R/PRE_FATE.params_PFGsoil.R
In MayaGueguen/RFate: Vegetation modelling with the FATE model
Defines functions
PRE_FATE.params_PFGsoil
Documented in
PRE_FATE.params_PFGsoil
### HEADER #####################################################################
##' @title Create \emph{SOIL} parameter files for a \code{FATE} simulation
##'
##' @name PRE_FATE.params_PFGsoil
##'
##' @author Maya Guéguen
##'
##' @description This script is designed to create parameter files containing
##' soil contribution and tolerance for each PFG (one file for each of them)
##' used in the soil module of \code{FATE}.
##'
##' @param name.simulation a \code{string} corresponding to the main directory
##' or simulation name of the \code{FATE} simulation
##' @param mat.PFG.soil a \code{data.frame} with 3 to 7 columns : \cr
##' \itemize{
##' \item \code{PFG},
##' \item \code{type}, (\emph{or \code{active_germ_low},
##' \code{active_germ_medium}, \code{active_germ_high}}) (\emph{or
##' \code{strategy_ag}})
##' \item \code{soil_contrib}, \code{soil_tol_min}, \code{soil_tol_max}
##' (\emph{or \code{strategy_contrib}})
##' }
##' (see \href{PRE_FATE.params_PFGsoil.html#details}{\code{Details}})
##' @param mat.PFG.tol (\emph{optional}) \cr
##' a \code{data.frame} with 2 to 4 columns : \cr
##' \itemize{
##' \item \code{PFG},
##' \item \code{lifeStage}, \code{resources}, \code{tolerance}
##' (\emph{or \code{strategy_tol}})
##' }
##' (see \href{PRE_FATE.params_PFGsoil.html#details}{\code{Details}})
##' @param opt.folder.name (\emph{optional}) \cr a \code{string} corresponding
##' to the name of the folder that will be created into the
##' \code{name.simulation/DATA/PFGS/SOIL/} directory to store the results
##'
##'
##' @details
##'
##' The \strong{soil module} allows the user to add the effect of
##' \strong{soil competition} within a primary vegetation succession. \cr \cr
##'
##' Several parameters, given within \code{mat.PFG.soil} or \code{mat.PFG.tol},
##' are required for each PFG in order to set up the soil competition :
##'
##' \describe{
##' \item{PFG}{the concerned plant functional group \cr \cr}
##'
##' \item{type}{or life-form, based on Raunkier. \cr It should be either
##' \code{H} (herbaceous), \code{C} (chamaephyte) or \code{P} (phanerophyte)
##' for now}
##' \item{(\emph{active_germ_low})}{an \code{integer} between \code{0} and
##' \code{10} corresponding to the proportion of seeds that will germinate for
##' \code{Low} soil condition}
##' \item{(\emph{active_germ_medium})}{an \code{integer} between \code{0} and
##' \code{10} corresponding to the proportion of seeds that will germinate for
##' \code{Medium} soil condition}
##' \item{(\emph{active_germ_high})}{an \code{integer} between \code{0} and
##' \code{10} corresponding to the proportion of seeds that will germinate for
##' \code{High} soil condition}
##' \item{(\emph{strategy_ag})}{a \code{string} to choose the germination
##' strategy : \cr \code{poor_lover}, \code{indifferent}, \code{rich_lover}
##' \cr \cr}
##'
##' \item{soil_contrib}{a value corresponding to the PFG preference for soil
##' fertility \cr (e.g. nitrogen value from Ellenberg or Flora Indicativa)}
##' \item{soil_tol_min}{the minimum soil value tolerated by the PFG (on the
##' same scale than \code{soil_contrib})}
##' \item{soil_tol_max}{the maximum soil value tolerated by the PFG (on the
##' same scale than \code{soil_contrib})}
##' \item{(\emph{strategy_contrib})}{a \code{string} to choose the
##' contribution strategy : \cr \code{ubiquist}, \code{tobedefined} \cr \cr}
##'
##' \item{lifeStage}{the concerned life stage (\code{Germinant},
##' \code{Immature}, \code{Mature})}
##' \item{resources}{the concerned soil condition (\code{Low},
##' \code{Medium}, \code{High})}
##' \item{tolerance}{an \code{integer} between \code{0} and \code{10}
##' corresponding to the proportion of surviving individuals}
##' \item{(\emph{strategy_tol})}{a \code{string} to choose the tolerance
##' strategy : \cr \code{ubiquist}, \code{tobedefined} \cr \cr}
##' }
##'
##' These values will allow to calculate or define a set of characteristics for
##' each PFG :
##'
##' \describe{
##' \item{ACTIVE_GERM}{proportion of seeds that will germinate for each soil
##' condition (\code{Low}, \code{Medium}, \code{High}) \cr \cr
##' Three methods to define these proportions are available :
##' \itemize{
##' \item from \strong{predefined scenarios} (using \code{strategy_ag}) :
##' \describe{
##' \item{}{\strong{\code{| _L_ _M_ _H_ |}}}
##' \item{}{\code{_______________}}
##' \item{poor_lover}{\code{| 80\% 90\% 50\% |}}
##' \item{indifferent}{\code{| 90\% 90\% 90\% |}}
##' \item{rich_lover}{\code{| 50\% 90\% 80\% |}}
##' }
##' \item from \strong{predefined rules} (using \code{type}) :
##' \itemize{
##' \item for \code{H} (herbaceous) : \code{80\%, 100\%, 50\%}
