% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/defaultControl.R
\name{defaultControl}
\alias{defaultControl}
\title{Control parameters for simulation models}
\usage{
defaultControl(
  transpirationMode = "Granier",
  soilDomains = "buckets",
  rhizosphereOverlap = "partial"
)
}
\arguments{
\item{transpirationMode}{String containing transpiration model (either 'Granier', 'Sperry' or 'Sureau'). See \code{\link{spwbInput}}.}

\item{soilDomains}{String containing soil hydrology model (either 'buckets', 'single', 'dual' or 'none'). Option 'none' is meant to be used when flows in the bulk soil are dealt with externally. For the remaining options, see \code{\link{hydrology_soilWaterBalance}}.}

\item{rhizosphereOverlap}{String indicating the assumption with respect to rhizosphere overlap:
\itemize{
\item{\code{total}: All plants extract water from the same pools.}
\item{\code{partial}: Plants partially share water pools, depending on soil moisture.}
\item{\code{none}: Plants extract water from totally-independent water pools.}
}}
}
\value{
A list, with the following options (default values in brackets):
\itemize{
\bold{General}:
\itemize{
\item{\code{verbose [= TRUE]}: Boolean flag to indicate console output during calculations. In function \code{fordyn} \code{verbose} is always set to FALSE.}
\item{\code{fillMissingRootParams [= TRUE]}: Boolean flag to indicate that initializing functions should provide estimates for Z50 and Z95 if these are missing in the forest data. Note that if \code{fillMissingRootParams} is set to \code{FALSE} then simulations may fail if the user does not provide values for Z50 and Z95 in tree or shrub data.}
\item{\code{fillMissingSpParams [= TRUE]}: Boolean flag to indicate that initializing functions should provide estimates for functional parameters if these are missing in the species parameter table \code{\link{SpParams}}. Note that if \code{fillMissingSpParams} is set to \code{FALSE} then simulations may fail if the user does not provide values for required parameters.}
\item{\code{fillMissingWithGenusParams [=TRUE]}: Boolean flag to indicate that initializing functions should provide estimates from genus value, if species-level values are missing in the species parameter table \code{\link{SpParams}} but genus-level ones are not.}
\item{\code{standResults [= TRUE]}: Boolean flag to keep stand-level results (in a data frame called 'Stand').}
\item{\code{soilResults [= TRUE]}: Boolean flag to keep soil-level results (in a list called 'Soil').}
\item{\code{soilPoolResults [= FALSE]}: Boolean flag to keep soil pool-level results (in a list called 'SoilPools'), if \code{rhizosphereOverlap!="total"}.}
\item{\code{snowResults [= TRUE]}: Boolean flag to keep snow results (in a data frame called 'Snow').}
\item{\code{plantResults [= TRUE]}: Boolean flag to keep plant-level water/energy/photosynthesis results (in a list called 'Plants').}
\item{\code{labileCarbonBalanceResults [= TRUE]}: Boolean flag to keep plant-level labile carbon balance results (in a list called 'LabileCarbonBalance').}
\item{\code{plantStructureResults [= TRUE]}: Boolean flag to keep plant-level structure results (in a list called 'PlantStructure').}
\item{\code{growthMortalityResults [= TRUE]}: Boolean flag to keep plant-level growth and mortality results (in a list called 'GrowthMortality').}
\item{\code{decompositionPoolResults [= TRUE]}: Boolean flag to keep decomposition pool results (in a data frame called 'DecompositionPools').}
\item{\code{leafResults [= TRUE]}: Boolean flag to keep leaf-level results (in elements called 'SunlitLeaves' and 'ShadeLeaves').}
\item{\code{temperatureResults [= TRUE]}: Boolean flag to keep temperature results (in elements called 'Temperature' and 'TemperatureLayers').}
\item{\code{subdailyResults [= FALSE]}: Boolean flag to force subdaily results to be stored (as a list called 'subdaily' of \code{\link{spwb_day}} objects, one by simulated date) in calls to \code{\link{spwb}}. In function \code{fordyn} \code{subdailyResults} is always set to FALSE.}
\item{\code{fireHazardResults [= FALSE]}: Boolean flag to force calculation of daily fire hazard.}
\item{\code{fireHazardStandardWind [= NA]}: Wind speed (in m/s) for fire-hazard estimation. If missing, actual wind-speed is used.}
\item{\code{fireHazardStandardDFMC [= NA]}: Dead fuel moisture content for fire-hazard estimation. If missing, estimation from current weather is used.}
}
\bold{Water balance} (functions \code{\link{spwb}}, \code{\link{pwb}} or \code{\link{spwb_day}}):
\itemize{
\item{\code{transpirationMode [= "Granier"]}: Transpiration model (either 'Granier', 'Sperry' or 'Sureau'). See \code{\link{spwbInput}}.}
\item{\code{soilFunctions [= "VG"]}: Soil water retention curve and conductivity functions, either 'SX' (for Saxton) or 'VG' (for Van Genuchten).
