medfate (version 4.7.0)

modifyParams: Modify parameters

Description

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)

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).

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 spwbInput or growthInput.

verbose

A logical flag to indicate that messages should be printed on the console.

Author

Miquel De Cáceres Ainsa, CREAF

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).

See Also

spwbInput, SpParamsMED, 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 

# 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$below
x1m$below

# Inspect dependencies: fine root distribution across soil layers
x1$belowLayers$V
x1m$belowLayers$V

# 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$soil
x1s$soil

# 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)