
@book{went_experimental_1957,
	title = {The experimental control of plant growth},
	volume = {17},
	publisher = {Chronica Botanica Co., Waltham, Mass., USA and The Ronald Press Co., New York, USA},
	author = {Went, Frits W},
	year = {1957},
	note = {tex.ids= went\_experimental\_1957-1},
}

@article{kader_comparison_2005,
	title = {A comparison of seed germination calculation formulae and the associated interpretation of resulting data},
	volume = {138},
	url = {https://www.royalsoc.org.au/images/pdf/journal/138_Kader.pdf},
	doi = {10.5962/p.361564},
	journal = {Journal and Proceedings of the Royal Society of New South Wales},
	author = {Kader, M. A.},
	year = {2005},
	pages = {65--75},
}

@article{goodchild_method_1971,
	title = {A method of measuring seed germination in physiological studies},
	volume = {35},
	issn = {0305-7364},
	url = {https://www.jstor.org/stable/42908843},
	doi = {10.1093/oxfordjournals.aob.a084504},
	abstract = {Methods of comparing germination curves are described and these are discussed in relation to the problem under consideration. In a study of chemical factors which modify seed germination (here all inhibitory), the changes in the rate of germination appeared to be associated with the inhibitory factors. These curves could be adequately described by orthogonal polynomial regressions. It is noted that some coefficients devised to represent the course of germination were not adequate for these purposes. The reasons are discussed.},
	number = {141},
	urldate = {2018-01-15},
	journal = {Annals of Botany},
	author = {Goodchild, N. A. and Walker, M. G.},
	year = {1971},
	pages = {615--621},
}

@article{al-mudaris_notes_1998,
	title = {Notes on various parameters recording the speed of seed germination},
	volume = {99},
	url = {https://www.jarts.info/index.php/tropenlandwirt/article/download/1495/671},
	number = {2},
	journal = {Der Tropenlandwirt - Journal of Agriculture in the Tropics and Subtropics},
	author = {Al-Mudaris, M. A.},
	year = {1998},
	pages = {147--154},
}

@article{edmond_effects_1958,
	title = {The effects of temperature, sand and soil, and acetone on germination of okra seed},
	volume = {71},
	journal = {Proceedings of the American Society for Horticultural Science},
	author = {Edmond, J. B. and Drapala, W. J.},
	year = {1958},
	note = {tex.ids= edmond\_effects\_1958-1},
	pages = {428--434},
}

@inproceedings{labouriau_uma_1983,
	title = {Uma nova linha de pesquisa na fisiologia da germinação das sementes},
	booktitle = {Anais do {XXXIV} {Congresso} {Nacional} de {Botânica}. {SBB}, {Porto} {Alegre}},
	publisher = {Sociedade Botânica do Brasil},
	author = {Labouriau, L. G.},
	year = {1983},
	note = {tex.ids= labouriau\_uma\_1983-1, labouriau\_uma\_1983-2, labouriau\_uma\_1983-3, labouriau\_uma\_1983-4},
	pages = {11--50},
}

@article{djavanshir_germination_1976,
	title = {Germination value-{A} new formula},
	volume = {25},
	url = {https://www.thuenen.de/media/institute/fg/PDF/Silvae_Genetica/1976/Vol._25_Heft_2/25_2_79.pdf},
	number = {2},
	journal = {Silvae Genetica},
	author = {Djavanshir, K. and Pourbeik, H.},
	year = {1976},
	pages = {79--83},
}

@inproceedings{george_influence_1961,
	title = {Influence of germination temperature on the expression of post-harvest dormancy in wheat},
	booktitle = {Crop {Science} {Abstracts}; {Western} {Society} of {Crop} {Science} {Annual} {Meeting}, 1961},
	publisher = {Western Society of Crop Science},
	author = {George, D. W.},
	year = {1961},
	pages = {15},
}

@book{khandakar_jute_1983,
	title = {Jute seed quality},
	publisher = {Bangladesh Agricultural Research Council, Dhaka},
	author = {Khandakar, A. L. and Bradbeer, J. W.},
	year = {1983},
	note = {tex.ids= khandakar\_jute\_1983-1},
}

@article{nichols_two_1968,
	title = {Two approaches to the study of germination data},
	volume = {33},
	number = {3},
	journal = {Proceedings of the International Seed Testing Association},
	author = {Nichols, M. A. and Heydecker, W.},
	year = {1968},
	pages = {531--540},
}

@article{edwards_temperature_1932,
	title = {Temperature relations of seed germination},
	volume = {7},
	issn = {0033-5770},
	url = {https://www.jstor.org/stable/2808419},
	doi = {10.1086/394417},
	number = {4},
	journal = {The Quarterly Review of Biology},
	author = {Edwards, Thomas I.},
	month = dec,
	year = {1932},
	note = {tex.ids= edwards\_temperature\_1932-1},
	pages = {428--443},
}

@article{khamassi_optimal_2013,
	title = {Optimal germination temperature assessed by indices and models in field bean (\emph{{Vicia} faba} {L}. var. \emph{minor})},
	volume = {78},
	issn = {1331-7768},
	url = {https://hrcak.srce.hr/104663},
	abstract = {This paper seeks to shed light on the effect of temperature on field bean (Vicia faba L. var. minor) germination and root elongation. Accordingly, the results were as follows: germination was faster at 20°C than at 5, 10, 15, 25 or...},
	language = {en},
	number = {2},
	journal = {Agriculturae Conspectus Scientificus},
	author = {Khamassi, Khalil and Harbaoui, Kalthoum and Jaime, A. Teixeira da Silva and Jeddi, Fayçal Ben},
	month = jun,
	year = {2013},
	note = {tex.ids= khamassi\_optimal\_2013-1},
	pages = {131--136},
}

@article{labouriau_germination_1976,
	title = {On the germination of seeds of \emph{{Calotropis} procera} ({Ait}.) {Ait}. f},
	volume = {48},
	number = {263-284},
	journal = {Anais da Academia Brasileira de Ciências},
	author = {Labouriau, L. G. and Valadares, M. E. B.},
	year = {1976},
	note = {tex.ids= labouriau\_germination\_1976-1},
}

@phdthesis{reddy_effect_1978,
	type = {Ph.{D}. {Thesis}},
	title = {Effect of temperature on seed dormancy and alpha-amylase activity during kernel maturation and germination in wheat (\emph{{Triticum} aestivum} {L}.) cultivars},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/1j92gb854},
	school = {Oregon State University},
	author = {Reddy, Lekkala Vijayasimha},
	year = {1978},
}

@article{schrader_seed_2000,
	title = {Seed germination and seedling growth of \emph{{Alnus} maritima} from its three disjunct populations},
	volume = {125},
	issn = {0003-1062, 2327-9788},
	url = {http://journal.ashspublications.org/content/125/1/128},
	doi = {10.21273/JASHS.125.1.128},
	abstract = {Genotypic variation and horticultural potential of Alnus maritima [Marsh.] Nutt. (seaside alder), a large shrub or small tree found naturally in only three small, disjunct populations, have not been studied. We examined effects of population of origin and environment on seed germination and growth and morphology of seedlings. The first experiment showed that 6 weeks of cold stratification optimized germination of half-sibling seeds from Oklahoma at 73.2\%. When this treatment was applied to multiple groups of half-siblings from all populations in a second experiment, seeds from Oklahoma had a higher germination percentage (55.0\%) than seeds from Georgia (31.4\%) and the Delmarva Peninsula (14.7\%). In a third experiment, morphology and growth of multiple groups of half-siblings from all three populations were compared in one environment. Leaves of seedlings from Oklahoma were longer (12.8 cm) and more narrow (2.15 length to width ratio) than leaves of seedlings from Georgia (12.0 cm long; ratio = 1.76) and the Delmarva Peninsula (11.6 cm long; ratio = 1.86). Seedlings from Oklahoma and Georgia accumulated dry weight at higher rates (181 and 160 mg·d-1, respectively) than seedlings from Delmarva (130 mg·d-1), while seedlings from Oklahoma and Delmarva were more densely foliated (0.72 and 0.64 leaves and lateral shoots per centimeter of primary stem, respectively) than those from Georgia (0.46 per cm). These differences indicate genetic divergence among the three disjunct populations and the potential to exploit genetic variation to select horticulturally superior A. maritima for use in managed landscapes.},
	language = {en},
	number = {1},
	urldate = {2018-12-12},
	journal = {Journal of the American Society for Horticultural Science},
	author = {Schrader, James A. and Graves, William R.},
	month = jan,
	year = {2000},
	pages = {128--134},
}

@article{allan_seedling_1962,
	title = {Seedling emergence rate of fall-sown wheat and its association with plant height and coleoptile length},
	volume = {54},
	issn = {0002-1962},
	url = {https://www.agronomy.org/publications/aj/abstracts/54/4/AJ0540040347},
	doi = {10.2134/agronj1962.00021962005400040022x},
	language = {en},
	number = {4},
	urldate = {2018-12-11},
	journal = {Agronomy Journal},
	author = {Allan, R. E. and Vogel, O. A. and Peterson, C. J.},
	year = {1962},
	pages = {347},
}

@article{bouton_germination_1976,
	title = {Germination in freshly harvested seed of centipedegrass},
	volume = {68},
	issn = {0002-1962},
	url = {https://www.agronomy.org/publications/aj/abstracts/68/6/AJ0680060991},
	doi = {10.2134/agronj1976.00021962006800060040x},
	language = {en},
	number = {6},
	urldate = {2018-12-11},
	journal = {Agronomy Journal},
	author = {Bouton, J. H. and Dudeck, A. E. and Smith, R. L.},
	year = {1976},
	pages = {991},
}

@article{grose_laboratory_1958,
	title = {Some laboratory germination responses of the seeds of river red gum, \emph{{Eucalyptus} camaldulensis} {Dehn}. {Syn}. \emph{{Eucalyptus} rostrata} {Schlecht}},
	volume = {6},
	issn = {0067-1924},
	url = {http://www.publish.csiro.au/?paper=BT9580129},
	doi = {10.1071/bt9580129},
	language = {en},
	number = {2},
	urldate = {2018-12-11},
	journal = {Australian Journal of Botany},
	author = {Grose, R. J. and Zimmer, W. J.},
	year = {1958},
	pages = {129},
}

@article{brown_representing_1988-2,
	title = {Representing cumulative germination. 2. {The} use of the weibull function and other empirically derived curves},
	volume = {61},
	issn = {0305-7364},
	doi = {10.1093/oxfordjournals.aob.a087535},
	abstract = {Abstract.  The Weibull, Morgan–Mercer–Flodin, Richards, Mitscherlich, Gompertz and logistic functions were each fitted to a wide range of cumulative germination},
	language = {en},
	number = {2},
	urldate = {2018-12-11},
	journal = {Annals of Botany},
	author = {Brown, R. F. and Mayer, D. G.},
	month = feb,
	year = {1988},
	pages = {127--138},
}

@article{brown_representing_1988,
	title = {Representing cumulative germination. 1. {A} critical analysis of single-value germination indices},
	volume = {61},
	issn = {0305-7364},
	doi = {10.1093/oxfordjournals.aob.a087534},
	abstract = {Several single-value germination indices, including Kotowski's coefficient of velocity, Maguire's speed of germination, Czabator's germination value, Diavanshir and Pourbiek's germination value, Timson's cumulative germination, Lehle and Putnam's Richards function index, Smith and Millett's sprouting index, and Tucker and Wright's regression index, were evaluated to test their ability to distinguish superior from inferior germination. All except Timson's cumulative germination method were essentially no better for ranking germination responses than data on total germination; Kotowski's coefficient of velocity, Smith and Millet's sprouting index, and Lehle and Putnam's Richards function index were markedly inferior. Because of the ambiguity inherent in any index that combines, into a single value, data about the onset, rate and extent of germination, none of the indices could be recommended as a way of summarizing germination.},
	language = {en},
	number = {2},
	journal = {Annals of Botany},
	author = {Brown, R. F. and Mayer, D. G.},
	month = feb,
	year = {1988},
	note = {tex.ids= brown\_representing\_1988-1},
	pages = {117--125},
}

@article{gordon_germination_1971,
	title = {The germination resistance test - {A} new test for measuring germination quality of cereals},
	volume = {51},
	issn = {0008-4220, 1918-1833},
	url = {http://www.nrcresearchpress.com/doi/10.4141/cjps71-036},
	doi = {10.4141/cjps71-036},
	language = {en},
	number = {2},
	urldate = {2018-12-11},
	journal = {Canadian Journal of Plant Science},
	author = {Gordon, Andrew G.},
	month = mar,
	year = {1971},
	pages = {181--183},
}

@article{mcnair_how_2012,
	title = {How to analyse seed germination data using statistical time-to-event analysis: {Non}-parametric and semi-parametric methods},
	volume = {22},
	issn = {0960-2585, 1475-2735},
	shorttitle = {How to analyse seed germination data using statistical time-to-event analysis},
	doi = {10.1017/s0960258511000547},
	language = {en},
	number = {02},
	urldate = {2018-12-11},
	journal = {Seed Science Research},
	author = {McNair, James N. and Sunkara, Anusha and Frobish, Daniel},
	month = jun,
	year = {2012},
	pages = {77--95},
}

@article{smith_germinating_1964,
	title = {Germinating and sprouting responses of the tomato at low temperatures},
	volume = {84},
	journal = {Proceedings of the American Society for Horticultural Science},
	author = {Smith, P. G. and Millet, A. H.},
	year = {1964},
	pages = {480--484},
}

@article{bonner_ideal_1967,
	title = {Ideal sowing depth for sweetgum seed},
	volume = {18},
	url = {https://rngr.net/publications/tpn/18-1/pdf.2005-05-13.4925080024/},
	number = {1},
	journal = {Tree Planters' Notes},
	author = {Bonner, F. T.},
	year = {1967},
	pages = {1--1},
}

@article{gordon_observations_1969,
	title = {Some observations on the germination energy tests for cereals},
	volume = {59},
	issn = {0097-1324},
	url = {https://www.jstor.org/stable/23432357},
	abstract = {[Investigations have shown that the number of grains of cereals germinating in germination tests is dependent upon the number of pre-germinated corns present, the amount of water added, the temperature of the added water, the temperature of germination, the relative position of the embryo to the level of water, the amount of oxygen present in the germination medium, the level of micro-organism infestation, the presence of dissolved ions in the germination medium, the length of storage at high temperatures and the moisture content of storage. As a result a set of conditions has been defined enabling exactly comparable tests to be made in different laboratories. The measured criteria of the test—the mean and standard deviation of the germination time—have been used for studying varietal differences in germination, for assessment of malting quality, for determining the optimum time for the start of malting, for investigating variety × location inter-actions of malting quality, for vigor studies and for the assessment of milling quality of wheat. This series of investigations has shown that the germination resistance test offers a simple, cheap reproducible method of measuring the germination characteristics of cereals. It has also shown that much useful information regarding the germination of cereals, not normally obtained from germinability tests can be gained. This sensitive technique can thus be used to study the effect of all external agencies on the germination of small grain cereals and with modifications in the moisture supply should also be adaptable to other non-gramineous seeds.]},
	urldate = {2018-12-11},
	journal = {Proceedings of the Association of Official Seed Analysts},
	author = {Gordon, Andrew G.},
	year = {1969},
	pages = {58--72},
}

@article{ellis_improved_1980,
	title = {Improved equations for the prediction of seed longevity},
	volume = {45},
	issn = {0305-7364},
	doi = {10.1093/oxfordjournals.aob.a085797},
	abstract = {Equations for predicting seed longevity in storage have been improved so that they now take into account variations within a species in initial seed quality—which is affected by genotype and pre-storage environment—and so that they are more accurate over a wider range of storage environments These improvements have been incorporated into a seed viability nomograph for barley (Hordeum distichum L.) which may be used to predict percentage viabihty of any seed lot after any time in any storage environment within the range −20 to 90 °C and 5–25 per cent moisture content. Applications of the improved equations to seed drying and to long-term seed storage for genetic conservation are discussed.},
	language = {en},
	number = {1},
	journal = {Annals of Botany},
	author = {Ellis, R. H. and Roberts, E. H.},
	month = jan,
	year = {1980},
	note = {Number: 1},
	pages = {13--30},
	file = {ellis1980.pdf:G\:\\OneDrive\\Aravind J\\Seed Viability equations\\Ellis and Roberts\\ellis1980.pdf:application/pdf},
}

@book{bradbeer_seed_1988,
	address = {Glasgow and London},
	title = {Seed {Dormancy} and {Germination}},
	url = {https://link.springer.com/book/10.1007/978-1-4684-7747-4},
	abstract = {The germination of seeds is a magical event, in which a pinch of dust-like material may give rise to all the power and the beauty of the growing plant. The mechanisms of seed dormancy, of the breaking of seed dormancy and of germination itself continue to remain shrouded in mystery, despite the best efforts of plant scientists. Perhaps we are getting there, but very slowly. This book considers germination and dormancy from the point of view of plant physiology. Plant physiologists attempt to understand the relation­ ship between plant form and function and to explain, in physical and chemical terms, plant growth and development. The place of germination and dormancy in plant ecophysiology is taken into account with attempts to understand the seed in its 'environment, whether the environment be natural, semi-natural or wholly artificial. In due course plant scientists hope to develop a precise understanding of germination and dormancy in cellular and molecular terms, and therefore there is some biochemistry in this book. Biochemists who wish to learn something about seeds should find this book useful.},
	language = {en},
	urldate = {2018-01-15},
	publisher = {Blackie},
	author = {Bradbeer, J. W.},
	year = {1988},
}

@article{kendrick_photocontrol_1969,
	title = {Photocontrol of germination in \emph{{Amaranthus} caudatus}},
	volume = {85},
	issn = {0032-0935, 1432-2048},
	doi = {10.1007/bf00381281},
	abstract = {SummaryGermination of Amaranthus caudatus is inhibited by light, far-red being the most effective part of the spectrum. At temperatures of 25° and below there is a low final germination percentage under continuous far-red whereas above 25° there is only a delaying effect. In the presence of a saturating concentration of gibberellic acid (GA3) at 25° seeds germinate under continuous far-red although they are delayed. At 25° seeds exposed to 48 hr far-red fail to germinate when transferred to darkness. This induced dormancy can be broken by a single short exposure to red light given at any time after the far-red illumination. This effect of short red can be reversed by a subsequent short period of far-red indicating that the seeds are phytochrome controlled. Although most seeds have escaped from the reversing effect of short far-red after an intervening dark period of 5 hours, germination is greatly reduced by continuous far-red at this time. Results of exposing seeds to varying periods of far-red before and after dark imbibition are interpreted in terms of a continual production of phytochrome in its active P fr form and a requirement for P fr action over a long period of time. Effects of intermittent and continuous low intensity far-red on the inhibition of germination provides further evidence for a low energy photoreaction involving phytochrome. Effects on Germination Index of continuous illumination with various light sources maintaining different P fr /P total ratios have been investigated. The results suggest that the proportion of phytochrome in the P fr form is the most important factor in the regulation of germination. A scheme for the phytochrome control of germination in Amaranthus caudatus is presented and possible explanations for the dependence on P fr /P total ratio are discussed.},
	language = {en},
	number = {4},
	journal = {Planta},
	author = {Kendrick, Richard E. and Frankland, Barry},
	month = dec,
	year = {1969},
	note = {tex.ids= kendrick\_photocontrol\_1969-1},
	pages = {326--339},
}

@article{ranal_how_2006,
	title = {How and why to measure the germination process?},
	volume = {29},
	issn = {0100-8404},
	doi = {10.1590/s0100-84042006000100002},
	number = {1},
	journal = {Brazilian Journal of Botany},
	author = {Ranal, Marli A. and de Santana, Denise Garcia},
	month = mar,
	year = {2006},
	note = {tex.ids= ranal\_how\_2006-1, ranal\_how\_2006-2},
	pages = {1--11},
}

@article{farooq_thermal_2005,
	title = {Thermal hardening: {A} new seed vigor enhancement tool in rice},
	volume = {47},
	issn = {1744-7909},
	shorttitle = {Thermal {Hardening}},
	doi = {10.1111/J.1744-7909.2005.00031.x},
	abstract = {Abstract:  In a laboratory study, indica and japonica rice (Oryza sativa L.) seeds were exposed to thermal hardening (heating followed by chilling followed by heating; chilling followed by heating followed by chilling; heating followed by chilling or chilling followed by heating). In indica rice, heating followed by chilling followed by heating resulted in decreased mean germination time, time to start germination, electrical conductivity of seed leachates, and time to 50\% germination, as well as increased germination index, energy of germination, radicle and plumule length, root length, root/shoot ratio, root fresh and dry weight, radicle and plumule growth rate, and shoot fresh weight. In japonica rice, chilling followed by heating followed by chilling performed better than all other treatments, including control. ( Managing editor: Ping HE)},
	language = {en},
	number = {2},
	journal = {Journal of Integrative Plant Biology},
	author = {Farooq, Muhammad and Basra, S. M. A. and Ahmad, Nazir and Hafeez, K.},
	month = feb,
	year = {2005},
	note = {tex.ids= farooq\_thermal\_2005-1},
	pages = {187--193},
}

@article{coolbear_effect_1984,
	title = {The effect of low temperature pre-sowing treatment on the germination performance and membrane integrity of artificially aged tomato seeds},
	volume = {35},
	issn = {0022-0957},
	url = {https://academic.oup.com/jxb/article/35/11/1609/719669},
	doi = {10.1093/jxb/35.11.1609},
	abstract = {Loss of seed viability and decrease in germination rate appear to be due to two independent sets of events occurring during artificial ageing in tomato (Lycopersicon esculentum Mill) seeds. Only the second category of physiological damage is reversible: a low temperature pre-sowing treatment being capable of greatly reducing the time to fifty percent germination of both unaged and aged seeds, but having no effect on germination capacity. Leakage of ionic solutes from the seeds did not increase following ageing, but there were considerable increases in losses of small organic molecules. Low temperature pretreatments did not reduce the rate of loss of either amino acids or reducing sugars from aged seeds. The implications of the use of artificial ageing in combination with low temperature pre-sowing treatments in the study of small seed physiology is discussed, as is the value of solute leakage studies in this kind of seed.},
	language = {en},
	number = {11},
	journal = {Journal of Experimental Botany},
	author = {Coolbear, P. and Francis, Adele and Grierson, D.},
	month = nov,
	year = {1984},
	note = {tex.ids= coolbear\_effect\_1984-1, coolbear\_effect\_1984-2},
	pages = {1609--1617},
}

@book{baskin_seeds_1998,
	address = {San Diego},
	title = {Seeds: {Ecology}, {Biogeography}, and {Evolution} of {Dormancy} and {Germination}},
	isbn = {0-12-080260-0},
	language = {English},
	publisher = {Academic Press},
	author = {Baskin, C. C. and Baskin, J. M.},
	year = {1998},
}

@article{khan_effect_1984,
	title = {The effect of salinity and temperature on the germination of polymorphic seeds and growth of \emph{{Atriplex} triangularis} {Willd}},
	volume = {71},
	issn = {0002-9122},
	doi = {10.2307/2443323},
	abstract = {Polymorphic seeds of Atriplex triangularis were germinated at various temperatures (5-15 C, 5-25 C, 10-20 C, 20-30 C) and salinity regimes (0 to 1.5\% NaCl) in order to determine their germinability and early seedling growth under these conditions. Larger seeds generally had a higher germination percentage in saline medium. The rate and percentage of germination decreased with increased salinity stress. A thermoperiod of 25 C day and 5 C night, 12 hr/12 hr, temperature enhanced germination of seeds. Early seedling growth is promoted in larger seeds at lower salinity, and at high-day and low-night temperatures. Polymorphic seeds have different physiological requirements which provide alternative situations for seed germination in natural habitats.},
	number = {4},
	journal = {American Journal of Botany},
	author = {Khan, M. A. and Ungar, I. A.},
	year = {1984},
	note = {tex.ids= khan\_effect\_1984-1, khan\_effect\_1984-2},
	pages = {481--489},
}

@book{bewley_seeds_1994,
	address = {New York, USA},
	title = {Seeds: {Physiology} of {Development} and {Germination}},
	isbn = {0-306-44748-7},
	shorttitle = {Seeds},
	url = {https://link.springer.com/book/10.1007/978-1-4899-1002-8},
	abstract = {The second edition of this book includes new information and concepts in areas of the subject where considerable advances have been made since the publication of the first edition in 1985. While some sections have been altered relatively little, others covering seed development, effects of abscisic acid and gibberellins on gene expression and some aspects of dormancy have been extensively...},
	language = {English},
	publisher = {Plenum Publishing Corporation},
	author = {Bewley, J. D. and Black, M.},
	year = {1994},
	note = {tex.ids= bewley\_seeds:\_1994, bewley\_seeds:\_1994-1, bewley\_seeds:\_1994-2
googlebooksid: W6EbrewcpDwC},
	file = {J. Derek Bewley, Michael Black (auth.) - Seeds_ Physiology of Development and Germination (1994, Springer) [10.1007_978-1-4899-1002-8] - libgen.li:G\:\\OneDrive\\Aravind J\\Books\\J. Derek Bewley, Michael Black (auth.) - Seeds_ Physiology of Development and Germination (1994, Springer) [10.1007_978-1-4899-1002-8] - libgen.li.pdf:application/pdf},
}

@article{haugland_experiments_1996,
	title = {Experiments on bioassay sensitivity in the study of allelopathy},
	volume = {22},
	doi = {10.1007/BF02028508},
	number = {10},
	journal = {Journal of Chemical Ecology},
	author = {Haugland, Espen and Brandsaeter, Lars Olav},
	year = {1996},
	note = {tex.ids= haugland\_experiments\_1996-1},
	pages = {1845--1859},
}

@article{timson_new_1965,
	title = {New method of recording germination data},
	volume = {207},
	copyright = {1965 Nature Publishing Group},
	issn = {1476-4687},
	doi = {10.1038/207216a0},
	abstract = {New Method of Recording Germination Data},
	language = {En},
	number = {4993},
	journal = {Nature},
	author = {Timson, J.},
	month = jul,
	year = {1965},
	note = {tex.ids= timson\_new\_1965-1},
	pages = {216},
}

@book{aosa_seed_1983,
	address = {Ithaca, NY, USA},
	title = {Seed {Vigor} {Testing} {Handbook}},
	language = {en},
	publisher = {Association of Official Seed Analysts},
	author = {AOSA},
	year = {1983},
	note = {tex.ids= aosa\_seed\_1983-1, aosa\_seed\_1983-2},
}

@article{throneberry_relation_1955,
	title = {Relation of respiratory and enzymatic activity to corn seed viability},
	volume = {30},
	issn = {0032-0889},
	doi = {10.1104/pp.30.4.337},
	number = {4},
	journal = {Plant Physiology},
	author = {Throneberry, Glyn O. and Smith, Frederick G.},
	month = jul,
	year = {1955},
	pages = {337--343},
}

@article{maguire_speed_1962,
	title = {Speed of germination - {Aid} in selection and evaluation for seedling emergence and vigor},
	volume = {2},
	issn = {0011-183X},
	doi = {10.2135/cropsci1962.0011183x000200020033x},
	language = {en},
	number = {2},
	journal = {Crop Science},
	author = {Maguire, James D.},
	year = {1962},
	note = {tex.ids= maguire\_speed\_1962-1, maguire\_speed\_1962-2},
	pages = {176--177},
}

@article{scott_review_1984,
	title = {Review of data analysis methods for seed germination},
	volume = {24},
	issn = {0011-183X},
	doi = {10.2135/cropsci1984.0011183x002400060043x},
	language = {en},
	number = {6},
	journal = {Crop Science},
	author = {Scott, S. J. and Jones, R. A. and Williams, W. A.},
	year = {1984},
	note = {tex.ids= scott\_review\_1984-1, scott\_review\_1984-2},
	pages = {1192--1199},
}

@article{ranal_effects_1999,
	title = {Effects of temperature on spore germination in some fern species from semideciduous mesophytic forest},
	volume = {89},
	issn = {00028444},
	doi = {10.2307/1547349},
	number = {2},
	journal = {American Fern Journal},
	author = {Ranal, Marli A.},
	month = apr,
	year = {1999},
	note = {tex.ids= ranal\_effects\_1999-1, ranal\_effects\_1999-2},
	pages = {149},
}

@article{quintanilla_effect_2000,
	title = {Effect of temperature on germination in northernmost populations of \emph{{Culcita} macrocarpa} and \emph{{Woodwardia} radicans}},
	volume = {2},
	issn = {1438-8677},
	doi = {10.1055/s-2000-16638},
	abstract = {Spore germination of Culcita macrocarpa C. Presl and Woodwardia radicans (L.) Sm. from nine populations at the northern limit of their distribution, in the northwest Iberian Peninsula, was investigated....},
	language = {en},
	number = {6},
	journal = {Plant Biology},
	author = {Quintanilla, L. G. and Pajarón, S. and Pangua, E. and Amigo, J.},
	month = nov,
	year = {2000},
	note = {tex.ids= quintanilla\_effect\_2000-1, quintanilla\_effect\_2000-2, quintanilla\_effect\_2000-3, quintanilla\_effect\_2000-4, quintanilla\_effect\_2000-5},
	pages = {612--617},
}

@incollection{ista_chapter_2015,
	title = {Chapter 5: {The} germination test},
	volume = {2015},
	shorttitle = {Chapter 5},
	url = {https://doi.org/10.15258/istarules.2015.05},
	booktitle = {International {Rules} for {Seed} {Testing}. {International} {Seed} {Testing} {Association}, {Zurich}, {Switzerland}.},
	publisher = {International Seed Testing Association},
	author = {{ISTA}},
	year = {2015},
	pages = {i--5--56},
}

@article{goloff_germination_1975,
	title = {A germination model for natural seed populations},
	volume = {52},
	issn = {0022-5193},
	doi = {10.1016/0022-5193(75)90001-6},
	abstract = {A general model for determining time and rate of germination under continuously changing temperatures and other environmental parameters is proposed. The seed population may vary in size and density. The principle of the model is based upon the adherence of seed germination to an Arrhenius type system. The model, with slight modifications, may be applied to many temperature or other environmentally dependent biological systems.},
	number = {2},
	journal = {Journal of Theoretical Biology},
	author = {Goloff, Alexander A. and Bazzaz, F. A.},
	month = aug,
	year = {1975},
	note = {tex.ids= goloff\_germination\_1975-2},
	pages = {259--283},
}

@article{tucker_estimating_1965,
	title = {Estimating rapidity of germination},
	volume = {5},
	issn = {0011-183X},
	doi = {10.2135/cropsci1965.0011183X000500050006x},
	language = {en},
	number = {5},
	journal = {Crop Science},
	author = {Tucker, Henry and Wright, L. Neal},
	year = {1965},
	pages = {398--399},
}

@article{primack_longevity_1985,
	title = {Longevity of individual flowers},
	volume = {16},
	doi = {10.1146/annurev.es.16.110185.000311},
	number = {1},
	urldate = {2018-01-15},
	journal = {Annual Review of Ecology and Systematics},
	author = {Primack, R. B.},
	year = {1985},
	note = {tex.ids= primack\_longevity\_1985-1},
	pages = {15--37},
}

@article{shannon_mathematical_1948,
	title = {A mathematical theory of communication},
	volume = {27},
	issn = {1538-7305},
	doi = {10.1002/j.1538-7305.1948.tb01338.x},
	language = {en},
	number = {3},
	journal = {Bell System Technical Journal},
	author = {Shannon, C. E.},
	month = jul,
	year = {1948},
	note = {tex.ids= shannon\_mathematical\_1948-1},
	pages = {379--423},
}

@book{heydecker_seed_1972,
	address = {University Park, USA},
	title = {Seed {Ecology}. {Proceedings} of the {Nineteenth} {Easter} {School} in {Agricultural} {Science}, {University} of {Nottingham}, 1972},
	publisher = {Pennsylvania State University Press},
	author = {Heydecker, W.},
	year = {1972},
}