##' \item for \code{C} (chamaephyte) or \code{P} (phanerophyte) :
##' \code{90\%, 100\%, 90\%}
##' }
##' \item from \strong{user data} : \cr
##' \emph{with the values contained within the \code{active_germ_low},
##' \code{active_germ_medium} and \code{active_germ_high} columns, if
##' provided \cr \cr}
##' }
##' }
##'
##' \item{SOIL_CONTRIB \cr SOIL_LOW \cr SOIL_HIGH}{
##' Two methods to define these values are available :
##' \itemize{
##' \item from \strong{predefined scenarios} (using
##' \code{strategy_contrib}) : \cr
##' \itemize{
##' \item the values give the \code{soil_tol_min}, \code{soil_contrib}
##' and \code{soil_tol_max}
##' \item with \code{L}: low soil, \code{M}: medium soil, \code{H}:
##' high soil \cr \cr
##' }
##' \describe{
##' \item{}{\strong{\code{| ___ L ___ | ___ M ___ | ___ H ___ |}}}
##' \item{}{\code{_____________________________________}}
##' \item{ubiquist}{\code{__________ 1.5 _ 2.5 _ 4.5 __________}}
##' \item{to be filled}{}
##' }
##' \item from \strong{user data} : \cr
##' \emph{with the values contained within the \code{soil_contrib},
##' \code{soil_tol_min} and \code{soil_tol_max} columns, if provided \cr \cr}
##' }
##' }
##'
##' \item{SOIL_TOL}{ defined for each life stage (\code{Germinant},
##' \code{Immature}, \code{Mature}) \cr and each soil condition (\code{Low},
##' \code{Medium}, \code{High}) \cr \cr
##' Three methods to define these tolerances are available :
##' \itemize{
##' \item from \strong{predefined scenarios} (using
##' \code{strategy_tol}) : \cr
##' \itemize{
##' \item the values give the percentage of surviving individuals to the
##' concerned conditions
##' \item with \code{g}: Germinant, \code{i}: Immature, \code{m}: Mature
##' \item with \code{L}: low soil, \code{M}: medium soil, \code{H}:
##' high soil \cr \cr
##' }
##' \describe{
##' \item{}{\strong{\code{| ___ g ___ | ___ i ___ | ___ m ___ |}}}
##' \item{}{\strong{\code{| _L _M_ H_ | _L _M_ H_ | _L _M_ H_ |}}}
##' \item{}{\code{_____________________________________}}
##' \item{ubiquist}{\code{| 90 100 90 | 90 100 90 | 90 100 90 |}}
##' \item{to be filled}{}
##' }
##' \item from \strong{predefined rules} :
##' \describe{
##' \item{(A)}{germinants are severely impacted by wrong soil conditions}
##' \item{(B)}{immatures are half impacted by wrong soil conditions}
##' \item{(C)}{matures are little impacted by wrong soil conditions}
##' }
##' \itemize{
##' \item the values give the percentage of surviving individuals to the
##' concerned conditions
##' \item with \code{g}: Germinant, \code{i}: Immature, \code{m}: Mature
##' \item with \code{L}: low soil, \code{M}: medium soil, \code{H}:
##' high soil \cr \cr
##' }
##' \describe{
##' \item{}{\strong{\code{| ___ g ___ | ___ i ___ | ___ m ___ |}}}
##' \item{}{\strong{\code{| _L _M_ H_ | _L _M_ H_ | _L _M_ H_ |}}}
##' \item{}{\code{_____________________________________}}
##' \item{}{\code{| 10 100 30 | 40 100 60 | 70 100 90 |}}
##' }
##' \item from \strong{user data} : \cr
##' \emph{with the values contained within the \code{lifeStage},
##' \code{resources} and \code{tolerance} columns, if provided}
##' }
##' }
##' }
##'
##'
##'
##' @return A \code{.txt} file per PFG into the
##' \code{name.simulation/DATA/PFGS/SOIL/} directory with the following
##' parameters :
##'
##' \describe{
##' \item{NAME}{name of the PFG}
##' \item{ACTIVE_GERM}{germination rates depending on soil conditions
##' \cr \emph{(from \code{0} to \code{10}, corresponding to 0 to 100\%)}}
##' \item{SOIL_CONTRIB}{contribution to the soil value of the pixel}
##' \item{SOIL_LOW}{lower value of soil supported by the PFG, \cr
##' defining the limit between \code{Low} and \code{Medium} soil resources
##' for this PFG}
##' \item{SOIL_HIGH}{upper value of soil supported by the PFG, \cr
##' defining the limit between \code{Medium} and \code{High} soil resources
##' for this PFG}
##' \item{SOIL_TOL}{soil tolerance table (in a single row). \cr
##' This is a vector of 9 numbers corresponding to the ability of the PFG to
##' survive or not :
##' \itemize{
##' \item at different life stages \emph{(Germinant (\code{Ge}), Immature
##' (\code{Im}), Mature (\code{Ma}))}
##' \item under different soil conditions \emph{(Low (\code{L}), Medium
##' (\code{M}) or High (\code{H}))}.
##' }
##' These parameters should be given in this order : \code{GeL, GeM, GeH, ImL,
##' ImM, ImH, MaL, MaM, MaH}
##' \cr \emph{(from \code{0} to \code{10}, corresponding to 0 to 100\%)}.
##' \cr \cr}
##' }
##'
##' A \code{SOIL_COMPLETE_TABLE.csv} file summarizing information for all
##' groups into the \code{name.simulation/DATA/PFGS/} directory.
##'
##' If the \code{opt.folder.name} has been used, the files will be into the
##' folder \code{name.simulation/DATA/PFGS/SOIL/opt.folder.name/}.