If \code{transpirationMode} is 'Sperry' or 'Sureau' then soilFunctions is forced to \code{'VG'}.
Only simulations with 'Granier' are allowed to use Saxton functions.}
\item{\code{truncateRootDistribution [= FALSE]}: Boolean flag to indicate that fine root distribution is to be truncated (i.e. Z100 is estimated from Z95 when not provided).}
\item{\code{VG_PTF}: String indicating the pedotransfer functions for van Genuchten parameters (either 'Toth' or 'Carsel').}
\item{\code{ndailysteps [= 24]}: Number of steps into which each day is divided for determination of soil water balance, stomatal conductance, transpiration and photosynthesis (24 equals 1-hour intervals).}
\item{\code{max_nsubsteps_soil [= 300]}: Maximum number of substeps for soil water balance solving.}
\item{\code{defaultWindSpeed [= 2.5]}: Default wind speed value (in m/s) to be used when missing from data. }
\item{\code{defaultCO2 [= 386]}: Default atmospheric (abovecanopy) CO2 concentration (in micromol·mol-1 = ppm). This value will be used whenever CO2 concentration is not specified in the weather input. }
\item{\code{defaultRainfallIntensityPerMonth [= c(1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 5.6, 5.6, 5.6, 5.6, 5.6, 1.5)]}: A vector of twelve values indicating the rainfall intensity (mm/h) per month.
By default synoptic storms (1.5 mm/h) are assumed between December and June, and convective storms (5.6 mm/h) are assumed between July and November.}
\item{\code{leafPhenology [= TRUE]}: Boolean flag to indicate the simulation of leaf phenology for winter-deciduous species.}
\item{\code{bareSoilEvaporation [= TRUE]}: Boolean flag to indicate the simulation of evaporation from bare soil.}
\item{\code{unlimitedSoilWater [= FALSE]}: Boolean flag to indicate the simulation of plant transpiration assuming that soil water is always at field capacity.}
\item{\code{unfoldingDD [= 300]}: Degree-days for complete leaf unfolding after budburst has occurred.}
\item{\code{interceptionMode [= "Gash1995"]}: Infiltration model, either "Gash1995" or "Liu2001".}
\item{\code{infiltrationMode [= "GreenAmpt1911"]}: Infiltration model, either "GreenAmpt1911" or "Boughton1989".}
\item{\code{infiltrationCorrection [= 5.0]}: Factor to correct infiltration amount in the GreenAmpt1911 model in single-domain simulations.}
\item{\code{soilDomains [= "buckets"]}: Either 'buckets' (for multi-bucket model), 'single' (for single-domain Richards model) or 'dual' (for dual-permeability model). See \code{\link{hydrology_soilWaterBalance}}.}
\item{\code{rhizosphereOverlap [= "partial"]}: A string indicating the degree of rhizosphere spatial overlap between plant cohorts:
\itemize{
\item{"none" - no overlap (independent water pools).}
\item{"partial" - plants partially share water pools, depending on soil moisture.}
\item{"total" - total overlap (plants extract from common soil pools).}
}
}
\item{\code{fullRhizosphereOverlapConductivity [= 0.01]}: The minimum soil hydraulic conductivity (in cm/day) allowing a full connectivity of water pools, when \code{rhizosphereOverlap = "partial"}.}
\item{\code{verticalLayerSize [= 100]}: Size of vertical layers (in cm) for the calculation of light extinction (and photosynthesis).}
\item{\code{windMeasurementHeight [= 200]}: Height (in cm) over the canopy corresponding to wind measurements.}