@article{stroup_rethinking_2015,
	title = {Rethinking the analysis of non-normal data in plant and soil science},
	volume = {107},
	issn = {0002-1962},
	url = {https://dl.sciencesocieties.org/publications/aj/abstracts/107/2/811},
	doi = {10.2134/agronj2013.0342},
	language = {en},
	number = {2},
	urldate = {2017-07-20},
	journal = {Agronomy Journal},
	author = {Stroup, Walter W.},
	year = {2015},
	pages = {811--827},
}

@article{hay_modelling_2014-1,
	title = {Modelling seed germination in response to continuous variables: {Use} and limitations of probit analysis and alternative approaches},
	volume = {24},
	issn = {0960-2585, 1475-2735},
	shorttitle = {Modelling seed germination in response to continuous variables},
	doi = {10.1017/s096025851400021x},
	language = {en},
	number = {03},
	urldate = {2018-12-11},
	journal = {Seed Science Research},
	author = {Hay, Fiona R. and Mead, Andrew and Bloomberg, Mark},
	month = sep,
	year = {2014},
	pages = {165--186},
	file = {modelling_seed_germination_in_response_to_continuous_variables_use_and_limitations_of_probit_analysis_and_alternative_approaches.pdf:G\:\\OneDrive\\Aravind J\\Seed Viability equations\\Others\\modelling_seed_germination_in_response_to_continuous_variables_use_and_limitations_of_probit_analysis_and_alternative_approaches.pdf:application/pdf},
}

@article{reddy_effect_1985,
	title = {Effect of temperature on seed dormancy of wheat},
	volume = {25},
	issn = {0011-183X},
	doi = {10.2135/cropsci1985.0011183X002500030007x},
	language = {en},
	number = {3},
	urldate = {2018-12-14},
	journal = {Crop Science},
	author = {Reddy, L. V. and Metzger, R. J. and Ching, T. M.},
	year = {1985},
	note = {tex.ids= reddy\_effect\_1985-1},
	pages = {455},
}

@misc{survival-package,
	title = {A {Package} for {Survival} {Analysis} in {S}},
	url = {https://CRAN.R-project.org/package=survival},
	author = {Therneau, Terry M},
	year = {2015},
	note = {version 2.38 },
}

@article{ritz_analysis_2013,
	title = {Analysis of germination data from agricultural experiments},
	volume = {45},
	issn = {1161-0301},
	doi = {10.1016/j.eja.2012.10.003},
	abstract = {Expensive agricultural experiments deserve to be analyzed as efficiently as possible by extracting as much information as possible from the data while respecting the experimental design. We consider experiments where germination in response to time elapsed is used to characterize germination performance and vigour. We formulate statistical models in a biologically meaningful framework in such a way that the inherent data structure, which centers around repeatedly monitoring seeds over time, is duly incorporated in the statistical analysis. Consequently, estimation and model checking procedures are based on treating the data as event times, that is, to record the time it takes for germination (the event of interest) to occur. The key result is that the use of appropriate statistical models is important in order to get a better appreciation of the uncertainty that is present in germination experiments.},
	urldate = {2019-02-04},
	journal = {European Journal of Agronomy},
	author = {Ritz, Christian and Pipper, Christian B. and Streibig, Jens C.},
	month = feb,
	year = {2013},
	pages = {1--6},
}

@book{gomes_curso_1960,
	title = {Curso {De} {Estatística} {Experimental}},
	url = {https://books.google.de/books?id=ZckqGwAACAAJ},
	publisher = {Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo},
	author = {Gomes, F. P.},
	year = {1960},
}

@article{negm_effects_1978,
	title = {Effects of ethylene and carbon dioxide on the germination of osmotically inhibited lettuce seed},
	volume = {62},
	copyright = {© 1978 American Society of Plant Biologists},
	issn = {0032-0889, 1532-2548},
	url = {http://www.plantphysiol.org/content/62/4/473},
	doi = {10.1104/pp.62.4.473},
	abstract = {Lettuce seeds ({<}em{>}Lactuca sativa{<}/em{>} L.) used in this study germinated 98\% at 25 C in light or dark. Their germination was completely inhibited by 0.20 {<}span class="small-caps"{>}m{<}/span{>} NaCl, 0.35 {<}span class="small-caps"{>}m{<}/span{>} mannitol, or polyethylene glycol 6000 (−7 bars) under continuous light when germination tests were made in Petri dishes. Approximately 50\% germination occurred in sealed flasks due to endogenously produced C$_{\textrm{2}}$H$_{\textrm{4}}$ and CO$_{\textrm{2}}$. Removal of either or both gases prevented germination. In the presence of endogenous CO$_{\textrm{2}}$, addition of C$_{\textrm{2}}$H$_{\textrm{4}}$ (0.5 to 16 microliters/liter) stimulated 95 to 100\% germination (after 5 days) only in the light, but the rate of germination was dependent on C$_{\textrm{2}}$H$_{\textrm{4}}$ concentration. At 16 microliters/liter C$_{\textrm{2}}$H$_{\textrm{4}}$, full germination occurred within 72 hours. Addition of up to 3.2\% CO$_{\textrm{2}}$ had no adverse effect on the C$_{\textrm{2}}$H$_{\textrm{4}}$ action. Higher concentrations or the complete absence of CO$_{\textrm{2}}$ reduced both rate and total germination. CO$_{\textrm{2}}$ alone was ineffective. Under these osmotic conditions the promotive effect of C$_{\textrm{2}}$H$_{\textrm{4}}$ was under the control of phytochrome.},
	language = {en},
	number = {4},
	urldate = {2020-01-24},
	journal = {Plant Physiology},
	author = {Negm, Fayek B. and Smith, Orrin E.},
	month = oct,
	year = {1978},
	pages = {473--476},
}

@article{lyon_rapid_1966,
	title = {Rapid method for determining numerical indexes for time-course curves},
	volume = {211},
	copyright = {1966 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/211330a0},
	doi = {10.1038/211330a0},
	abstract = {IN reporting experiments with biological processes such as abscission, germination, and dormancy, where results are observed and recorded periodically, most investigators have found it convenient to present the data as time-course curves. While time-course curves such as those shown for abscission in Fig. 1 are useful in indicating the initiation and the total amount of abscission, as well as the slope of the response curves (rate), they cannot readily be compared numerically. For comparison of the results of large numbers of treatments in individual experiments, or of groups of experiments, and for statistical analyses, numerical designations are necessary. The time required for 50 or 100 per cent abscission and the percentage abscission at an arbitrary time after treatment are designations commonly used. Neither of these methods allows a satisfactory comparison of data frequently encountered in research. For example, comparison of the data represented by curves 1, 2, and 3 in Fig. 1 on the basis of the time to 50 or 100 per cent abscission is impossible as not all the curves reach either of these levels by the end of the experiment. This problem is intensified when treatments retard or inhibit abscission. Furthermore, the relationship of the curves changes with time, and thus comparison of the percentage abscission at an arbitrary time represents only a small part of the information in the curve.},
	language = {en},
	number = {5046},
	urldate = {2020-01-24},
	journal = {Nature},
	author = {Lyon, J. L. and Coffelt, R. J.},
	month = jul,
	year = {1966},
	pages = {330--330},
}

@article{melville_seed_1980,
	title = {Seed germination and early seedling vigor in progenies of inbred strawberry selections},
	volume = {15},
	number = {6, I},
	journal = {HortScience},
	author = {Melville, A. H. and Galletta, G. J. and Draper, A. D. and Ng, T. J.},
	year = {1980},
	pages = {749--750},
}

@article{fakorede_variability_1981,
	title = {Variability for seedling vigour in maize},
	volume = {17},
	issn = {1469-4441, 0014-4797},
	url = {https://www.cambridge.org/core/journals/experimental-agriculture/article/variability-for-seedling-vigour-in-maize/BEA116DC65520A6FD9B1652881C46983},
	doi = {10.1017/s0014479700011455},
	abstract = {Considerable variation in seedling vigour was observed among 36 maize populations; genotypic variances were generally high for emergence percentage (E\%), emergence index (EI), dry-matter accumulation and relative growth rate (RGR). Broadsense heritability values and environmental variances indicated that E\% and EI would be more reliable indices for seedling vigour than emergence rate index (ERI). The expression of growth rate (GR) was influenced more by the environment than the genetic constitution of seedlings; GR was not therefore an effective indicator for seedling vigour, and RGR would be preferred because it was more heritable and less influenced by the environment.},
	language = {en},
	number = {2},
	urldate = {2020-01-23},
	journal = {Experimental Agriculture},
	author = {Fakorede, M. A. B. and Ojo, D. K.},
	month = apr,
	year = {1981},
	pages = {195--201},
}

@article{hsu_planting_1986,
	title = {Planting date effects on seedling development of perennial warm-season forage grasses. {I}. {Field} emergence},
	volume = {78},
	copyright = {© American Society of Agronomy},
	issn = {1435-0645},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/agronj1986.00021962007800010008x},
	doi = {10.2134/agronj1986.00021962007800010008x},
	abstract = {Slow establishment of perennial warm-season forage grasses is a problem in their utilization to improve animal production in summer when cool-season grasses are less productive. A field experiment was conducted to determine temperature effects on field emergence, estimate base temperature required for emergence in the field, and provide insight toward optimum planting dates for warm-season perennial forage grasses. Big bluestem (BB) (Andropogon gerardiiVitman), Causasian bluestem (CB) [Bothriochloa caucasica(Trin.) C. E. Hubb.], indiangrass (IG) [Sorghartrum nutans(L.) Nash], switchgrass (SG) (Panicum virgatumL.), and an annual species, crabgrass (CG) [Digitaria sanguinalis(L.) Scop.] were compared in a split-plot field experiment with five replications. Unchilled seeds of each species were planted at approximately 2-week intervals in a Mexico silt loam soil (fine, montmorillonitic, mesic Udollic Ochraqualf) near Columbia, MO from early April to late June in 1982 and 1983. Emerging seedlings were recorded frequently. The logistic function was used to fit the emergence data. No emergence data were obtained for CG since natural emergence also occurred. Maximum emergence percentage was obtained following planting on 30 Apr. and 2 June 1982, and 6 and 16 May 1983. Indiangrass had the highest emergence percentages of pure live seed with 38 and 51\% in 1982 and 1983, respectively, followed by SG, BB, and CB. Survival percentage of emerged seedlings averaged about 90\%, but was reduced to near 70\% on late plantings when soil dried out rapidly. Entries with high emergence percentages also had their highest emergence rates (ER) at Et50(time to reach 50\% of final emergence). Corrected ER index and ER50(reciprocal of Et50) were closely correlated (r= 0.99, P{<}0.01). Both are good indices for evaluating speed of emergence. However, ER50is based on actual measurements and has more agronomic significance and biological meaning. Base temperatures required for emergence in 1982 were estimated as 9.4, 9.9, 10.8, and 11.4 °C for IG, BB, SG, and CB, respectively. For 1983 temperatures were 10.0, 10.8, 10.4, and 9.5 °C, respectively. The data suggest optimum planting dates for these species between late April and mid-May to maximize emergence percentage and reduce risks of high temperature and soil moisture stress.},
	language = {en},
	number = {1},
	urldate = {2020-01-23},
	journal = {Agronomy Journal},
	author = {Hsu, F. H. and Nelson, C. J.},
	year = {1986},
	pages = {33--38},
}

@article{chopra_effect_1980,
	title = {Effect of soil temperature alteration by soil covers on seedling emergence of wheat (\emph{{Triticum} aestivum} {L}.) sown on two dates},
	volume = {57},
	issn = {1573-5036},
	url = {https://doi.org/10.1007/BF02139648},
	doi = {10.1007/bf02139648},
	abstract = {A field study was conducted to evaluate the effect of soil temperature altered by various ways of soil coveringviz control (T1), transparent polyethylene (T2), black polyethylene (T3), rice straw (T4), rice straw applied only during night (T5) and farm yard manure (T6) on seedling emergence of wheat sown on November 30, 1978 and January 6, 1979. Maximum increase in soil temperature occurred under transparent polyethylene cover. Temperature alterations were relatively smaller under other treatments and was minimum under farm yard manure cover. With both sowings, the effect of various ways of soil covering on seedling emergence depended on the magnitude of soil temperature alteration caused by them. It was hastened markedly under transparent polyethylene cover and only slightly under black polyethylene cover. Continuous soil covering with rice straw slowed down seedling emergence while covering only during night hastened it slightly. Farm yard manure cover showed negligible effect on seedling emergence. Seedling emergence response to an increase in soil temperature was higher with second sowing when temperature was relatively lower than with first sowing. The result suggests the possibility of expediting seedling emergence of wheat sown under low temperature condition by transparent polyethylene cover. Seedling emergence was only slightly influenced by other soil covers.},
	language = {en},
	number = {1},
	urldate = {2020-01-23},
	journal = {Plant and Soil},
	author = {Chopra, Usha K. and Chaudhary, T. N.},
	month = feb,
	year = {1980},
	pages = {125--129},
}

@article{chaudhary_effect_1970,
	title = {Effect of temperature associated with levels of bulk density on rice seedling emergence},
	volume = {33},
	issn = {1573-5036},
	url = {https://doi.org/10.1007/BF01378199},
	doi = {10.1007/bf01378199},
	abstract = {A laboratory study was conducted to find out the effect of temperatures on rice seedling emergence under different levels of bulk density. The temperatures ranging from 10 to 40°C in increments of 5°C were maintained constant with ±1°C accuracy. The bulk density levels were 1.3, 1.5, 1.7, and 1.9 g cm−3. Aluminum cylinders with top open and bottom provided with a removable 20-mesh brass screen, were used as soil containers. The moisture content in soil was always above field capacity which could be accomplished by placing the cylinders in a tray in which water level was maintained constant to 5 cm depth.},
	language = {en},
	number = {1},
	urldate = {2020-01-23},
	journal = {Plant and Soil},
	author = {Chaudhary, T. N. and Ghildyal, B. P.},
	month = aug,
	year = {1970},
	pages = {87--90},
}

@article{fakorede_relation_1980,
	title = {Relation between seedling vigor and selection for yield improvement in maize},
	volume = {25},
	number = {3},
	journal = {Maydica},
	author = {Fakorede, M. A. B. and Ayoola, A. O.},
	year = {1980},
	pages = {135--147},
}

@article{fakorede_heterotic_1983,
	title = {Heterotic effects and association of seedling vigour with mature characteristics and grain yield in some tropical maize cultivars},
	volume = {28},
	journal = {Maydica},
	author = {Fakorede, M. A. B. and Agbana, S. B.},
	year = {1983},
	pages = {327--338},
}

@article{mock_cold_1972,
	title = {Cold tolerance in adapted maize populations},
	volume = {12},
	issn = {0011-183X, 1435-0653},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.2135/cropsci1972.0011183X001200040021x},
	doi = {10.2135/cropsci1972.0011183x001200040021x},
	language = {en},
	number = {4},
	urldate = {2020-01-23},
	journal = {Crop Science},
	author = {Mock, J.  J. and Eberhart, S. A.},
	month = jul,
	year = {1972},
	pages = {466--469},
}

@article{erbach_tillage_1982,
	title = {Tillage for continuous corn and corn-soybean rotation},
	volume = {25},
	doi = {10.13031/2013.33638},
	number = {4},
	journal = {Transactions of the ASAE},
	author = {Erbach, Donald C.},
	year = {1982},
	pages = {906--0911},
}

@article{bilbro_soil_1982,
	title = {Soil crusts and cotton emergence relationships},
	volume = {25},
	doi = {10.13031/2013.33750},
	number = {6},
	journal = {Transactions of the ASAE},
	author = {Bilbro, J. D. and Wanjura, D. F.},
	year = {1982},
	pages = {1484--1487},
}

@article{shmueli_emergence_1971,
	title = {Emergence, early growth, and salinity of five vegetable crops germinated by sprinkle and trickle irrigation in an arid zone},
	volume = {6},
	journal = {HortScience},
	author = {Shmueli, M. and Goldberg, D.},
	year = {1971},
	pages = {563--565},
}

@article{czabator_germination_1962,
	title = {Germination value: {An} index combining speed and completeness of pine seed germination},
	volume = {8},
	issn = {0015-749X},
	doi = {10.1093/forestscience/8.4.386},
	number = {4},
	journal = {Forest Science},
	author = {Czabator, Felix J},
	year = {1962},
	note = {tex.ids= czabator\_germination\_1962-1, czabator\_germination\_1962-2},
	pages = {386--396},
}

@article{el-kassaby_seed_2008,
	title = {Seed germination: {Mathematical} representation and parameters extraction},
	volume = {54},
	issn = {0015-749X},
	shorttitle = {Seed {Germination}},
	doi = {10.1093/forestscience/54.2.220},
	abstract = {A method for mathematically describing cumulative seed germination using the four-parameter Hill function is described. The function's four parameters allowed both direct or indirect biological interpretation of germination behavior and the impact of seed pretreatments on germination improvement. Three parameters, a, b, and c, allowed direct assessment of germination capacity (\%), the shape and steepness of the germination course, and germination speed (time to reach 50\% germination). The fourth parameter y0 permitted estimation of the lag time (germination onset). The mathematical expression of cumulative seed germination of unstratified and stratified seed made it possible to quantitatively estimate seedlot dormancy and the amount of germination improvement caused by a specific seed pretreatment. This was accomplished by estimating the area between the two cumulative germination curves through integration. The utility of the proposed approach was demonstrated using germination data from wind-pollinated, individual genotypes (half-sib families) of lodgepole pine (Pinus contorta var. latifolia) and bulk seedlots of lodgepole pine and white spruce (Picea glauca).},
	language = {en},
	number = {2},
	journal = {Forest Science},
	author = {El-Kassaby, Yousry A. and Moss, Ian and Kolotelo, Dave and Stoehr, Michael},
	month = apr,
	year = {2008},
	note = {tex.ids= el-kassaby\_seed\_2008-1},
	pages = {220--227},
}

@article{evetts_germination_1972,
	title = {Germination and seedling development of common milkweed and other species},
	volume = {20},
	issn = {0043-1745, 1550-2759},
	doi = {10.1017/S004317450003589x},
	abstract = {Common milkweed (Asclepias syriaca L.) seed did not survive storage in water for 1, 2, and 12 months at 40, 30, and 5 C, respectively; but under dry storage seed viability was destroyed only at 40 C for 5 months. Stratifying common milkweed seed in water at 5 C was more effective in breaking dormancy than at 22 C. Mechanical scarification also caused a significant increase in germination. Exogenous 6-furfurylamino purine (kinetin) and gibberellic acid-3 (GA) increased germination while indole-3-acetic acid (IAA) had no effect. The optimum germination temperature scheme for common milkweed was an alternating 20 to 30 C, the maximum between 35 and 40 C, and the minimum between 15 and 20 C. Common milkweed seedlings were more susceptible to moisture stress than kochia [Kochia scoparia (L.) Schrad.] but less susceptible than hemp dogbane (Apocynum cannabinum L.) and sunflower (Helianthus annuus L.). In a greenhouse study common milkweed was less drought tolerant than eight other weed species. Common milkweed seedlings tolerated wider pH ranges than honeyvine milkweed [Ampelamus albidus (Nutt.) Britt.], kochia, and sunflower. Common milkweed seedlings were less tolerant to salt solutions than four other species. Common milkweed emerged from 6-cm depths in Sharpsburg silty clay loam (sicl) at 20 or 30 C but only from the 3-cm depth at an alternating 20 to 30 C. Results from root box studies showed that common and honeyvine milkweed produced less shoot and root weight than kochia and sunflower and had a lower growth rate index of roots than sunflower. Common milkweed seedlings resprouted 21 days after planting when clipped at ground level. As days from planting to clipping increased, sprouting activity increased.},
	language = {en},
	number = {4},
	journal = {Weed Science},
	author = {Evetts, L. L. and Burnside, O. C.},
	month = jul,
	year = {1972},
	note = {tex.ids= evetts\_germination\_1972-1},
	pages = {371--378},
}

@book{de_santana_alise_2004,
	address = {Brasília},
	title = {Análise {Da} {Germinação}: {Um} {Enfoque} {Estatístico}},
	publisher = {Universidade de Brasília},
	author = {de Santana, D. G. and Ranal, Marli A.},
	year = {2004},
	note = {tex.ids= de2004analise, de\_santana\_alise\_2004-1},
}

@article{wardle_allelopathic_1991,
	title = {Allelopathic influence of nodding thistle (\emph{{Carduus} nutans} {L}.) seeds on germination and radicle growth of pasture plants},
	volume = {34},
	issn = {0028-8233, 1175-8775},
	doi = {10.1080/00288233.1991.10423358},
	language = {en},
	number = {2},
	journal = {New Zealand Journal of Agricultural Research},
	author = {Wardle, D. A. and Ahmed, M. and Nicholson, K. S.},
	month = apr,
	year = {1991},
	note = {tex.ids= wardle\_allelopathic\_1991-1},
	pages = {185--191},
}

@book{labouriau_germinacao_1983,
	title = {A {Germinação} {Das} {Sementes}},
	publisher = {Organização dos Estados Americanos. Programa Regional de Desenvolvimento Científico e Tecnológico. Série de Biologia. Monografia 24},
	author = {Labouriau, L. G.},
	year = {1983},
	note = {tex.ids= labouriau\_germinacao\_1983-1},
}

@article{kotowski_temperature_1926,
	title = {Temperature relations to germination of vegetable seeds},
	volume = {23},
	journal = {Proceedings of the American Society for Horticultural Science},
	author = {Kotowski, Feliks},
	year = {1926},
	pages = {176--184},
}

@article{perez_characterizing_2013,
	title = {Characterizing \emph{{Ipomopsis} rubra} ({Polemoniaceae}) germination under various thermal scenarios with non-parametric and semi-parametric statistical methods},
	volume = {238},
	issn = {0032-0935, 1432-2048},
	doi = {10.1007/s00425-013-1935-8},
	language = {en},
	number = {4},
	urldate = {2021-05-14},
	journal = {Planta},
	author = {Pérez, Hector E. and Kettner, Keith},
	month = oct,
	year = {2013},
	pages = {771--784},
}

@article{seglias_germination_2020,
	title = {Germination behaviour of forbs native to the southwestern {United} {States} following exposure to short-term seed bank conditions (−20\&deg;{C})},
	volume = {30},
	issn = {0960-2585, 1475-2735},
	doi = {10.1017/S096025852000001X},
	abstract = {Seeds are increasingly being stored in seed banks for ex situ conservation, food security, and restoration reserves. Although it is hypothesized that seeds of many species can survive the dry, freezer conditions (−20°C) of seed banks for many years, shelf life is unknown for many species. In particular, changes to dormancy and germination requirements following freezer storage have not yet been studied extensively. To improve our understanding of how seed dormancy and germination respond to seed banking conditions, we evaluated seed of six restoration-priority species in the southwestern United States, which is a region of increasing restoration need. Germination tendencies of seeds that were and were not exposed to a −20°C treatment for 4–6 months were evaluated under 22 cold-moist stratification and incubation treatments to broadly assess changes to dormancy and germination requirements and speed. Direct or indirect (via interactions with stratification and/or incubation treatments) differences in dormancy breaking and germination were observed in seeds for four of the six species studied. Specifically, storage temperature accounted for differences in the final germination proportion, germination during stratification, and/or rate of germination in five of the six species. Notably, seeds of the one species that exhibit a combination of physiological and physical dormancy showed significant differences in all germination measures. However, while significant differences were found between seeds exposed to short-term seed bank storage and those that were not, these differences were small and may not be biologically meaningful, indicating that seed banking these species should not change how they are used for restoration or reintroduction purposes.},
	language = {en},
	number = {2},
	urldate = {2021-05-14},
	journal = {Seed Science Research},
	author = {Seglias, Alexandra E. and Finch, Jessamine and Kramer, Andrea T.},
	month = jun,
	year = {2020},
	pages = {81--91},
}

@mastersthesis{gardner_using_2017,
	address = {Gainesville, Florida},
	title = {Using seed biology to conserve \emph{{Harperocallis} flava}, a federally endangered endemic plant of the {Florida} panhandle},
	url = {https://ufdc.ufl.edu/UFE0051546/00001/citation},
	language = {en},
	urldate = {2021-05-14},
	school = {University of Florida},
	author = {Gardner, Amber Grey},
	year = {2017},
}

@inproceedings{shafi_nonlinear_1991,
	address = {Manhattan, Kansas},
	title = {Nonlinear estimation of growth curve models for germination data analysis},
	doi = {10.4148/2475-7772.1415},
	booktitle = {Proceedings of the 1991 {Kansas} {State} {University} {Conference} on {Applied} {Statistics} in {Agriculture}},
	publisher = {Kansas State University},
	author = {Shafi, B. and Price, W. J. and Swensen, J. B. and Murray, G. A.},
	editor = {Milliken, George A. and Schwenke, James R.},
	year = {1991},
	pages = {19--42},
}

@article{olvera-carrillo_germination_2003,
	title = {Germination of the hard seed coated \emph{{Opuntia} tomentosa} {SD}, a cacti from the {México} valley},
	volume = {55},
	doi = {10.1016/S0140-1963(02)00268-9},
	number = {1},
	journal = {Journal of Arid Environments},
	author = {Olvera-Carrillo, Yadira and Márquez-Guzmán, Judith and Barradas, Vı́ctor L. and Sánchez-Coronado, Ma Esther and Orozco-Segovia, Alma},
	year = {2003},
	note = {ISBN: 0140-1963
Publisher: Elsevier},
	pages = {29--42},
}

@article{romano_germination_2020,
	title = {Germination data analysis by time-to-event approaches},
	volume = {9},
	issn = {2223-7747},
	doi = {10.3390/plants9050617},
	abstract = {Germination data are analyzed by several methods, which can be mainly classified as germination indexes and traditional regression techniques to fit non-linear parametric functions to the temporal sequence of cumulative germination. However, due to the nature of germination data, often different from other biological data, the abovementioned methods may present some limits, especially when ungerminated seeds are present at the end of an experiment. A class of methods that could allow addressing these issues is represented by the so-called “time-to-event analysis”, better known in other scientific fields as “survival analysis” or “reliability analysis”. There is relatively little literature about the application of these methods to germination data, and some reviews dealt only with parts of the possible approaches such as either non-parametric and semi-parametric or parametric ones. The present study aims to give a contribution to the knowledge about the reliability of these methods by assessing all the main approaches to the same germination data provided by sugar beet (Beta vulgaris L.) seeds cohorts. The results obtained confirmed that although the different approaches present advantages and disadvantages, they could generally represent a valuable tool to analyze germination data providing parameters whose usefulness depends on the purpose of the research.},
	language = {en},
	number = {5},
	urldate = {2021-05-16},
	journal = {Plants},
	author = {Romano, Alessandro and Stevanato, Piergiorgio},
	month = may,
	year = {2020},
	pages = {617},
}

@article{onofri_new_2010,
	title = {A new method for the analysis of germination and emergence data of weed species: {Survival} analysis for germination and emergence data},
	volume = {50},
	issn = {00431737},
	doi = {10.1111/j.1365-3180.2010.00776.x},
	language = {en},
	number = {3},
	urldate = {2021-05-16},
	journal = {Weed Research},
	author = {Onofri, A and Gresta, F and Tei, F},
	month = jun,
	year = {2010},
	pages = {187--198},
}

@article{onofri_cure_2011,
	title = {The cure model: an improved way to describe seed germination?: {The} cure model for seed germination?},
	volume = {51},
	issn = {00431737},
	shorttitle = {The cure model},
	doi = {10.1111/j.1365-3180.2011.00870.x},
	language = {en},
	number = {5},
	urldate = {2021-05-16},
	journal = {Weed Research},
	author = {Onofri, A and Mesgaran, M B and Tei, F and Cousens, R D},
	month = oct,
	year = {2011},
	pages = {516--524},
}

@inproceedings{gunjaca_survival_2000,
	address = {Pula, Croatia},
	title = {Survival analysis of the wheat germination data},
	isbn = {953-96769-1-6},
	booktitle = {Proceedings of the 22nd {International} {Conference} on {Information} {Technology} {Interfaces}},
	publisher = {IEEE},
	author = {Gunjača, Jerko and Šarčević, Hrvoje},
	editor = {Kalpić, Damir and Dobrić, Vesna Hljuz},
	year = {2000},
	pages = {307--310},
}

@article{manso_modelling_2013,
	title = {Modelling seed germination in forest tree species through survival analysis. {The} \emph{{Pinus} pinea} {L}. case study},
	volume = {289},
	issn = {03781127},
	doi = {10.1016/j.foreco.2012.10.028},
	language = {en},
	urldate = {2021-05-16},
	journal = {Forest Ecology and Management},
	author = {Manso, Rubén and Fortin, Mathieu and Calama, Rafael and Pardos, Marta},
	month = feb,
	year = {2013},
	pages = {515--524},
}

@article{janssen_method_1973,
	title = {A method of recording germination curves},
	volume = {37},
	issn = {1095-8290, 0305-7364},
	url = {https://academic.oup.com/aob/article/152977/A},
	doi = {10.1093/oxfordjournals.aob.a084738},
	language = {en},
	number = {4},
	urldate = {2021-05-18},
	journal = {Annals of Botany},
	author = {Janssen, J. G. M.},
	month = sep,
	year = {1973},
	pages = {705--708},
}

@article{cao_computing_2011,
	title = {Computing statistical indices for hydrothermal times using weed emergence data},
	volume = {149},
	issn = {1469-5146, 0021-8596},
	url = {https://www.cambridge.org/core/journals/journal-of-agricultural-science/article/abs/computing-statistical-indices-for-hydrothermal-times-using-weed-emergence-data/9F2284AF53949E4A20CC3631C2659369},
	doi = {10.1017/S002185961100030X},
	abstract = {Hydrothermal time (HTT) is a valuable environmental synthesis to predict weed emergence. However, weed scientists face practical problems in determining the best soil depth at which to calculate it. Two different types of measures are proposed for this: moment-based indices and probability density-based indices. Due to the monitoring process, it is not possible to observe the exact emergence time of every seedling; therefore, emergence times are not observed individually, seedling by seedling, but in an aggregated way. To address these facts, some new methods to estimate the proposed indices are derived, using grouped data estimators and kernel density estimators. The proposed methods have been exemplified with an emergence data set of Bromus diandrus. The results indicate that hydrothermal timing at 50 mm is more useful than that at 10 mm.},
	language = {en},
	number = {6},
	urldate = {2021-05-17},
	journal = {The Journal of Agricultural Science},
	author = {Cao, R. and Francisco-Fernández, M. and Anand, A. and Bastida, F. and González-Andújar, J. L.},
	month = dec,
	year = {2011},
	note = {Publisher: Cambridge University Press},
	pages = {701--712},
}

@article{reyes_nonparametric_2016,
	title = {Nonparametric kernel density estimation for general grouped data},
	volume = {28},
	issn = {1048-5252},
	url = {https://doi.org/10.1080/10485252.2016.1163348},
	doi = {10.1080/10485252.2016.1163348},
	abstract = {Interval-grouped data are defined, in general, when the event of interest cannot be directly observed and it is only known to have been occurred within an interval. In this framework, a nonparametric kernel density estimator is proposed and studied. The approach is based on the classical Parzen–Rosenblatt estimator and on the generalisation of the binned kernel density estimator. The asymptotic bias and variance of the proposed estimator are derived under usual assumptions, and the effect of using non-equally spaced grouped data is analysed. Additionally, a plug-in bandwidth selector is proposed. Through a comprehensive simulation study, the behaviour of both the estimator and the plug-in bandwidth selector considering different scenarios of data grouping is shown. An application to real data confirms the simulation results, revealing the good performance of the estimator whenever data are not heavily grouped.},
	number = {2},
	urldate = {2021-05-17},
	journal = {Journal of Nonparametric Statistics},
	author = {Reyes, Miguel and Francisco-Fernández, Mario and Cao, Ricardo},
	month = apr,
	year = {2016},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/10485252.2016.1163348},
	pages = {235--249},
}