##'
##'
##' @keywords FATE, simulation, soil tolerance, nitrogen
##'
##' @seealso \code{\link{PRE_FATE.skeletonDirectory}},
##' \code{\link{PRE_FATE.params_PFGsuccession}}
##'
##' @examples
##'
##' ## Create a skeleton folder with the default name ('FATE_simulation')
##' PRE_FATE.skeletonDirectory()
##'
##' ## Create PFG soil parameter files
##' PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
##' , mat.PFG.soil = data.frame(PFG = c("PFG1", "PFG2", "PFG3")
##' , type = c("H", "H", "C")
##' , soil_contrib = c(2.5, 3, 4.8)
##' , soil_tol_min = c(2, 3, 3)
##' , soil_tol_max = c(3, 3, 6)))
##'
##' @export
##'
##' @importFrom utils write.table
##'
## END OF HEADER ###############################################################
PRE_FATE.params_PFGsoil = function(
name.simulation
, mat.PFG.soil
, mat.PFG.tol = NULL
, opt.folder.name = NULL
){
#############################################################################
.testParam_existFolder(name.simulation, "DATA/PFGS/SOIL/")
## CHECK parameter mat.PFG.soil
if (.testParam_notDf(mat.PFG.soil))
{
.stopMessage_beDataframe("mat.PFG.soil")
} else
{
if (nrow(mat.PFG.soil) == 0 || !(ncol(mat.PFG.soil) %in% c(3, 5, 7)))
{
.stopMessage_numRowCol("mat.PFG.soil", c("PFG", "type", "(active_germ_low)", "(active_germ_medium)"
, "(active_germ_high)", "(strategy_ag)", "soil_contrib"
, "soil_tol_min", "soil_tol_max", "(strategy_contrib)"))
} else
{
notCorrect = switch(as.character(ncol(mat.PFG.soil))
, "3" = (.testParam_notColnames(mat.PFG.soil, c("PFG", "type", "strategy_contrib")) &&
.testParam_notColnames(mat.PFG.soil, c("PFG", "strategy_ag", "strategy_contrib")))
, "5" = (.testParam_notColnames(mat.PFG.soil, c("PFG", "type", "soil_contrib"
, "soil_tol_min", "soil_tol_max")) &&
.testParam_notColnames(mat.PFG.soil, c("PFG", "active_germ_low"
, "active_germ_medium"
, "active_germ_high"
, "strategy_contrib")) &&
.testParam_notColnames(mat.PFG.soil, c("PFG", "strategy_ag", "soil_contrib"
, "soil_tol_min", "soil_tol_max")))
, "7" = .testParam_notColnames(mat.PFG.soil, c("PFG", "active_germ_low"
, "active_germ_medium"
, "active_germ_high", "soil_contrib"
, "soil_tol_min", "soil_tol_max"))
, TRUE)
if (notCorrect){
.stopMessage_columnNames("mat.PFG.soil", c("PFG", "type", "(active_germ_low)", "(active_germ_medium)"
, "(active_germ_high)", "(strategy_ag)", "soil_contrib"
, "soil_tol_min", "soil_tol_max", "(strategy_contrib)"))
}
}
mat.PFG.soil$PFG = as.character(mat.PFG.soil$PFG)
.testParam_samevalues.m("mat.PFG.soil$PFG", mat.PFG.soil$PFG)
.testParam_notChar.m("mat.PFG.soil$PFG", mat.PFG.soil$PFG)
if (sum(colnames(mat.PFG.soil) == "type") == 1)
{
mat.PFG.soil$type = as.character(mat.PFG.soil$type)
.testParam_notInValues.m("mat.PFG.soil$type", mat.PFG.soil$type, c("H", "C", "P"))
}
if (sum(colnames(mat.PFG.soil) == "active_germ_low") == 1)
{
.testParam_NAvalues.m("mat.PFG.soil$active_germ_low", mat.PFG.soil$active_germ_low)
.testParam_notInValues.m("mat.PFG.soil$active_germ_low", mat.PFG.soil$active_germ_low, 0:10)
.testParam_NAvalues.m("mat.PFG.soil$active_germ_medium", mat.PFG.soil$active_germ_medium)
.testParam_notInValues.m("mat.PFG.soil$active_germ_medium", mat.PFG.soil$active_germ_medium, 0:10)
.testParam_NAvalues.m("mat.PFG.soil$active_germ_high", mat.PFG.soil$active_germ_high)
.testParam_notInValues.m("mat.PFG.soil$active_germ_high", mat.PFG.soil$active_germ_high, 0:10)
}
if (sum(colnames(mat.PFG.soil) == "strategy_ag") == 1)
{
mat.PFG.soil$strategy_ag = as.character(mat.PFG.soil$strategy_ag)
.testParam_notInValues.m("mat.PFG.soil$strategy_ag", mat.PFG.soil$strategy_ag
, c("poor_lover", "indifferent", "rich_lover"))
}
if (sum(colnames(mat.PFG.soil) == "soil_contrib") == 1)
{
.testParam_notNum.m("mat.PFG.soil$soil_contrib", mat.PFG.soil$soil_contrib)
.testParam_NAvalues.m("mat.PFG.soil$soil_contrib", mat.PFG.soil$soil_contrib)
.testParam_notNum.m("mat.PFG.soil$soil_tol_min", mat.PFG.soil$soil_tol_min)
.testParam_NAvalues.m("mat.PFG.soil$soil_tol_min", mat.PFG.soil$soil_tol_min)
.testParam_notNum.m("mat.PFG.soil$soil_tol_max", mat.PFG.soil$soil_tol_max)
.testParam_NAvalues.m("mat.PFG.soil$soil_tol_max", mat.PFG.soil$soil_tol_max)
if (sum(mat.PFG.soil$soil_tol_min > mat.PFG.soil$soil_contrib) > 0){
stop(paste0("Wrong type of data!\n `mat.PFG.soil$soil_tol_min` must contain "
, "values equal or inferior to `mat.PFG.soil$soil_contrib`"))
}
if (sum(mat.PFG.soil$soil_tol_max < mat.PFG.soil$soil_contrib) > 0){
stop(paste0("Wrong type of data!\n `mat.PFG.soil$soil_tol_max` must contain "
, "values equal or superior to `mat.PFG.soil$soil_contrib`"))
}
}
if (sum(colnames(mat.PFG.soil) == "strategy_contrib") == 1)
{
