Routines to modify species parameter table or model input objects
Usage
modifySpParams(SpParams, customParams, subsetSpecies = TRUE)
modifyCohortParams(x, customParams, verbose = TRUE)
modifyInputParams(x, customParams, verbose = TRUE)Arguments
- SpParams
A species parameter data frame, typically
SpParamsMED.- customParams
A data frame or a named vector with new parameter values (see details).
- subsetSpecies
A logical flag to indicate that the output data frame should include only those species mentioned in
customParams.- x
A model input object of class
spwbInputorgrowthInput.- verbose
A logical flag to indicate that messages should be printed on the console.
Value
Function modifySpParams returns a modified species parameter data frame.
Functions modifyCohortParams and modifyInputParams return a modified spwbInput or growthInput object. Note that modifications may affect other parameters beyond those indicated in customParams, as a result of parameter dependencies (see examples).
Details
When calling function modifySpParams, customParams should be a data frame with as many rows as species
and as many columns as parameters to modify, plus a column called 'Name' or 'Species' to match species names between the two tables. In both
cases, the function will match input strings with column 'Name' of x. Alternatively, customParams can contain a column 'SpIndex' for
matching of species indices, but this is deprecated.
When calling modifyCohortParams, customParams can be a data frame with as many rows as cohorts
and as many columns as parameters to modify, plus a column called 'Cohort' which will be matched with the cohort names
given by spwbInput or growthInput.
Alternatively, customParams can be a named list or named numeric vector as for modifyInputParams.
When calling modifyInputParams, customParams must be either a named list or a named numeric vector.
Cohort parameters are specified using the syntax "<cohortName>/<paramName>" for names (e.g. "T2_176/Z50" to modify parameter 'Z50' of cohort 'T2_176').
Soil layer parameters are specified using the syntax "<paramName>@#layer" for names, where #layer is the layer index (e.g. "rfc@1" will modify the rock fragment content of soil layer 1).
Control parameters are specified using either "<paramName>" (e.g "phloemConductanceFactor") or "<paramName>$<subParamName>" (e.g "maximumRelativeGrowthRates$leaf").
It may seem unnecessary to modify soil or control parameters via a function, but modifyInputParams is called from optimization functions (see optimization).
Examples
#Load example daily meteorological data
data(examplemeteo)
#Load example plot plant data
data(exampleforest)
#Default species parameterization
data(SpParamsMED)
#Define soil with default soil params (4 layers)
examplesoil <- defaultSoilParams(4)
#Initialize control parameters
control <- defaultControl("Granier")
#Initialize input
x1 <- spwbInput(exampleforest,examplesoil, SpParamsMED, control)
# Cohort name for Pinus halepensis
PH_coh <- paste0("T1_", SpParamsMED$SpIndex[SpParamsMED$Name=="Pinus halepensis"])
PH_coh
#> [1] "T1_148"
# Modify Z50 and Z95 of Pinus halepensis cohort
customParams <- c(200,2000)
names(customParams) <- paste0(PH_coh,c("/Z50", "/Z95"))
x1m <- modifyInputParams(x1, customParams)
# Inspect original and modified objects
x1$below
#> Z50 Z95 Z100
#> T1_148 100 600 NA
#> T2_168 300 1000 NA
#> S1_165 200 1000 NA
x1m$below
#> Z50 Z95 Z100 fineRootBiomass coarseRootSoilVolume
#> T1_148 200 2000 NA NA 0
#> T2_168 300 1000 NA NA 0
#> S1_165 200 1000 NA NA 0
# Inspect dependencies: fine root distribution across soil layers
x1$belowLayers$V
#> 1 2 3 4
#> T1_148 0.8604899 0.1194556 0.01511005 0.004944476
#> T2_168 0.5008953 0.4505941 0.04064831 0.007862284
#> S1_165 0.6799879 0.2737911 0.03567632 0.010544678
x1m$belowLayers$V
#> 1 2 3 4
#> T1_148 0.6402830 0.2655064 0.06472163 0.029488953
#> T2_168 0.5008953 0.4505941 0.04064831 0.007862284
#> S1_165 0.6799879 0.2737911 0.03567632 0.010544678
# Modify rock fragment content and sand proportion of soil layer 1
x1s <- modifyInputParams(x1, c("rfc@1" = 5, "sand@1" = 10))
# Inspect original and modified soils
x1$soil
#> widths sand clay usda om nitrogen bd rfc macro Ksat VG_alpha
#> 1 300 25 25 Silt loam NA NA 1.5 25 0.0485 5401.471 89.16112
#> 2 700 25 25 Silt loam NA NA 1.5 45 0.0485 5401.471 89.16112
#> 3 1000 25 25 Silt loam NA NA 1.5 75 0.0485 5401.471 89.16112
#> 4 2000 25 25 Silt loam NA NA 1.5 95 0.0485 5401.471 89.16112
#> VG_n VG_theta_res VG_theta_sat W Temp
#> 1 1.303861 0.041 0.423715 1 NA
#> 2 1.303861 0.041 0.423715 1 NA
#> 3 1.303861 0.041 0.423715 1 NA
#> 4 1.303861 0.041 0.423715 1 NA
x1s$soil
#> widths sand clay usda om nitrogen bd rfc macro Ksat VG_alpha
#> 1 300 10 25 Silt loam NA NA 1.5 5 0.0167 7046.523 97.10141
#> 2 700 25 25 Silt loam NA NA 1.5 45 0.0485 5401.471 89.16112
#> 3 1000 25 25 Silt loam NA NA 1.5 75 0.0485 5401.471 89.16112
#> 4 2000 25 25 Silt loam NA NA 1.5 95 0.0485 5401.471 89.16112
#> VG_n VG_theta_res VG_theta_sat W Temp
#> 1 1.240345 0.041 0.426520 1 NA
#> 2 1.303861 0.041 0.423715 1 NA
#> 3 1.303861 0.041 0.423715 1 NA
#> 4 1.303861 0.041 0.423715 1 NA
# When modifying growth input objects dependencies increase
x1 <- growthInput(exampleforest,examplesoil, SpParamsMED, control)
customParams <- c(2000,2)
names(customParams) <- paste0(PH_coh,c("/Al2As", "/LAI_live"))
x1m <- modifyInputParams(x1, customParams)