@article{reyes_bandwidth_2017,
	title = {Bandwidth selection in kernel density estimation for interval-grouped data},
	volume = {26},
	issn = {1863-8260},
	url = {https://doi.org/10.1007/s11749-017-0523-9},
	doi = {10.1007/s11749-017-0523-9},
	abstract = {When interval-grouped data are available, the classical Parzen–Rosenblatt kernel density estimator has to be modified to get a computable and useful approach in this context. The new nonparametric grouped data estimator needs of the choice of a smoothing parameter. In this paper, two different bandwidth selectors for this estimator are analyzed. A plug-in bandwidth selector is proposed and its relative rate of convergence obtained. Additionally, a bootstrap algorithm to select the bandwidth in this framework is designed. This method is easy to implement and does not require Monte Carlo. Both proposals are compared through simulations in different scenarios. It is observed that when the sample size is medium or large and grouping is not heavy, both bandwidth selection methods have a similar and good performance. However, when the sample size is large and under heavy grouping scenarios, the bootstrap bandwidth selector leads to better results.},
	language = {en},
	number = {3},
	urldate = {2021-05-17},
	journal = {TEST},
	author = {Reyes, Miguel and Francisco-Fernández, Mario and Cao, Ricardo},
	month = sep,
	year = {2017},
	pages = {527--545},
}

@article{gonzalez-andujar_comparative_2016,
	title = {A comparative study between nonlinear regression and nonparametric approaches for modelling {Phalaris} paradoxa seedling emergence},
	volume = {56},
	copyright = {© 2016 European Weed Research Society},
	issn = {1365-3180},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/wre.12216},
	doi = {10.1111/wre.12216},
	abstract = {Parametric nonlinear regression (PNR) models are used widely to fit weed seedling emergence patterns to soil microclimatic indices. However, such approximation has been questioned, mainly due to several statistical limitations. Alternatively, nonparametric approaches can be used to overcome the problems presented by PNR models. Here, we used an emergence data set of Phalaris paradoxa to compare both approaches. Mean squared error and correlation results indicated higher accuracy for the descriptive ability but similar poor performance for predictive ability of the nonparametric approach in comparison with the PNR approach. These results suggest that our nonparametric cumulative distribution function approach is a valuable alternative to the classical parametric nonlinear regression models to describe complex emergence patterns for P. paradoxa, but not to predict them.},
	language = {en},
	number = {5},
	urldate = {2021-05-17},
	journal = {Weed Research},
	author = {Gonzalez‐Andujar, J. L. and Francisco‐Fernandez, M. and Cao, R. and Reyes, M. and Urbano, J. M. and Forcella, F. and Bastida, F.},
	year = {2016},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/wre.12216},
	pages = {367--376},
}

@article{graziani_hydrothermal_2009,
	title = {Hydrothermal and thermal time models for the invasive grass, \emph{{Arundo} donax}},
	volume = {90},
	issn = {03043770},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0304377008001241},
	doi = {10.1016/j.aquabot.2008.06.003},
	language = {en},
	number = {1},
	urldate = {2021-05-18},
	journal = {Aquatic Botany},
	author = {Graziani, Anthony and Steinmaus, Scott J.},
	month = jan,
	year = {2009},
	pages = {78--84},
}

@article{dumur_use_1990,
	title = {Use of the weibull function to calculate cardinal temperatures in faba bean},
	volume = {41},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/41.11.1423},
	doi = {10.1093/jxb/41.11.1423},
	language = {en},
	number = {11},
	urldate = {2021-05-18},
	journal = {Journal of Experimental Botany},
	author = {Dumur, D. and Pilbeam, C. J. and Craigon, J.},
	year = {1990},
	pages = {1423--1430},
}

@article{chantre_germination_2009,
	title = {Germination parameterization and development of an after-ripening thermal-time model for primary dormancy release of \emph{{Lithospermum} arvense} seeds},
	volume = {103},
	issn = {1095-8290, 0305-7364},
	url = {https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mcp070},
	doi = {10.1093/aob/mcp070},
	language = {en},
	number = {8},
	urldate = {2021-05-18},
	journal = {Annals of Botany},
	author = {Chantre, Guillermo R. and Batlla, Diego and Sabbatini, Mario R. and Orioli, Gustavo},
	month = jun,
	year = {2009},
	note = {tex.ids= chantre\_germination\_2009-1},
	pages = {1291--1301},
	file = {Full Text:C\:\\Users\\J. Aravind\\Zotero\\storage\\RIQA7U8A\\Chantre et al. - 2009 - Germination parameterization and development of an after-ripening thermal-time model for primary dor.pdf:application/pdf},
}

@article{dahal_effects_1990-1,
	title = {Effects of priming and endosperm integrity on seed germination rates of tomato genotypes: {I}. {Germination} at suboptimal temperature},
	volume = {41},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Effects of priming and endosperm integrity on seed germination rates of tomato genotypes},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/41.11.1431},
	doi = {10.1093/jxb/41.11.1431},
	language = {en},
	number = {11},
	urldate = {2021-05-18},
	journal = {Journal of Experimental Botany},
	author = {Dahal, Peetambar and Bradford, Kent J. and Jones, Richard A.},
	year = {1990},
	pages = {1431--1439},
}

@article{dahal_hydrothermal_1994,
	title = {Hydrothermal time analysis of tomato seed germination at suboptimal temperature and reduced water potential},
	volume = {4},
	issn = {0960-2585, 1475-2735},
	url = {https://www.cambridge.org/core/product/identifier/S096025850000204X/type/journal_article},
	doi = {10.1017/S096025850000204X},
	abstract = {Both temperature (\emph{T}) and water potential (ψ) have consistent and quantifiable effects on the rate and extent of seed germination (radicle emergence). Germination at suboptimal \emph{T} can be characterized on the basis of thermal time, or the \emph{T} in excess of a base (\emph{T$_{\textrm{b}}$}) multiplied by the time to a given percentage germination (\emph{t$_{\textrm{g}}$}). Similarly, germination at reduced ψ can be characterized on a hydrotime basis, or the ψ in excess of a base (ψ$_{\textrm{\emph{b}}}$) multiplied by \emph{t$_{\textrm{g}}$}. Within a seed population, the variation in thermal times to germination for a specific percentage (\emph{g}) is based upon the normal distribution of ψ$_{\textrm{\emph{b}}}$ values among seeds (ψ$_{\textrm{\emph{b}}}$(\emph{g})). Germination responses across a range of suboptimal \emph{T} and ψ might be accounted for by a general hydrothermal time model incorporating both \emph{T} and ψ components. We tested this hypothesis for tomato (\emph{Lycopersicon esculentum} Mill.) seeds of two genotypes differing in germination rates and tolerance of suboptimal \emph{T} and ψ. For combinations of \emph{T} (10−25°C) and ψ (0 to −0.9 MPa), a general hydrothermal time model accounted for approximately 75\% of the variation in times to germination within the seed populations of both genotypes, and over 96\% of the variation in median germination rates. However, ψ$_{\textrm{\emph{b}}}$(\emph{g}) distributions were sensitive to both the \emph{T} and ψ of imbibition, resulting in a poor fit of the model to specific time course data. Analysis of germination timing separately for low and high ψ ranges within a given \emph{T} resulted in specific models accounting for 88−99\% of the variation in individual germination times and \&gt;99\% of the variation in madian germination rates. Thus, for a given \emph{T} and ψ range, the hydrotime model closely matched tomato seed germination time courses. Accumulated hydrothermal time accounted well for germination rates at ψ\&gt; −0.5 MPa across suboptimal \emph{T} if ψ$_{\textrm{\emph{b}}}$(\emph{g}) was allowed to vary with \emph{T}. Germination did not show a consistent response to \emph{T} at ψ \&lt; −0.5 MPa, and estimated \emph{T}$_{\textrm{\emph{b}}}$ values varied over different \emph{T} ranges. Generalization of the hydrothermal time model across the entire range of suboptimal \emph{T} and ψ was limited by physiological adjustments of the seeds to their current environment. The hydrothermal time model detected and quantified these adjustment processes that would otherwise not be evident from inspection of germination time courses. Temperature and water potential influence the time to germination via physiological mechanisms that reciprocally interact.},
	language = {en},
	number = {2},
	urldate = {2021-05-18},
	journal = {Seed Science Research},
	author = {Dahal, Peetambar and Bradford, Kent J.},
	month = jun,
	year = {1994},
	pages = {71--80},
}

@article{dahal_effects_1990,
	title = {Effects of priming and endosperm integrity on seed germination rates of tomato genotypes: {II}. {Germination} at reduced water potential},
	volume = {41},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Effects of priming and endosperm integrity on seed germination rates of tomato genotypes},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/41.11.1441},
	doi = {10.1093/jxb/41.11.1441},
	language = {en},
	number = {11},
	urldate = {2021-05-18},
	journal = {Journal of Experimental Botany},
	author = {Dahal, Peetambar and Bradford, Kent J.},
	year = {1990},
	pages = {1441--1453},
}

@article{craufurd_development_1996,
	title = {Development in cowpea (\emph{{Vigna} unguiculata}). {I}. {The} influence of temperature on seed germination and seedling emergence},
	volume = {32},
	issn = {0014-4797, 1469-4441},
	url = {https://www.cambridge.org/core/product/identifier/S0014479700025801/type/journal_article},
	doi = {10.1017/S0014479700025801},
	abstract = {The base (T$_{\textrm{b}}$), optimum (T$_{\textrm{o}}$) and ceiling (T$_{\textrm{ce}}$) temperature for 50\% seed germination and seedling emergence, and the thermal time at sub-optimal temperatures (θ$_{\textrm{1}}$), were examined in experiments with a range of cowpea genotypes from different habitats and latitudes. There was substantial genotypic variation in seed germination for T$_{\textrm{b}}$ and T$_{\textrm{o}}$, but not for T$_{\textrm{ce}}$. There was no evidence that genotypes from semi-arid habitats had higher values of T$_{\textrm{o}}$ or T$_{\textrm{ce}}$, but estimates of T$_{\textrm{b}}$ for seed germination were related to latitude and were highest in genotypes originating from close to the equator. The significance of these responses as a component of developmental plasticity in relation to the adaptation of cowpeas is discussed.},
	language = {en},
	number = {1},
	urldate = {2021-05-18},
	journal = {Experimental Agriculture},
	author = {Craufurd, P. Q. and Ellis, R. H. and Summerfield, R. R. J. and Menin, L.},
	month = jan,
	year = {1996},
	note = {tex.ids= craufurd\_development\_1996-1
publisher: Cambridge University Press},
	pages = {1--12},
}

@article{covell_influence_1986,
	title = {The influence of temperature on seed germination rate in grain legumes: {I}. {A} comparison of chickpea, lentil, soyabean and cowpea at constant temperatures},
	volume = {37},
	issn = {0022-0957, 1460-2431},
	shorttitle = {The influence of temperature on seed germination rate in grain legumes},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/37.5.705},
	doi = {10.1093/jxb/37.5.705},
	language = {en},
	number = {5},
	urldate = {2021-05-18},
	journal = {Journal of Experimental Botany},
	author = {Covell, S. and Ellis, R. H. and Roberts, E. H. and Summerfield, R. J.},
	year = {1986},
	pages = {705--715},
}

@article{chejara_factors_2008,
	title = {Factors affecting germination of coolatai grass ( \emph{{Hyparrhenia} hirta} )},
	volume = {56},
	issn = {0043-1745, 1550-2759},
	url = {https://www.cambridge.org/core/product/identifier/S0043174500017811/type/journal_article},
	doi = {10.1614/WS-07-163.1},
	abstract = {Coolatai grass is an invasive, perennial grass from Africa and the Middle East that has infested large areas of northern New South Wales, Australia, and also occurs in other Australian states. An understanding of the seed germination ecology of Coolatai grass can assist in predicting its potential distribution and developing effective management strategies. The effects of various environmental factors on Coolatai grass seed germination were investigated in a series of laboratory experiments. The effect of diurnal alternating temperatures (5–45 C) with a 12-h photoperiod were examined on a thermogradient plate. Seed germination occurred at almost all temperature combinations from 5 to 45 C. At moderate temperatures the speed of seed germination was very high; at 30/20 C more than 80\% of seeds were germinated within 12 h. Germination was slightly enhanced by the presence of light, but length of photoperiod did not affect germination. Germination at neutral pH was over 90\%, and declined to 65\% at acidic (pH 4) and alkaline (pH 10) pH levels. Germination was completely inhibited at an osmotic stress of −0.55 MPa or greater and was reduced by 50\% at −0.37 MPa. Greater germination in relatively dry soil conditions compared with native species may contribute to the establishment of this species in the field. Results indicate that Coolatai grass seeds can germinate over a wide range of diurnal temperatures, light regimes, pH levels, and under marginal water stress. These characteristics help explain the successful invasion of Coolatai grass and provide evidence that this species is capable of establishing in many parts of Australia.},
	language = {en},
	number = {4},
	urldate = {2021-05-18},
	journal = {Weed Science},
	author = {Chejara, Vinod K. and Kristiansen, Paul and Whalley, Ralph D. B. and Sindel, Brian M. and Nadolny, Christopher},
	month = aug,
	year = {2008},
	pages = {543--548},
}

@article{bloomberg_hydrothermal_2009,
	title = {Hydrothermal time germination models for radiata pine ( \emph{{Pinus} radiata} {D}. {Don})},
	volume = {19},
	issn = {0960-2585, 1475-2735},
	url = {https://www.cambridge.org/core/product/identifier/S0960258509990031/type/journal_article},
	doi = {10.1017/S0960258509990031},
	abstract = {The objective of this study was to fit a hydrothermal germination model to germination data for a seedlot of radiata pine ({<}span class="italic"{>}Pinus radiata{<}/span{>} D. Don). Seeds were incubated for 50\&nbsp;d at constant temperatures and water potentials ({<}span class="italic"{>}T{<}/span{>}\&nbsp;=\&nbsp;12.5–32.5°C, Ψ\&nbsp;=\&nbsp;0 to −\&nbsp;1.2\&nbsp;MPa). Most seeds completed germination within 50\&nbsp;d, but for low Ψ and/or non-optimal temperatures ({<}span class="italic"{>}T{<}/span{>}\&nbsp;\&lt;\&nbsp;17.5°C, {<}span class="italic"{>}T{<}/span{>}\&gt;25°C) many seeds did not complete germination. In general, germination data conformed to the hydrothermal model. Departures from the model were encountered for slow-germinating seeds at suboptimal temperatures ({<}span class="italic"{>}T{<}/span{>}\&nbsp;≤\&nbsp;20°C). To account for these departures, two alternative hydrothermal models were fitted with an additional term for an upwards shift in seed base water potential with increasing time to germination. The alternative models more correctly predicted germination time than the original model. Similarly, reduced percentage germination at supra-optimal temperatures ({<}span class="italic"{>}T{<}/span{>}\&gt;20°C) was explained by including a term in the hydrothermal model which shifted the base water potential of seeds upwards towards zero, which in turn reduced the predicted rate that hydrothermal time would be accumulated by seeds. The rate of this upwards shift in base water potential was dependent on time to complete germination and ambient water potential as well as supra-optimal temperature.},
	language = {en},
	number = {3},
	urldate = {2021-05-18},
	journal = {Seed Science Research},
	author = {Bloomberg, M. and Sedcole, J.R. and Mason, E.G. and Buchan, G.},
	month = sep,
	year = {2009},
	pages = {171--182},
}

@article{bradford_water_1994,
	title = {Water relations of lettuce seed thermoinhibition. {I}. {Priming} and endosperm effects on base water potential},
	volume = {4},
	issn = {0960-2585, 1475-2735},
	url = {http://www.journals.cambridge.org/abstract_S0960258500001938},
	doi = {10.1017/S0960258500001938},
	language = {en},
	number = {01},
	urldate = {2021-05-18},
	journal = {Seed Science Research},
	author = {Bradford, Kent J. and Somasco, Oscar A.},
	month = mar,
	year = {1994},
}

@article{bradford_quantifying_2008,
	title = {Quantifying the sensitivity of barley seed germination to oxygen, abscisic acid, and gibberellin using a population-based threshold model},
	volume = {59},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erm315},
	doi = {10.1093/jxb/erm315},
	language = {en},
	number = {2},
	urldate = {2021-05-18},
	journal = {Journal of Experimental Botany},
	author = {Bradford, Kent J. and Benech-Arnold, Roberto L. and Côme, Daniel and Corbineau, Françoise},
	month = feb,
	year = {2008},
	pages = {335--347},
}

@article{zuk-golaszewska_effect_2007,
	title = {Effect of scarification on seed germination of red clover in hydrotime model terms},
	volume = {35},
	issn = {02510952, 18195717},
	url = {http://www.ingentaconnect.com/content/ista/sst/2007/00000035/00000002/art00008},
	doi = {10.15258/sst.2007.35.2.08},
	number = {2},
	urldate = {2021-05-18},
	journal = {Seed Science and Technology},
	author = {Zuk-Gołaszewska, K. and Bochenek, A. and Gołaszewski, J.},
	month = jul,
	year = {2007},
	pages = {326--336},
}

@article{thomas_interaction_2010,
	title = {The interaction of temperature, water availability and fire cues regulates seed germination in a fire-prone landscape},
	volume = {162},
	issn = {0029-8549, 1432-1939},
	url = {http://link.springer.com/10.1007/s00442-009-1456-0},
	doi = {10.1007/s00442-009-1456-0},
	language = {en},
	number = {2},
	urldate = {2021-05-18},
	journal = {Oecologia},
	author = {Thomas, Paul Bengt and Morris, E. Charles and Auld, Tony D. and Haigh, Anthony M.},
	month = feb,
	year = {2010},
	pages = {293--302},
}

@article{rowse_hydrothermal_2003,
	title = {Hydrothermal threshold models can describe the germination response of carrot ( \emph{{Daucus} carota} ) and onion ( \emph{{Allium} cepa} ) seed populations across both sub‐ and supra‐optimal temperatures},
	volume = {158},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1046/j.1469-8137.2003.00707.x},
	doi = {10.1046/j.1469-8137.2003.00707.x},
	language = {en},
	number = {1},
	urldate = {2021-05-18},
	journal = {New Phytologist},
	author = {Rowse, Hr and Finch‐Savage, We},
	month = apr,
	year = {2003},
	pages = {101--108},
}

@article{alvarado_hydrothermal_2005,
	title = {Hydrothermal time analysis of seed dormancy in true (botanical) potato seeds},
	volume = {15},
	issn = {0960-2585, 1475-2735},
	url = {https://www.cambridge.org/core/product/identifier/S0960258505000085/type/journal_article},
	doi = {10.1079/SSR2005198},
	abstract = {As seed dormancy is released within a seed population, both the rate and percentage of germination increase progressively with increasing dose of a dormancy-breaking treatment or condition. Population-based models can account for this behaviour on the basis of shifting response thresholds as dormancy is alleviated. In particular, hydrothermal time analysis of germination sensitivity to water potential (Ψ) and temperature ({<}span class="italic"{>}T{<}/span{>}) can describe these features of seed behaviour. We used the hydrothermal time model to analyse the effects of dormancy-breaking treatments on germination of dormant true (botanical) potato ({<}span class="italic"{>}Solanum tuberosum{<}/span{>} L.) seeds (TPS). After-ripening (37°C and 4\% seed moisture content) of TPS for 7 or 30 days partially or fully alleviated primary dormancy. The median base water potential required to prevent germination [Ψ{<}span class="sub"{>}b{<}/span{>}(50)] decreased from –0.25 MPa in control seeds to –0.87 MPa and –1.83 MPa after 7 and 30 days of after-ripening, respectively. In contrast, the base temperature for germination ({<}span class="italic"{>}T{<}/span{>}{<}span class="sub"{>}b{<}/span{>}) was relatively unaffected (0–3.3°C). Fluridone (50 μM), an inhibitor of abscisic acid (ABA) biosynthesis, also promoted germination of dormant TPS and lowered Ψ{<}span class="sub"{>}b{<}/span{>}(50), indicating a role for {<}span class="italic"{>}de novo{<}/span{>} synthesis of ABA during dormancy maintenance. Moist chilling (3 days at 4°C) or gibberellin (100 μM) alleviated secondary dormancy and lowered Ψ{<}span class="sub"{>}b{<}/span{>}(50) values from –0.08 MPa to –0.36 and –0.87 MPa, respectively. The hydrothermal time model allows quantification of dormancy levels and explains why changes in germination speed and percentage are closely correlated during dormancy alleviation.},
	language = {en},
	number = {2},
	urldate = {2021-05-18},
	journal = {Seed Science Research},
	author = {Alvarado, Veria and Bradford, Kent J.},
	month = jun,
	year = {2005},
	pages = {77--88},
}

@article{zhang_modified_2013,
	title = {A modified thermal time model to predict germination rate of ryegrass and tall fescue at constant temperatures},
	volume = {53},
	issn = {0011-183X, 1435-0653},
	url = {https://onlinelibrary.wiley.com/doi/10.2135/cropsci2012.02.0085},
	doi = {10.2135/cropsci2012.02.0085},
	language = {en},
	number = {1},
	urldate = {2021-05-18},
	journal = {Crop Science},
	author = {Zhang, Hongxiang and McGill, Craig R. and Irving, Louis J. and Kemp, Peter D. and Zhou, Daowei},
	month = jan,
	year = {2013},
	pages = {240--249},
}

@article{zambrano-navea_hydrothermal_2013,
	title = {A hydrothermal seedling emergence model for \emph{{Conyza} bonariensis}},
	volume = {53},
	issn = {00431737},
	url = {http://doi.wiley.com/10.1111/wre.12020},
	doi = {10.1111/wre.12020},
	language = {en},
	number = {3},
	urldate = {2021-05-18},
	journal = {Weed Research},
	author = {Zambrano-Navea, C and Bastida, F and Gonzalez-Andujar, J L},
	editor = {Davis, Adam},
	month = jun,
	year = {2013},
	pages = {213--220},
}

@article{shafii_estimation_2001,
	title = {Estimation of cardinal temperatures in germination data analysis},
	volume = {6},
	issn = {1085-7117, 1537-2693},
	url = {http://link.springer.com/10.1198/108571101317096569},
	doi = {10.1198/108571101317096569},
	language = {en},
	number = {3},
	urldate = {2021-05-18},
	journal = {Journal of Agricultural, Biological, and Environmental Statistics},
	author = {Shafii, Bahman and Price, William J.},
	month = sep,
	year = {2001},
	pages = {356--366},
}

@article{scott_cold_1985,
	title = {Cold tolerance in tomato. {I}. {Seed} germination and early seedling growth of \emph{{Lycopersicon} esculentum}},
	volume = {65},
	issn = {0031-9317, 1399-3054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.1985.tb08678.x},
	doi = {10.1111/j.1399-3054.1985.tb08678.x},
	language = {en},
	number = {4},
	urldate = {2021-05-18},
	journal = {Physiologia Plantarum},
	author = {Scott, S. Jeffrey and Jones, R. A.},
	month = dec,
	year = {1985},
	pages = {487--492},
}

@article{ni_germination_1993,
	title = {Germination and dormancy of abscisic acid- and gibberellin-deficient mutant tomato (\emph{{Lycopersicon} esculentum}) seeds (sensitivity of germination to abscisic acid, gibberellin, and water potential)},
	volume = {101},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/101/2/607-617/6065968},
	doi = {10.1104/pp.101.2.607},
	language = {en},
	number = {2},
	urldate = {2021-05-18},
	journal = {Plant Physiology},
	author = {Ni, B. R. and Bradford, K. J.},
	month = feb,
	year = {1993},
	pages = {607--617},
}

@article{ni_quantitative_1992,
	title = {Quantitative models characterizing seed germination responses to abscisic acid and osmoticum},
	volume = {98},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/98/3/1057-1068/6087674},
	doi = {10.1104/pp.98.3.1057},
	language = {en},
	number = {3},
	urldate = {2021-05-18},
	journal = {Plant Physiology},
	author = {Ni, Bing-Rui and Bradford, Kent J.},
	month = mar,
	year = {1992},
	pages = {1057--1068},
}

@article{kebreab_modelling_1999,
	title = {Modelling the effects of water stress and temperature on germination rate of \emph{{Orobanche} aegyptiaca} seeds},
	volume = {50},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/50.334.655},
	doi = {10.1093/jxb/50.334.655},
	language = {en},
	number = {334},
	urldate = {2021-05-18},
	journal = {Journal of Experimental Botany},
	author = {Kebreab, E. and Murdoch, A. J.},
	month = may,
	year = {1999},
	pages = {655--664},
}

@article{kebreab_quantitative_1999,
	title = {A quantitative model for loss of primary dormancy and induction of secondary dormancy in imbibed seeds of \emph{{Orobanche}} spp},
	volume = {50},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/50.331.211},
	doi = {10.1093/jxb/50.331.211},
	language = {en},
	number = {331},
	urldate = {2021-05-18},
	journal = {Journal of Experimental Botany},
	author = {Kebreab, E. and Murdoch, A. J.},
	month = feb,
	year = {1999},
	pages = {211--219},
}

@article{ellis_safe_1983,
	title = {Safe procedures for the removal of rice seed dormancy},
	volume = {11},
	journal = {Seed Science and Technology},
	author = {Ellis, R. H. and Hong, T. D. and Roberts, E. H.},
	year = {1983},
	pages = {77--112},
}

@article{gianinetti_seed_2007,
	title = {Seed dormancy in red rice. {XII}: {Population}-based analysis of dry-afterripening with a hydrotime model},
	volume = {17},
	doi = {10.1017/S0960258507841523},
	number = {4},
	journal = {Seed Science Research},
	author = {Gianinetti, Alberto and Cohn, Marc Alan},
	year = {2007},
	note = {tex.ids= gianinetti\_seed\_2007-1
ISBN: 0960-2585
publisher: Cambridge University Press},
	pages = {253},
}

@article{bradford_applications_2004,
	title = {Applications of hydrotime analysis in seed testing},
	journal = {Seed Technology},
	author = {Bradford, Kent J. and Still, David W.},
	year = {2004},
	note = {ISBN: 1096-0724
Publisher: JSTOR},
	pages = {75--85},
}

@inproceedings{dahal_concept_1993,
	address = {Paris},
	title = {The concept of hydrothermal time in seed germination and priming},
	booktitle = {Proceedings of the {Fourth} {International} {Workshop} on {Seeds}: {Basic} and {Applied} {Aspects} of {Seed} {Biology}, {Vol}. 3.},
	publisher = {Association pour la Formation Professionnelle de l’Interprofession Semences},
	author = {Dahal, P. and Bradford, K. J. and Haigh, A. M.},
	editor = {Come, D and Corbineau, F},
	year = {1993},
	pages = {1009--1014},
}

@article{kaplan_nonparametric_1958,
	title = {Nonparametric estimation from incomplete observations},
	volume = {53},
	issn = {0162-1459},
	doi = {10.1080/01621459.1958.10501452},
	abstract = {In lifetesting, medical follow-up, and other fields the observation of the time of occurrence of the event of interest (called a death) may be prevented for some of the items of the sample by the previous occurrence of some other event (called a loss). Losses may be either accidental or controlled, the latter resulting from a decision to terminate certain observations. In either case it is usually assumed in this paper that the lifetime (age at death) is independent of the potential loss time; in practice this assumption deserves careful scrutiny. Despite the resulting incompleteness of the data, it is desired to estimate the proportion P(t) of items in the population whose lifetimes would exceed t (in the absence of such losses), without making any assumption about the form of the function P(t). The observation for each item of a suitable initial event, marking the beginning of its lifetime, is presupposed. For random samples of size N the product-limit (PL) estimate can be defined as follows: List and label the N observed lifetimes (whether to death or loss) in order of increasing magnitude, so that one has 0≤t 1ǐ≤t 2ǐ≤ … ≤t N ǐ. Then P(t)= II. [(N – r)/(N – r + 1)], where r assumes those values for which tr ≤t and for which tr ǐ measures the time to death. This estimate is the distribution, unrestricted as to form, which maximizes the likelihood of the observations. Other estimates that are discussed are the actuarial estimates (which are also products, but with the number of factors usually reduced by grouping); and reduced-sample (RS) estimates, which require that losses not be accidental, so that the limits of observation (potential loss times) are known even for those items whose deaths are observed. When no losses occur at ages less than t, the estimate of P(t) in all cases reduces to the usual binomial estimate, namely, the observed proportion of survivors. * Prepared while the authors were at Bell Telephone Laboratories and Johns Hopkins University respectively. The work was aided by a grant from the Office of Naval Research.},
	number = {282},
	urldate = {2021-05-18},
	journal = {Journal of the American Statistical Association},
	author = {Kaplan, E. L. and Meier, Paul},
	month = jun,
	year = {1958},
	note = {Publisher: Taylor \& Francis
\_eprint: https://www.tandfonline.com/doi/pdf/10.1080/01621459.1958.10501452},
	pages = {457--481},
}

@article{hunter_analysis_1984,
	title = {The analysis of data from germination tests},
	volume = {102},
	doi = {10.1017/S0021859600041642},
	number = {1},
	journal = {Journal of Agricultural Science},
	author = {Hunter, E. A. and Glasbey, C. A. and Naylor, R. E. L.},
	year = {1984},
	pages = {207--213},
}

@inproceedings{finch-savage_use_2000,
	address = {Merida, Mexico},
	title = {Use of threshold germination models under variable field conditions},
	doi = {10.1079/9780851994048.0489},
	abstract = {The potential of four threshold models to predict germination patterns (in carrot cv. Nantes) recorded in 15 different field environments was investigated. Thermal time tended to underestimate the time to germination and hydrothermal time tended to overestimate the time to germination. The prediction was improved under some conditions by incorporating hydrothermal priming time to take account of...},
	language = {English},
	urldate = {2021-05-17},
	booktitle = {Seed biology: {Advances} and {Applications}. {Proceedings} of the {Sixth} {International} {Workshop} on {Seeds}, {Merida}, {Mexico}, 1999.},
	publisher = {CABI, Wallingford, UK},
	author = {Finch-Savage, W. E. and Phelps, K. and Peach, L. and Steckel, J. R. A.},
	editor = {Black, Michael and Bradford,, Kent J. and Vázquez-Ramos, Jorge},
	year = {2000},
	note = {Publisher: CABI Publishing},
	pages = {489--497},
}

@article{golaszewski_computational_2008,
	title = {A computational procedure for hydrotime concept of seed germination},
	volume = {45},
	number = {1},
	journal = {Biometrical Letters},
	author = {Gołaszewski, Janusz and Bochenek, Anna},
	year = {2008},
	pages = {55--67},
}

@article{watt_development_2010,
	title = {Development of a hydrothermal time seed germination model which uses the {Weibull} distribution to describe base water potential},
	volume = {221},
	issn = {0304-3800},
	url = {https://www.sciencedirect.com/science/article/pii/S0304380010000566},
	doi = {10.1016/j.ecolmodel.2010.01.017},
	abstract = {Seed germination has been modelled extensively using hydrothermal time (HTT) models, that predict time to germination as a function of the extent to which seedbed temperature, T, and water potential, Ψ, exceed the base temperature, Tb, and base water potential, Ψb, of each seed percentile, g. Within a seed population the variation in time to germination arises from variation in Ψb(g) modelled by a normal distribution. We tested the assumption of normality in the distribution of Ψb(g) by germinating seed of two unrelated species with non-dormant seed (Buddleja davidii (Franch.) and Pinus radiata D. Don) across a range of constant Ψ at sub-optimal T. When incorporated into a HTT model the Weibull distribution more accurately described both the right skewed distribution of Ψb(g) and germination time course over sub-optimal T than the HTT based on the normal distribution, for both species. Given the flexibility of the Weibull distribution this model not only provides a useful method for predicting germination but also a means of determining the distribution of Ψb(g).},
	language = {en},
	number = {9},
	urldate = {2021-05-17},
	journal = {Ecological Modelling},
	author = {Watt, Michael S. and Xu, Vega and Bloomberg, Mark},
	month = may,
	year = {2010},
	pages = {1267--1272},
}