mat.PFG.soil$strategy_contrib = as.character(mat.PFG.soil$strategy_contrib)
.testParam_notInValues.m("mat.PFG.soil$strategy_contrib", mat.PFG.soil$strategy_contrib
, c("full_light", "pioneer", "ubiquist", "semi_shade", "undergrowth"))
}
}
## CHECK parameter mat.PFG.tol
if (!is.null(mat.PFG.tol))
{
if (.testParam_notDf(mat.PFG.tol))
{
.stopMessage_beDataframe("mat.PFG.tol")
} else
{
if (nrow(mat.PFG.tol) == 0 || !(ncol(mat.PFG.tol) %in% c(2, 4)))
{
.stopMessage_numRowCol("mat.PFG.tol", c("PFG", "lifeStage", "resources", "tolerance", "(strategy_tol)"))
} else
{
notCorrect = switch(as.character(ncol(mat.PFG.tol))
, "2" = .testParam_notColnames(mat.PFG.tol, c("PFG", "strategy_tol"))
, "4" = .testParam_notColnames(mat.PFG.tol, c("PFG", "lifeStage", "resources", "tolerance"))
, TRUE)
if (notCorrect){
.stopMessage_columnNames("mat.PFG.tol", c("PFG", "lifeStage", "resources", "tolerance", "(strategy_tol)"))
}
}
mat.PFG.tol$PFG = as.character(mat.PFG.tol$PFG)
.testParam_notChar.m("mat.PFG.tol$PFG", mat.PFG.tol$PFG)
if (sum(colnames(mat.PFG.tol) == "lifeStage") == 1)
{
.testParam_notInValues.m("mat.PFG.tol$lifeStage", mat.PFG.tol$lifeStage, c("Germinant", "Immature", "Mature"))
.testParam_notInValues.m("mat.PFG.tol$resources", mat.PFG.tol$resources, c("Low", "Medium", "High"))
.testParam_NAvalues.m("mat.PFG.tol$tolerance", mat.PFG.tol$tolerance)
.testParam_notInValues.m("mat.PFG.tol$tolerance", mat.PFG.tol$tolerance, 0:10)
}
if (sum(colnames(mat.PFG.tol) == "strategy_tol") == 1)
{
mat.PFG.tol$strategy_tol = as.character(mat.PFG.tol$strategy_tol)
.testParam_notInValues.m("mat.PFG.tol$strategy_tol", mat.PFG.tol$strategy_tol
, c("full_light", "pioneer", "ubiquist", "semi_shade", "undergrowth"))
}
}
}
## CHECK parameter opt.folder.name
opt.folder.name = .getParam_opt.folder.name(opt.folder.name
, paste0(name.simulation, "/DATA/PFGS/SOIL/"))
#############################################################################
no.PFG = nrow(mat.PFG.soil)
## GET PFG NAME
NAME = as.character(mat.PFG.soil$PFG)
#############################################################################
## GET GERMINATION RATE depending on soil conditions
## = these rates should express a deviation from the
## germination rate in optimal conditions (=100%)
## = for each soil condition (Low, Medium, High)
## 11 levels : 0 = 0 %
## 1 = 10 %
## 2 = 20 %
## 3 = 30 %
## 4 = 40 %
## 5 = 50 %
## 6 = 60 %
## 7 = 70 %
## 8 = 80 %
## 9 = 90 %
## 10 = 100 %
ACTIVE_GERM = matrix(10, nrow = 3, ncol = no.PFG)
if (sum(colnames(mat.PFG.soil) == "type") == 1)
{
## woody species have little variation in germination rate depending on soil conditions
ACTIVE_GERM[c(1,3), which(mat.PFG.soil$type %in% c("C", "P"))] = 9
## herbaceous germinate less in richer soil
ACTIVE_GERM[1, which(mat.PFG.soil$type == "H")] = 8 ## low soil conditions
ACTIVE_GERM[3, which(mat.PFG.soil$type == "H")] = 5 ## high soil conditions
} else if (sum(colnames(mat.PFG.soil) == "active_germ_low") == 1 ||
sum(colnames(mat.PFG.soil) == "active_germ_medium") == 1 ||
sum(colnames(mat.PFG.soil) == "active_germ_high") == 1)
{
if (sum(colnames(mat.PFG.soil) == "active_germ_low") == 1)
{
ACTIVE_GERM[1, ] = mat.PFG.soil$active_germ_low
}
if (sum(colnames(mat.PFG.soil) == "active_germ_medium") == 1)
{
ACTIVE_GERM[2, ] = mat.PFG.soil$active_germ_medium
}
if (sum(colnames(mat.PFG.soil) == "active_germ_high") == 1)
{
ACTIVE_GERM[3, ] = mat.PFG.soil$active_germ_high
}
} else if (sum(colnames(mat.PFG.soil) == "strategy_ag") == 1)
{
for (i in 1:no.PFG){
ACTIVE_GERM[, i] = switch(mat.PFG.soil$strategy_ag[i]
, poor_lover = c(8, 9, 5)
, indifferent = c(9, 9, 9)
, rich_lover = c(5, 9, 8)
)
}
} else
{
warning(paste0("Missing data! The `ACTIVE_GERM` parameter has not been set. "
, "Please check."))
}
#############################################################################
if (sum(colnames(mat.PFG.soil) == "soil_contrib") == 1)
{
## GET SOIL CONTRIBUTION
SOIL_CONTRIB = as.numeric(mat.PFG.soil$soil_contrib)
## GET SOIL TOLERANCE LIMITS
SOIL_LOW = as.numeric(mat.PFG.soil$soil_tol_min)
SOIL_HIGH = as.numeric(mat.PFG.soil$soil_tol_max)
} else if (sum(colnames(mat.PFG.soil) == "strategy_contrib") == 1)
{
SOIL_CONTRIB = SOIL_LOW = SOIL_HIGH = vector(length = no.PFG)
for (i in 1:no.PFG){
tmp = switch(mat.PFG.soil$strategy_contrib[i]
# , full_light = c(1,1,1,0,0,1,0,0,1)
# , pioneer = c(1,1,1,0,1,1,0,1,1)
, ubiquist = c(2.5, 1, 4)
# , semi_shade = c(1,1,0,1,1,0,1,1,1)
# , undergrowth = c(1,1,0,1,1,0,1,1,0)
)
SOIL_CONTRIB[i] = tmp[1]
SOIL_LOW[i] = tmp[2]
SOIL_HIGH[i] = tmp[3]
}
} else
{
warning(paste0("Missing data! The `SOIL_CONTRIB`, `SOIL_LOW` and "
, "`SOIL_HIGH` parameters have not been set. "
, "Please check."))