\item{\code{segmentedXylemVulnerability [= TRUE/FALSE]}: If \code{FALSE} leaf and root vulnerability curves will be equal to those of stem. By default, \code{segmentedXylemVulnerability = TRUE} for \code{transpirationMode = "Sperry"} and \code{segmentedXylemVulnerability = FALSE} for \code{transpirationMode = "Sureau"}.}
\item{\code{leafCavitationEffects, stemCavitationEffects [= FALSE/TRUE]}: A flag indicating whether cavitation effects on conductance of leaves and stem are applied. Only relevant for \code{transpirationMode = "Sperry"}.}
\item{\code{leafCavitationRecovery, stemCavitationRecovery [= "rate"]}: A string indicating how recovery of previous cavitation leaf/stem xylem is done (only relevant for functions \code{\link{spwb}} and \code{\link{spwb_day}}):
\itemize{
\item{"none" - no recovery.}
\item{"annual" - every first day of the year.}
\item{"rate" - following a rate of new leaf or sapwood formation.}
\item{"total" - instantaneous complete recovery.}
}
}
\item{\code{cavitationRecoveryMaximumRate [= 0.05]}: Maximum rate of daily refilling of embolized conduits as sapwood area per leaf area (in cm2·m-2·day-1).}
\item{\code{cavitationInducedDefoliation [= TRUE]}: Whether leaf hydraulic impairment induces defoliation (88 \% PLC will correspond to 50 \% defoliation).}
\item{\code{lfmcComponent [= "fine"]}: Plant component used to estimate LFMC, either "leaf" or "fine" (for fine fuel).}
}
\bold{Water balance} (functions \code{\link{spwb}}, \code{\link{pwb}} or \code{\link{spwb_day}} when \code{traspirationMode = "Granier"} only):
\itemize{
\item{\code{hydraulicRedistributionFraction [= 0.1]}: Fraction of plant transpiration corresponding to hydraulic redistribution.}
}
\bold{Water balance} (functions \code{\link{spwb}}, \code{\link{pwb}} or \code{\link{spwb_day}} when \code{traspirationMode = "Sperry"} or \code{traspirationMode = "Sureau"}):
\itemize{
\item{\code{nsubsteps_canopy [= 3600]}: Number of substeps into which each step is divided for multi-layer canopy energy balance solving.}
\item{\code{multiLayerBalance [= FALSE]}: Flag to indicate multiple canopy energy balance. If \code{FALSE}, canopy is considered a single layer for energy balance.}
\item{\code{sapFluidityVariation [= TRUE]}: Flag to indicate that temperature affects sap fluidity (and indirectly plant conductance).}
\item{\code{TPhase_gmin [= 37.5]}: Temperature for transition phase of gmin.}
\item{\code{Q10_1_gmin [= 1.2]}: Temperature dependance of gmin when T less than or equal to TPhase.}
\item{\code{Q10_2_gmin [= 4.8]}: Temperature dependance of gmin when T greater than TPhase.}
\item{\code{taper [= TRUE]}: Whether taper of xylem conduits is accounted for when calculating aboveground stem conductance from xylem conductivity.}
\item{\code{thermalCapacityLAI [= 1000000]}: Thermal canopy capacitance per LAI unit.}
\item{\code{rootRadialConductance [= 4]}: Radial conductance in roots (mmol·s-1·m-2·MPa-1).}
\item{\code{averageFracRhizosphereResistance [= 0.15]}: Fraction to total continuum (leaf+stem+root+rhizosphere) resistance that corresponds to rhizosphere (averaged across soil water potential values).}
\item{\code{boundaryLayerSize [= 2000]}: Size of the boundary layer (in cm) over the canopy (relevant for multi-layer canopy energy balance).}
}

\bold{Water balance} (functions \code{\link{spwb}}, \code{\link{pwb}} or \code{\link{spwb_day}} when \code{traspirationMode = "Sperry"} only):
\itemize{