@article{washitani_convenient_1987,
	title = {A convenient screening test system and a model for thermal germination responses of wild plant seeds: {Behaviour} of model and real seeds in the system},
	volume = {10},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-3040.ep11604111},
	doi = {10.1111/1365-3040.ep11604111},
	abstract = {A convenient test system for screening the thermal germination behaviour of seeds was developed for both basic and applied research in seed germination ecophysiology. Only two temperature-controlled facilities, a test period of about a month and a relatively small number of sample seeds arc needed to obtain information on the thermal-germination parameters of individual seed populations, such as lower or higher limit temperatures, and thermal times required for germination. In the test system, the germination performances of sample seed populations were compared under two temperature regimes: a gradually increasing temperature regime and a gradually decreasing temperature regime, in which the seeds were subjected to gradually changing temperatures in the range of 4 36°C. In order to assess the effects of various values for thermal-germination parameters on the patterns of germination performance in the system, the behaviour of model seeds characterized by a definite set of thermal germination parameters were investigated. Referring to the results of the simulations, the actual germination patterns of some wild-seed populations in the test system were interpreted in terms of thermal-germination parameters.},
	language = {en},
	number = {7},
	urldate = {2021-05-17},
	journal = {Plant, Cell \& Environment},
	author = {Washitani, I.},
	year = {1987},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1365-3040.ep11604111},
	pages = {587--598},
}

@article{rawlins_predicting_2012,
	title = {Predicting germination in semi-arid wildland seedbeds {II}. {Field} validation of wet thermal-time models},
	volume = {76},
	issn = {00988472},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0098847211002450},
	doi = {10.1016/j.envexpbot.2011.10.004},
	language = {en},
	urldate = {2021-05-17},
	journal = {Environmental and Experimental Botany},
	author = {Rawlins, Jennifer K. and Roundy, Bruce A. and Egget, Dennis and Cline, Nathan},
	month = feb,
	year = {2012},
	pages = {68--73},
}

@article{rowse_model_1999,
	title = {A model of the effects of water stress on seed advancement and germination},
	volume = {143},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1046/j.1469-8137.1999.00455.x},
	doi = {10.1046/j.1469-8137.1999.00455.x},
	abstract = {A model of seed germination is proposed which uses a variable with the units of an osmotic potential (virtual osmotic potential) to integrate the effect of a constant or a varying water potential. This differs from existing models that describe the effects of fixed water potentials on germination, or the effects of fixed priming water potentials on the subsequent germination at a fixed water potential. When a seed is sown, the virtual osmotic potential is assumed to fall at a rate that depends on the ambient water potential, and on the difference between its current and a minimum value. Radicle growth is assumed to initiate when the difference between the ambient water potential and the virtual osmotic potential exceeds a threshold. The germination of carrot and onion seeds at various fixed potentials below 0 MPa was well described by the virtual osmotic potential model. The model was also used to simulate the results of experiments in which seeds were given a single step change in water potential.},
	language = {en},
	number = {2},
	urldate = {2021-05-17},
	journal = {New Phytologist},
	author = {Rowse, H. R. and McKEE, J. M. T. and Higgs, E. C.},
	year = {1999},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1469-8137.1999.00455.x},
	pages = {273--279},
}

@article{vleeshouwers_modelling_2000,
	title = {Modelling field emergence patterns in arable weeds},
	volume = {148},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1046/j.1469-8137.2000.00773.x},
	doi = {10.1046/j.1469-8137.2000.00773.x},
	abstract = {A model was developed to simulate weed emergence patterns after soil cultivation. In the model, the consecutive processes of dormancy release, germination and pre-emergence growth were modelled in separate modules. Input variables of the model were: date of soil cultivation, soil temperature and soil penetration resistance. Output variables of the model were: seedling density and timing of seedling emergence. The model was parameterized for Polygonum persicaria, Chenopodium album and Spergula arvensis with data from previous field and laboratory experiments. The model was evaluated with data from an experiment, in which emergence of P. persicaria, C. album and S. arvensis was monitored in field plots that were cultivated once only, at one of five dates in the spring. At the same time as the field observations on seedling emergence, seasonal changes in seed dormancy of the buried weed seeds were assessed by testing the germination of seed lots that were buried in envelopes. From a comparison between field observations and simulated data, it appeared that the model overestimated the rate of dormancy release in spring, whereas germination and pre-emergence growth were simulated well. In general, therefore, both the numbers of emerging seedlings and the timing of emergence could be predicted accurately, when dormancy was not simulated but introduced from experimental data. Improvement of predictions of field emergence of weeds should mainly focus on increasing the precision of the simulation of dormancy release. Close correlations were found between seedbed temperature and both the extent and rate of seedling emergence, but analysis with the simulation model revealed that they were only partly based on causal relationships, so that they have limited predictive value.},
	language = {en},
	number = {3},
	urldate = {2021-05-17},
	journal = {New Phytologist},
	author = {Vleeshouwers, L. M. and Kropff, M. J.},
	year = {2000},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1469-8137.2000.00773.x},
	pages = {445--457},
}

@article{onofri_experimental_2014,
	title = {Experimental design and parameter estimation for threshold models in seed germination},
	volume = {54},
	issn = {00431737},
	url = {http://doi.wiley.com/10.1111/wre.12095},
	doi = {10.1111/wre.12095},
	language = {en},
	number = {5},
	urldate = {2021-05-17},
	journal = {Weed Research},
	author = {Onofri, A and Mesgaran, M B and Neve, P and Cousens, R D},
	editor = {Bastiaans, Lammert},
	month = oct,
	year = {2014},
	pages = {425--435},
}

@article{onofri_hydrothermal-time--event_2018,
	title = {Hydrothermal-time-to-event models for seed germination},
	volume = {101},
	issn = {11610301},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1161030118301692},
	doi = {10.1016/j.eja.2018.08.011},
	language = {en},
	urldate = {2021-05-17},
	journal = {European Journal of Agronomy},
	author = {Onofri, Andrea and Benincasa, Paolo and Mesgaran, Mohsen B. and Ritz, Christian},
	month = nov,
	year = {2018},
	pages = {129--139},
}

@inproceedings{phelps_statistical_1997,
	address = {Dordrecht},
	series = {Current {Plant} {Science} and {Biotechnology} in {Agriculture}},
	title = {A statistical perspective on threshold type germination models},
	isbn = {978-94-011-5716-2},
	url = {https://doi.org/10.1007/978-94-011-5716-2_40},
	doi = {10.1007/978-94-011-5716-2_40},
	abstract = {A need for empirical germination models that would give reliable predictions under field conditions led us to look critically at the statistical assumptions made in the concepts of thermal and hydrothermal time. Doubts were raised about the unquestioning description of rate temperature relationships by straight lines and the subsequent extrapolation of base temperatures from them. An alternative method where base temperatures are estimated from final percentage germination is suggested. This removes the linearity constraint from the rate temperature relationship and should have better predictive properties at low temperatures. An advantage of the method is that it predicts both the timing and percentage of seeds which will germinate in a given time interval. Thus it provides a unifying hypothesis which may aid interpretation of results from alternating temperature studies. Generalization of the method to include water potential is described and the methods are illustrated with several data sets.},
	language = {en},
	urldate = {2021-05-17},
	booktitle = {Basic and {Applied} {Aspects} of {Seed} {Biology}: {Proceedings} of the {Fifth} {International} {Workshop} on {Seeds}, {Reading}, 1995},
	publisher = {Springer Netherlands},
	author = {Phelps, K. and Finch-Savage, W. E.},
	editor = {Ellis, R. H. and Black, M. and Murdoch, A. J. and Hong, T. D.},
	year = {1997},
	pages = {361--368},
}

@article{moltchanova_comparison_2020,
	title = {Comparison of three different statistical approaches (non-linear least-squares regression, survival analysis and {Bayesian} inference) in their usefulness for estimating hydrothermal time models of seed germination},
	volume = {30},
	issn = {0960-2585, 1475-2735},
	url = {https://www.cambridge.org/core/journals/seed-science-research/article/abs/comparison-of-three-different-statistical-approaches-nonlinear-leastsquares-regression-survival-analysis-and-bayesian-inference-in-their-usefulness-for-estimating-hydrothermal-time-models-of-seed-germination/4B67BA1B07F635F017864AA073C3D4EB},
	doi = {10.1017/S0960258520000082},
	abstract = {Hydrothermal time (HTT) models describe the time course of seed germination for a population of seeds under specific temperature and water potential conditions. The parameters of the HTT model are usually estimated using either a linear regression, non-linear least squares estimation or a generalized linear regression model. There are problems with these approaches, including loss of information, and censoring and lack of independence in the germination data. Model estimation may require optimization, and this can have a heavy computational burden. Here, we compare non-linear regression with survival and Bayesian methods, to estimate HTT models for germination of two clover species. All three methods estimated similar HTT model parameters with similar root mean squared errors. However, the Bayesian approach allowed (1) efficient estimation of model parameters without the need for computation-intensive methods and (2) easy comparison of HTT parameters for the two clover species. HTT models that accounted for a species effect were superior to those that did not. Inspection of credibility intervals and estimated posterior distributions for the Bayesian HTT model shows that it is credible that most HTT model parameters were different for the two clover species, and these differences were consistent with known biological differences between species in their germination behaviour.},
	language = {en},
	number = {1},
	urldate = {2021-05-17},
	journal = {Seed Science Research},
	author = {Moltchanova, Elena and Sharifiamina, Shirin and Moot, Derrick J. and Shayanfar, Ali and Bloomberg, Mark},
	month = mar,
	year = {2020},
	note = {Publisher: Cambridge University Press},
	pages = {64--72},
}

@article{mesgaran_importance_2013,
	title = {Importance of distribution function selection for hydrothermal time models of seed germination},
	volume = {53},
	issn = {00431737},
	url = {http://doi.wiley.com/10.1111/wre.12008},
	doi = {10.1111/wre.12008},
	language = {en},
	number = {2},
	urldate = {2021-05-17},
	journal = {Weed Research},
	author = {Mesgaran, M B and Mashhadi, H R and Alizadeh, H and Hunt, J and Young, K R and Cousens, R D},
	editor = {Andersson, Lars},
	month = apr,
	year = {2013},
	pages = {89--101},
}

@article{leon_characterization_2015,
	title = {Characterization and modeling of itchgrass (\emph{{Rottboellia} cochinchinensis}) biphasic seedling emergence patterns in the tropics},
	volume = {63},
	issn = {0043-1745, 1550-2759},
	url = {https://bioone.org/journals/weed-science/volume-63/issue-3/WS-D-14-00172.1/Characterization-and-Modeling-of-Itchgrass-Rottboellia-cochinchinensis-Biphasic-Seedling-Emergence/10.1614/WS-D-14-00172.1.full},
	doi = {10.1614/WS-D-14-00172.1},
	abstract = {Itchgrass is an aggressive weed species in tropical agroecosystems. Because of phytosanitary restrictions to exports, pineapple producers must use a zero tolerance level for this species. An understanding of itchgrass seedling emergence would help producers to better time POST control. The objective of the present study was to characterize itchgrass seedling emergence patterns and develop a predictive model. Multiple field experiments were conducted in four agricultural fields in Costa Rica between 2010 and 2011 for a total of 9 site-years. Itchgrass consistently showed a biphasic emergence pattern, with a first emergence phase that was faster and more consistent across site-years than the second one. Weibull logistic models based on chronological time (R2adj = 0.92) and thermal time with Tbase = 20 C (R2adj = 0.92) provided the best fit for the combined emergence data for two experimental locations in 2010. Both models predicted itchgrass seedling emergence adequately for most site-years, but the thermal-time model was more accurate (R2adj = 0.64 to 0.86) than the chronological model (R2adj = 0.31 to 0.74), especially when temperatures were high. Both models showed high accuracy in the first emergence phase but tended to underestimate emergence rate during the second phase. The models predicted 50\% emergence at 14 d or 80 growing degree days and the stabilization of the first emergence phase at approximately 25 d or 200 growing degree days. Thus, these models can be used to properly time itchgrass POST control. More research is needed to understand the regulatory mechanisms responsible for the variability of the second emergence phase.Nomenclature: Itchgrass, Rottboellia cochinchinensis (Lour.) W.D. Clayton, pineapple, Ananas comosus (L.) Merr.},
	number = {3},
	urldate = {2021-05-17},
	journal = {Weed Science},
	author = {Leon, Ramon G. and Izquierdo, Jordi and González-Andújar*, José Luis},
	month = jul,
	year = {2015},
	note = {Publisher: Weed Science Society of America},
	pages = {623--630},
}

@article{mesgaran_water_2017,
	title = {Water availability shifts the optimal temperatures for seed germination: {A} modelling approach},
	volume = {351},
	issn = {0304-3800},
	url = {https://www.sciencedirect.com/science/article/pii/S030438001630521X},
	doi = {10.1016/j.ecolmodel.2017.02.020},
	abstract = {Hydrothermal time (HTT) models have been widely applied to describe the germination responses of seeds to temperature and water. Some HTT models assume that the thermoinhibition of germination is caused by an upward shift in base water potential Ψb(g) that only happens above the optimum temperature To, and that To is a parameter independent of the water stress level. However, the available data suggest that these assumptions may be invalid in practice. We introduce a new HTT model that uses a log-logistic distribution for Ψb(g) and assumes a linear increase in Ψb(g) across both sub- and supra-optimal temperature ranges. We also provide explicit mathematical solutions for estimating To and other cardinal temperatures within a HTT modelling framework. Germination data were obtained for two winter annual plant species (Hordeum spontaneum and Phalaris minor) and used to build and test the model. For both species, the linear upward shift in Ψb(g) was confirmed across both sub-and supra-optimal ranges, while the hydrotime constant θH decreased nonlinearly with temperature. This interplay between θH and Ψb(g) resulted in a curvilinear germination rate response to temperature that accounts for thermoinhibition of germination at high temperatures. The optimal temperature decreased proportionally with decreasing water potential and became cooler for higher (slower) germination fractions than for the lower (faster) ones. The new modelling approach not only gave good fits to germination data (with root mean square errors {<}10\%), but also provided useful insights about the adaptive strategies evolved by plant species to optimize their germination timing under the various temperature and moisture environments.},
	language = {en},
	urldate = {2021-05-17},
	journal = {Ecological Modelling},
	author = {Mesgaran, Mohsen B. and Onofri, Andrea and Mashhadi, Hamid R. and Cousens, Roger D.},
	month = may,
	year = {2017},
	pages = {87--95},
}

@article{kochy_hydrothermal_2007,
	title = {Hydrothermal time model of germination: {Parameters} for 36 {Mediterranean} annual species based on a simplified approach},
	volume = {8},
	issn = {14391791},
	shorttitle = {Hydrothermal time model of germination},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1439179106000375},
	doi = {10.1016/j.baae.2006.04.002},
	language = {en},
	number = {2},
	urldate = {2021-05-17},
	journal = {Basic and Applied Ecology},
	author = {Köchy, Martin and Tielbörger, Katja},
	month = mar,
	year = {2007},
	pages = {171--182},
}

@article{hardegree_hydrothermal_2015,
	title = {Hydrothermal germination models: {Comparison} of two data-fitting approaches with probit optimization},
	volume = {55},
	copyright = {Copyright © by the Crop Science Society of America, Inc.},
	issn = {1435-0653},
	shorttitle = {Hydrothermal germination models},
	url = {https://acsess.onlinelibrary.wiley.com/doi/abs/10.2135/cropsci2014.10.0703},
	doi = {10.2135/cropsci2014.10.0703},
	abstract = {Probit models for estimating hydrothermal germination rate yield model parameters that have been associated with specific physiological processes. The desirability of linking germination response to seed physiology must be weighed against expectations of model fit and the relative accuracy of predicted germination response. Computationally efficient empirical models have been proposed that do not require a priori assumptions about model shape parameters, but the accuracy of these models has not been compared to the more common probit-optimization procedure. Thirteen seedlots, representing six native perennial rangeland grasses and an invasive annual weed, were germinated over the constant temperature range of 3 to 36°C and water potential range of 0 to -2.5 MPa. Hydrothermal germination models were generated using probit optimization, optimized regression, and statistical gridding. These models were evaluated for the pattern and magnitude of residual model error and the relative magnitude of predictive errors under field-simulated temperature and moisture conditions. Residual model errors in predictions of germination rate were greatest for the probit optimization procedure. Statistical gridding and optimized regression produced lower predictive model error, but the latter procedure could not resolve germination response for slower-germinating seed populations. The more computationally efficient and accurate regression and statistical-gridding procedures may be desirable for identifying germination strategies and syndromes that are based on predicted response to simulated conditions of field temperature and moisture.},
	language = {en},
	number = {5},
	urldate = {2021-05-17},
	journal = {Crop Science},
	author = {Hardegree, Stuart P. and Walters, Christina T. and Boehm, Alex R. and Olsoy, Peter J. and Clark, Patrick E. and Pierson, Frederick B.},
	year = {2015},
	note = {\_eprint: https://acsess.onlinelibrary.wiley.com/doi/pdf/10.2135/cropsci2014.10.0703},
	pages = {2276--2290},
}

@article{leblanc_calibration_2004,
	title = {Calibration and validation of a common lambsquarters (\emph{{Chenopodium} album}) seedling emergence model},
	volume = {52},
	issn = {0043-1745},
	url = {https://www.jstor.org/stable/4046792},
	doi = {10.1614/P2002-109},
	abstract = {Studies were conducted to calibrate and validate a mathematical model previously developed to predict common lambsquarters seedling emergence at different corn seedbed preparation times. The model was calibrated for different types of soil by adjusting the base temperature of common lambsquarters seedling emergence to the soil texture. A relationship was established with the sand mineral fraction of the soil and was integrated into the model. The calibrated model provided a good fit of the field data and was accurate in predicting cumulative weed emergence in different soil types. The validation was done using data collected independently at a site located 80 km from the original experimental area. There were no differences between observed and predicted values. The accuracy of the model is very satisfactory because the emergence of common lambsquarters populations was accurately predicted at the 95\% probability level. This model is one of the first to take into consideration seedbed preparation time and soil texture. This common lambsquarters emergence model could be adapted to model other weed species whose emergence is limited by low spring temperature.},
	number = {1},
	urldate = {2021-05-17},
	journal = {Weed Science},
	author = {Leblanc, Maryse L. and Cloutier, Daniel C. and Stewart, Katrine A. and Hamel, Chantal},
	year = {2004},
	note = {Publisher: [Cambridge University Press, Weed Science Society of America]},
	pages = {61--66},
}

@article{hardegree_predicting_2006,
	title = {Predicting germination response to temperature. {I}. {Cardinal}-temperature models and subpopulation-specific regression},
	volume = {97},
	issn = {1095-8290, 0305-7364},
	url = {http://academic.oup.com/aob/article/97/6/1115/207352/Predicting-Germination-Response-to-Temperature-I},
	doi = {10.1093/aob/mcl071},
	language = {en},
	number = {6},
	urldate = {2021-05-17},
	journal = {Annals of Botany},
	author = {Hardegree, Stuart P.},
	month = jun,
	year = {2006},
	pages = {1115--1125},
}

@article{hardegree_hydrothermal_2018,
	title = {Hydrothermal germination models: {Assessment} of the wet‐thermal approximation of potential field response},
	volume = {58},
	issn = {0011-183X, 1435-0653},
	shorttitle = {Hydrothermal germination models},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.2135/cropsci2017.11.0666},
	doi = {10.2135/cropsci2017.11.0666},
	language = {en},
	number = {5},
	urldate = {2021-05-17},
	journal = {Crop Science},
	author = {Hardegree, Stuart P. and Roundy, Bruce A. and Walters, Christina T. and Reeves, Patrick A. and Richards, Christopher M. and Moffet, Corey A. and Sheley, Roger L. and Flerchinger, Gerald N.},
	month = sep,
	year = {2018},
	pages = {2042--2049},
}

@article{gummerson_effect_1986,
	title = {The effect of constant temperatures and osmotic potentials on the germination of sugar beet},
	volume = {37},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/37.6.729},
	doi = {10.1093/jxb/37.6.729},
	abstract = {The germination-time curves for a series of experiments at constant temperatures and osmotic potentials were analysed to produce a relationship between germination, time, temperature and osmotic potential. The analysis involved the concept of hydrothermal time which is a combination of potential above a base potential, temperature above a base temperature and time. For most of the population of sugar-beet seeds examined, the hydrothermal time required for germination was constant. The base temperatures of the seeds were similar but the base potentials varied between seeds. Analysis of the times to germination of fractions of the seed population, grouped according to the order in which they germinated, showed that the base potentials were almost normally distributed An equation using this distribution can be used to predict the time course of germination over a wide range of temperatures and potentials. The equation uses five parameters to describe a seed population: the proportion of live seeds, the hydrothermal time required for germination, the base temperature and the mean and standard deviation of base potential.},
	number = {6},
	urldate = {2021-05-17},
	journal = {Journal of Experimental Botany},
	author = {Gummerson, R. J.},
	month = jun,
	year = {1986},
	pages = {729--741},
}

@article{gianinetti_basic_2020,
	title = {Basic features of the analysis of germination data with generalized linear mixed models},
	volume = {5},
	issn = {2306-5729},
	url = {https://www.mdpi.com/2306-5729/5/1/6},
	doi = {10.3390/data5010006},
	language = {en},
	number = {1},
	urldate = {2021-05-17},
	journal = {Data},
	author = {Gianinetti, Alberto},
	month = jan,
	year = {2020},
	pages = {6},
	file = {data-05-00006-v3.pdf:G\:\\OneDrive\\IPK Docs\\germination modeling\\GLMM\\data-05-00006-v3.pdf:application/pdf},
}

@article{garcia-huidobro_time_1982,
	title = {Time, temperature and germination of pearl millet (\emph{{Pennisetum} typhoides} {S}. \& {H}.): {I}. {Constant} temperature},
	volume = {33},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/33.2.288},
	doi = {10.1093/jxb/33.2.288},
	abstract = {The germination of pearl millet (Pennisetum typhoides S. \&amp; H.) seeds was investigated at constant temperatures between 12 °C and 47 °C on a thermal gradient plate.The rate of germination increased linearly with temperature from a base Tb to a sharply defined optimum To beyond which the rate decreased linearly with temperature, reaching zero at Tm. The linearity of the response both above and below To allowed time and temperature to be combined in a thermal time at which a specified fraction of the seeds germinated. Within the population Tb and Tm were constant.},
	number = {2},
	urldate = {2021-05-17},
	journal = {Journal of Experimental Botany},
	author = {Garcia-Huidobro, J. and Monteith, J. L. and Squire, G. R.},
	month = apr,
	year = {1982},
	pages = {288--296},
}

@article{bradford_interpreting_2018,
	title = {Interpreting biological variation: {Seeds}, populations and sensitivity thresholds},
	volume = {28},
	issn = {0960-2585, 1475-2735},
	shorttitle = {Interpreting biological variation},
	url = {https://www.cambridge.org/core/product/identifier/S0960258518000156/type/journal_article},
	doi = {10.1017/S0960258518000156},
	language = {en},
	number = {3},
	urldate = {2021-05-17},
	journal = {Seed Science Research},
	author = {Bradford, Kent J.},
	month = sep,
	year = {2018},
	pages = {158--167},
}

@article{bradford_population-based_1993,
	title = {A population-based threshold model describing the relationship between germination rates and seed deterioration},
	volume = {44},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/44.7.1225},
	doi = {10.1093/jxb/44.7.1225},
	abstract = {The time required for germination increases prior to the loss of viability as seeds deteriorate during storage. We have developed a population-based threshold model that can quantify and predict seed germination times and percentages after various ageing periods under constant conditions. The model assumes that each seed has a maximum potential lifetime, the values of which vary in a normal distribution among individual seeds, and that the time to germination of a particular seed is inversely proportional to the remaining difference between the accumulated ageing period and the maximum lifetime of that seed. This model described with reasonable accuracy the germination time-courses of lettuce (Lactuca sativa L.) seeds after increasing periods of controlled deterioration at 10\% moisture content (fresh weight basis) and 40 °C. In seeds of high initial quality, two phases of deterioration were detected, a relatively slow phase before significant loss of viability occurred and a more rapid phase once viability began to decline. Prehydration and redrying treatments that shortened the time to germination also reduced or eliminated the initial lag phase before the loss of viability began. Seed germination rates after different ageing periods can be normalized on a common ‘ageing-time’ scale, emphasizing the continuous and progressive nature of deteriorative processes in seeds. The model predicted, and the data confirmed, that there was a critical imbibition time after which no additional normal seedlings would germinate. This critical imbibition time for a given seed lot was independent of the ageing period. The maximum lifetime threshold model, in conjunction with previous population-based models of seed viability during storage, can provide a quantitative description of seed germination rates and normal or abnormal seedling percentages throughout the storage life of a seed lot.},
	number = {7},
	urldate = {2021-05-17},
	journal = {Journal of Experimental Botany},
	author = {Bradford, Kent J. and Tarquis, Ana M. and Durán, José M.},
	month = jul,
	year = {1993},
	pages = {1225--1234},
}

@article{colbach_construction_2007,
	title = {Construction and evaluation of {ALOMYSYS} modelling the effects of cropping systems on the blackgrass life-cycle: {From} seedling to seed production},
	volume = {201},
	issn = {0304-3800},
	shorttitle = {Construction and evaluation of {ALOMYSYS} modelling the effects of cropping systems on the blackgrass life-cycle},
	url = {https://www.sciencedirect.com/science/article/pii/S0304380006004455},
	doi = {10.1016/j.ecolmodel.2006.09.018},
	abstract = {Blackgrass (Alopecurus myosuroides Huds.) is an annual weed frequently found in winter crops and increasingly tolerant to herbicides. To manage this weed with less or no herbicides, the model ALOMYSYS was developed to quantify the effects of cropping systems on the demography of blackgrass. The sub-model for seed survival, dormancy, germination and pre-emergent growth was described in a previous paper. This paper presents the sub-model quantifying seedling survival, tillering, heading, flowering and seed production, as a function of the weed emergence date and density (predicted by the seed bank sub-model), the crops grown in the field, the cultivation techniques used to manage the crop (tillage, sowing, herbicides, nitrogen, harvest) and the climate (temperature, rainfall). The sub-model is based on the annual life-cycle of blackgrass; the relationship between the various life-stages depends on the model input variables and on the characteristics of the weed population (e.g. tillering decreases with weed density, herbicide efficacy decreases with plant stage and density, etc.). The equations describing the life-stages and processes were deduced from previous greenhouse experiments and field trials. The resulting model was evaluated by comparing the simulations to independent field observations. This validation showed the model to accurately predict weed stages for a given year as well as the dynamics over the years, in contrasted cropping systems. The model can thus be used to evaluate and design new cropping systems for integrated crop protection.},
	language = {en},
	number = {3},
	urldate = {2021-05-17},
	journal = {Ecological Modelling},
	author = {Colbach, N. and Chauvel, B. and Gauvrit, C. and Munier-Jolain, N. M.},
	month = mar,
	year = {2007},
	pages = {283--300},
}

@article{bradford_threshold_2005,
	title = {Threshold models applied to seed germination ecology},
	doi = {10.1111/j.1469-8137.2004.01302.x},
	journal = {New Phytologist},
	author = {Bradford, Kent J.},
	year = {2005},
	note = {ISBN: 0028-646X
Publisher: JSTOR},
	pages = {338--341},
}

@inproceedings{bradford_hydrotime_1997,
	address = {Dordrecht},
	series = {Current {Plant} {Science} and {Biotechnology} in {Agriculture}},
	title = {The hydrotime concept in seed germination and dormancy},
	isbn = {978-94-011-5716-2},
	url = {https://doi.org/10.1007/978-94-011-5716-2_39},
	doi = {10.1007/978-94-011-5716-2_39},
	abstract = {The hydrotime concept has been developed to describe the relationship between water potential (ψ) and seed germination rates. In analogy with thermal time, hydrotime is the accumulated ψ units (MPa) above a base or threshold value (ψb) multiplied by the time of imbibition at that ψ. The germination rate (inverse of time to radicle emergence) increases linearly as the seed ψ increases above ψb. As ψb values vary among individual seeds, the amount by which the ψ exceeds ψb also varies among seeds, resulting in the typical right-skewed sigmoid germination time courses. Factors which influence seed germination kinetics alter the mean ψb of the seed lot, with higher (more positive) values resulting in an inhibition of germination or imposition of dormancy and lower (more negative) values being associated with rapid germination and high vigour. The induction or alleviation of dormancy involves physiological shifts in the ψb distribution, allowing a seed population to track both long-term and short-term environmental conditions to enhance seedling survival.},
	language = {en},
	urldate = {2021-05-17},
	booktitle = {Basic and {Applied} {Aspects} of {Seed} {Biology}: {Proceedings} of the {Fifth} {International} {Workshop} on {Seeds}, {Reading}, 1995},
	publisher = {Springer Netherlands},
	author = {Bradford, K. J.},
	editor = {Ellis, R. H. and Black, M. and Murdoch, A. J. and Hong, T. D.},
	year = {1997},
	pages = {349--360},
}

@article{bradford_water_1990,
	title = {A water relations analysis of seed germination rates},
	volume = {94},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.94.2.840},
	doi = {10.1104/pp.94.2.840},
	abstract = {Seed germination culminates in the initiation of embryo growth and the resumption of water uptake after imbibition. Previous applications of cell growth models to describe seed germination have focused on the inhibition of radicle growth rates at reduced water potential (Ψ). An alternative approach is presented, based upon the timing of radicle emergence, to characterize the relationship of seed germination rates to Ψ. Using only three parameters, a `hydrotime constant' and the mean and standard deviation in minimum or base Ψ among seeds in the population, germination time courses can be predicted at any Ψ, or normalized to a common time scale equal to that of seeds germinating in water. The rate of germination of lettuce (Lactuca sativa L. cv Empire) seeds, either intact or with the endosperm envelope cut, increased linearly with embryo turgor. The endosperm presented little physical resistance to radicle growth at the time of radicle emergence, but its presence markedly delayed germination. The length of the lag period after imbibition before radicle emergence is related to the time required for weakening of the endosperm, and not to the generation of additional turgor in the embryo. The rate of endosperm weakening is sensitive to Ψ or turgor.},
	number = {2},
	urldate = {2021-05-17},
	journal = {Plant Physiol.},
	author = {Bradford, Kent J.},
	month = oct,
	year = {1990},
	pages = {840--849},
}

@article{bradford_applications_2002,
	title = {Applications of hydrothermal time to quantifying and modeling seed germination and dormancy},
	volume = {50},
	issn = {0043-1745},
	url = {https://www.jstor.org/stable/4046371},
	doi = {10.1614/0043-1745(2002)050[0248:AOHTTQ]2.0.CO;2},
	abstract = {Knowledge and prediction of seasonal weed seedling emergence patterns is useful in weed management programs. Seed dormancy is a major factor influencing the timing of seedling emergence, and once dormancy is broken, environmental conditions determine the rate of germination and seedling emergence. Seed dormancy is a population-based phenomenon, because individual seeds are independently sensing their environment and responding physiologically to the signals they perceive. Mathematical models based on characterizing the variation that occurs in germination times among individual seeds in a population can describe and quantity environmental and after-ripening effects on seed dormancy. In particular, the hydrothermal time model can describe and quantify the effects of temperature and water potential on seed germination. This model states that the time to germination of a given seed fraction is inversely proportional to the amount by which a given germination factor (e.g., temperature or water potential) exceeds a threshold level for that factor. The hydrothermal time model provides a robust method for understanding how environmental factors interact to result in the germination phenotype (i.e., germination pattern over time) of a seed population. In addition, other factors that influence seed dormancy and germination act by causing the water potential thresholds of the seed population to shift to higher or lower values. This relatively simple model can describe and quantify the germination behavior of seeds across a wide array of environmental conditions and dormancy states, and can be used as an input to more general models of seed germination and seedling emergence in the field.},
	number = {2},
	urldate = {2021-05-17},
	journal = {Weed Science},
	author = {Bradford, Kent J.},
	year = {2002},
	pages = {248--260},
}

@article{boddy_population-based_2012,
	title = {Population-based threshold models describe weed germination and emergence patterns across varying temperature, moisture and oxygen conditions},
	volume = {49},
	issn = {00218901},
	url = {http://doi.wiley.com/10.1111/j.1365-2664.2012.02206.x},
	doi = {10.1111/j.1365-2664.2012.02206.x},
	language = {en},
	number = {6},
	urldate = {2021-05-17},
	journal = {Journal of Applied Ecology},
	author = {Boddy, Louis G. and Bradford, Kent J. and Fischer, Albert J.},
	editor = {Firn, Jennifer},
	month = dec,
	year = {2012},
	pages = {1225--1236},
}