}
no.class = seq(min(round(SOIL_CONTRIB))
, max(round(SOIL_CONTRIB))
, 1)
cat("\n ---------- INFORMATION : SOIL \n")
cat("\n Classes : ", no.class)
cat("\n Number of classes : ", max(no.class))
cat("\n Number of PFG within each class (contribution) : "
, table(cut(SOIL_CONTRIB, breaks = 1:max(no.class))))
cat("\n")
#############################################################################
## GET SOIL TOLERANCE
## = for each life stage (Germinant, Immature, Mature)
## = for each soil condition (Low, Medium, High)
## 11 levels : 0 = 0 %
## 1 = 10 %
## 2 = 20 %
## 3 = 30 %
## 4 = 40 %
## 5 = 50 %
## 6 = 60 %
## 7 = 70 %
## 8 = 80 %
## 9 = 90 %
## 10 = 100 %
SOIL_TOL = matrix(10, nrow = 3 * 3, ncol = no.PFG)
if (is.null(mat.PFG.tol))
{
SOIL_TOL[1, ] = 1 ## Germinant - Low soil conditions
SOIL_TOL[3, ] = 3 ## Germinant - High soil conditions
SOIL_TOL[4, ] = 4 ## Immature - Low soil conditions
SOIL_TOL[6, ] = 6 ## Immature - High soil conditions
SOIL_TOL[7, ] = 7 ## Mature - Low soil conditions
SOIL_TOL[9, ] = 9 ## Mature - High soil conditions
} else
{
if (sum(colnames(mat.PFG.tol) == "lifeStage") == 1)
{
for (ii in 1:nrow(mat.PFG.tol))
{
LS_res = paste0(mat.PFG.tol$lifeStage[ii], "_", mat.PFG.tol$resources[ii])
ind_ii = switch(LS_res
, Germinant_Low = 1
, Germinant_Medium = 2
, Germinant_High = 3
, Immature_Low = 4
, Immature_Medium = 5
, Immature_High = 6
, Mature_Low = 7
, Mature_Medium = 8
, Mature_High = 9
)
SOIL_TOL[ind_ii, which(NAME == mat.PFG.tol$PFG[ii])] = mat.PFG.tol$tolerance[ii]
}
} else if (sum(colnames(mat.PFG.tol) == "strategy_tol") == 1)
{
for (i in 1:no.PFG){
SOIL_TOL[, i] = switch(mat.PFG.tol$strategy_tol[i]
# , full_light = c(1,1,1,0,0,1,0,0,1)
# , pioneer = c(1,1,1,0,1,1,0,1,1)
, ubiquist = c(9,10,9,9,10,9,9,10,9)
# , semi_shade = c(1,1,0,1,1,0,1,1,1)
# , undergrowth = c(1,1,0,1,1,0,1,1,0)
)
}
} else
{
warning("Missing data! The `SOIL_TOL` parameter has not been set. Please check.")
}
}
#############################################################################
names.params.list = mat.PFG.soil$PFG
names.params.list.sub = c("NAME", "SOIL_CONTRIB"
, "SOIL_LOW", "SOIL_HIGH"
, "ACTIVE_GERM", "SOIL_TOL")
params.list = lapply(names.params.list.sub, function(x) { return(get(x)) })
params.csv = t(do.call(rbind, params.list))
colnames(params.csv) = c("NAME"
, "SOIL_CONTRIB"
, "SOIL_LOW"
, "SOIL_HIGH"
, paste0("ACTIVE_GERM_for_", c("L", "M", "H"))
, paste0("SOIL_TOL_for_",
c("GeL", "GeM", "GeH"
, "ImL", "ImM", "ImH"
, "MaL", "MaM", "MaH"))
)
write.table(params.csv
, file = paste0(name.simulation
, "/DATA/PFGS/"
, ifelse(opt.folder.name == ""
, ""
, sub("/$", "_", opt.folder.name))
, "SOIL_COMPLETE_TABLE.csv")
, row.names = FALSE
, col.names = TRUE)
#############################################################################
params.list = lapply(1:no.PFG, function(x) {
lapply(names.params.list.sub, function(y) {
val = get(y)
if (is.null(nrow(val))){
val = val[x]
} else {
val = val[, x]
}
return(val)
})
})
for (i in 1:length(params.list)) {
params = params.list[[i]]
names(params) = names.params.list.sub
.createParams(params.file = paste0(name.simulation
, "/DATA/PFGS/SOIL/"
, opt.folder.name
, "SOIL_"
, names.params.list[i],
".txt")
, params.list = params)
}
cat("\n> Done!\n")
cat("\n Complete table of information about PFG soil parameters can be find in "
, paste0(name.simulation, "/DATA/PFGS/"), "folder.")
cat("\n")
}
MayaGueguen/RFate documentation built on Oct. 17, 2020, 8:06 a.m.
R Package Documentation
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Defines functions PRE_FATE.params_PFGsoil
Documented in PRE_FATE.params_PFGsoil
### HEADER #####################################################################
##' @title Create \emph{SOIL} parameter files for a \code{FATE} simulation
##'
##' @name PRE_FATE.params_PFGsoil
##'
##' @author Maya Guéguen
##'
##' @description This script is designed to create parameter files containing
##' soil contribution and tolerance for each PFG (one file for each of them)
##' used in the soil module of \code{FATE}.