\item{\code{numericParams}: A list with the following elements:
\itemize{
\item{\code{maxNsteps [= 400]}: Maximum number of steps in supply function.}
\item{\code{ntrial [= 200]}: Number of iteration trials when finding root of equation system.}
\item{\code{psiTol [= 0.0001]}: Tolerance value for water potential.}
\item{\code{ETol [= 0.0001]}: Tolerance value for flow.}
}
}
}

\bold{Water balance} (functions \code{\link{spwb}}, \code{\link{pwb}} or \code{\link{spwb_day}} when \code{traspirationMode = "Sureau"} only):
\itemize{
\item{\code{plantCapacitance [= TRUE]}: Whether the effect of (symplasmic) plant water compartments is considered in simulations.}
\item{\code{cavitationFlux [= TRUE]}: Whether the effect of water flux generated by cavitation of apoplasmic tissues is considered in simulations.}
\item{\code{leafCuticularTranspiration [= TRUE]}: Whether the effect of leaf cuticular transpiration is considered in simulations.}
\item{\code{stemCuticularTranspiration [= FALSE]}: Whether the effect of stem cuticular transpiration is considered in simulations.}
\item{\code{C_SApoInit [= 2.0e-5]}: Maximum capacitance of the stem apoplasm (mmol·m-2).}
\item{\code{C_LApoInit [= 1.0e-5]}: Maximum capacitance of the leaf apoplasm (mmol·m-2).}
\item{\code{k_SSym [= 0.26]}: Conductance from stem apoplasm to stem symplasm (mmol·s-1·m-2·MPa-1).}
\item{\code{fractionLeafSymplasm [= 0.5]}: Fraction of the leaf resistance from leaf apoplasm to leaf symplasm ([0-1]).}
\item{\code{gs_NightFrac [= 0.05]}: Stomatal conductance at night as fraction of maximum stomatal conductance ([0-1]).}
\item{\code{stomatalSubmodel [= "Baldocchi"]}: Stomatal regulation sub-model, either "Jarvis" or "Baldocchi".}
\item{\code{JarvisPAR [= 0.003]}: Parameter regulating the response of stomatal conductance to light (PAR) in the Jarvis model.}
\item{\code{fTRBToLeaf [= 0.8]}: Fraction of surface of bark exposed to air per leaf area.}
}

\bold{Forest growth} (functions \code{\link{growth}} or \code{\link{growth_day}}):
\itemize{
\item{\code{subdailyCarbonBalance [= FALSE]}: Boolean flag to indicate that labile carbon balance should be conducted at sub-daily steps (applies only to transpirationMode = "Sperry").}
\item{\code{allowDessication [= TRUE]}: Boolean flag to indicate that mortality by dessication is allowed.}
\item{\code{allowStarvation [= TRUE]}: Boolean flag to indicate that mortality by starvation is allowed.}
\item{\code{sinkLimitation [= TRUE]}: Boolean flag to indicate that temperature and turgor limitations to growth are applied.}
\item{\code{shrubDynamics [= TRUE]}: Boolean flag to allow the application of demographic processes to shrubs.}
\item{\code{herbDynamics [= TRUE]}: Boolean flag to allow dynamic herb leaf area as a function of shading due to leaf area of woody cohorts.}
\item{\code{allocationStrategy [= "Al2As"]}: Strategy for allocation (either "Plant_kmax", for constant maximum plant conductance, or "Al2As" for constant Huber value).}
\item{\code{phloemConductanceFactor [= 0.2])}: Factor to transform stem xylem conductance to stem phloem conductance (only for transpirationMode = "Sperry").}
\item{\code{nonSugarConcentration [= 0.25]}: Non-sugar (inorganic) solute concentration  (mol·l-1) in cells.}