@article{bakhshandeh_population-based_2020,
	title = {Population-based threshold models: {A} reliable tool for describing aged seeds response of rapeseed under salinity and water stress},
	volume = {176},
	issn = {00988472},
	shorttitle = {Population-based threshold models},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0098847220301039},
	doi = {10.1016/j.envexpbot.2020.104077},
	language = {en},
	urldate = {2021-05-17},
	journal = {Environmental and Experimental Botany},
	author = {Bakhshandeh, Esmaeil and Jamali, Mohsen},
	month = aug,
	year = {2020},
	pages = {104077},
}

@incollection{bradford_water_1995,
	address = {New York},
	title = {Water relations in seed germination},
	booktitle = {Marcel {Dekker} {Inc}., {New} {York}},
	publisher = {Marcel Dekker Inc.},
	author = {Bradford, K. J.},
	editor = {Kigel, J. and Galili, G.},
	year = {1995},
	pages = {291--295},
}

@article{allen_when_2003,
	title = {When and how many? {Hydrothermal} models and the prediction of seed germination},
	volume = {158},
	issn = {0028-646X},
	shorttitle = {When and how many?},
	url = {https://www.jstor.org/stable/1514074},
	doi = {10.1046/j.1469-8137.2003.00729.x},
	number = {1},
	urldate = {2021-05-17},
	journal = {The New Phytologist},
	author = {Allen, Phil},
	year = {2003},
	note = {Publisher: [Wiley, New Phytologist Trust]},
	pages = {1--3},
}

@article{atashi_application_2015,
	title = {Application of a hydrothermal time seed germination model using the weibull distribution to describe base water potential in zucchini (\emph{{Cucurbita} pepo} l.)},
	volume = {34},
	issn = {1435-8107},
	url = {https://doi.org/10.1007/s00344-014-9452-y},
	doi = {10.1007/s00344-014-9452-y},
	abstract = {Seed germination has been modeled extensively using hydrothermal time (HTT) models. Generally, a normal distribution for base water potential ψb(g)and a linear upward shift in ψb(g)with increasing temperature were used within these models to relate variation in ψb(g)to the variation in time to germination of a given fraction of seeds. However, little research has tested these assumptions. Therefore, the main purpose of this study was to test the assumption of normality in the distribution of ψb(g)by germinating zucchini (Cucurbita pepo L.) seed with non-dormant seed across a range of constant ψ at sub- and supra-optimal temperatures. Zucchini seeds were incubated at six constant temperature regimes (15, 20, 25, 30, 35, and 37 °C) at each of the following osmotic potentials (0, −0.15, −0.30, −0.45, and −0.60 MPa). Results indicate that when incorporated into an HTT model, the Weibull distribution (R2 = 0.85; RMSE = 11.89) more accurately described ψb(g)and germination course over sub- and supra-optimal temperatures than HTT based on a normal distribution (R2 = 0.77; RMSE = 14.80). According to these models, base temperature and base water potential for the 50th percentile (ψb(50)) were estimated at 9.38 °C for both models and −1.27 and −1.31 MPa by the normal and Weibull distribution, respectively. Given the flexibility of the Weibull distribution this model not only provides a useful method for predicting germination but also a means for determining the distribution of ψb(g).},
	language = {en},
	number = {1},
	urldate = {2021-05-17},
	journal = {Journal of Plant Growth Regulation},
	author = {Atashi, Sadegh and Bakhshandeh, Esmaeil and Mehdipour, Mozde and Jamali, Mohsen and Teixeira da Silva, Jaime A.},
	month = mar,
	year = {2015},
	pages = {150--157},
}

@incollection{allen_modeling_2007,
	title = {Modeling of seed dormancy},
	copyright = {Copyright © 2007 by Blackwell Publishing Ltd},
	isbn = {978-0-470-98884-8},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470988848.ch4},
	language = {en},
	urldate = {2021-05-17},
	booktitle = {Annual {Plant} {Reviews} {Volume} 27: {Seed} {Development}, {Dormancy} and {Germination}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Allen, Phil S. and Benech‐Arnold, Roberto L. and Batlla, Diego and Bradford, Kent J.},
	editor = {Bradford, Kent J. and Nonogaki, Hiro},
	year = {2007},
	doi = {10.1002/9780470988848.ch4},
	note = {Section: 4
\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470988848.ch4},
	pages = {72--112},
}

@article{alvarado_hydrothermal_2002,
	title = {A hydrothermal time model explains the cardinal temperatures for seed germination},
	volume = {25},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-3040.2002.00894.x},
	doi = {10.1046/j.1365-3040.2002.00894.x},
	abstract = {Temperature (T) and water potential (y) are two primary environmental regulators of seed germination. Seeds exhibit a base or minimum T for germination (Tb), an optimum T at which germination is most rapid (To), and a maximum or ceiling T at which germination is prevented (Tc). Germination at suboptimal T can be characterized on the basis of thermal time, or the T in excess of Tb multiplied by the time to a given germination percentage (tg). Similarly, germination at reduced y can be characterized on a hydrotime basis, or tg multiplied by the y in excess of a base or threshold y that just prevents germination (yb). Within a seed population, the variation in thermal times to germination among different seed fractions (g) is based on a normal distribution of yb values among seeds (yb(g)). Germination responses across a range of suboptimal T and y can be described by a general hydrothermal time model that combines the T and y components, but this model does not account for the decrease in germination rates and percentages when T exceeds To. We report here that supra-optimal temperatures shift the ψb(g) distribution of a potato (Solanum tuberosum L.) seed population to more positive values, explaining why both germination rates and percentages are reduced as T increases above To. A modified hydrothermal time model incorporating changes in ψb(g) at T {>} To describes germination timing and percentage across all T and ψ at which germination can occur and provides physiologically relevant indices of seed behaviour.},
	language = {en},
	number = {8},
	urldate = {2021-05-17},
	journal = {Plant, Cell \& Environment},
	author = {Alvarado, V. and Bradford, K. J.},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-3040.2002.00894.x},
	pages = {1061--1069},
}

@article{jardim_amorim_use_2021,
	title = {The use of the generalized linear model to assess the speed and uniformity of germination of corn and soybean seeds},
	volume = {11},
	issn = {2073-4395},
	doi = {10.3390/agronomy11030588},
	abstract = {The use of seeds with high physiological quality allows rapid growth and establishment of seedlings in the field to be obtained. Therefore, the accuracy of the information obtained during the determination of the physiological quality of seeds is of great importance. The objective was to use generalized linear models, investigating which link function (Probit, Logit and Complementary log-log) is suitable to predict T50 and uniformity during germination of soybean and corn seeds. To perform the experiments, we used seeds from five commercial hybrids and/or cultivars of corn and soybean. The germination speed was calculated by counting the germinated seeds and the results were expressed in the form of proportions. Germination uniformity was calculated by the difference in the times required for germination. The best model was selected according to the criteria of the test of Deviance, AIC and BIC. The Logit model showed accurate results for most cultivars. The evaluation of germination in the form of proportions considering the assumption of binomial response is satisfactory, and the choice of the link function is dependent on the characteristics of each lot and/or species evaluated. The use of this methodology makes it possible to estimate any germination time and uniformity.},
	language = {en},
	number = {3},
	urldate = {2021-05-14},
	journal = {Agronomy},
	author = {Jardim Amorim, Deoclecio and Pereira dos Santos, Amanda Rithieli and Nunes da Piedade, Gabriela and Quelvia de Faria, Rute and Amaral da Silva, Edvaldo Aparecido and Pereira Sartori, Maria Márcia},
	month = mar,
	year = {2021},
	pages = {588},
}

@article{rathod_introduction_2020,
	title = {Introduction to survival analysis and application in agricultural research},
	volume = {1},
	url = {https://foodandscientificreports.com/details/introduction-to-survival-analysis-and-application-in-agricultural-research.html},
	number = {4},
	journal = {Food and Scientific Reports},
	author = {Rathod, Santosha and Saha, Amit and Sinha, Kanchan},
	year = {2020},
	pages = {28--30},
}

@article{berry_curve_1988,
	title = {Curve fitting of germination data using the {Richards} function},
	volume = {11},
	issn = {1365-3040},
	doi = {10.1111/j.1365-3040.1988.tb01135.x},
	abstract = {Abstract. The fitting of the generalized Richards function to germination data by using two nested iterative and least squares regression procedures to estimate the four parameters (all of which can be associated with features of biological growth) is demonstrated. The program also involves a procedure of parallel curve analysis which makes comparisons between two curves by examining the whole process represented by the curve and not just a point or portion thereof. Excellent agreement between observed and expected values was obtained by analyzing data which defined patterns of germination exhibiting a range of rates and final percentages. The program also calculates a number of derived quantities including maximum daily rate of germination and time to 50\% of final germination.},
	language = {en},
	number = {3},
	urldate = {2022-02-23},
	journal = {Plant, Cell \& Environment},
	author = {Berry, G. J. and Cawood, R. J. and Flood, R. G.},
	year = {1988},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3040.1988.tb01135.x},
	pages = {183--188},
}

@article{hsu_mathematical_1984,
	title = {A mathematical model to utilize the logistic function in germination and seedling growth},
	volume = {35},
	issn = {0022-0957},
	doi = {10.1093/jxb/35.11.1629},
	abstract = {Several models have been proposed to describe germination rates, but most are limited in statistical analysis and biological meaning of indices. Therefore, a mathematical model is proposed to utilize the logistic function. The function was defined as an overall response including time, temperature, and the interaction between time and temperature. Cumulative germination percentages over time were used to develop the model.Germination tests were conducted on indiangrass (Sorghastrum nutans (L.) Nash) strain ‘IG-2C-F1’, at constant temperatures of 9, 12, 15, 20, 25, and 30 °C. The function fitted the observed data over six temperatures at r2 = 0.99. Time to reach 10\% of final germination (Gt10) increased from 2.5 d at 30 °C to 44.0 d at 9 °C, and Gt50 (time to reach 50\% of final germination) increased from 3.6 d at 30 °C to 53.8 d at 9 °C. True germination rate (\% d−1) for each temperature was maximum at Gt50. A linear model of 1/Gt50 versus temperature was used to estimate the base temperature of 8.3 °C for germination. An Arrhenius plot indicated a change occurred between 20 °C and 25 °C for temperature response of germination. Published data on hypocotyl growth of Cucumis melo L. were recalculated using the model. Absolute growth rates showed a temperature response similar to the published weighted-mean elongation rates. Base temperature for hypocotyl growth of C. melo was estimated as 8.8 °C. The proposed model proved to be useful in calculating and interpreting germination and growth kinetics.},
	number = {11},
	urldate = {2022-02-23},
	journal = {Journal of Experimental Botany},
	author = {Hsu, F. H. and Nelson, C. J. and Chow, W. S.},
	month = nov,
	year = {1984},
	pages = {1629--1640},
}

@article{onofri_analysing_2019,
	title = {Analysing censored data in agricultural research: {A} review with examples and software tips},
	volume = {174},
	issn = {1744-7348},
	shorttitle = {Analysing censored data in agricultural research},
	doi = {10.1111/aab.12477},
	abstract = {Metric data are usually assessed on a continuous scale with good precision, but sometimes agricultural researchers cannot obtain precise measurements of a variable. Values of such a variable cannot then be expressed as real numbers (e.g., 1.51 or 2.56), but often can be represented by intervals into which the values fall (e.g., from 1 to 2 or from 2 to 3). In this situation, statisticians talk about censoring and censored data, as opposed to missing data, where no information is available at all. Traditionally, in agriculture and biology, three methods have been used to analyse such data: (a) when intervals are narrow, some form of imputation (e.g., mid-point imputation) is used to replace the interval and traditional methods for continuous data are employed (such as analyses of variance [ANOVA] and regression); (b) for time-to-event data, the cumulative proportions of individuals that experienced the event of interest are analysed, instead of the individual observed times-to-event; (c) when intervals are wide and many individuals are collected, non-parametric methods of data analysis are favoured, where counts are considered instead of the individual observed value for each sample element. In this paper, we show that these methods may be suboptimal: The first one does not respect the process of data collection, the second leads to unreliable standard errors (SEs), while the third does not make full use of all the available information. As an alternative, methods of survival analysis for censored data can be useful, leading to reliable inferences and sound hypotheses testing. These methods are illustrated using three examples from plant and crop sciences.},
	language = {en},
	number = {1},
	urldate = {2022-02-23},
	journal = {Annals of Applied Biology},
	author = {Onofri, Andrea and Piepho, Hans-Peter and Kozak, Marcin},
	year = {2019},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/aab.12477},
	pages = {3--13},
}

@article{roh_maturity_2004,
	title = {Maturity and temperature stratification affect the germination of \emph{{Styrax} japonicus} seeds},
	volume = {79},
	doi = {10.1080/14620316.2004.11511820},
	number = {4},
	journal = {The Journal of Horticultural Science and Biotechnology},
	author = {Roh, Mark and Bentz, Jo-Ann and Wang, Paul and Li, Ercheng and Koshioka, Masaji},
	year = {2004},
	note = {Publisher: Taylor \& Francis},
	pages = {645--651},
}

@article{vallance_studies_1950,
	title = {Studies on the germination of the seeds of \emph{{Striga} hermonthica} {I}. {The} influence of moisture-treatment, stimulant-dilution, and after-ripening on germination},
	volume = {14},
	doi = {10.1093/oxfordjournals.aob.a083251},
	number = {55},
	journal = {Annals of Botany},
	author = {Vallance, KB},
	year = {1950},
	note = {Publisher: JSTOR},
	pages = {347--363},
}

@article{richardson_use_2018,
	title = {Use of auto-germ to model germination timing in the sagebrush-steppe},
	volume = {8},
	issn = {20457758},
	doi = {10.1002/ece3.4591},
	language = {en},
	number = {23},
	urldate = {2022-06-14},
	journal = {Ecology and Evolution},
	author = {Richardson, William C. and Whitaker, Dallin R. and Sant, Kyler P. and Barney, Nicholas S. and Call, Ryan S. and Roundy, Bruce A. and Aanderud, Zachary T. and Madsen, Matthew D.},
	month = dec,
	year = {2018},
	pages = {11533--11542},
}

@article{heydecker_clarity_1966,
	title = {Clarity in recording germination data},
	volume = {210},
	doi = {10.1038/210753b0},
	journal = {Nature},
	author = {Heydecker, Walter},
	year = {1966},
	note = {Publisher: Springer},
	pages = {753--754},
}

@article{talska_comparison_2020,
	title = {A comparison of seed germination coefficients using functional regression},
	volume = {8},
	issn = {2168-0450},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aps3.11366},
	doi = {10.1002/aps3.11366},
	abstract = {Premise Seed germination over time is characterized by a sigmoid curve, called a germination curve, in which the percentage (or absolute number) of seeds that have completed germination is plotted against time. A number of individual coefficients have been developed to characterize this germination curve. However, as germination is considered to be a qualitative developmental response of an individual seed that occurs at one time point, but individual seeds within a given treatment respond at different time points, it has proven difficult to develop a single index that satisfactorily incorporates both percentage and rate. The aim of this paper is to develop a new coefficient, the continuous germination index (CGI), which quantifies seed germination as a continuous process, and to compare the CGI with other commonly used indexes. Methods To create the new index, the germination curves were smoothed using nondecreasing splines and the CGI was derived as the area under the resulting spline. For the comparison of the CGI with other common indexes, a regression model with functional response was developed. Results Using both an experimentally obtained wild pea (Pisum sativum subsp. elatius) seed data set and a hypothetical data set, we showed that the CGI is able to characterize the germination process better than most other indices. The CGI captures the local behavior of the germination curves particularly well. Discussion The CGI can be used advantageously for the characterization of the germination process. Moreover, B-spline coefficients extracted by its construction can be employed for the further statistical processing of germination curves using functional data analysis methods.},
	language = {en},
	number = {8},
	urldate = {2023-05-03},
	journal = {Applications in Plant Sciences},
	author = {Talská, Renáta and Machalová, Jitka and Smýkal, Petr and Hron, Karel},
	year = {2020},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/aps3.11366},
	pages = {e11366},
	file = {aps3.11366.pdf:G\:\\OneDrive\\IPK Docs\\germination modeling\\CGI\\aps3.11366.pdf:application/pdf},
}

@article{hradilova_variation_2019,
	title = {Variation in wild pea (\emph{{Pisum} sativum} subsp. \emph{elatius}) seed dormancy and its relationship to the environment and seed coat traits},
	volume = {7},
	issn = {2167-8359},
	url = {https://peerj.com/articles/6263},
	doi = {10.7717/peerj.6263},
	abstract = {Background Seed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue. Methods Seeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA). Results Seed total germination ranged from 0\% to 100\%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92\%), (2) dormant at both treatments (29 acc., 15\%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80\%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g−1) than those of non-dormant (mean 1.77 mg g−1) and responsive accessions (mean 1.87 mg g−1). Each soil and bioclimatic variable and also germination responsivity (representing synthetic variable characterizing germination pattern of seeds) was spatially clustered. However, only one environmental variable (BIO7, i.e., annual temperature range) was significantly related to germination responsivity. Non-dormant and responsive accessions covered almost whole range of BIO7 while dormant accessions are found in the environment with higher annual temperature, smaller temperature variation, seasonality and milder winter. Ecological niche modelling showed a more localized potential distribution of dormant group. Seed dormancy in the wild pea might be part of a bet-hedging mechanism for areas of the Mediterranean basin with more unpredictable water availability in an otherwise seasonal environment. This study provides the framework for analysis of environmental aspects of physical seed dormancy.},
	language = {en},
	urldate = {2023-05-03},
	journal = {PeerJ},
	author = {Hradilová, Iveta and Duchoslav, Martin and Brus, Jan and Pechanec, Vilém and Hýbl, Miroslav and Kopecký, Pavel and Smržová, Lucie and Štefelová, Nikola and Vaclávek, Tadeáš and Bariotakis, Michael and Machalová, Jitka and Hron, Karel and Pirintsos, Stergios and Smýkal, Petr},
	month = jan,
	year = {2019},
	note = {Publisher: PeerJ Inc.},
	pages = {e6263},
	file = {peerj-6263.pdf:G\:\\OneDrive\\IPK Docs\\germination modeling\\CGI\\peerj-6263.pdf:application/pdf},
}

@phdthesis{hradilova_seed_2019,
	address = {Olomouc, Czech Republic},
	type = {{PhD} {Thesis}},
	title = {Seed dormancy as the key domestication trait in legumes},
	url = {https://theses.cz/id/lc7p93/Hradilov_disertan_prce_a_autorefert_3.10.2019.pdf},
	school = {Palacký University Olomouc},
	author = {Hradilová, Iveta},
	year = {2019},
	file = {Hradilov_disertan_prce_a_autorefert_3.10.2019.pdf:G\:\\OneDrive\\IPK Docs\\germination modeling\\CGI\\Hradilov_disertan_prce_a_autorefert_3.10.2019.pdf:application/pdf},
}

@article{lehle_quantification_1982,
	title = {Quantification of allelopathic potential of sorghum residues by novel indexing of {Richards}' function fitted to cumulative cress seed germination curves},
	volume = {69},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.69.5.1212},
	doi = {10.1104/pp.69.5.1212},
	abstract = {The inhibitory activity of aqueous extracts of field-grown sorghum (Sorghum bicolor cv. Bird-a-boo) herbage and roots was quantitatively indexed by three aspects of cumulative cress (Lepidium sativum cv. Curlycress) seed germination: the germination onset; weighted mean rate; and final germination percentage. Extract potency was greatest for herbage collected four weeks after planting but declined sharply thereafter as the plants matured. About 91\% of the inhibitory activity obtained from four-week-old herbage was in a low molecular weight fraction. Differential effects of herbage and root extracts on cress seed germination suggest that the nature and/or proportion of biologically active substances extractable from these plant parts is dissimilar.},
	number = {5},
	urldate = {2023-05-03},
	journal = {Plant Physiology},
	author = {Lehle, Fredric R. and Putnam, Alan R.},
	month = may,
	year = {1982},
	pages = {1212--1216},
}

@article{bonner_weibull_1976,
	title = {The {Weibull} function: {A} new method of comparing seed vigor},
	volume = {1},
	issn = {0146-3071},
	shorttitle = {The weibull function},
	url = {https://www.jstor.org/stable/23430404},
	abstract = {The three-parameter Weibull function can be used to compare germination responses and to quantify the differences for use in statistical analyses. Data from germination of several lots of white oak and sweetgum were used to illustrate how the Weibull parameters reflect quantitative differences in seed vigor. Besides vigor comparisons, other possible uses of the Weibull are in tests of prechill treatments, chemical treatments, and varietal or geographic seed source differences.},
	number = {1},
	urldate = {2023-05-03},
	journal = {Journal of Seed Technology},
	author = {Bonner, F. T. and Dell, T. R.},
	year = {1976},
	note = {Publisher: Association of Official Seed Analysts},
	pages = {96--103},
}

@article{becerra-vazquez_seed_2018,
	title = {Seed longevity of five tropical species from {South}-{Eastern} {Mexico}: {Changes} in seed germination during storage},
	volume = {11},
	issn = {1940-0829, 1940-0829},
	url = {http://journals.sagepub.com/doi/10.1177/1940082918779489},
	doi = {10.1177/1940082918779489},
	language = {en},
	urldate = {2023-05-03},
	journal = {Tropical Conservation Science},
	author = {Becerra-Vázquez, Ángel G. and Sánchez-Nieto, Sobeida and Coates, Rosamond and Flores-Ortiz, César M. and Orozco-Segovia, Alma},
	month = jan,
	year = {2018},
	pages = {194008291877948},
}

@article{brown_germination_1987,
	title = {Germination of \emph{{Aristida} armata} under constant and alternating temperatures and its analysis with the cumulative weibull distribution as a model},
	volume = {35},
	issn = {1444-9862},
	url = {https://www.publish.csiro.au/bt/bt9870581},
	doi = {10.1071/bt9870581},
	abstract = {Germination of Aristida armata was compared at different temperatures on a thermogradient plate. Temperatures ranged from 10°C to 50°C with day/night differentials of 0, 5, 10 and 15°C. Alternating temperatures improved overall germination, particularly at the extremes of temperature. Average temperatures of 35°C and higher were fatal to many seeds. Day temperatures of 17.5°C and lower inhibited germination but did not prevent subsequent germination under warmer conditions. There was little variation in the rate of germination with incubation under constant temperatures. Under alternating temperatures, maximum germination occurred at lower temperatures than those under which germination rate was greatest. A four-parameter cumulative Weibull distribution was used to summarise cumulative germination. The distribution has the general form: Y = M(1-exp[- \{k(t - I)\}c]), where Y is the total germination at time t, M is the final total germination, k is germination rate, I is the interval between the start of incubation and the start of germination, and c is a shape parameter. In nearly all cases, the fitted function had a coefficient of determination greater than 0.98. The Weibull distribution allows reconstruction of the original germination data with minimal distortion and its use is recommended for both the analysis and modelling of germination responses.},
	language = {en},
	number = {5},
	urldate = {2023-05-03},
	journal = {Australian Journal of Botany},
	author = {Brown, R. F.},
	year = {1987},
	note = {Publisher: CSIRO PUBLISHING},
	pages = {581--591},
}

@article{larsen_use_2004,
	title = {Use of germination curves to describe variation in germination characteristics in three turfgrass species},
	volume = {44},
	issn = {1435-0653},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.2135/cropsci2004.8910},
	doi = {10.2135/cropsci2004.8910},
	abstract = {Germination characteristics are important for the establishment success of grass species. The objective of this study was to study the variation in germination characteristics within and among cultivars in three grass species by use of a curve-fitting procedure. The study included 20 seed lots of slender creeping red fescue (Festuca rubra L. var. littoralis Vasey), 19 lots of perennial ryegrass (Lolium perenne L.), and 16 lots of Kentucky bluegrass (Poa pratensis L.), and the seed lots represented four, four, and five cultivars, respectively. Seeds of each seed lot were germinated in standard tests, and germination was recorded daily. Germination time courses were described for each replicate of each seed lot, using a generalized hyperbolic multinomial distribution. The function efficiently described all observed germination time courses, and germination was summarized as three characteristics of biological significance: final germination percentage (FGP), mean germination time (MGT), and time from 25 to 75\% germination (T25-75). For each of the characteristics, an ANOVA was performed. Cultivar differences were tested against variation between seed lots within cultivars. Within all three species, there were significant cultivar differences in FGP, and cultivars of red fescue and Kentucky bluegrass also differed significantly in MGT and T25-75 Cultivar variation was 53 to 99\% larger than seed lot variation within cultivars, but in some cases, seed lots within cultivars differed considerably in germination characteristics. Cultivars should, therefore, be represented by more than one seed lot and cultivar differences should be tested against seed lot differences to get valid test results.},
	language = {en},
	number = {3},
	urldate = {2023-05-03},
	journal = {Crop Science},
	author = {Larsen, Søren Ugilt and Bibby, Bo Martin},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2135/cropsci2004.8910},
	pages = {891--899},
}

@article{oneill_fitting_2004,
	title = {Fitting and comparing seed germination models with a focus on the inverse normal distribution},
	volume = {46},
	issn = {1467-842X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1467-842X.2004.00335.x},
	doi = {10.1111/j.1467-842X.2004.00335.x},
	abstract = {This paper reviews current methods for fitting a range of models to censored seed germination data and recommends adoption of a probability-based model for the time to germination. It shows that, provided the probability of a seed eventually germinating is not on the boundary, maximum likelihood estimates, their standard errors and the resultant deviances are identical whether only those seeds which have germinated are used or all seeds (including seeds ungerminated at the end of the experiment). The paper recommends analysis of deviance when exploring whether replicate data are consistent with a hypothesis that the underlying distributions are identical, and when assessing whether data from different treatments have underlying distributions with common parameters. The inverse normal distribution, otherwise known as the inverse Gaussian distribution, is discussed, as a natural distribution for the time to germination (including a parameter to measure the lag time to germination). The paper explores some of the properties of this distribution, evaluates the standard errors of the maximum likelihood estimates of the parameters and suggests an accurate approximation to the cumulative distribution function and the median time to germination. Additional material is on the web, at http://www.agric.usyd.edu.au/staff/oneill/.},
	language = {en},
	number = {3},
	urldate = {2023-05-03},
	journal = {Australian \& New Zealand Journal of Statistics},
	author = {O'Neill, Michael E. and Thomson, Peter C. and Jacobs, Brent C. and Brain, Phil and Butler, Ruth C. and Turner, Heather and Mitakda, Bernadetha},
	year = {2004},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1467-842X.2004.00335.x},
	pages = {349--366},
}

@article{lambers_benefits_2005,
	title = {The benefits of seed banking for red maple (\emph{{Acer} rubrum}): {Maximizing} seedling recruitment},
	volume = {35},
	issn = {0045-5067},
	shorttitle = {The benefits of seed banking for red maple ({Acer} rubrum)},
	url = {https://cdnsciencepub.com/doi/abs/10.1139/x05-017},
	doi = {10.1139/x05-017},
	abstract = {Seed banking is assumed to be unimportant for temperate trees, because their seeds are short-lived in soils. However, even short-term seed banking could increase recruitment and affect population dynamics of seed-banking trees. To investigate this possibility, we examined early life-history stages of red maple (Acer rubrum L.), an abundant seed-banking tree in eastern forests. We found that seed banking benefits red maple by increasing germination when seedling survival is likely. Most red maple seeds germinate soon after spring dispersal, when seedling survival is high, or postpone germination to the following growing season, once seedling survival becomes less likely late in the summer. This occurs because seed dormancy increases during the growing season, matching a concurrent decrease in seedling survival. Our results and those of other studies suggest seed dormancy is increased by the same environmental factors (low light and low moisture) that also decrease seedling survival. We speculate that early life-history traits, including seed banking, may have contributed to this species' increased abundance in eastern deciduous forests in the last century.},
	number = {4},
	urldate = {2023-05-03},
	journal = {Canadian Journal of Forest Research},
	author = {Lambers, Janneke Hille Ris and Clark, James S},
	month = apr,
	year = {2005},
	note = {Publisher: NRC Research Press},
	pages = {806--813},
}

@article{guedes_nonlinear_2014,
	title = {Nonlinear models applied to seed germination of \emph{{Rhipsalis} cereuscula} {Haw} ({Cactaceae})},
	volume = {36},
	issn = {18062563, 18078664},
	url = {http://periodicos.uem.br/ojs/index.php/ActaSciTechnol/article/view/21192},
	doi = {10.4025/actascitechnol.v36i4.21192},
	number = {4},
	urldate = {2023-05-03},
	journal = {Acta Scientiarum. Technology},
	author = {Guedes, Terezinha Aparecida and Rossi, Robson Marcelo and Martins, Ana Beatriz Tozzo and Janeiro, Vanderly and Carneiro, José W. P.},
	year = {2014},
	pages = {651--656},
}

@article{ochuodho_statistical_2006,
	title = {Statistical evaluation of the germination of \emph{{Cleome} gynandra} {L}. seeds},
	volume = {23},
	doi = {10.1080/02571862.2006.10634771},
	number = {4},
	journal = {South African Journal of Plant and Soil},
	author = {Ochuodho, J. A. and Modi, A. T.},
	year = {2006},
	note = {Publisher: Taylor \& Francis},
	pages = {310--315},
}

@article{torres_analysis_1989,
	title = {Analysis of germination curves of aged fennel seeds by mathematical models},
	volume = {29},
	issn = {0098-8472},
	url = {https://www.sciencedirect.com/science/article/pii/0098847289900166},
	doi = {10.1016/0098-8472(89)90016-6},
	abstract = {Mature fennel seeds (Foeniculum vulgare Mill. cv. amargo) were collected from cultivated plants grown in experimental fields in 1982, 1984 and 1986. Germination tests (25°C in darkness) were conducted after 1, 3 and 5 years of seed storage at room temperature. Three mathematical models (monomolecular, logistic and Gompertz) were used to analyzed cumulative germination curves over time. The results of these fittings were compared in terms of graphical representation, statistical criteria and biological relevance. The logistic model \{G = A[1+exp (β-Kt)]−1\} was finally selected to describe the shape of germination curves of aged fennel seeds. This model showed a flexible and biologically realistic form and gave a good similarity to experimental data, thus confirming the plasticity of this function.},
	language = {en},
	number = {3},
	urldate = {2023-05-03},
	journal = {Environmental and Experimental Botany},
	author = {Torres, M. and Frutos, G.},
	month = jul,
	year = {1989},
	pages = {409--415},
}

@article{thornley_germination_1977,
	title = {Germination of seeds and spores},
	volume = {41},
	issn = {0305-7364},
	url = {https://www.jstor.org/stable/42765299},
	doi = {10.1093/oxfordjournals.aob.a085425},
	number = {176},
	urldate = {2023-05-03},
	journal = {Annals of Botany},
	author = {Thornley, J. H. M.},
	year = {1977},
	note = {Publisher: Oxford University Press},
	pages = {1363--1365},
}

@article{campbell_new_1979,
	title = {A new basis for characterizing germination},
	volume = {4},
	issn = {0146-3071},
	url = {https://www.jstor.org/stable/23432731},
	abstract = {Procedures for characterizing seed lots (i.e., by mean and variation of days to germination, peak germination date, and other useful properties) are commonly complicated because frequency of days to germination does not have a normal distribution. A procedure is presented for minimizing this problem. Tests of a seed lot of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) subjected to differing stratification periods and germination temperatures indicated that it is the rates at which seed embryos develop toward germination rather than days to germination that have a normal distribution. Consequently, by transforming cumulative percentages of germination to probits (a means for converting a normal sigmoid curve to a straight line) and fitting a straight line to probits regressed on rates rather than on days—or by plotting percentages on probit-scaled graph paper—the resulting intercept and regression coefficient can be used to easily calculate all the standard properties for characterizing a seed lot.},
	number = {2},
	urldate = {2023-05-03},
	journal = {Journal of Seed Technology},
	author = {Campbell, Robert K. and Sorensen, Frank C.},
	year = {1979},
	note = {Publisher: Association of Official Seed Analysts},
	pages = {24--34},
}

