| Title: | Fundamental Formulas for Plant Physiology | 
| Version: | 1.0.0 | 
| Description: | Functions tailored for scientific and student communities involved in plant science research. Functionalities encompass estimation chlorophyll content according to Arnon (1949) <doi:10.1104/pp.24.1.1>, determination water potential of Polyethylene glycol(PEG)6000 as in Michel and Kaufmann (1973) <doi:10.1104/pp.51.5.914> and functions related to estimation of yield related indices like Abiotic tolerance index as given by Moosavi et al.(2008)<doi:10.22059/JDESERT.2008.27115>, Geometric mean productivity (GMP) by Fernandez (1992) <ISBN:92-9058-081-X>, Golden Mean by Moradi et al.(2012)<doi:10.14207/ejsd.2012.v1n3p543>, HAM by Schneider et al.(1997)<doi:10.2135/cropsci1997.0011183X003700010007x>,MPI and TOL by Hossain etal., (1990)<doi:10.2135/cropsci1990.0011183X003000030030x>, RDI by Fischer et al. (1979)<doi:10.1071/AR9791001>,SSI by Fisher et al.(1978)<doi:10.1071/AR9780897>, STI by Fernandez (1993)<doi:10.22001/wvc.72511>,YSI by Bouslama & Schapaugh (1984)<doi:10.2135/cropsci1984.0011183X002400050026x>, Yield index by Gavuzzi et al.(1997)<doi:10.4141/P96-130>. | 
| License: | GPL (≥ 3) | 
| URL: | https://github.com/rameshram96/plantphysioR | 
| BugReports: | https://github.com/rameshram96/plantphysioR/issues | 
| Depends: | R (≥ 2.10) | 
| Suggests: | testthat (≥ 3.0.0) | 
| Config/testthat/edition: | 3 | 
| Encoding: | UTF-8 | 
| LazyData: | true | 
| RoxygenNote: | 7.3.1 | 
| NeedsCompilation: | no | 
| Packaged: | 2024-03-27 05:49:50 UTC; Ramesh_PhD | 
| Author: | Ramesh Ramasamy | 
| Maintainer: | Ramesh Ramasamy <ramesh.rahu96@gmail.com> | 
| Repository: | CRAN | 
| Date/Publication: | 2024-03-27 10:10:03 UTC | 
plantphysioR: Fundamental Formulas for Plant Physiology
Description
 
Functions tailored for scientific and student communities involved in plant science research. Functionalities encompass estimation chlorophyll content according to Arnon (1949) doi:10.1104/pp.24.1.1, determination water potential of Polyethylene glycol(PEG)6000 as in Michel and Kaufmann (1973) doi:10.1104/pp.51.5.914 and functions related to estimation of yield related indices like Abiotic tolerance index as given by Moosavi et al.(2008)doi:10.22059/JDESERT.2008.27115, Geometric mean productivity (GMP) by Fernandez (1992) <ISBN:92-9058-081-X>, Golden Mean by Moradi et al.(2012)doi:10.14207/ejsd.2012.v1n3p543, HAM by Schneider et al.(1997)doi:10.2135/cropsci1997.0011183X003700010007x,MPI and TOL by Hossain etal., (1990)doi:10.2135/cropsci1990.0011183X003000030030x, RDI by Fischer et al. (1979)doi:10.1071/AR9791001,SSI by Fisher et al.(1978)doi:10.1071/AR9780897, STI by Fernandez (1993)doi:10.22001/wvc.72511,YSI by Bouslama & Schapaugh (1984)doi:10.2135/cropsci1984.0011183X002400050026x, Yield index by Gavuzzi et al.(1997)doi:10.4141/P96-130.
Author(s)
Maintainer: Ramesh Ramasamy ramesh.rahu96@gmail.com (ORCID)
See Also
Useful links:
- Report bugs at https://github.com/rameshram96/plantphysioR/issues 
Abiotic Tolerance Index (ATI)
Description
Calculate abiotic tolerance index according to Moosavi et al. (2008)
Usage
ATI(Yp, Ys, Mp, Ms)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under Stress condition | 
| Mp | Mean yield of all the genotypes under stress condition | 
| Ms | Mean yield of all the genotypes under control condition | 
Value
ATI
References
Moosavi SS, Samadi YB, Naghavi MR, Zali AA, Dashti H, Pourshahbazi A (2008) Introduction of new indices to identify relative drought tolerance and resistance in wheat genotypes. Desert. 12: 165-178.