##'
##' @param name.simulation a \code{string} corresponding to the main directory
##' or simulation name of the \code{FATE} simulation
##' @param mat.PFG.soil a \code{data.frame} with 3 to 7 columns : \cr
##' \itemize{
##' \item \code{PFG},
##' \item \code{type}, (\emph{or \code{active_germ_low},
##' \code{active_germ_medium}, \code{active_germ_high}}) (\emph{or
##' \code{strategy_ag}})
##' \item \code{soil_contrib}, \code{soil_tol_min}, \code{soil_tol_max}
##' (\emph{or \code{strategy_contrib}})
##' }
##' (see \href{PRE_FATE.params_PFGsoil.html#details}{\code{Details}})
##' @param mat.PFG.tol (\emph{optional}) \cr
##' a \code{data.frame} with 2 to 4 columns : \cr
##' \itemize{
##' \item \code{PFG},
##' \item \code{lifeStage}, \code{resources}, \code{tolerance}
##' (\emph{or \code{strategy_tol}})
##' }
##' (see \href{PRE_FATE.params_PFGsoil.html#details}{\code{Details}})
##' @param opt.folder.name (\emph{optional}) \cr a \code{string} corresponding
##' to the name of the folder that will be created into the
##' \code{name.simulation/DATA/PFGS/SOIL/} directory to store the results
##'
##'
##' @details
##'
##' The \strong{soil module} allows the user to add the effect of
##' \strong{soil competition} within a primary vegetation succession. \cr \cr
##'
##' Several parameters, given within \code{mat.PFG.soil} or \code{mat.PFG.tol},
##' are required for each PFG in order to set up the soil competition :
##'
##' \describe{
##' \item{PFG}{the concerned plant functional group \cr \cr}
##'
##' \item{type}{or life-form, based on Raunkier. \cr It should be either
##' \code{H} (herbaceous), \code{C} (chamaephyte) or \code{P} (phanerophyte)
##' for now}
##' \item{(\emph{active_germ_low})}{an \code{integer} between \code{0} and
##' \code{10} corresponding to the proportion of seeds that will germinate for
##' \code{Low} soil condition}
##' \item{(\emph{active_germ_medium})}{an \code{integer} between \code{0} and
##' \code{10} corresponding to the proportion of seeds that will germinate for
##' \code{Medium} soil condition}
##' \item{(\emph{active_germ_high})}{an \code{integer} between \code{0} and
##' \code{10} corresponding to the proportion of seeds that will germinate for
##' \code{High} soil condition}
##' \item{(\emph{strategy_ag})}{a \code{string} to choose the germination
##' strategy : \cr \code{poor_lover}, \code{indifferent}, \code{rich_lover}
##' \cr \cr}
##'
##' \item{soil_contrib}{a value corresponding to the PFG preference for soil
##' fertility \cr (e.g. nitrogen value from Ellenberg or Flora Indicativa)}
##' \item{soil_tol_min}{the minimum soil value tolerated by the PFG (on the
##' same scale than \code{soil_contrib})}
##' \item{soil_tol_max}{the maximum soil value tolerated by the PFG (on the
##' same scale than \code{soil_contrib})}
##' \item{(\emph{strategy_contrib})}{a \code{string} to choose the
##' contribution strategy : \cr \code{ubiquist}, \code{tobedefined} \cr \cr}
##'
##' \item{lifeStage}{the concerned life stage (\code{Germinant},
##' \code{Immature}, \code{Mature})}
##' \item{resources}{the concerned soil condition (\code{Low},
##' \code{Medium}, \code{High})}
##' \item{tolerance}{an \code{integer} between \code{0} and \code{10}
##' corresponding to the proportion of surviving individuals}
##' \item{(\emph{strategy_tol})}{a \code{string} to choose the tolerance
##' strategy : \cr \code{ubiquist}, \code{tobedefined} \cr \cr}
##' }
##'
##' These values will allow to calculate or define a set of characteristics for
##' each PFG :
##'
##' \describe{
##' \item{ACTIVE_GERM}{proportion of seeds that will germinate for each soil
##' condition (\code{Low}, \code{Medium}, \code{High}) \cr \cr
##' Three methods to define these proportions are available :
##' \itemize{
##' \item from \strong{predefined scenarios} (using \code{strategy_ag}) :
##' \describe{
##' \item{}{\strong{\code{| _L_ _M_ _H_ |}}}
##' \item{}{\code{_______________}}
##' \item{poor_lover}{\code{| 80\% 90\% 50\% |}}
##' \item{indifferent}{\code{| 90\% 90\% 90\% |}}
##' \item{rich_lover}{\code{| 50\% 90\% 80\% |}}
##' }
##' \item from \strong{predefined rules} (using \code{type}) :
##' \itemize{
##' \item for \code{H} (herbaceous) : \code{80\%, 100\%, 50\%}
##' \item for \code{C} (chamaephyte) or \code{P} (phanerophyte) :
##' \code{90\%, 100\%, 90\%}
##' }
##' \item from \strong{user data} : \cr
##' \emph{with the values contained within the \code{active_germ_low},
##' \code{active_germ_medium} and \code{active_germ_high} columns, if
##' provided \cr \cr}
##' }
##' }
##'
##' \item{SOIL_CONTRIB \cr SOIL_LOW \cr SOIL_HIGH}{
##' Two methods to define these values are available :
##' \itemize{
##' \item from \strong{predefined scenarios} (using
##' \code{strategy_contrib}) : \cr
##' \itemize{
##' \item the values give the \code{soil_tol_min}, \code{soil_contrib}
##' and \code{soil_tol_max}
##' \item with \code{L}: low soil, \code{M}: medium soil, \code{H}:
##' high soil \cr \cr
##' }
##' \describe{
##' \item{}{\strong{\code{| ___ L ___ | ___ M ___ | ___ H ___ |}}}