@article{ketabi_estimation_2016,
	title = {Estimation of the cardinal temperatures for germination of four \emph{{Satureja}} species growing in {Iran}},
	volume = {62},
	doi = {10.1515/hepo-2016-0001},
	number = {1},
	journal = {Herba Polonica},
	author = {Ketabi, Hamed Zarif and Khazaei, Hamid Reza and Nezami, Ahmad and Aghadaei, S. R. T.},
	year = {2016},
	note = {Publisher: -},
}

@article{schimpf_representation_1977,
	title = {Representation of germination curves with the logistic function},
	volume = {41},
	issn = {0305-7364},
	doi = {10.1093/oxfordjournals.aob.a085423},
	abstract = {The fitting of the logistic function to germination progress data by simple linear regression is demonstrated. Acceptable goodness of fit is obtained for both fast and slowly-germinating seed populations. The rate and final percentage of germination are positively correlated in these experiments, although mathematically independent. The rate appears to be more sensitive to environmental conditions during germination than is the final percentage. The limitations of the logistic function and the desirability of a standard means of expressing germination rates are discussed.},
	number = {6},
	urldate = {2023-05-03},
	journal = {Annals of Botany},
	author = {Schimpf, D. J. and Flint, S. D. and Palmblad, I. G.},
	month = nov,
	year = {1977},
	pages = {1357--1360},
}

@article{bentsink_natural_2010,
	title = {Natural variation for seed dormancy in {Arabidopsis} is regulated by additive genetic and molecular pathways},
	volume = {107},
	url = {https://www.pnas.org/doi/abs/10.1073/pnas.1000410107},
	doi = {10.1073/pnas.1000410107},
	abstract = {Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways.},
	number = {9},
	urldate = {2023-05-03},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Bentsink, Leónie and Hanson, Johannes and Hanhart, Corrie J. and Blankestijn-de Vries, Hetty and Coltrane, Colin and Keizer, Paul and El-Lithy, Mohamed and Alonso-Blanco, Carlos and de Andrés, M. Teresa and Reymond, Matthieu and van Eeuwijk, Fred and Smeekens, Sjef and Koornneef, Maarten},
	month = mar,
	year = {2010},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {4264--4269},
	file = {Bentsink et al. - 2010 - Natural variation for seed dormancy in Arabidopsis:G\:\\OneDrive\\Documents\\Seed dormancy\\DSDS50\\logistic\\Bentsink et al. - 2010 - Natural variation for seed dormancy in Arabidopsis.pdf:application/pdf},
}

@article{xu_germination_2016,
	title = {Germination and early seedling growth of \emph{{Pinus} densata} {Mast}. provenances},
	volume = {27},
	issn = {1007-662X, 1993-0607},
	url = {http://link.springer.com/10.1007/s11676-015-0186-x},
	doi = {10.1007/s11676-015-0186-x},
	language = {en},
	number = {2},
	urldate = {2023-05-03},
	journal = {Journal of Forestry Research},
	author = {Xu, Yulan and Cai, Nianhui and He, Bin and Zhang, Ruili and Zhao, Wei and Mao, Jianfeng and Duan, Anan and Li, Yue and Woeste, Keith},
	month = apr,
	year = {2016},
	pages = {283--294},
}

@article{wu_effects_2001,
	title = {Effects of moist chilling and solid matrix priming on germination of loblolly pine (\emph{{Pinus} taeda} {L}.) seeds},
	volume = {21},
	issn = {1573-5095},
	url = {https://doi.org/10.1023/A:1010606720727},
	doi = {10.1023/A:1010606720727},
	abstract = {Loblolly pine (Pinus taeda L.) seeds from sources with a mild climate under maritime influence (North Carolina) required shorter moist chilling to achieve maximum germination vigor than seeds from sources with a harsher continental climate (Oklahoma). Solid matrix priming (SMP) for 6 d achieved as much as 60 d of moist chilling to improve rapidity, synchrony and completeness of germination for three of the four families studied. SMP after moist chilling increased the rapidity, synchrony and completeness of germination. The benefit of SMP was greatest for non-stratified seeds and the benefit decreased with length of moist chilling. In general, delaying planting for one week after SMP had minor effects on germination when seeds were kept in the SMP matrix at 4°C. Delayed planting after SMP can increase germination rapidity and synchrony of seeds that have received long moist chilling and reduce the benefit of SMP in non-moist-chilled seeds.},
	language = {en},
	number = {1},
	urldate = {2023-05-03},
	journal = {New Forests},
	author = {Wu, Luguang and Hallgren, Stephen W. and Ferris, David M. and Conway, Kenneth E.},
	month = jan,
	year = {2001},
	pages = {1--16},
}

@article{gonzalez2002effects,
	title = {Effects of priming on germination of \emph{{Buddleja} cordata} ssp. \emph{cordata} ({Loganiaceae}) seeds and possible ecological significance},
	volume = {30},
	number = {3},
	journal = {Seed Science and Technology},
	author = {González-Zertuche, L and Orozco-Segovia, A and Baskin, C and Baskin, JM},
	year = {2002},
	note = {Publisher: INTERNATIONAL SEED TESTING ASSOCIATION ISTA},
	pages = {535--548},
}

@article{takahashi1996desempenho,
	title = {Desempenho germinativo de sementes de \emph{{Stevia} rebaudiana} ({Bert}) {Bertoni} sob diferentes temperaturas},
	volume = {18},
	doi = {10.17801/0101-3122/rbs.v18n1p6-9},
	number = {1},
	journal = {Revista Brasileira de Sementes},
	author = {Takahashi, Luciana and Melges, Elena and Carneiro, José Walter P.},
	year = {1996},
	pages = {6--9},
}

@article{cristaudo_assessment_2014,
	title = {Assessment of daily heat pulse regimes on the germination of six \emph{{Amaranthus}} species},
	volume = {54},
	issn = {1365-3180},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/wre.12085},
	doi = {10.1111/wre.12085},
	abstract = {In Mediterranean environments, thermal requirements for seed germination of Amaranthus species are met in spring. Nonetheless, seedlings of these species start emerging in the field from late winter, although the theoretical heat sum thresholds required for germination are not likely to be reached under field conditions. We hypothesised that soil thermal fluctuations can reduce the heat requirements of these species. Cardinal temperatures and thermal times of six Amaranthus species (A. albus, A. cruentus, A. deflexus, A. graecizans, A. retroflexus and A. viridis) were determined on non-dormant seeds at constant temperatures ranging from 10 to 40°C. Subsequently, germination response to heat pulses was studied by imposing a thermal fluctuation regime of 32/8°C with two different thermoperiods of 3/21 and 6/18 h. In the two thermoperiods, exposure to 32°C was imposed for a different number of days: from 1 to 12 and from 1 to 6 heat pulses cycles in the 3/21 and 6/18 h thermoperiods respectively. Cumulative germination, germination rate and mean germination time were evaluated. Heat sum requirements and final germination percentage were affected by thermoperiod and number of thermal cycles. Amaranthus spp. germination was higher and faster when seeds were submitted to 6 h compared with 3 + 3 h of heat pulses. Our data showed that heat sum requirements for germination may change depending on the way in which varying temperatures are imposed on germinating seeds.},
	language = {en},
	number = {4},
	urldate = {2023-05-03},
	journal = {Weed Research},
	author = {Cristaudo, A. and Gresta, F. and Catara, S. and Mingo, A.},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/wre.12085},
	pages = {366--376},
}

@article{dias_describing_2001,
	title = {Describing phytotoxic effects on cumulative germination},
	volume = {27},
	issn = {1573-1561},
	url = {https://doi.org/10.1023/A:1005644808956},
	doi = {10.1023/A:1005644808956},
	abstract = {Phytotoxic studies strongly depend on evaluation of germination responses, which implies the need for adequate procedures to account for distinct aspects of the germinative process. For this, indices, comparisons among treatments at various times, and model fitting have been proposed. The objective of this work is to compare the three approaches and select the one providing the greatest insight and precision. Speed of germination, speed of accumulated germination, the coefficient of the rate of germination, comparisons at each determination time, including final germination, and the parameters of the Weibull function were examined. The Weibull function proved the best approach to describe the germination process, providing not only the same type of information about the speed of germination, with greater precision, but also additional information about the initiation and shape of the germination response curve.},
	language = {en},
	number = {2},
	urldate = {2023-05-03},
	journal = {Journal of Chemical Ecology},
	author = {Dias, L. S.},
	month = feb,
	year = {2001},
	pages = {411--418},
}

@article{larsen_use_2004-2,
	title = {Use of the hydrothermal time model to analyse interacting effects of water and temperature on germination of three grass species},
	volume = {14},
	issn = {1475-2735, 0960-2585},
	url = {https://www.cambridge.org/core/journals/seed-science-research/article/abs/use-of-the-hydrothermal-time-model-to-analyse-interacting-effects-of-water-and-temperature-on-germination-of-three-grass-species/2581D1C218221E26E211628AF40D6086},
	doi = {10.1079/SSR2003153},
	abstract = {The temperate grass species, red fescue (Festuca rubra ssp. litoralis), perennial ryegrass (Lolium perenne) and Kentucky bluegrass (Poa pratensis), are often sown in mixtures for turfgrass. Differences in germination response to environmental conditions often result in different establishment success. The three species were compared in a study of imbibition at reduced water potential (Ψ) and in a study of the effects of Ψ and temperature on germination. In all three species, imbibition rate and extent were reduced with decreasing Ψ, causing a prolonged lag-phase before germination, particularly in Kentucky bluegrass. In perennial ryegrass and Kentucky bluegrass, water content at radicle emergence decreased non-linearly with decreasing Ψ, with a lower asymptote expressing the critical water content for germination. Seeds were germinated in factorial combinations of two temperatures (10 and 25°C) and nine Ψ levels (–2 to 0 MPa). Kentucky bluegrass required a longer thermal time to germinate than the other species and exhibited conditional dormancy at 25°C, which affected the use of the thermal time model. The effects of Ψ were described by a hydrotime model. Kentucky bluegrass had higher base water potential (Ψb) and required a longer hydrotime for germination than the other species. However, Ψb increased with temperature in Kentucky bluegrass and red fescue, but decreased in perennial ryegrass, and the base temperatures also changed with Ψ. The interacting effects of Ψ and temperature affected the ability of the hydrothermal time model to predict germination performance across all temperature and Ψ conditions.},
	language = {en},
	number = {1},
	urldate = {2023-05-03},
	journal = {Seed Science Research},
	author = {Larsen, Søren Ugilt and Bailly, Christophe and Côme, Daniel and Corbineau, Françoise},
	month = mar,
	year = {2004},
	note = {Publisher: Cambridge University Press},
	pages = {35--50},
}

@article{sri-ngernyuang_survival_2003,
	title = {Survival and germination of an experimental seed bank population of two species of {Lauraceae} in a tropical montane forest in {Thailand}},
	volume = {8},
	issn = {1610-7403},
	url = {https://doi.org/10.1007/s10310-003-0042-2},
	doi = {10.1007/s10310-003-0042-2},
	abstract = {The survival and germination traits of two tropical species of Lauraceae, Lindera metcalfiana and Litsea cubeba, were investigated in a 2-year burial experiment and subsequent germination tests of sequentially excavated seeds. Fresh seeds extracted from fruit were packed in aluminum mesh bags and buried 5 cm deep in a mature montane forest in northern Thailand (1700 m altitude). No seed mortality was recorded for Litsea, but Lindera experienced 26\%–48\% mortality after being buried for 122 days. These seeds did not germinate in the forest soil during the 2-year experimental period. We found that fresh seeds of these two species did not germinate even under open conditions, suggesting that the seeds are initially deeply dormant after dispersal. In contrast, 29\%–60\% of excavated Lindera seeds germinated under open conditions after being buried for 30–753 days, and excavated Litsea seeds began to germinate after being buried for 408 days. These findings suggest that seeds enter a state of enforced dormancy. The ratio of germinable seeds peaked 184 days after burial in Lindera (33\%) and 930 days after burial in Litsea (91\%). The longer period of deep dormancy in Litsea prior to enforced dormancy is concordant with the fact that for regeneration Litsea requires larger-scale disturbance than Lindera.},
	language = {en},
	number = {4},
	urldate = {2023-05-03},
	journal = {Journal of Forest Research},
	author = {Sri-ngernyuang, Kriangsak and Chai-Udom, Kwanchai and Kanzaki, Mamoru and Ohkubo, Tatsuhiro and Yamakura, Takuo},
	month = nov,
	year = {2003},
	pages = {311--316},
}

@article{hageseth_kinetics_1975,
	title = {Kinetics and thermodynamics of isothermal seed germination},
	volume = {53},
	issn = {00225193},
	doi = {10.1016/0022-5193(75)90102-2},
	language = {en},
	number = {1},
	urldate = {2023-05-04},
	journal = {Journal of Theoretical Biology},
	author = {Hageseth, G. T. and Joyner, R. D.},
	month = sep,
	year = {1975},
	pages = {51--65},
}

@article{berrie_use_1981,
	title = {The use of population parameters in the analysis of germination of lettuce seed},
	volume = {51},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.1981.tb02703.x},
	doi = {10.1111/j.1399-3054.1981.tb02703.x},
	abstract = {Probit analysis was used to determine the parameters of the germinating population of lettuce seed. Seeds were induced to germinate under different conditions and it was shown that with light induced germination the germinating populations were the same. However, when gibberellic acid (GA3) was the inductive agent then the germinating populations were not the same being concentration dependent. – This type of analysis offers a rigorous comparison of different inductive treatments.},
	language = {en},
	number = {2},
	urldate = {2023-05-04},
	journal = {Physiologia Plantarum},
	author = {Berrie, Alex. M. M. and Taylor, Graham C. D.},
	year = {1981},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.1981.tb02703.x},
	pages = {229--233},
}

@article{orozco-segovia_mathematical_1996,
	title = {A mathematical model that uses {Gaussian} distribution to analyze the germination of \emph{{Manfreda} brachystachya} ({Agavaceae}) in a thermogradient},
	volume = {98},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.1996.tb05696.x},
	doi = {10.1111/j.1399-3054.1996.tb05696.x},
	abstract = {Germination of nondormant seeds of Manfreda brachystachya (Agavaceae) was analyzed at temperatures ranging from 11–35°C. Maximum germination (95\%) occurred at 25°C. An exponential sigmoid relationship was found between time and cumulative germination. Germination rate for every subpopulation (10–90\% germination) was estimated by means of a normal distribution analysis. The kurtosis indicated die amplitude of the range of temperatures where the highest germination rates were concentrated, and the skew indicated sharply inhibitory temperatures in the range of temperatures used. Based on analysis of the normal distribution models for each subpopulation, we calculated a theoretical function which described germination rate over the temperature range considered: F(T,χ) = A × exp[−B(C−1)2], where A is the function that describes germination rate for each subpopulation (characterized by the percentage [χ] at optimal temperature); B is a shape parameter, 1/(σG2); and C is the ratio between each germination temperature (T) and the optimal germination temperature. The Gaussian curves were used to calculate thermal time, and base and ceiling temperatures. Germination thermal time ranged from 1 333 to 2 373°C h, and base and ceiling temperatures were 10.44 ± 0.7°C and 39.54 ± 0.7°C, respectively. There was a linear relationship between thermal time and cumulative percentage of germination of the subpopulations. Based on fitted curves for each subpopulation, the use of a general model for all the subpopulations has been proven: F8 = A × exp[−5.9437(C−1)2], where changes in the curves for each subpopulation depended on temperature only.},
	language = {en},
	number = {3},
	urldate = {2023-05-04},
	journal = {Physiologia Plantarum},
	author = {Orozco-Segovia, Alma and González-Zertuche, Lourdes and Mendoza, Ana and Orozco, Susana},
	year = {1996},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.1996.tb05696.x},
	pages = {431--438},
}

@article{quinones-huatangari_analysis_2023,
	title = {Analysis of germination curves of \emph{{Cinchona} officinalis} {L}. ({Rubiaceae})using sigmoidal mathematical models},
	volume = {2023},
	issn = {1687-8159},
	url = {https://www.hindawi.com/journals/ija/2023/1360608/},
	doi = {10.1155/2023/1360608},
	abstract = {Seed germination is the fundamental phenomenon that determines the successful growth and development of each plant species, even more so in Cinchona officinalis, which is a forest species that stands out for its medicinal importance. The objective of this work was to determine the best sigmoidal mathematical model describing the germination of C. officinalis. For the germination test, a completely randomized design was used with six treatments and three replicates per treatment; 100°C. officinalis seeds were used per replicate, and 1800 seeds were needed in the trial. Gompertz sigmoidal, logistic, and von Bertalanffy models were used to analyse the germination curves of C. officinalis. The results of these adjustments were analysed based on the graphic representation and statistical criteria (Akaike’s value (), , and ). The results suggest that the Gompertz and logistic models have a better graphic representation, showing values close to those observed, while the von Bertalanffy model shows negative germination values. According to the statistical criteria, the lowest AIC and the highest were obtained. and with the Gompertz model, followed by the logistic model and von Bertalanffy. It is concluded that the Gompertz model can represent the shape of the germination curves of C. officinalis for the six treatments of the test.},
	language = {en},
	urldate = {2023-05-04},
	journal = {International Journal of Agronomy},
	author = {Quiñones-Huatangari, Lenin and Huaccha-Castillo, Annick Estefany and Fernandez-Zarate, Franklin Hitler and Morales-Rojas, Eli and Marrufo-Jiménez, Jenny Del Milagro and Mejía-Córdova, Leslie Lizbeth},
	month = jan,
	year = {2023},
	note = {Publisher: Hindawi},
	pages = {e1360608},
}

@article{mees_generalized_1984,
	title = {The generalized gamma distribution: {A} model for seed germination curves [{Weibull} model]},
	issn = {0006-3436},
	shorttitle = {The generalized gamma distribution},
	language = {French},
	urldate = {2023-05-04},
	journal = {Biometrie - Praximetrie},
	author = {Mees, E. and Gerard, G.},
	year = {1984},
}

@article{bould_model_1981,
	title = {A model for seed germination curves},
	abstract = {A mathematical model has been developed which describes the germination curve as a function of time. Unlike much of the previous work on the subject a recognisable growth equation or statistical distribution has not been used as the starting point. Instead it has been assumed that the simplest situation arises where each seed in a population has the same probability of germinating in unit time. More complex situations are modelled by assuming that the population comprises more than one sub-group where the probability of a seed germination in unit time is constant with a sub-group but varies between sub-groups. The shape of the curve is determined by the number of sub-groups and the extent to which they overlap. Starting with the basic equation for the simplest situation a range of curve shapes can be developed by building into the basic equation a second equation to describe the relationship between the probability (q) of a seed not germinating in unit time and time itself. Proofs are given for the shape of the curve for the basic equation and where there is a linear relationship between q and time and llog(, e) q and time. Examples are given of the model fitted to observed data.},
	language = {English},
	urldate = {2023-05-04},
	journal = {Seed Science and Technology},
	author = {Bould, A. and Abrol, B. K.},
	year = {1981},
}

@article{bridges_modeling_1989,
	title = {Modeling distributions of crop and weed seed germination time},
	volume = {37},
	issn = {0043-1745},
	url = {https://www.jstor.org/stable/4045136},
	doi = {10.1017/S0043174500072702},
	abstract = {Research was conducted to determine the utility of a single, temperature-independent Weibull function for describing cumulative seed germination under several temperature regimes with 14 sets of weed and crop seed germination data. A modified cumulative Weibull function was derived to distribute germination times for individuals within the population and distributed the occurrence of germination given ample sample size and appropriate sample interval. The descriptive and predictive attributes of the stochastic model component are well suited for incorporation into seed germination models and are likely applicable to models to predict distribution of times for other developmental processes of plants.},
	number = {5},
	urldate = {2023-05-04},
	journal = {Weed Science},
	author = {Bridges, David C. and Wu, Hsin-I and Sharpe, Peter J. H. and Chandler, James M.},
	year = {1989},
	note = {Publisher: [Cambridge University Press, Weed Science Society of America]},
	pages = {724--729},
}

@article{chen_estimation_2021,
	title = {Estimation of thermal time model parameters for seed germination in 15 species: {The} importance of distribution function},
	volume = {31},
	issn = {0960-2585, 1475-2735},
	shorttitle = {Estimation of thermal time model parameters for seed germination in 15 species},
	url = {https://www.cambridge.org/core/journals/seed-science-research/article/abs/estimation-of-thermal-time-model-parameters-for-seed-germination-in-15-species-the-importance-of-distribution-function/B0E4FF6A54FDB053259254A1DEC6700A},
	doi = {10.1017/S0960258521000040},
	abstract = {Thermal time models have been widely applied to predict temperature requirements for seed germination. Generally, a log-normal distribution for thermal time [θT(g)] is used in such models at suboptimal temperatures to examine the variation in time to germination arising from variation in θT(g) within a seed population. Recently, additional distribution functions have been used in thermal time models to predict seed germination dynamics. However, the most suitable kind of the distribution function to use in thermal time models, especially at suboptimal temperatures, has not been determined. Five distributions (log-normal, Gumbel, logistic, Weibull and log-logistic) were used in thermal time models over a range of temperatures to fit the germination data for 15 species. The results showed that a more flexible model with the log-logistic distribution, rather than the log-normal distribution, provided the best explanation of θT(g) variation in 13 species at suboptimal temperatures. Thus, at least at suboptimal temperatures, the log-logistic distribution is an appropriate candidate among the five distributions used in this study. Therefore, the distribution of parameters [θT(g)] should be considered when using thermal time models to prevent large deviations; furthermore, an appropriate equation should be selected before using such a model to make predictions.},
	language = {en},
	number = {2},
	urldate = {2023-05-04},
	journal = {Seed Science Research},
	author = {Chen, Dali and Chen, Xianglai and Wang, Jingjing and Zhang, Zuxin and Wang, Yan and Jia, Cunzhi and Hu, Xiaowen},
	month = jun,
	year = {2021},
	note = {Publisher: Cambridge University Press},
	pages = {83--90},
}

@article{brown_problems_1986,
	title = {Problems in applying {Thornley}'s model of germination},
	volume = {57},
	issn = {0305-7364},
	url = {https://doi.org/10.1093/oxfordjournals.aob.a087093},
	doi = {10.1093/oxfordjournals.aob.a087093},
	abstract = {Thornley's adaptation of Kendall's model was tested on 46 sets of germination data. The model provided a good empirical description of cumulative germination but the necessary calculations were very complex. It was concluded that either the assumption of sequential germination stages or the assumption of a common linear rate constant between stages, or both, were unsatisfactory and that simpler and more useful mathematical means of describing the time-course of germination were available.},
	number = {1},
	urldate = {2023-05-04},
	journal = {Annals of Botany},
	author = {Brown, R. F. and Mayer, D. G.},
	month = jan,
	year = {1986},
	pages = {49--53},
}

@article{ellis_influence_1987,
	title = {The influence of temperature on seed germination rate in grain legumes: {III}. {A} comparison of five faba bean genotypes at constant temperatures using a new screening method},
	volume = {38},
	issn = {0022-0957, 1460-2431},
	shorttitle = {The influence of temperature on seed germination rate in grain legumes},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/38.6.1033},
	doi = {10.1093/jxb/38.6.1033},
	language = {en},
	number = {6},
	urldate = {2023-05-04},
	journal = {Journal of Experimental Botany},
	author = {Ellis, R. H. and Simon, G. and Covell, S.},
	year = {1987},
	pages = {1033--1043},
}

@article{white_influence_1993,
	title = {The influence of temperature on seed germination in cultivars of common bean},
	volume = {44},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/44.12.1795},
	doi = {10.1093/jxb/44.12.1795},
	language = {en},
	number = {12},
	urldate = {2023-05-04},
	journal = {Journal of Experimental Botany},
	author = {White, Jeffrey W. and Montes-R, Consuelo},
	year = {1993},
	pages = {1795--1800},
}

@article{roman_modeling_1999-1,
	title = {Modeling germination and seedling elongation of common lambsquarters (\emph{{Chenopodium} album})},
	volume = {47},
	issn = {0043-1745, 1550-2759},
	url = {https://www.cambridge.org/core/journals/weed-science/article/abs/modeling-germination-and-seedling-elongation-of-common-lambsquarters-chenopodium-album/8132553DF2F1A44A32F6D71B3ADF1835},
	doi = {10.1017/S0043174500091554},
	abstract = {The ability to predict time of weed seedling emergence relative to the crop is an important component of a mechanistic model describing weed and crop competition. In this paper, we hypothesized that the process of germination could be described by the interaction of temperature and water potential and that the rate of seedling shoot and radicle elongation vary as a function of temperature. To test these hypotheses, incubator studies were conducted using seeds and seedlings of common lambsquarters. Probit analysis was used to account for variation in cardinal temperatures and base water potentials and to develop parameters for a new mathematical model that describes seed germination and shoot and radicle elongation in terms of hydrothermal time and temperature, respectively. This hydrothermal time model describes the phenology of seed germination using a single curve, generated from the relationship of temperature and water potential.},
	language = {en},
	number = {2},
	urldate = {2023-05-04},
	journal = {Weed Science},
	author = {Roman, Erivelton S. and Thomas, A. Gordon and Murphy, Stephen D. and Swanton, Clarence J.},
	month = apr,
	year = {1999},
	note = {Publisher: Cambridge University Press},
	pages = {149--155},
}

@article{villa-morales_stochastic_2020,
	title = {A stochastic model for germination},
	volume = {27},
	issn = {2215-3373, 1409-2433},
	url = {https://revistas.ucr.ac.cr/index.php/matematica/article/view/34109},
	doi = {10.15517/rmta.v27i2.34109},
	abstract = {Assuming that the germination process of a seed passes through several stages (or states), including a state of non-germination, we model this phenomenon by means of a continuous-time Markov chain. The distribution of the germination time and the average of the first germination is obtained. In particular, when the duration of the process at each stage is on average the same we see that the proposed model adjusts rather well some experimental data.},
	number = {2},
	urldate = {2023-05-04},
	journal = {Revista de Matemática: Teoría y Aplicaciones},
	author = {Villa-Morales, José},
	month = jun,
	year = {2020},
	pages = {355--365},
}

@article{thornley_germination_1986,
	title = {A germination model: {Responses} to time and temperature},
	volume = {123},
	issn = {0022-5193},
	shorttitle = {A germination model},
	url = {https://www.sciencedirect.com/science/article/pii/S0022519386802156},
	doi = {10.1016/S0022-5193(86)80215-6},
	abstract = {A compartmental model for seed germination is constructed and analyzed. The main components of the model are a discrete delay, and two intermediate states from which low and high temperature processes giving loss in seed viability can occur. The Arrhenius equation and a related equation are used to describe the temperature dependence of the rate constants of the model. The ensuing twelve-parameter model is analytically soluble, and makes realistic predictions about the temperature responses of germinability, germination rate, and the time course of germination, giving both sigmoidal and non-sigmoidal responses.},
	language = {en},
	number = {4},
	urldate = {2023-05-04},
	journal = {Journal of Theoretical Biology},
	author = {Thornley, J. H. M.},
	month = dec,
	year = {1986},
	pages = {481--492},
}

@incollection{bradford_applying_2022,
	series = {Burleigh {Dodds} {Series} in {Agricultural} {Science}},
	title = {Applying population-based threshold models to quantify and improve seed quality attributes},
	isbn = {978-1-78676-917-6},
	url = {https://shop.bdspublishing.com/store/bds/detail/product/3-190-9781801463584},
	abstract = {Achieving rapid and uniform stand establishment in crops requires a combination of high-quality seeds and appropriate environmental conditions. In particular, temperature and soil moisture (or water potential) are the major factors influencing germination in the field. In this chapter, we focus on the application of population-based threshold (PBT) models to characterize seed germination time courses and how environmental and technological inputs influence them. Viewing seed quality as a product of the behavior of populations of individual seeds is critical for understanding the causes and consequences of poor performance. Quantitatively characterizing seed population features enables their use in seed sorting and seed enhancement, and provides phenotypes for use in research, breeding, conservation and restoration. We believe that PBT models are essential tools to enable full utilization of new advances in seed technology to improve seed quality and enable successful stand establishment in agriculture or in natural settings.},
	urldate = {2023-05-05},
	booktitle = {Advances in {Seed} {Science} and {Technology} for {More} {Sustainable} {Crop} {Productio}},
	publisher = {Burleigh Dodds Science Publishing},
	author = {Bradford, Kent J. and Bello, Pedro},
	editor = {Buitink, Julia and Leprince, Olivier},
	month = jul,
	year = {2022},
	doi = {10.19103/AS.2022.0105.05},
	pages = {67--154},
}

@article{harrison_brief_2018,
	title = {A brief introduction to mixed effects modelling and multi-model inference in ecology},
	volume = {6},
	issn = {2167-8359},
	url = {https://peerj.com/articles/4794},
	doi = {10.7717/peerj.4794},
	abstract = {The use of linear mixed effects models (LMMs) is increasingly common in the analysis of biological data. Whilst LMMs offer a flexible approach to modelling a broad range of data types, ecological data are often complex and require complex model structures, and the fitting and interpretation of such models is not always straightforward. The ability to achieve robust biological inference requires that practitioners know how and when to apply these tools. Here, we provide a general overview of current methods for the application of LMMs to biological data, and highlight the typical pitfalls that can be encountered in the statistical modelling process. We tackle several issues regarding methods of model selection, with particular reference to the use of information theory and multi-model inference in ecology. We offer practical solutions and direct the reader to key references that provide further technical detail for those seeking a deeper understanding. This overview should serve as a widely accessible code of best practice for applying LMMs to complex biological problems and model structures, and in doing so improve the robustness of conclusions drawn from studies investigating ecological and evolutionary questions.},
	language = {en},
	urldate = {2023-05-06},
	journal = {PeerJ},
	author = {Harrison, Xavier A. and Donaldson, Lynda and Correa-Cano, Maria Eugenia and Evans, Julian and Fisher, David N. and Goodwin, Cecily E.D. and Robinson, Beth S. and Hodgson, David J. and Inger, Richard},
	month = may,
	year = {2018},
	pages = {e4794},
}

@inproceedings{stroup_non-normal_2013,
	address = {Kansas State University},
	title = {Non-normal data in agricultural experiments},
	url = {https://newprairiepress.org/agstatconference/2013/proceedings/8},
	doi = {10.4148/2475-7772.1018},
	language = {en},
	urldate = {2023-05-06},
	booktitle = {Proceedings of the 25th {Conference} on {Applied} {Statistics} in {Agriculture}},
	author = {Stroup, W. W.},
	month = apr,
	year = {2013},
}

@article{naylor_using_2007,
	title = {Using segmented regression to analyse the response of germination to temperature},
	volume = {35},
	doi = {10.15258/sst.2007.35.3.02},
	number = {3},
	journal = {Seed Science and Technology},
	author = {Naylor, R. E. L.},
	year = {2007},
	note = {Publisher: International Seed Testing Association},
	pages = {539--549},
}