\item{\code{equilibriumOsmoticConcentration [=  c(leaf = 0.8, sapwood = 0.6)]}: Equilibrium osmotic concentrations (mol·l-1) for leaf and sapwood cells. The difference between leaf and sapwood values helps maintaining phloem transport. The equilibrium sugar concentration is \code{equilibriumOsmoticConcentration - nonSugarConcentration} defaults to \code{[= c(leaf = 0.55, sapwood = 0.35)]}. }
\item{\code{minimumRelativeStarchForGrowth [= 0.50]}: Default minimum concentration of storage carbon (starch), relative to the maximum storage capacity, for sapwood growth to occur, when not specified via SpParams (\code{RSSG}). }
\item{\code{constructionCosts [= c(leaf = 1.5, sapwood = 1.47, fineroot = 1.30)]}: Default construction costs, including respiration and structural carbon, per dry weight of new tissue (g gluc · g dry -1) when not specified via SpParams (\code{CCleaf}, \code{CCsapwood} and \code{CCfineroot}).}
\item{\code{senescenceRates [= c(sapwood = 0.0001261398, fineroot = 0.001897231)]}: Default senescence rates (day-1) for sapwood and fineroots when not specified via SpParams (\code{SRsapwood} and \code{SRfineroot}). Defaults are equivalent to 9\%, 5\% and 50\% annual turnover for gymnosperm sapwood, angiosperm sapwood and fine roots, respectively.}
\item{\code{maximumRelativeGrowthRates [=   c(leaf = 0.09, cambium = 0.005, sapwood = 0.002, fineroot = 0.1)]}: Default maximum relative growth rates for leaves (m2 leaf ·cm-2 sapwood· day-1), tree sapwood (cm2 sapwood· cm-1 cambium · day-1), shrub sapwood (cm2 sapwood ·cm-2 sapwood· day-1) and fine roots (g dw · g dw -1 · day -1) when not specified via SpParams (\code{RGRleafmax}, \code{RGRcambiummax} , \code{RGRsapwoodmax} and \code{RGRfinerootmax}, respectively).}
\item{\code{mortalityMode [= "density/deterministic"]}: String describing how mortality is applied. Current accepted values are combinations of "cohort" vs "density" (for whole-cohort mortality vs reduction of stem density) and "deterministic" vs. "stochastic".}
\item{\code{mortalityBaselineRate [= 0.0015]}: Default deterministic proportion or probability specifying the baseline reduction of cohort's density occurring in a year (for \code{mortalityMode = "density/deterministic" or "density/stochastic").}}
\item{\code{mortalityRelativeSugarThreshold [= 0.4]}: Threshold of stem sugar concentration relative to the equilibrium sugar concentration, resulting in an increased starvation mortality rate/probability whenever levels are below.}
\item{\code{mortalityRWCThreshold [= 0.4]}: Threshold of stem relative water content resulting in increased mortality rate/probability whenever levels are below.}
\item{\code{recrTreeDBH [= 1]}: Default DBH (cm) for recruited trees  (when species parameter \code{RecrTreeDBH} is missing).}
\item{\code{recrTreeDensity [= 3000]}: Default density (ind·ha-1) for recruited trees  (when species parameter \code{RecrTreeDensity} is missing).}
\item{\code{ingrowthTreeDBH [= 7.5]}: Default DBH (cm) for ingrowth trees  (when species parameter \code{IngrowthTreeDBH} is missing).}
\item{\code{ingrowthTreeDensity [= 127]}: Default density (ind·ha-1) for ingrowth trees  (when species parameter \code{IngrowthTreeDensity} is missing).}
\item{\code{decompositionAnnualBaseRates}: Vector of base annual decomposition rates (in yr-1) for different pools.}
\item{\code{decompositionAnnualTurnoverRate [= 0.1]}: Annual turnover time for biome in the CENTURY model.}
}
\bold{Forest dynamics} (function \code{\link{fordyn}}):
\itemize{