##' \item{}{\code{_____________________________________}}
##' \item{ubiquist}{\code{__________ 1.5 _ 2.5 _ 4.5 __________}}
##' \item{to be filled}{}
##' }
##' \item from \strong{user data} : \cr
##' \emph{with the values contained within the \code{soil_contrib},
##' \code{soil_tol_min} and \code{soil_tol_max} columns, if provided \cr \cr}
##' }
##' }
##'
##' \item{SOIL_TOL}{ defined for each life stage (\code{Germinant},
##' \code{Immature}, \code{Mature}) \cr and each soil condition (\code{Low},
##' \code{Medium}, \code{High}) \cr \cr
##' Three methods to define these tolerances are available :
##' \itemize{
##' \item from \strong{predefined scenarios} (using
##' \code{strategy_tol}) : \cr
##' \itemize{
##' \item the values give the percentage of surviving individuals to the
##' concerned conditions
##' \item with \code{g}: Germinant, \code{i}: Immature, \code{m}: Mature
##' \item with \code{L}: low soil, \code{M}: medium soil, \code{H}:
##' high soil \cr \cr
##' }
##' \describe{
##' \item{}{\strong{\code{| ___ g ___ | ___ i ___ | ___ m ___ |}}}
##' \item{}{\strong{\code{| _L _M_ H_ | _L _M_ H_ | _L _M_ H_ |}}}
##' \item{}{\code{_____________________________________}}
##' \item{ubiquist}{\code{| 90 100 90 | 90 100 90 | 90 100 90 |}}
##' \item{to be filled}{}
##' }
##' \item from \strong{predefined rules} :
##' \describe{
##' \item{(A)}{germinants are severely impacted by wrong soil conditions}
##' \item{(B)}{immatures are half impacted by wrong soil conditions}
##' \item{(C)}{matures are little impacted by wrong soil conditions}
##' }
##' \itemize{
##' \item the values give the percentage of surviving individuals to the
##' concerned conditions
##' \item with \code{g}: Germinant, \code{i}: Immature, \code{m}: Mature
##' \item with \code{L}: low soil, \code{M}: medium soil, \code{H}:
##' high soil \cr \cr
##' }
##' \describe{
##' \item{}{\strong{\code{| ___ g ___ | ___ i ___ | ___ m ___ |}}}
##' \item{}{\strong{\code{| _L _M_ H_ | _L _M_ H_ | _L _M_ H_ |}}}
##' \item{}{\code{_____________________________________}}
##' \item{}{\code{| 10 100 30 | 40 100 60 | 70 100 90 |}}
##' }
##' \item from \strong{user data} : \cr
##' \emph{with the values contained within the \code{lifeStage},
##' \code{resources} and \code{tolerance} columns, if provided}
##' }
##' }
##' }
##'
##'
##'
##' @return A \code{.txt} file per PFG into the
##' \code{name.simulation/DATA/PFGS/SOIL/} directory with the following
##' parameters :
##'
##' \describe{
##' \item{NAME}{name of the PFG}
##' \item{ACTIVE_GERM}{germination rates depending on soil conditions
##' \cr \emph{(from \code{0} to \code{10}, corresponding to 0 to 100\%)}}
##' \item{SOIL_CONTRIB}{contribution to the soil value of the pixel}
##' \item{SOIL_LOW}{lower value of soil supported by the PFG, \cr
##' defining the limit between \code{Low} and \code{Medium} soil resources
##' for this PFG}
##' \item{SOIL_HIGH}{upper value of soil supported by the PFG, \cr
##' defining the limit between \code{Medium} and \code{High} soil resources
##' for this PFG}
##' \item{SOIL_TOL}{soil tolerance table (in a single row). \cr
##' This is a vector of 9 numbers corresponding to the ability of the PFG to
##' survive or not :
##' \itemize{
##' \item at different life stages \emph{(Germinant (\code{Ge}), Immature
##' (\code{Im}), Mature (\code{Ma}))}
##' \item under different soil conditions \emph{(Low (\code{L}), Medium
##' (\code{M}) or High (\code{H}))}.
##' }
##' These parameters should be given in this order : \code{GeL, GeM, GeH, ImL,
##' ImM, ImH, MaL, MaM, MaH}
##' \cr \emph{(from \code{0} to \code{10}, corresponding to 0 to 100\%)}.
##' \cr \cr}
##' }
##'
##' A \code{SOIL_COMPLETE_TABLE.csv} file summarizing information for all
##' groups into the \code{name.simulation/DATA/PFGS/} directory.
##'
##' If the \code{opt.folder.name} has been used, the files will be into the
##' folder \code{name.simulation/DATA/PFGS/SOIL/opt.folder.name/}.
##'
##'
##' @keywords FATE, simulation, soil tolerance, nitrogen
##'
##' @seealso \code{\link{PRE_FATE.skeletonDirectory}},
##' \code{\link{PRE_FATE.params_PFGsuccession}}
##'
##' @examples
##'
##' ## Create a skeleton folder with the default name ('FATE_simulation')
##' PRE_FATE.skeletonDirectory()
##'
##' ## Create PFG soil parameter files
##' PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
##' , mat.PFG.soil = data.frame(PFG = c("PFG1", "PFG2", "PFG3")
##' , type = c("H", "H", "C")
##' , soil_contrib = c(2.5, 3, 4.8)
##' , soil_tol_min = c(2, 3, 3)
##' , soil_tol_max = c(3, 3, 6)))
##'
##' @export
##'
##' @importFrom utils write.table
##'
## END OF HEADER ###############################################################
PRE_FATE.params_PFGsoil = function(
name.simulation
, mat.PFG.soil
, mat.PFG.tol = NULL
, opt.folder.name = NULL
){
#############################################################################
.testParam_existFolder(name.simulation, "DATA/PFGS/SOIL/")
## CHECK parameter mat.PFG.soil
if (.testParam_notDf(mat.PFG.soil))
{
.stopMessage_beDataframe("mat.PFG.soil")
} else
{