@article{ellis_influence_1986,
	title = {The influence of temperature on seed germination rate in grain legumes: {II}. intraspecific variation in chickpea ({<}i{>}{Cicer} arietinum{<}i{>} l.) at constant temperatures},
	volume = {37},
	issn = {0022-0957},
	shorttitle = {The influence of temperature on seed germination rate in grain legumes},
	url = {https://doi.org/10.1093/jxb/37.10.1503},
	doi = {10.1093/jxb/37.10.1503},
	abstract = {Positive linear relationships were shown between constant temperatures and the rates of progress of germination to different percentiles, G, for single populations of each of five genotypes of chickpea (Cicer anetinum L.). The base temperature, Tb, at which the rate of germination is zero, was 0·0°C for all germination percentiles of all genotypes. The optimum temperature, To(G), at which rate of germination is most rapid, varied between the five genotypes and also between percentiles within at least one population. Over the sub-optimal temperature range, i.e. from Tb to To(G), the distribution of thermal times within each population was normal. Consequently a single equation was applied to describe the influence of sub-optimal temperatures on rate of germination of all seeds within each population of each genotype. The precision with which optimum temperature, Tb(G), could be defined varied between populations. In each of three genotypes there was a negative linear relationship between temperature above Tb(G) and rate of germination. For all seeds within any of these three populations thermal time at supra-optimal temperatures was constant. Variation in the time taken to germinate at supra-optimal temperatures was a consequence of normal variation in the ceiling temperature, To(G)—the temperature at or above which rate of progress to germination percentile G is zero. A new approach to defining the response of seed germination rate to temperature is proposed for use in germplasm screening programmes.In two populations final percentage germination was influenced by temperature. The optimum constant temperature for maximum final germination was between 10°C and 15°C in these populations; approximately 15°C cooler than the optimum temperature for rate of germination. It is suggested that laboratory tests of chickpea germination should be carried out at temperatures between 10°C and 15°C.},
	number = {10},
	urldate = {2023-05-08},
	journal = {Journal of Experimental Botany},
	author = {Ellis, R. H. and Covell, S. and Roberts, E. H. and Summerfield, R. J.},
	month = oct,
	year = {1986},
	pages = {1503--1515},
}

@article{onofri_unified_2022,
	title = {A unified framework for the analysis of germination, emergence, and other time-to-event data in weed science},
	volume = {70},
	issn = {0043-1745, 1550-2759},
	url = {https://www.cambridge.org/core/journals/weed-science/article/unified-framework-for-the-analysis-of-germination-emergence-and-other-timetoevent-data-in-weed-science/7DB0E039C9013D3E8F44FE32A3F42B88},
	doi = {10.1017/wsc.2022.8},
	abstract = {Germination and emergence assays represent the most notable examples of time-to-event data in agriculture and related disciplines. In spite of the peculiar characteristics of this type of data, there has been little effort to establish a specific and comprehensive framework for their analyses. Indeed, a brief survey of the literature shows that germination and emergence data, along with other phenological measurements such as flowering time, have been analyzed through myriad approaches, giving rise to confusion and uncertainty among scientists and practitioners as to what may represent the best statistical practice. This lack of coherence in statistical approach may reduce the efficiency of research, while making the communication of results and the cross-study comparisons extremely challenging. Here, we attempt to provide a coherent framework and protocol for the analyses of germination/emergence and other time-to-event data in weed science and related disciplines, together with a software implementation in the form of a new R package. We propose a similar approach to biological assays in ecotoxicology, based on: (1) fitting a time-to-event model to describe the whole time course of events; (2) comparing time-to-event curves across experimental treatments, and (3) deriving further information from the fitted model to better focus on some traits of interest. The most appropriate methods to accomplish this procedure were carefully selected from the framework of survival analysis and related sources and were modified to comply with the specific needs of weed, seed, and plant sciences. Finally, they were implemented in the new R package drcte. In this article, we describe the procedure and its limitations by way of providing examples of several types of germination/emergence assays. We highlight that our proposed procedure can also serve as the first step of data analyses, with its output subsequently submitted to traditional or meta-analytic approaches.},
	language = {en},
	number = {3},
	urldate = {2023-05-08},
	journal = {Weed Science},
	author = {Onofri, Andrea and Mesgaran, Mohsen B. and Ritz, Christian},
	month = may,
	year = {2022},
	note = {Publisher: Cambridge University Press},
	pages = {259--271},
}

@article{liu_hydrothermal_2020,
	title = {Hydrothermal sensitivities of seed populations underlie fluctuations of dormancy states in an annual plant community},
	volume = {101},
	issn = {0012-9658, 1939-9170},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/ecy.2958},
	doi = {10.1002/ecy.2958},
	language = {en},
	number = {3},
	urldate = {2023-05-10},
	journal = {Ecology},
	author = {Liu, Shuangshuang and Bradford, Kent J. and Huang, Zhenying and Venable, D. Lawrence},
	month = mar,
	year = {2020},
}

@article{donohue_applying_2015,
	title = {Applying developmental threshold models to evolutionary ecology},
	volume = {30},
	issn = {01695347},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S016953471400250X},
	doi = {10.1016/j.tree.2014.11.008},
	language = {en},
	number = {2},
	urldate = {2023-05-10},
	journal = {Trends in Ecology \& Evolution},
	author = {Donohue, Kathleen and Burghardt, Liana T. and Runcie, Daniel and Bradford, Kent J. and Schmitt, Johanna},
	month = feb,
	year = {2015},
	pages = {66--77},
}

@article{hawkins_secondary_2017,
	title = {Secondary dormancy induction and release in \emph{{Bromus} tectorum} seeds: the role of temperature, water potential and hydrothermal time},
	volume = {27},
	issn = {0960-2585, 1475-2735},
	shorttitle = {Secondary dormancy induction and release in \emph{{Bromus} tectorum} seeds},
	url = {https://www.cambridge.org/core/product/identifier/S0960258516000258/type/journal_article},
	doi = {10.1017/S0960258516000258},
	language = {en},
	number = {1},
	urldate = {2023-05-10},
	journal = {Seed Science Research},
	author = {Hawkins, K. K. and Allen, P.S. and Meyer, S.E.},
	month = mar,
	year = {2017},
	pages = {12--25},
}

@article{meyer_predicting_2009,
	title = {Predicting seed dormancy loss and germination timing for \emph{{Bromus} tectorum} in a semi-arid environment using hydrothermal time models},
	volume = {19},
	issn = {0960-2585, 1475-2735},
	url = {https://www.cambridge.org/core/product/identifier/S0960258509990122/type/journal_article},
	doi = {10.1017/S0960258509990122},
	language = {en},
	number = {4},
	urldate = {2023-05-10},
	journal = {Seed Science Research},
	author = {Meyer, Susan E. and Allen, Phil S.},
	month = dec,
	year = {2009},
	pages = {225--239},
}

@article{bello_single-seed_2016,
	title = {Single-seed oxygen consumption measurements and population-based threshold models link respiration and germination rates under diverse conditions},
	volume = {26},
	issn = {0960-2585, 1475-2735},
	url = {https://www.cambridge.org/core/journals/seed-science-research/article/singleseed-oxygen-consumption-measurements-and-populationbased-threshold-models-link-respiration-and-germination-rates-under-diverse-conditions/ABCB1892AB7DF0B465DCD38BF6BA5F92},
	doi = {10.1017/S0960258516000179},
	abstract = {Seed germination is responsive to diverse environmental, hormonal and chemical signals. Germination rates (i.e. speed and distribution in time) reveal information about timing, uniformity and extent of germination in seed populations and are sensitive indicators of seed vigour and stress tolerance. Population-based threshold (PBT) models have been applied to describe germination responses to temperature, water potential, hormones, ageing and oxygen. However, obtaining detailed data on germination rates of seed populations requires repeated observations at frequent times to construct germination time courses, which is labour intensive and often impractical. Recently, instruments have been developed to measure repeatedly the respiration (oxygen consumption) of individual seeds following imbibition, providing complete respiratory time courses for populations of individual seeds in an automated manner. In this study, we demonstrate a new approach that enables the use of single-seed respiratory data, rather than germination data, to characterize the responses of seed populations to diverse conditions. We applied PBT models to single-seed respiratory data and compared the results to similar analyses of germination time courses. We found consistent and quantitatively comparable relationships between seed respiratory and germination patterns in response to temperature, water potential, abscisic acid, gibberellin, respiratory inhibitors, ageing and priming. This close correspondence between seed respiration and germination time courses enables the use of semi-automated respiratory measurements to assess seed vigour and quality parameters. It also raises intriguing questions about the fundamental relationship between the respiratory capacities of seeds and the rates at which they proceed toward completion of germination.},
	language = {en},
	number = {3},
	urldate = {2023-05-10},
	journal = {Seed Science Research},
	author = {Bello, Pedro and Bradford, Kent J.},
	month = sep,
	year = {2016},
	note = {Publisher: Cambridge University Press},
	pages = {199--221},
}

@article{tatari_application_2020,
	title = {Application of the hydrotime model to assess seed priming effects on the germination of rapeseed (\emph{{Brassica} napus} {L}.) in response to water stress},
	volume = {98},
	issn = {1916-2790},
	url = {https://cdnsciencepub.com/doi/10.1139/cjb-2019-0192},
	doi = {10.1139/cjb-2019-0192},
	abstract = {Our aim was to determine whether the parameters of the hydrotime model can be used to compare the effects of seed priming treatments on germination. Seeds of three rapeseed cultivars (‘H61’, ‘H4815’, and ‘DK003’) were exposed to priming treatments and then their germination was tested at different water potentials. Seed priming improved the germination percentage, which was higher in ‘H4815’ than in the other two cultivars, and it increased germination rate (decreased θH) and uniformity (decreased σψb). The increase in germination rate was higher in PEG-osmoprimed than in NaCl-osmoprimed and hydroprimed seeds. The base water potential allowing 50\% germination () also was affected by seed priming, but the response of cultivars to different priming treatments varied. Compared with the control seeds, hydropriming of ‘H61’ seeds shifted ψb(50) toward negative values, whereas NaCl-osmopriming of ‘H4815’ seeds shifted ψb(50) toward negative values. On the other hand, priming of ‘DK003’ seeds shifted ψb(50) to more positive values and increased susceptibility to water stress. After dormancy-breaking and dormancy-induction treatments, ψb(50) shifted to more negative or positive values, indicating the release of primary dormancy and induction of dormancy, respectively. Therefore, priming treatments should be selected, depending on the environmental conditions anticipated to prevail during the germination of rapeseed seeds.},
	number = {5},
	urldate = {2023-05-10},
	journal = {Botany},
	author = {Tatari, Samaneh and Ghaderi-Far, Farshid and Yamchi, Ahad and Siahmarguee, Asieh and Shayanfar, Ali and Baskin, Carol C.},
	month = may,
	year = {2020},
	note = {Publisher: NRC Research Press},
	pages = {283--291},
}

@mastersthesis{bello_analytical_2021,
	title = {Analytical and {Computational} {Tools} to {Assess} {Seed} {Quality} and {Model} {Germination} {Rates}},
	school = {University of California, Davis},
	author = {Bello, Pedro Henrique Nogueira},
	year = {2021},
	note = {ISBN: 9798738650796},
}

@article{still_using_1998,
	title = {Using hydrotime and {ABA}-time models to quantify seed quality of {Brassicas} during development},
	volume = {123},
	issn = {2327-9788, 0003-1062},
	url = {https://journals.ashs.org/jashs/view/journals/jashs/123/4/article-p692.xml},
	doi = {10.21273/JASHS.123.4.692},
	abstract = {With many seed crops, the most difficult production decision is when to harvest. In indeterminate crops such as Brassica species, early harvests result in immature seed of low vigor while late harvests risk seed deterioration and seed loss due to shattering. To provide a biological basis on which to determine harvest timing, we have characterized seed development in rape seed (Brassica napus L. `Weststar') and red cabbage (Brassica oleracea L. Group Capitata) using population-based hydrotime and ABA-time models. These models provide information relevant to assessing physiological maturity, and therefore, seed quality. The hydrotime and ABA-time models quantify germination rate, the uniformity of germination, viability, and the sensitivity of germination to water potential and ABA. Indices derived from these models, along with maximum germination and t50 values, were used to determine physiological maturity (maximum seed quality) of the seeds during development. The overall trends in seed development were similar in both species: as seeds matured, germination became more uniform and less sensitive to low Ψ and externally applied ABA. The models accurately described germination time courses and final germination percentages except for seeds imbibed at very high concentrations of ABA. In rape seed, physiological maturity was attained several days after maximum seed dry mass, while in red cabbage physiological maturity occurred at or after maximum seed dry mass. Vigor indices were correlated with easily discerned traits such as moisture content and silique phenotypic characteristics. The results of these experiments suggest that hydrotime and ABA-time models can be successfully used to provide a biological basis on which to determine harvest in brassicas.},
	language = {en\_US},
	number = {4},
	urldate = {2023-05-10},
	journal = {Journal of the American Society for Horticultural Science},
	author = {Still, David W. and Bradford, Kent J.},
	month = jul,
	year = {1998},
	note = {Publisher: American Society for Horticultural Science
Section: Journal of the American Society for Horticultural Science},
	pages = {692--699},
}

@article{dorado_germination_2009,
	title = {Germination patterns in naturally chilled and nonchilled seeds of fierce thornapple ( \emph{{Datura} ferox} ) and velvetleaf ( \emph{{Abutilon} theophrasti} )},
	volume = {57},
	issn = {0043-1745, 1550-2759},
	url = {https://www.cambridge.org/core/product/identifier/S0043174500018543/type/journal_article},
	doi = {10.1614/WS-08-122.1},
	abstract = {Seeds from natural populations of fierce thornapple and velvetleaf collected in a corn-growing area in central Spain were incubated at a range of constant temperatures and water potentials to model the progress of germination on the basis of the accumulation of hydrothermal time. Previous to the germination tests, the seeds were treated in two different ways: (1) dark storage under dry conditions (nonchilled seeds), and (2) burying in the original soil at 10-cm depth during 2 mo in winter (naturally chilled seeds). The results indicated different mechanisms inhibiting germination in both weed species. Whereas fierce thornapple displayed some type of embryo dormancy, the lack of germination in velvetleaf appeared to be entirely due to the seed coat. On the other hand, significant differences between nonchilled and naturally chilled seeds in fierce thornapple were observed, mainly due to the decrease in the mean base water potential of the 50th percentile in the latter, which indicated a loss of dormancy by exposure of the seeds to natural conditions. Hydrothermal time appears to be a good description of the germination patterns in both weed species, but in the case of fierce thornapple, only for naturally chilled seeds. Thus, the development of the hydrothermal model in fierce thornapple raises some questions for consideration concerning the influence of the type of seeds (conditions of storage, pretreatments of the seeds before germination tests) on its germination capacity.},
	language = {en},
	number = {2},
	urldate = {2023-05-25},
	journal = {Weed Science},
	author = {Dorado, José and Fernández-Quintanilla, César and Grundy, Andrea C.},
	month = apr,
	year = {2009},
	pages = {155--162},
}

@techreport{chen_new_2022,
	type = {preprint},
	title = {A new framework for modelling seed germination and seedling tillering of winter wheat in the field},
	url = {https://www.researchsquare.com/article/rs-1469115/v1},
	abstract = {Abstract
          Aims
 Seed germination is regulated by multiple environmental cues in the field and understanding their relationship is critical to planning seed drilling and subsequent seedling management but challenging due to the trade-off impact of some environmental stimuli on metabolic reactions involved in the germination.
Methods
 We develop a new framework by introducing a physiological dimension over which the metabolic reactions associated with seed germination can be modelled as a moving dynamic event. The influence of environmental cues and the heterogeneity of seeds is described by an average germination rate and a dispersion coefficient. Winter wheat seeds were drilled at different dates in field plots under different soil water contents, and the time course of germination in all treatments and the subsequent tillering development are used to validate the model.
Results
 The model accurately reproduces the time course of germination in all treatments. We find that the average germination rate increases asymptotically rather than linearly as the temperature increases within the base-suboptimal temperature range, and that there is an optimal soil water content at which the germination rate peaks due to the trade-off impact of soil water on seed imbibition and soil anaerobicity. The average germination rate and the dispersion coefficient are closely related.
Conclusions
 Using soil water content instead of matric potential in our model can naturally describe the simultaneous impact of soil water on soil anaerobicity and seed imbibition, and the physiological dimension can be extended to combine seed germination and seedling tillering development as a continued physiological process.},
	urldate = {2023-05-25},
	institution = {In Review},
	author = {Chen, Jinping and Whalley, Peter A. and Li, Zhongyang and Gao, Yang and Zhang, Xiaoxian and Hawkesford, Malcolm J. and Whalley, W. Richard},
	month = apr,
	year = {2022},
	doi = {10.21203/rs.3.rs-1469115/v1},
}

@article{malavert_role_2020,
	title = {The role of seed water content for the perception of temperature signals that drive dormancy changes in \emph{{Polygonum} aviculare} buried seeds},
	volume = {48},
	issn = {1445-4416, 1445-4416},
	url = {https://www.publish.csiro.au/fp/FP20011},
	doi = {10.1071/FP20011},
	abstract = {Seedling emergence in the field is strongly related to the dynamics of dormancy release and induction of the seed bank, which is mainly regulated by soil temperature. However, there is limited information on how temperature-driven effects on dormancy changes are modulated by the seed hydration-level. We investigated the effect of seed water content (SWC) on the dormancy release and dormancy induction in Polygonum aviculare L. seeds. We characterised quantitatively the interaction between seed water content (SWC) and temperature through the measurement of changes in the lower limit temperature for seed germination (Tl) during dormancy changes for seeds with different SWC. These relationships were inserted in existing population-based threshold models and were run against field obtained data. The model considering SWC was able to predict P. aviculare field emergence patterns. However, failure to consider SWC led to overestimations in the emergence size and timing. Our results show that in humid temperate habitats, the occurrence of eventual water shortages during late-winter or spring (i.e. short periods of water content below 31\% SWC) can affect soil temperature effects on seed dormancy, and might lead reductions in the emergence size rather than to significant temporal displacements in the emergence window. In conclusion, SWC plays an important role for the perception of temperature signals that drive dormancy changes in buried seeds.},
	language = {en},
	number = {1},
	urldate = {2023-05-23},
	journal = {Functional Plant Biology},
	author = {Malavert, Cristian and Batlla, Diego and Benech-Arnold, Roberto L. and Malavert, Cristian and Batlla, Diego and Benech-Arnold, Roberto L.},
	month = jul,
	year = {2020},
	note = {Publisher: CSIRO PUBLISHING},
	pages = {28--39},
}

@article{afzal_quantifying_2022,
	title = {Quantifying the germination response of \emph{{Parthenium} hysterophorus} at various temperatures and water potentials by using population-based threshold model},
	volume = {13},
	doi = {10.3389/fpls.2022.961378},
	journal = {Frontiers in Plant Science},
	author = {Afzal, Irfan and Akram, Muhammad and Javed, Talha and Ali, Faryal and Kalaji, Hazem M. and Wróbel, Jacek and Telesiński, Arkadiusz and Mojski, Jacek and Ahmed, Mohamed AA},
	year = {2022},
	note = {Publisher: Frontiers Media SA},
}

@article{bradford_understanding_2023,
	title = {Understanding seed behavior: populations of individuals},
	issn = {0567-7572, 2406-6168},
	shorttitle = {Understanding seed behavior},
	url = {https://www.actahort.org/books/1365/1365_1.htm},
	doi = {10.17660/ActaHortic.2023.1365.1},
	number = {1365},
	urldate = {2023-05-23},
	journal = {Acta Horticulturae},
	author = {Bradford, K.J. and Bello, P.},
	month = apr,
	year = {2023},
	pages = {1--16},
}

@article{yasin_effect_2016,
	title = {Effect of reduced oxygen concentration on the germination behavior of vegetable seeds},
	volume = {57},
	issn = {2211-3460},
	url = {https://doi.org/10.1007/s13580-016-0170-1},
	doi = {10.1007/s13580-016-0170-1},
	abstract = {Oxygen (O2) in the soil is necessary for the germination of seeds, but it can be reduced by excessive water contents, compaction, compression, and hard surfaces. Reduced O2 concentrations may change the germination success (proportion of seeds germinated; d) and speed (time to reach 50\% germination; t50) of seeds. Independent laboratory experiments tested the germination of nine economically valuable vegetable species at five O2 concentrations (20.9, 15, 10, 5, and 2.5\%). Members of the Asteraceae (butterhead lettuce and iceberg lettuce) and Brassicaceae (broccoli and white cabbage) families germinated best at 20.9\% O2 and 15\% O2, but were also able to germinate at 5-2.5\% O2. Members of the Apiaceae (carrot, celeriac, and parsley) were sensitive to 5-2.5\% O2 concentrations, which reduced their d and increased their t50. The germination rate of Swiss chard (Amaranthaceae) consistently declined as O2 concentrations reduced from 20.9\% O2 to 2.5\% O2. There was a slight variation in the germination response to O2 concentration between the morphotypes of Brassica oleracea, (white cabbage, broccoli and cauliflower), although it was unclear whether this was related to seed age, genetic variation, or the conditions experienced during seed production or storage. The seeds of the Brassicaceae (broccoli and white cabbage) and Asteraceae (butterhead lettuce and iceberg lettuce) were less sensitive to reduced O2 concentrations and therefore may be more suitable for soils suffering from low O2 concentrations, such as compacted soils with hard surfaces or waterlogged soils.},
	language = {en},
	number = {5},
	urldate = {2023-05-23},
	journal = {Horticulture, Environment, and Biotechnology},
	author = {Yasin, Muhammad and Andreasen, Christian},
	month = oct,
	year = {2016},
	pages = {453--461},
}

@article{wang_quantitative_2009,
	title = {Quantitative description of the effect of stratification on dormancy release of grape seeds in response to various temperatures and water contents},
	volume = {60},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erp178},
	doi = {10.1093/jxb/erp178},
	abstract = {The effect of stratification on dormancy release of grape seeds crossing from the sub- to the supraoptimal range of temperatures and water contents was analysed by modified threshold models. The stratification impacted on dormancy release in three different ways: (i) dormancy was consistently released with prolonged stratification time when stratified at temperatures of \&lt;15 °C; (ii) at 15 °C and 20 °C, the stratification effect initially increased, and then decreased with extended time; and (iii) stratification at 25 °C only reduced germinable seeds. These behaviours indicated that stratification could not only release primary dormancy but also induce secondary dormancy in grape seed. The rate of dormancy release changed linearly in two phases, while induction increased exponentially with increasing temperature. The thermal time approaches effectively quantified dormancy release only at suboptimal temperature, but a quantitative method to integrate the occurrence of dormancy release and induction at the same time could describe it well at either sub- or supraoptimal temperatures. The regression with the percentage of germinable seeds versus stratification temperature or water content within both the sub- and supraoptimal range revealed how the optimal temperature (Tso) and water content (Wso) for stratification changed. The Tso moved from 10.6 °C to 5.3 °C with prolonged time, while Wso declined from \&gt;0.40 g H2O g DW−1 at 5 °C to ∼0.23 g H2O g DW−1 at 30 °C. Dormancy release in grape seeds can occur across a very wide range of conditions, which has important implications for their ability to adapt to a changeable environment in the wild.},
	number = {12},
	urldate = {2023-05-23},
	journal = {Journal of Experimental Botany},
	author = {Wang, W. Q. and Song, S. Q. and Li, S. H. and Gan, Y. Y. and Wu, J. H. and Cheng, H. Y.},
	month = aug,
	year = {2009},
	pages = {3397--3406},
}

@article{boddy_stratification_2013,
	title = {Stratification requirements for seed dormancy alleviation in a wetland weed},
	volume = {8},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071457},
	doi = {10.1371/journal.pone.0071457},
	abstract = {Echinochloaoryzicola(syn.E. phyllopogon) is an exotic weed of California rice paddies that has evolved resistance to multiple herbicides. Elimination of seedlingsthroughcertain weed control methods can limit the spread of this weed, but is contingent on accurate predictions of germination and emergence timing, which are influenced by seed dormancy levels.In summer annuals, dormancy can often be relieved through stratification, a period of prolonged exposure to cold and moist conditions.We used population-based threshold models to quantify the effects of stratification on seed germination of four E. Oryzicola populations at a range of water potential (Ψ) and oxygen levels. We also determined how stratification temperatures, moisture levels and durations contributed to dormancy release. Stratification released dormancy by decreasing base Ψ and hydrotimerequired for germination and by eliminating any germination sensitivity to oxygen. Stratification also increased average germination rates (GR), which were used as a proxy for relative dormancy levels. Alternating temperatures nearly doubled GR in all populations, indicating that seeds could be partially dormant despite achieving high final germination percentages. Stratification at Ψ = 0 MPa increased GR compared to stratification at lower water potentials, demonstrating that Ψ contributed to regulating dormancy release. Maximum GR occurred after 2-4 weeks of stratification at 0 MPa; GR were often more rapid for herbicide-resistant than for herbicide-susceptible seeds, implying greater dormancy in the latter. Manipulation of field conditions to promote dormancy alleviation of E. oryzicola seeds might improve the rate and uniformity of germination for seed bank depletion through seedling weed control. Our results suggest field soil saturation in winter would contribute towards E. oryzicola dormancy release and decrease the time to seedling emergence.},
	language = {en},
	number = {9},
	urldate = {2023-05-23},
	journal = {PLOS ONE},
	author = {Boddy, Louis G. and Bradford, Kent J. and Fischer, Albert J.},
	month = sep,
	year = {2013},
	note = {tex.ids= boddy\_stratification\_2013-1
publisher: Public Library of Science},
	pages = {e71457},
	file = {Full Text:C\:\\Users\\J. Aravind\\Zotero\\storage\\TP6XFASJ\\Boddy et al. - 2013 - Stratification requirements for seed dormancy alleviation in a wetland weed.pdf:application/pdf},
}

@article{batlla_changes_2005,
	title = {Changes in the light sensitivity of buried \emph{{Polygonum} aviculare} seeds in relation to cold-induced dormancy loss: {Development} of a predictive model},
	volume = {165},
	issn = {0028-646X},
	shorttitle = {Changes in the light sensitivity of buried polygonum aviculare seeds in relation to cold-induced dormancy loss},
	url = {https://www.jstor.org/stable/1514724},
	doi = {10.1111/j.1469-8137.2004.01262.x},
	abstract = {• The effect of cold (stratification) temperature on changes in the sensitivity of Polygonum aviculare seeds to light was investigated. • Seeds buried in pots were stored under stratification temperatures (1.6, 7 and 12°C) for 137 d. Seeds exhumed at regular intervals during storage were exposed to different light treatments. Germination responses obtained for seeds exposed to different light treatments and stratification temperatures were used to develop a model to predict the sensitivity of buried seeds to light. • Seed sensitivity to light increased as dormancy loss progressed, showing the successive acquisition of low-fluence responses (LFR), very low-fluence responses (VLFR), and the loss of the light requirement for germination for a fraction of the seed population. These changes were inversely correlated to stratification temperature, allowing the use of a thermal time index to relate observed changes in seed light sensitivity to stratification temperature. • The rate of increase in sensitivity of P. aviculare seeds to light during stratification is inversely correlated to soil temperature, and these changes in light sensitivity could be predicted in relation to temperature using thermal-time models.},
	number = {2},
	urldate = {2023-05-23},
	journal = {The New Phytologist},
	author = {Batlla, Diego and Benech-Arnold, Roberto Luis},
	year = {2005},
	note = {Publisher: [Wiley, New Phytologist Trust]},
	pages = {445--452},
}

@article{malavert_light_2021,
	title = {Light sensitivity changes during dormancy induction in \emph{{Polygonum} aviculare} {L}. seeds: development of a predictive model of annual changes in seed-bank light sensitivity in relation to soil temperature},
	volume = {61},
	issn = {1365-3180},
	shorttitle = {Light sensitivity changes during dormancy induction in {Polygonum} aviculare {L}. seeds},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/wre.12463},
	doi = {10.1111/wre.12463},
	abstract = {Seeds of weed species require light to terminate dormancy and give way to germination. It is documented that sensitivity to light in Polygonum aviculare seeds increases during dormancy release. However, it is not known whether this sensitivity is lost during dormancy induction. The aim of this study was to investigate and quantify the changes in dormancy level of P. aviculare seeds during secondary dormancy induction as measured by changes in sensitivity to light in relation to soil temperature. Polygonum aviculare seeds were stratified at 5ºC until obtaining a minimum dormancy level. The seeds were then induced into secondary dormancy by burying them in pots containing soil which were stored at 10, 15, 20 and 25ºC for different time-periods. Polygonum aviculare seeds were exhumed periodically, exposed to different light treatments (Pfr/Ptotal-pythochrome = 0.76, 0.03 and 7.6 × 10−4) or darkness, and incubated at 15ºC to test germination. Our results showed that the high sensitivity to light acquired during dormancy release and decreased during dormancy induction at a rate that was temperature-dependent. These changes in sensitivity to light were quantified as a function of the accumulation of thermal-time over a base-temperature of 7.9ºC during dormancy induction and were coupled with previous thermal-time index established for the dormancy release process. Both thermal-time indices allowed us to develop a model for the prediction of cyclic changes in sensitivity to light in relation to the thermal environment experienced by the seeds during burial. This model constitutes a valuable tool for predicting weed emergence in the field and to design management practices accordingly.},
	language = {en},
	number = {2},
	urldate = {2023-05-23},
	journal = {Weed Research},
	author = {Malavert, Cristian and Batlla, Diego and Benech-Arnold, Roberto L.},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/wre.12463},
	pages = {115--125},
}

@article{fernandez_farnocchia_regulation_2019,
	title = {Regulation of seed dormancy by the maternal environment is instrumental for maximizing plant fitness in \emph{{Polygonum} aviculare}},
	volume = {70},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erz269},
	doi = {10.1093/jxb/erz269},
	abstract = {Emergence at an appropriate time and place is critical for maximizing plant fitness and hence sophisticated mechanisms such as seed dormancy have evolved. Although maternal influence on different aspects of dormancy behavior has been identified, its impact under field conditions and its relation to plant fitness has not been fully determined. This study examined maternal effects in Polygonum aviculare on release of seed primary dormancy, responses to alternating temperatures, induction into secondary dormancy, and field emergence patterns as influenced by changes in the sowing date and photoperiod experienced by the mother plant. Maternal effects were quantified using population threshold models that allowed us to simulate and interpret the experimental results. We found that regulation of dormancy in P. aviculare seeds by the maternal environment is instrumental for maximizing plant fitness in the field. This regulation operates by changing the dormancy level of seeds dispersed at different times (as a consequence of differences in the sowing dates of mother plants) in order to synchronize most emergence to the seasonal period that ultimately guarantees the highest reproductive output of the new generation. Our results also showed that maternal photoperiod, which represents a clear seasonal cue, is involved in this regulation.},
	number = {18},
	urldate = {2023-05-23},
	journal = {Journal of Experimental Botany},
	author = {Fernández Farnocchia, Rocío B and Benech-Arnold, Roberto L and Batlla, Diego},
	month = sep,
	year = {2019},
	pages = {4793--4806},
}

@article{fernandez_farnocchia_optimization_2021,
	title = {Optimization of timing of next-generation emergence in \emph{{Amaranthus} hybridus} is determined via modulation of seed dormancy by the maternal environment},
	volume = {72},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erab141},
	doi = {10.1093/jxb/erab141},
	abstract = {The timing of emergence of weed species has critical ecological and agronomical implications. In several species, emergence patterns largely depend on the level of dormancy of the seedbank, which is modulated by specific environmental factors. In addition, environmental conditions during seed maturation on the mother plant can have marked effects on the dormancy level at the time of seed dispersal. Hence, the maternal environment has been suggested to affect seedbank dormancy dynamics and subsequent emergence; however, this modulation has not been adequately examined under field conditions, and the mechanisms involved are only partly understood. Combining laboratory and field experiments with population-based models, we investigated how dormancy level and emergence in the field are affected by the sowing date and photoperiod experienced by the mother plant in Amaranthus hybridus, a troublesome weed worldwide. The results showed that an earlier sowing date and a longer photoperiod enhanced the level of dormancy by increasing the dormancy imposed by both the embryo and the seed coat. However, this did not affect the timing and extent of emergence in the field; on the contrary, the variations in dormancy level contributed to synchronizing the emergence of the next generation of plants with the time period that maximized population fitness. Our results largely correspond with effects previously observed in other species such as Polygonum aviculare and Arabidopsis, suggesting a common effect exists within different species.},
	number = {12},
	urldate = {2023-05-23},
	journal = {Journal of Experimental Botany},
	author = {Fernández Farnocchia, Rocio Belen and Benech-Arnold, Roberto Luis and Mantese, Anita and Batlla, Diego},
	month = may,
	year = {2021},
	pages = {4283--4297},
}