\item{\code{allowSeedBankDynamics [= TRUE]}: Boolean flag to indicate that seed production and seed bank dynamics is simulated.}
\item{\code{allowRecruitment [= TRUE]}: Boolean flag to indicate that recruitment from seeds is allowed.}
\item{\code{allowResprouting [= TRUE]}: Boolean flag to indicate that resprouting is allowed.}
\item{\code{recruitmentMode [= "annual/stochastic"]}: String describing how recruitment from seeds is applied. Current accepted values are "annual/deterministic", "annual/stochastic", "daily/deterministic" or "daily/stochastic".}
\item{\code{removeEmptyCohorts [= TRUE]}: Boolean flag to indicate the removal of cohorts whose density is too low.}
\item{\code{minimumTreeCohortDensity [= 1]}: Threshold of tree density resulting in cohort removal.}
\item{\code{minimumShrubCohortCover [= 0.01]}: Threshold of shrub cover resulting in cohort removal.}
\item{\code{dynamicallyMergeCohorts [= TRUE]}: Boolean flag to indicate that cohorts should be merged when possible. This option speeds up calculations but results in a loss of cohort identity and reinitialization of many state variables.}
\item{\code{keepCohortsWithID [= TRUE]}: Boolean flag to indicate that cohorts having a non-missing value in a column \code{"ID"} (if present) should not be merged or removed.}
\item{\code{seedRain [= NULL]}: Vector of species names whose seed rain is to be added to seed bank, regardless of local seed production.}
\item{\code{seedProductionTreeHeight [= 300]}: Default minimum tree height for producing seeds (when species parameter \code{SeedProductionHeight} is missing).}
\item{\code{seedProductionShrubHeight [= 30]}: Default minimum shrub height for producing seeds (when species parameter \code{SeedProductionHeight} is missing).}
\item{\code{probRecr [= 0.05]}: Default annual probability of seed-recruitment (when species parameter \code{ProbRecr} is missing).}
\item{\code{minTempRecr [= 0]}: Default threshold of minimum average temperature of the coldest month necessary for recruiting from seeds (when species parameter \code{MinTempRecr} is missing).}
\item{\code{minMoistureRecr [= 0.3]}: Default threshold of minimum moisture index (annual precipitation over annual ETP) necessary for seed-recruiting (when species parameter \code{MinMoistureRecr} is missing).}
\item{\code{minFPARRecr [= 10]}: Default threshold of minimum fraction of PAR (in \%)  reaching the ground necessary for recruiting (when species parameter \code{MinFPARRecr} is missing).}
\item{\code{recrAge [= 5]}: Default recruitment age (in yrs).}
\item{\code{recrTreeHeight [= 620]}: Default height (cm) for recruited trees  (when species parameter \code{RecrTreeHeight} is missing).}
\item{\code{recrShrubCover [= 1]}: Default cover (\%) for shrubs recruited from seed  (when species parameter \code{RecrShrubCover} is missing).}
\item{\code{recrShrubHeight [= 25]}: Default height (cm) for recruited shrubs  (when species parameter \code{RecrShrubHeight} is missing).}
}
}
}
\description{
Creates a list control parameters default values for simulations
}
\details{
The function returns a list with default parameters.
Users can change those defaults that need to be set to other values and use the list as input for model functions.
The relevant parameters are different for each model function.
}
\seealso{
\code{\link{spwbInput}}, \code{\link{spwb}}, \code{\link{growth}}, \code{\link{fordyn}}
}
\author{
Miquel De \enc{Cáceres}{Caceres} Ainsa, CREAF
}