Examples
ATI(500, 350, 400, 300)
Drought resistant index (DRI)
Description
The genotype with high values of this index will be more suitable for drought stress condition
Usage
DRI(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
DRI
Examples
DRI(500, 350)
Golden Mean (GM)
Description
Calculates Golden mean value using Moradi et al.,(2012)
Usage
Golden_mean(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
GM
References
Moradi H, Akbari GA, Khorasani SK, Ramshini HA (2012) Evaluation of drought tolerance in corn (Zea Mays L.) new hybrids with using stress tolerance indices. Eur J Sustain Dev 1. (3): 543-560
Examples
Golden_mean(500, 350)
Harmonic Mean
Description
Harmonic Mean
Usage
HAM(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
Harmonic mean
References
Schneider, K. A., Rosales‐Serna, R., Ibarra‐Perez, F., Cazares‐Enriquez, B., Acosta‐Gallegos, J. A., Ramirez‐Vallejo, P., ... & Kelly, J. D. (1997). Improving common bean performance under drought stress. Crop science, 37(1), 43-50.
Examples
HAM(500, 350)
Relative Drought Index (RDI)
Description
Calculates relative drought index according to Fisher and Wood (1979)
Usage
R_drought_index(Yp, Ys, Mp, Ms)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
| Mp | Mean Yield of all the genotypes under control Condition | 
| Ms | Mean Yield of all the genotypes under stress Condition | 
Value
RDI
References
Fischer RA, Wood JT (1979) Drought resistance in spring wheat cultivars III. Yield association with morphological traits. Aust J Agr Res. 30: 1001-1020
Examples
R_drought_index(500, 350, 400, 300)
Yield reduction ratio (YR)
Description
lesser the YR value more stable under stress conditions
Usage
YR_ratio(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
YR
Examples
YR_ratio(500, 350)
Yield reduction index or Yield Stability Index (YSI)
Description
Higer YSI value depicts that particular genotype is stable under both normal and stressed conditions
Usage
YSI(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
YSI
References
Bouslama, M., & Schapaugh Jr, W. T. (1984). Stress tolerance in soybeans. I. Evaluation of three screening techniques for heat and drought tolerance 1. Crop science, 24(5), 933-937.
Examples
YSI(500, 350)
Yield index (YI)
Description
Yield index (YI)
Usage
Y_index(Ys, Ms)
Arguments
| Ys | Yield under stress condition | 
| Ms | Mean Yield of all the genotypes under stress Condition | 
Value
Yield Index
References
Gavuzzi, P., Rizza, F., Palumbo, M., Campanile, R. G., Ricciardi, G. L., & Borghi, B. (1997). Evaluation of field and laboratory predictors of drought and heat tolerance in winter cereals. Canadian journal of plant science, 77(4), 523-531.
Examples
Y_index(500, 300)
All indices combined
Description
Function to all the indices related to biomass/ yield under different growth conditions
Usage
all_indices(Yp, Ys, Mp, Ms)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
| Mp | Mean yield of all the genotypes under control condition | 
| Ms | Mean yiels of all the genotyps under Stress condition | 
Value
Indices Combined
Examples
Mp <- mean(yield_data$Yp)
Ms <- mean(yield_data$Ys)
Yp <- yield_data$Yp
Ys <- yield_data$Ys
all_indices(Yp, Ys, Mp, Ms)
Calculate Polyethylene glycol (PEG) 6000 requirement
Description
Calculate Amount of PEG6000 required to reach desired water potential at given temperature
Usage
calculate_PEG_6000(C, bar)
Arguments
| C | Temperature of solution in degree centigrade | 
| bar | Water potential in bars | 
Value
PEG6000 required
References
Michel, B. E., & Kaufmann, M. R. (1973). The osmotic potential of polyethylene glycol 6000. Plant physiology, 51(5), 914-916.
Examples
calculate_PEG_6000(25, -4)
Total carotenoids content
Description
Calculate total carotenoids using Method by Lichtenthaler (1987)
Usage
caro_total(A470, A663, A646, fresh_weight)
Arguments
| A470 | Absorbance at 470nm | 
| A663 | Absorbance at 663nm | 
| A646 | Absorbance at 646nm | 
| fresh_weight | Fresh weight of the sample used in grams | 
Value
Carotenoids concentration in µg/ml
References
Lichtenthaler, H. K. (1987). Chlorophylls and carotenoids: pigments of photosynthetic biomembranes. In Methods in enzymology (Vol. 148, pp. 350-382). Academic Press.