@article{seal_seed_2018,
	title = {Seed germination niche of the halophyte \emph{{Suaeda} maritima} to combined salinity and temperature is characterised by a halothermal time model},
	volume = {155},
	issn = {00988472},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0098847218306269},
	doi = {10.1016/j.envexpbot.2018.06.035},
	language = {en},
	urldate = {2023-05-22},
	journal = {Environmental and Experimental Botany},
	author = {Seal, Charlotte E. and Barwell, Louise J. and Flowers, Timothy J. and Merrett Wade, Ellie and Pritchard, Hugh W.},
	month = nov,
	year = {2018},
	pages = {177--184},
}

@article{bair_hydrothermal_2006,
	title = {A hydrothermal after-ripening time model for seed dormancy loss in \emph{{Bromus} tectorum} {L}.},
	volume = {16},
	issn = {1475-2735, 0960-2585},
	url = {https://www.cambridge.org/core/journals/seed-science-research/article/abs/hydrothermal-afterripening-time-model-for-seed-dormancy-loss-in-bromus-tectorum-l/4B1F14DB4A84ECC4D5DC0E5E1E4F48B2},
	doi = {10.1079/SSR2005237},
	abstract = {After-ripening, the loss of dormancy under dry conditions, is associated with a decrease in mean base water potential for germination of Bromus tectorum L. seeds. After-ripening rate is a linear function of temperature above a base temperature, so that dormancy loss can be quantified using a thermal after-ripening time (TAR) model. To incorporate storage water potential into TAR, we created a hydrothermal after-ripening time (HTAR) model. Seeds from two B. tectorum populations were stored under controlled temperatures (20 or 30 °C) and water potentials (−400 to −40 MPa). Subsamples were periodically removed from each storage treatment and incubated at 15 or 25 °C to determine germination time courses. Dormancy status (mean base water potential) was calculated from each time course using hydrothermal time equations developed for each seed collection. Seeds stored at −400 MPa did not after-ripen. At water potentials from −400 to −150 MPa, the rate of after-ripening increased approximately linearly with increasing water potential. Between −150 and −80 MPa, there was no further increase in after-ripening rate, while at −40 MPa seeds did not after-ripen and showed loss of vigour. These results suggest that the concept of critical water potential thresholds, previously shown to be associated with metabolic activity and desiccation damage in partially hydrated seeds, is also relevant to the process of after-ripening. The HTAR model generally improved field predictions of dormancy loss when the soil was very dry. Reduced after-ripening rate under such conditions provides an ecologically relevant explanation of how seeds prolong dormancy at high summer soil temperatures.},
	language = {en},
	number = {1},
	urldate = {2023-05-23},
	journal = {Seed Science Research},
	author = {Bair, Necia B. and Meyer, Susan E. and Allen, Phil S.},
	month = mar,
	year = {2006},
	note = {Publisher: Cambridge University Press},
	pages = {17--28},
}

@article{christensen_hydrothermal_1996,
	title = {A hydrothermal time model of seed after-ripening in \emph{{Bromus} tectorum} {L}.},
	volume = {6},
	issn = {1475-2735, 0960-2585},
	url = {https://www.cambridge.org/core/journals/seed-science-research/article/abs/hydrothermal-time-model-of-seed-afterripening-in-bromus-tectorum-l/26D06833EB397A8A4A62E8B7876A5780},
	doi = {10.1017/S0960258500003214},
	abstract = {Bromus tectorum L. is an invasive winter annual grass with seeds that lose dormancy through the process of dry after-ripening. This paper proposes a model for after-ripening of B. tectorum seeds based on the concept of hydrothermal time. Seed germination time course curves are modelled using five parameters: a hydrothermal time constant, the fraction of viable seeds in the population, base temperature, mean base water potential and the standard deviation of base water potentials in the population. It is considered that only mean base water potential varies as a function of storage duration and incubation temperature following after-ripening. All other parameters are held constant throughout after-ripening and at all incubation temperatures. Data for model development are from seed germination studies carried out at four water potentials (0, −0.5, −1.0 and −1.5 MPa) at each of two constant incubation temperatures (15 and 25°C) following different storage intervals including recently harvested, partially after-ripened (stored for 4, 9 or 16 weeks at 20°C) and fully after-ripened (stored for 14 weeks at 40°C). The model was fitted using a repeated probit regression method, and for the two seed populations studied gave R2 values of 0.898 and 0.829. Germination time course curves predicted by the model generally had a good fit when compared with observed curves at the incubation temperature/water potential treatment combinations for different after-ripening intervals. Changes in germination time course curves during after-ripening of B. tectorum can largely be explained by decreases in the mean base water potential. The simplicity and good fit of the model give it considerable potential for extension to simulation of after-ripening under field conditions.},
	language = {en},
	number = {4},
	urldate = {2023-05-23},
	journal = {Seed Science Research},
	author = {Christensen, Maren and Meyer, Susan E. and Allen, Phil S.},
	month = dec,
	year = {1996},
	note = {tex.ids= christensen\_hydrothermal\_1996-1
publisher: Cambridge University Press},
	pages = {155--164},
}

@article{bradford_relationship_1994,
	title = {Relationship between accumulated hydrothermal time during seed priming and subsequent seed germination rates},
	volume = {4},
	issn = {1475-2735, 0960-2585},
	url = {https://www.cambridge.org/core/journals/seed-science-research/article/abs/relationship-between-accumulated-hydrothermal-time-during-seed-priming-and-subsequent-seed-germination-rates/4C04CD735BDEE5A9F76B8035421FCEBC#},
	doi = {10.1017/S0960258500002038},
	abstract = {Seed germination rates are sensitive to both temperature (T) and water potential (ψ). The times to germination of seeds imbibed at suboptimal T and/or reduced ψ are inversely proportional to the amounts by which T exceeds a base temperature (Tb) and ψ exceeds a base water potential (ψb). Germination rates across a range of suboptimal T and ψ can be normalized on the basis of the hydrothermal time accumulated in excess of these thresholds. However, seeds can also progress metabolically toward germination even at T or ψ too low to allow radicle emergence to occur. Seeds preimbibed at low ψ and dried back, or primed, germinate more rapidly upon subsequent reimbibition. We show here that the increase in germination rates of tomato (Lycopersicon esculentum Mill.) seeds resulting from seed priming is linearly related to the hydrothermal time accumulated during the priming treatment. The threshold temperature (Tmin = 7.05°C) and water potential (ψmin = −2.50 MPa) for metabolic advancement were considerably lower than the corresponding thresholds for radicle emergence of the same seed lot (Tb = 11°C; ψb = −0.71 MPa), allowing the accumulation of hydrothermal priming time that is subsequently expressed as more rapid germination when T or ψ increase. The hydrothermal time model can now be applied to quantify and analyse germination rates of seeds across the entire range of suboptimal T and ψ at which metabolic progress toward radicle emergence is possible.},
	language = {en},
	number = {2},
	urldate = {2023-05-23},
	journal = {Seed Science Research},
	author = {Bradford, Kent J. and Haigh, Anthony M.},
	month = jun,
	year = {1994},
	note = {Publisher: Cambridge University Press},
	pages = {63--69},
}

@article{batlla_framework_2015,
	title = {A framework for the interpretation of temperature effects on dormancy and germination in seed populations showing dormancy},
	volume = {25},
	issn = {0960-2585, 1475-2735},
	url = {https://www.cambridge.org/core/product/identifier/S0960258514000452/type/journal_article},
	doi = {10.1017/S0960258514000452},
	abstract = {Abstract
            Temperature is a key factor affecting both dormancy and germination. In non-dormant seeds, when temperature is within the thermal range permissive for germination, it just regulates germination velocity, while in seeds presenting dormancy it can also be affecting dormancy level, dormancy termination and the expression of dormancy itself. This dual effect of temperature on dormancy and germination often leads to misinterpretation of obtained germination results and confounds the analysis of temperature effects in seed populations presenting some degree of dormancy. In the present paper we discuss the effect of temperature in the regulation of dormancy level and its implications in dormancy expression, as an attempt to construct a conceptual framework that allows distinguishing between the effects of temperature on dormancy and germination. Finally, we present examples of how a better understanding of these effects could help us to interpret the mixed effects of temperature on both processes during incubation of seeds presenting dormancy.},
	language = {en},
	number = {2},
	urldate = {2023-05-23},
	journal = {Seed Science Research},
	author = {Batlla, Diego and Benech-Arnold, Roberto L.},
	month = jun,
	year = {2015},
	pages = {147--158},
}

@mastersthesis{bair_hydrothermal_2004,
	title = {A hydrothermal after-ripening time model for seed dormancy loss in \emph{{Bromus} tectorum} {L}.},
	url = {https://scholarsarchive.byu.edu/etd/533},
	abstract = {After-ripening, the loss of dormancy under dry conditions, is associated with a decrease in mean base water potential for germination of Bromus tectorum L. seeds. After-ripening rate is a linear function of temperature above a base temperature, so that dormancy loss can be quantified using a thermal after-ripening time (TAR) model. To incorporate storage water potential into TAR, we created a hydrothermal after-ripening time (HTAR) model. Seeds from two B. tectorum populations were stored under controlled temperatures (20 or 30 °C) and water potentials (−400 to −40 MPa). Subsamples were periodically removed from each storage treatment and incubated at 15 or 25 °C to determine germination time courses. Dormancy status (mean base water potential) was calculated from each time course using hydrothermal time equations developed for each seed collection. Seeds stored at −400 MPa did not after-ripen. At water potentials from −400 to −150 MPa, the rate of after-ripening increased approximately linearly with increasing water potential. Between −150 and −80 MPa, there was no further increase in after-ripening rate, while at −40 MPa seeds did not after-ripen and showed loss of vigour. These results suggest that the concept of critical water potential thresholds, previously shown to be associated with metabolic activity and desiccation damage in partially hydrated seeds, is also relevant to the process of after-ripening. The HTAR model generally improved field predictions of dormancy loss when the soil was very dry. Reduced after-ripening rate under such conditions provides an ecologically relevant explanation of how seeds prolong dormancy at high summer soil temperatures.},
	language = {en},
	urldate = {2023-05-23},
	school = {Department of Plant and Animal Science, Brigham Young University},
	author = {Bair, Necia B.},
	month = aug,
	year = {2004},
}

@article{patane_modeling_2016,
	title = {Modeling seed germination of unprimed and primed seeds of sweet sorghum under {PEG}-induced water stress through the hydrotime analysis},
	volume = {38},
	issn = {1861-1664},
	url = {https://doi.org/10.1007/s11738-016-2135-5},
	doi = {10.1007/s11738-016-2135-5},
	abstract = {The effects of reduced water potential (ψ) on seed germination at 25 and 15 °C in unprimed (UP) and primed (P) seeds of two cultivars of sweet sorghum (cv. Keller and cv. Makueni local), were analyzed through the hydrotime model. Six ψ (from 0 to −1.0 MPa) in polyethylene glycol 6000 (PEG) solutions were used for the tests. Seeds were primed in 250 g/L PEG solution at 15 °C for 48 h. Decreasing ψ of imbibition solution reduced and delayed germination. At 15 °C seeds germinated less and slower than at 25 °C at any ψ. Seeds of cv. Makueni local exhibited a greater sensitivity to water stress in terms of germination percentage, than seeds of cv. Keller, but they were faster in germination. Osmopriming was beneficial for seed germination, both in terms of final percentage and rate, at any temperature and ψ. The hydrotime analysis revealed that predicted θH constant was increased when temperature was reduced to 15 °C and at this temperature median base water potential [ψb(50)] for germination was higher (less negative) than at 25 °C. Seed priming shifted ψb(50) towards more negative values and reduced θH requirements for germination. At 25 °C the two cultivars behaved similarly while at 15 °C cv. Keller exhibited a ψb more negative but required a greater θH to germinate, indicating a greater water-stress tolerance but a slower germination, than cv. Makueni local. The application of the model allows to identify water stress tolerant cultivars during germination, to include into breeding programs for the selection of well-performing cultivars under stress conditions.},
	language = {en},
	number = {5},
	urldate = {2023-05-23},
	journal = {Acta Physiologiae Plantarum},
	author = {Patanè, Cristina and Saita, Alessandro and Tubeileh, Ashraf and Cosentino, Salvatore L. and Cavallaro, Valeria},
	month = apr,
	year = {2016},
	pages = {115},
}

@article{dahal_respiration_1996,
	title = {Respiration and germination rates of tomato seeds at suboptimal temperatures and reduced water potentials},
	volume = {47},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/47.7.941},
	doi = {10.1093/jxb/47.7.941},
	abstract = {Suboptimal temperature (T) affects germination rates (reciprocal of time to radicle emergence) on a thermal time basis; that is, the T in excess of a base or minimum temperature multiplied by the time to a given per cent germination [tg) is a constant. Respiration rates are also sensitive to T, and proportional relationships are often found between respiration rates and germination rates. Reduced water potential (ψ) delays seed germination on a hydrotime basis (i.e. the ψ in excess of a base water potential multiplied by tg is a constant). It was tested whether respiration rates prior to radicle emergence vary in proportion to T and ψ as expected from the thermal and hydrotime models. Respiration rates (C02 evolution) of cold-tolerant, rapidly germinating (PI 341988) and cold-sensitive, more slowly germinating (T5) tomato [Lycopersicon esculentum Mill.) seeds were evaluated over a range of T and ψ conditions. For both genotypes, respiration rates until the beginning of radicle emergence were related to T on a thermal time basis and increased approximately linearly with ψ above -2.0 MPa, consistent with the hydrotime model. Respiration rates were uniquely related to germination rates, regardless of whether germination timing was affected by T, ψ, or genotype. However, germination timing was unaffected when respiration rates were manipulated by varying 02 partial pressure. Thus, while both germination and respiration rates vary with T and ψ consistent with thermal and hydrotime models of biological time, respiration rates per se were not the limiting factor in germination timing of tomato seeds.},
	number = {7},
	urldate = {2023-05-23},
	journal = {Journal of Experimental Botany},
	author = {Dahal, Peetambar and Kim, Nahm-Su and Bradford, Kent J.},
	month = jul,
	year = {1996},
	pages = {941--947},
}

@article{cheng_hydrothermal_1999,
	title = {Hydrothermal time analysis of tomato seed germination responses to priming treatments},
	volume = {50},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/50.330.89},
	doi = {10.1093/jxb/50.330.89},
	abstract = {Controlled hydration of seeds followed by drying (seed priming) is used to break dormancy, speed germination, and improve uniformity of radicle emergence. To date, empirical trials are used to predict optimal priming conditions for a given seed lot. Since priming is based upon seed water relations, it was hypothesized that the sensitivity of germination to reduced water potential before priming might be mechanistically related to, and therefore predictive of, priming responsiveness. Analyses of germination of 13 tomato (Lycopersicon esculentum Mill.) seed lots at two temperatures (15 °C and 20 °C) and three water potentials (0, −0.28 and −0.43 MPa) showed that seed lot germination responses could be quantitatively characterized by parameters derived from thermal time, hydrotime, and hydrothermal time models (R2=0.73–0.99). Six of the seed lots were primed at two temperatures (15 °C and 20 °C) and three water potentials (−1.0, −1.5 and −2.0 MPa) for various durations, dried, and their subsequent germination rates analysed according to hydropriming time and hydrothermal priming time models. The responses of germination rates to priming were characterized by hydropriming time (θHP) and hydrothermal priming time (θHTP) constants and the minimum water potential (ψmin) and temperature (Tmin) for achieving a priming effect. The values of ψmin and Tmin varied relatively little among tomato seed lots, and the generalized values of ψmin= −2.39 MPa and Tmin=9.10 °C accounted for 74\% (15 °C), 57\% (20 °C), and 62\% (across both temperatures) of the increase in germination rates following priming. Nonetheless, while the hydrothermal time models described germination patterns both before and after priming, there was relatively little predictive relationship between them.},
	number = {330},
	urldate = {2023-05-23},
	journal = {Journal of Experimental Botany},
	author = {Cheng, Zhiyuan and Bradford, Kent J.},
	month = jan,
	year = {1999},
	pages = {89--99},
}

@article{bradford_sensitivity_1994,
	title = {Sensitivity thresholds and variable time scales in plant hormone action},
	volume = {105},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/105/4/1029-1036/6068149},
	doi = {10.1104/pp.105.4.1029},
	language = {en},
	number = {4},
	urldate = {2023-05-22},
	journal = {Plant Physiology},
	author = {Bradford, K. J. and Trewavas, A. J.},
	month = aug,
	year = {1994},
	pages = {1029--1036},
}

@article{finch-savage_development_2005,
	title = {Development of combined imbibition and hydrothermal threshold models to simulate maize (\emph{{Zea} mays}) and chickpea (\emph{{Cicer} arietinum}) seed germination in variable environments},
	volume = {165},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.2004.01272.x},
	doi = {10.1111/j.1469-8137.2004.01272.x},
	abstract = {• The ability of hydrothermal time (HTT) and virtual osmotic potential (VOP) models to describe the kinetics of maize (Zea mays) and chickpea (Cicer arietinum) seed germination under variable conditions of water potential was investigated with a view to gaining an improved understanding of the impact of on-farm seed priming on seedling establishment through simulation. • Germination and/or imbibition time courses were recorded over a wide range of constant temperatures and water potentials and simple stepwise changes in water potential. • Both models adequately described germination under constant environmental conditions, but not conditions of water potential that varied. To test the hypothesis that this inaccuracy resulted from the use of ambient water potential, a parsimonious model of seed imbibition was developed to calibrate the HTT and VOP models (IHTT and IVOP) and drive them with estimates of seed water potential. • The IHTT and IVOP models described germination during stepwise changes in water potential more accurately than the conventional models, and should contribute to improved predictions of germination time in the field.},
	language = {en},
	number = {3},
	urldate = {2023-05-22},
	journal = {New Phytologist},
	author = {Finch-Savage, W. E. and Rowse, H. R. and Dent, K. C.},
	year = {2005},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2004.01272.x},
	pages = {825--838},
}

@article{durr_ranges_2015,
	title = {Ranges of critical temperature and water potential values for the germination of species worldwide: {Contribution} to a seed trait database},
	volume = {200},
	issn = {01681923},
	shorttitle = {Ranges of critical temperature and water potential values for the germination of species worldwide},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0168192314002482},
	doi = {10.1016/j.agrformet.2014.09.024},
	language = {en},
	urldate = {2023-05-22},
	journal = {Agricultural and Forest Meteorology},
	author = {Dürr, C. and Dickie, J.B. and Yang, X.-Y. and Pritchard, H.W.},
	month = jan,
	year = {2015},
	pages = {222--232},
}

@article{batlla_quantitative_2003,
	title = {A quantitative analysis of seed responses to cycle-doses of fluctuating temperatures in relation to dormancy: {Development} of a thermal time model for \emph{{Polygonum} aviculare} {L}. seeds},
	volume = {13},
	issn = {1475-2735, 0960-2585},
	shorttitle = {A quantitative analysis of seed responses to cycle-doses of fluctuating temperatures in relation to dormancy},
	url = {https://www.cambridge.org/core/journals/seed-science-research/article/abs/quantitative-analysis-of-seed-responses-to-cycledoses-of-fluctuating-temperatures-in-relation-to-dormancy-development-of-a-thermal-time-model-for-polygonum-aviculare-l-seeds/DB160010FFAB60A5FEB31F7C9ED106AE},
	doi = {10.1079/SSR2003137},
	abstract = {The sensitivity of Polygonum aviculare L. seeds to the dormancy-breaking effect of cycle-doses of fluctuating temperature changes as seeds lose dormancy due to storage under stratification temperatures. Sensitivity changes during seed stratification were characterized by a decrease in the number of cycles required to saturate the germination response, and by a progressive loss of the requirement for temperature fluctuations for dormancy breakage in increasing fractions of the seed population. The rate of these changes was dependent on the temperature at which seeds were stored for stratification; lower storage temperatures produced higher rates of change than higher storage temperatures. Germination curves, obtained in response to the effect of fluctuating temperature cycle-doses for seeds stratified at variable temperatures and times of storage, were brought to a common stratification thermal time (Stt) scale by accumulating thermal time units under a threshold temperature for dormancy loss to occur. Results showed that those seeds that had accumulated similar Stt units during stratification under different storage temperatures presented a similar germination response. Therefore, response-curve functions were adjusted to germination data of exhumed seeds that had accumulated similar Stt, obtaining a family of germination response curves in relation to Stt accumulation during storage. Based on these results, a simulation model was constructed relating dynamic changes in the parameters that determine germination response curves in relation to Stt accumulation. The model was tested against independent data, showing a good description of the dynamics of changes in the fraction of the seed population requiring temperature fluctuation for dormancy breakage as dormancy release progressed.},
	language = {en},
	number = {3},
	urldate = {2023-05-22},
	journal = {Seed Science Research},
	author = {Batlla, Diego and Verges, Virginia and Benech-Arnold, Roberto Luis},
	month = sep,
	year = {2003},
	note = {Publisher: Cambridge University Press},
	pages = {197--207},
}

@article{grundy_modelling_2000,
	title = {Modelling the germination of \emph{{Stellaria} media} using the concept of hydrothermal time},
	volume = {148},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1046/j.1469-8137.2000.00778.x},
	doi = {10.1046/j.1469-8137.2000.00778.x},
	language = {en},
	number = {3},
	urldate = {2023-05-22},
	journal = {New Phytologist},
	author = {Grundy, A. C. and Phelps, K. and Reader, R. J. and Burston, S.},
	month = dec,
	year = {2000},
	pages = {433--444},
}

@article{bakhshandeh_new_2020,
	title = {A new halothermal time model describes seed germination responses to salinity across both sub- and supra-optimal temperatures},
	volume = {42},
	issn = {0137-5881, 1861-1664},
	url = {https://link.springer.com/10.1007/s11738-020-03126-9},
	doi = {10.1007/s11738-020-03126-9},
	language = {en},
	number = {8},
	urldate = {2023-05-22},
	journal = {Acta Physiologiae Plantarum},
	author = {Bakhshandeh, Esmaeil and Bradford, Kent J. and Pirdashti, Hemmatollah and Vahabinia, Fatemeh and Abdellaoui, Raoudha},
	month = aug,
	year = {2020},
	pages = {137},
}

@article{watt_key_2012,
	title = {Key features of the seed germination response to high temperatures},
	volume = {196},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04280.x},
	doi = {10.1111/j.1469-8137.2012.04280.x},
	language = {en},
	number = {2},
	urldate = {2023-05-22},
	journal = {New Phytologist},
	author = {Watt, Michael S. and Bloomberg, Mark},
	month = oct,
	year = {2012},
	pages = {332--336},
}

@article{bierhuizen_aspects_1974,
	title = {Some aspects of seed germination in vegetables. 1. {The} determination and application of heat sums and minimum temperature for germination},
	volume = {2},
	issn = {0304-4238},
	url = {https://www.sciencedirect.com/science/article/pii/0304423874900296},
	doi = {10.1016/0304-4238(74)90029-6},
	abstract = {Germination can be predicted at optimal soil moisture conditions by means of a heat sum in degree days (S) and a minimum temperature for germination in °C (Tmin). These constants were analysed for 31 vegetables in a temperature range between 3 and 25°C. Some practical consequences of the combined effects of S and Tmin on germination are given.},
	language = {en},
	number = {3},
	urldate = {2023-05-22},
	journal = {Scientia Horticulturae},
	author = {Bierhuizen, J. F. and Wagenvoort, W. A.},
	month = sep,
	year = {1974},
	pages = {213--219},
}

@book{stroup_generalized_2016,
	edition = {1st},
	title = {Generalized {Linear} {Mixed} {Models}: {Modern} {Concepts}, {Methods} and {Applications}},
	isbn = {978-1-4398-1513-7},
	shorttitle = {Generalized {Linear} {Mixed} {Models}},
	language = {eng},
	publisher = {CRC Press},
	author = {Stroup, Walter W.},
	year = {2016},
	note = {OCLC: 991276468},
	file = {(Chapman & Hall_CRC Texts in Statistical Science) Stroup, Walter W - Generalized Linear Mixed Models _ Modern Concepts, Methods and Applications-CRC Press (2012).pdf:G\:\\OneDrive\\Aravind J\\Books\\(Chapman & Hall_CRC Texts in Statistical Science) Stroup, Walter W - Generalized Linear Mixed Models _ Modern Concepts, Methods and Applications-CRC Press (2012).pdf:application/pdf},
}

@misc{chau_gslnls_2023,
	title = {gslnls: {GSL} {Nonlinear} {Least}-{Squares} {Fitting}},
	copyright = {GPL-3},
	shorttitle = {gslnls},
	url = {https://cran.r-project.org/web/packages/gslnls/index.html},
	abstract = {An R interface to nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.},
	urldate = {2023-08-12},
	author = {Chau, Joris},
	month = jan,
	year = {2023},
}

@book{galassi_gnu_2009,
	address = {Bristol},
	edition = {3. ed},
	title = {{GNU} {Scientific} {Library} {Reference} {Manual}: {For} {GSL} {Version} 1.12},
	isbn = {978-0-9546120-7-8},
	shorttitle = {Gnu {Scientific} {Library} {Reference} {Manual}},
	language = {eng},
	publisher = {Network Theory},
	editor = {Galassi, Mark},
	year = {2009},
}

@article{wood_priming_2010,
	title = {Priming increases the storability and changes the water sorption properties of \emph{{Rhododendron} griersonianum} seeds},
	volume = {38},
	doi = {10.15258/sst.2010.38.3.16},
	number = {3},
	journal = {Seed Science and Technology},
	author = {Wood, I.P. and Hay, F.R.},
	month = oct,
	year = {2010},
	note = {Number: 3},
	pages = {682--691},
}

@article{carvalho_why_2018,
	title = {Why analyze germination experiments using {Generalized} {Linear} {Models}?},
	volume = {40},
	issn = {2317-1545, 2317-1537},
	url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S2317-15372018000300281&lng=en&tlng=en},
	doi = {10.1590/2317-1545v40n3185259},
	abstract = {Abstract: We compared the goodness of fit and efficiency of models for germination. Generalized Linear Models (GLMs) were performed with a randomized component corresponding to the percentage of germination for a normal distribution or to the number of germinated seeds for a binomial distribution. Lower levels of Akaikes’s Information Criterion (AIC) and Bayesian Information Criterion (BIC) combined, data adherence to simulated envelopes of normal plots and corrected confidence intervals for the means guaranteed the binomial model a better fit, justifying the importance of GLMs with binomial distribution. Some authors criticize the inappropriate use of analysis of variance (ANOVA) for discrete data such as copaiba oil, but we noted that all model assumptions were met, even though the species had dormant seeds with irregular germination.
          , 
            Resumo: A qualidade do ajuste e eficiência de modelos de germinação foram comparadas. Modelos Lineares Generalizados (MLGs) foram executados com o componente aleatório correspondendo ao percentual de germinação para a distribuição normal e o número de sementes germinadas para a distribuição binomial. Baixos valores do Critério de Informação de Akaike (AIC) e do Critério de Informação Bayesiano (BIC), ajuste aos envelopes simulados dos Normal plots e intervalos de confiança corretos para as médias justificam a importância do uso dos MLGs com distribuição binomial. Alguns autores criticam o uso inapropriado da análise de variância (ANOVA) para dados discretos como a germinação de copaíba, mas todas as pressuposições do modelo foram atendidas, mesmo a espécie possuindo sementes dormentes e germinação irregular.},
	number = {3},
	urldate = {2024-06-07},
	journal = {Journal of Seed Science},
	author = {Carvalho, Fábio Janoni and Santana, Denise Garcia De and Araújo, Lúcio Borges De},
	month = sep,
	year = {2018},
	pages = {281--287},
	file = {Carvalho et al. - 2018 - Why analyze germination experiments using Generali.pdf:G\:\\OneDrive\\IPK Docs\\germination modeling\\GLMM\\Carvalho et al. - 2018 - Why analyze germination experiments using Generali.pdf:application/pdf},
}

@article{humplik_Bayesian_2020,
	title = {Bayesian approach for analysis of time-to-event data in plant biology},
	volume = {16},
	issn = {1746-4811},
	url = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-020-0554-1},
	doi = {10.1186/s13007-020-0554-1},
	abstract = {Abstract
            
              Background
              Plants, like all living organisms, metamorphose their bodies during their lifetime. All the developmental and growth events in a plant’s life are connected to specific points in time, be it seed germination, seedling emergence, the appearance of the first leaf, heading, flowering, fruit ripening, wilting, or death. The onset of automated phenotyping methods has brought an explosion of such time-to-event data. Unfortunately, it has not been matched by an explosion of adequate data analysis methods.
            
            
              Results and discussion
              In this paper, we introduce the Bayesian approach towards time-to-event data in plant biology. As a model example, we use seedling emergence data of maize under control and stress conditions but the Bayesian approach is suitable for any time-to-event data (see the examples above). In the proposed framework, we are able to answer key questions regarding plant emergence such as these: (1) Do seedlings treated with compound A emerge earlier than the control seedlings? (2) What is the probability of compound A increasing seedling emergence by at least 5 percent?
            
            
              Conclusion
              Proper data analysis is a fundamental task of general interest in life sciences. Here, we present a novel method for the analysis of time-to-event data which is applicable to many plant developmental parameters measured in field or in laboratory conditions. In contrast to recent and classical approaches, our Bayesian computational method properly handles uncertainty in time-to-event data and it is capable to reliably answer questions that are difficult to address by classical methods.},
	language = {en},
	number = {1},
	urldate = {2024-12-13},
	journal = {Plant Methods},
	author = {Humplík, Jan F. and Dostál, Jakub and Ugena, Lydia and Spíchal, Lukáš and De Diego, Nuria and Vencálek, Ondřej and Fürst, Tomáš},
	month = dec,
	year = {2020},
	pages = {14},
	file = {Humplík et al. - 2020 - Bayesian approach for analysis of time-to-event data in plant biology:G\:\\OneDrive\\Documents\\Eigene Dateien\\Oats - Longevity\\Seed Germination measurements\\Germination\\Bayesian\\Humplík et al. - 2020 - Bayesian approach for analysis of time-to-event data in plant biology.pdf:application/pdf},
}

@article{gholamhoseini_sesame_2024,
	title = {Sesame {Germination} {Dynamics}: {Unravelling} {Sesame}’s {Response} to {Salinity} and {Temperature} {Variability}},
	volume = {3},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2674-1024},
	shorttitle = {Sesame {Germination} {Dynamics}},
	url = {https://www.mdpi.com/2674-1024/3/1/6},
	doi = {10.3390/seeds3010006},
	abstract = {Sesame (Sesamum indicum), a highly valued oilseed, faces challenges in cultivation, especially in regions susceptible to environmental stressors. This study investigates the interactive effects of salinity and temperature on sesame seed germination. Two cultivars, Darab 1 and Oltan, were subjected to various salinity levels (−3 to −12 bars) and temperatures (15 °C, 20 °C, and 25 °C). Results revealed that at 15 °C, salinity levels beyond -3 bars significantly reduced germination, while at 25 °C, 40\% and 62\% germination rates were recorded even at −12 bars for Darab 1 and Oltan, respectively. This study highlights the importance of temperature in mitigating the inhibitory effects of salinity on germination. Germination speed exhibited a decline with increasing salinity, particularly at lower temperatures. Shoot and root lengths and dry weights decreased with rising salinity, but Oltan demonstrated greater tolerance than Darab 1. The research emphasises the species-specific nature of temperature-salinity interactions and the intraspecific variability among sesame cultivars. Notably, Oltan, adapted to arid regions with elevated temperatures, displayed increased tolerance to salinity stress. These findings contribute to understanding sesame’s resilience to environmental stressors, aiding in developing resilient cultivars for challenging agricultural landscapes. Overall, temperature is pivotal in influencing sesame seed germination and early seedling growth under salinity stress, offering insights for optimised cultivation practices.},
	language = {en},
	number = {1},
	urldate = {2024-11-26},
	journal = {Seeds},
	author = {Gholamhoseini, Majid and Dolatabadian, Aria},
	month = mar,
	year = {2024},
	note = {Number: 1
Publisher: Multidisciplinary Digital Publishing Institute},
	pages = {76--87},
}