Examples
caro_total(0.7, 0.041, 0.025, 1)
Chlorophyll'a' Concentration by Arnon method
Description
Calculates Chlorophyll a Concentration according to Arnon(1949) method
Usage
chl_a(A663, A645, v, w)
Arguments
| A663 | Absorbance at 663nm | 
| A645 | Absorbance at 645nm | 
| v | Final volume of solvent used in ml | 
| w | Fresh weight of the sample used in grams | 
Value
Chlorophyll a in mg/g of fresh weight
References
Arnon, D. I. (1949). Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant physiology, 24(1), 1. doi:10.1104/pp.24.1.1
Examples
chl_a(0.025, 0.041, 15, 1)
Chlorophyll b concentration
Description
Calculates Chlorophyll b Concentration according to Arnon(1949) method
Usage
chl_b(A645, A663, v, w)
Arguments
| A645 | Absorbance at 645nm | 
| A663 | Absorbance at 663nm | 
| v | Final volume of solvent used in ml | 
| w | Fresh weight of the sample used in grams | 
Value
Chlorophyll b in mg/g of fresh weight
References
Arnon, D. I. (1949). Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant physiology, 24(1), 1. doi:10.1104/pp.24.1.1
Examples
chl_b(0.041, 0.025, 15, 1)
Total chlorophyll (a+b) concentration
Description
Calculate Total chlorophyll (a+b) concentration using method by Arnon (1949)
Usage
chl_total(A645, A663, v, w)
Arguments
| A645 | Absorbance at 645nm | 
| A663 | Absorbance at 663nm | 
| v | Final volume of solvent used in ml | 
| w | Fresh weight of the sample used in grams | 
Value
Total chlorophyll (a+b) in mg/g of fresh weight
References
Arnon, D. I. (1949). Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant physiology, 24(1), 1. doi:10.1104/pp.24.1.1
Examples
chl_total(0.041, 0.025, 15, 1)
Geometric mean productivity (GMP) by Fernandez (1992)
Description
The genotype with high values of this index will be more desirable
Usage
gmp(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
GMP
References
Fernandez, G. C. (1993). Effective selection criteria for assessing plant stress tolerance.
Examples
gmp(5, 3)
Mean productivity Index (MPI)- by Hossain et al., (1990)
Description
The genotype with high values of this index will be more desirable
Usage
mp_index(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
Mean productivity Index
References
Hossain, A. B. S., Sears, R. G., Cox, T. S., & Paulsen, G. M. (1990). Desiccation tolerance and its relationship to assimilate partitioning in winter wheat. Crop Science, 30(3), 622-627.
Water potential of Polyethylene glycol (PEG) 6000
Description
Calculate the corresponding water potential of PEG6000 when dissolved in 1l of water
Usage
peg_6000(peg, C)
Arguments
| peg | Amount PEG600O in grams | 
| C | Temperature of the solution in degree centigrade | 
Value
Water potential in bars
References
Michel, B. E., & Kaufmann, M. R. (1973). The osmotic potential of polyethylene glycol 6000. Plant physiology, 51(5), 914-916.
Examples
peg_6000(20, 25)
Stress susceptibility index (SSI) by Fischer and Maurer (1978)
Description
The genotype with high SSI < 1 are more resistant to drought stress conditions
Usage
ss_index(Yp, Ys, Ms, Mp)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under Stress condition | 
| Ms | Mean yield of all the genotypes under control condition | 
| Mp | Mean yield of all the genotypes under stress condition | 
Value
SSI
References
Fischer, R. A., & Maurer, R. (1978). Drought resistance in spring wheat cultivars. I. Grain yield responses. Australian Journal of Agricultural Research, 29(5), 897-912.
Examples
ss_index(500, 350, 450, 370)
Calculate Stress tolerance index (STI) suggested by Fernandez (1992)
Description
The genotype with high STI values will be tolerant to drought
Usage
st_index(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
STI
References
Fernandez, G. C. (1993). Effective selection criteria for assessing plant stress tolerance.
Examples
st_index(500, 350)
Tolerance index -TOL by Hossain et al., (1990)
Description
Higher the TOL value indicates the genotype is tolerant to stress
Usage
tol_index(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
TOL
References
Hossain, A. B. S., Sears, R. G., Cox, T. S., & Paulsen, G. M. (1990). Desiccation tolerance and its relationship to assimilate partitioning in winter wheat. Crop Science, 30(3), 622-627.
Examples
tol_index(500, 350)
Example data
Description
Yield data of rice in kg/ha under two different growth conditions
Usage
yield_data
Format
A data frame with 50 rows and 3 variables:
- Genotype
- character Genotype 
- Yp
- integer Yield under control condition 
- Ys
- integer Yield under drought condition 
Source
Simulated data, no external source were used
References
No external reference
Yield Reduction
Description
Claculate percent yield reduction over control
Usage
yield_reduction(Yp, Ys)
Arguments
| Yp | Yield under control condition | 
| Ys | Yield under stress condition | 
Value
YR
Examples
yield_reduction(500, 350)