if (nrow(mat.PFG.soil) == 0 || !(ncol(mat.PFG.soil) %in% c(3, 5, 7)))
{
.stopMessage_numRowCol("mat.PFG.soil", c("PFG", "type", "(active_germ_low)", "(active_germ_medium)"
, "(active_germ_high)", "(strategy_ag)", "soil_contrib"
, "soil_tol_min", "soil_tol_max", "(strategy_contrib)"))
} else
{
notCorrect = switch(as.character(ncol(mat.PFG.soil))
, "3" = (.testParam_notColnames(mat.PFG.soil, c("PFG", "type", "strategy_contrib")) &&
.testParam_notColnames(mat.PFG.soil, c("PFG", "strategy_ag", "strategy_contrib")))
, "5" = (.testParam_notColnames(mat.PFG.soil, c("PFG", "type", "soil_contrib"
, "soil_tol_min", "soil_tol_max")) &&
.testParam_notColnames(mat.PFG.soil, c("PFG", "active_germ_low"
, "active_germ_medium"
, "active_germ_high"
, "strategy_contrib")) &&
.testParam_notColnames(mat.PFG.soil, c("PFG", "strategy_ag", "soil_contrib"
, "soil_tol_min", "soil_tol_max")))
, "7" = .testParam_notColnames(mat.PFG.soil, c("PFG", "active_germ_low"
, "active_germ_medium"
, "active_germ_high", "soil_contrib"
, "soil_tol_min", "soil_tol_max"))
, TRUE)
if (notCorrect){
.stopMessage_columnNames("mat.PFG.soil", c("PFG", "type", "(active_germ_low)", "(active_germ_medium)"
, "(active_germ_high)", "(strategy_ag)", "soil_contrib"
, "soil_tol_min", "soil_tol_max", "(strategy_contrib)"))
}
}
mat.PFG.soil$PFG = as.character(mat.PFG.soil$PFG)
.testParam_samevalues.m("mat.PFG.soil$PFG", mat.PFG.soil$PFG)
.testParam_notChar.m("mat.PFG.soil$PFG", mat.PFG.soil$PFG)
if (sum(colnames(mat.PFG.soil) == "type") == 1)
{
mat.PFG.soil$type = as.character(mat.PFG.soil$type)
.testParam_notInValues.m("mat.PFG.soil$type", mat.PFG.soil$type, c("H", "C", "P"))
}
if (sum(colnames(mat.PFG.soil) == "active_germ_low") == 1)
{
.testParam_NAvalues.m("mat.PFG.soil$active_germ_low", mat.PFG.soil$active_germ_low)
.testParam_notInValues.m("mat.PFG.soil$active_germ_low", mat.PFG.soil$active_germ_low, 0:10)
.testParam_NAvalues.m("mat.PFG.soil$active_germ_medium", mat.PFG.soil$active_germ_medium)
.testParam_notInValues.m("mat.PFG.soil$active_germ_medium", mat.PFG.soil$active_germ_medium, 0:10)
.testParam_NAvalues.m("mat.PFG.soil$active_germ_high", mat.PFG.soil$active_germ_high)
.testParam_notInValues.m("mat.PFG.soil$active_germ_high", mat.PFG.soil$active_germ_high, 0:10)
}
if (sum(colnames(mat.PFG.soil) == "strategy_ag") == 1)
{
mat.PFG.soil$strategy_ag = as.character(mat.PFG.soil$strategy_ag)
.testParam_notInValues.m("mat.PFG.soil$strategy_ag", mat.PFG.soil$strategy_ag
, c("poor_lover", "indifferent", "rich_lover"))
}
if (sum(colnames(mat.PFG.soil) == "soil_contrib") == 1)
{
.testParam_notNum.m("mat.PFG.soil$soil_contrib", mat.PFG.soil$soil_contrib)
.testParam_NAvalues.m("mat.PFG.soil$soil_contrib", mat.PFG.soil$soil_contrib)
.testParam_notNum.m("mat.PFG.soil$soil_tol_min", mat.PFG.soil$soil_tol_min)
.testParam_NAvalues.m("mat.PFG.soil$soil_tol_min", mat.PFG.soil$soil_tol_min)
.testParam_notNum.m("mat.PFG.soil$soil_tol_max", mat.PFG.soil$soil_tol_max)
.testParam_NAvalues.m("mat.PFG.soil$soil_tol_max", mat.PFG.soil$soil_tol_max)
if (sum(mat.PFG.soil$soil_tol_min > mat.PFG.soil$soil_contrib) > 0){
stop(paste0("Wrong type of data!\n `mat.PFG.soil$soil_tol_min` must contain "
, "values equal or inferior to `mat.PFG.soil$soil_contrib`"))
}
if (sum(mat.PFG.soil$soil_tol_max < mat.PFG.soil$soil_contrib) > 0){
stop(paste0("Wrong type of data!\n `mat.PFG.soil$soil_tol_max` must contain "
, "values equal or superior to `mat.PFG.soil$soil_contrib`"))
}
}
if (sum(colnames(mat.PFG.soil) == "strategy_contrib") == 1)
{
mat.PFG.soil$strategy_contrib = as.character(mat.PFG.soil$strategy_contrib)
.testParam_notInValues.m("mat.PFG.soil$strategy_contrib", mat.PFG.soil$strategy_contrib
, c("full_light", "pioneer", "ubiquist", "semi_shade", "undergrowth"))
}
}
## CHECK parameter mat.PFG.tol
if (!is.null(mat.PFG.tol))
{
if (.testParam_notDf(mat.PFG.tol))
{
.stopMessage_beDataframe("mat.PFG.tol")
} else
{
if (nrow(mat.PFG.tol) == 0 || !(ncol(mat.PFG.tol) %in% c(2, 4)))
{
.stopMessage_numRowCol("mat.PFG.tol", c("PFG", "lifeStage", "resources", "tolerance", "(strategy_tol)"))
} else
{
notCorrect = switch(as.character(ncol(mat.PFG.tol))
, "2" = .testParam_notColnames(mat.PFG.tol, c("PFG", "strategy_tol"))
, "4" = .testParam_notColnames(mat.PFG.tol, c("PFG", "lifeStage", "resources", "tolerance"))
, TRUE)
if (notCorrect){
.stopMessage_columnNames("mat.PFG.tol", c("PFG", "lifeStage", "resources", "tolerance", "(strategy_tol)"))
}
}
mat.PFG.tol$PFG = as.character(mat.PFG.tol$PFG)
.testParam_notChar.m("mat.PFG.tol$PFG", mat.PFG.tol$PFG)
if (sum(colnames(mat.PFG.tol) == "lifeStage") == 1)
{
.testParam_notInValues.m("mat.PFG.tol$lifeStage", mat.PFG.tol$lifeStage, c("Germinant", "Immature", "Mature"))
.testParam_notInValues.m("mat.PFG.tol$resources", mat.PFG.tol$resources, c("Low", "Medium", "High"))
.testParam_NAvalues.m("mat.PFG.tol$tolerance", mat.PFG.tol$tolerance)
.testParam_notInValues.m("mat.PFG.tol$tolerance", mat.PFG.tol$tolerance, 0:10)
}
if (sum(colnames(mat.PFG.tol) == "strategy_tol") == 1)
{
mat.PFG.tol$strategy_tol = as.character(mat.PFG.tol$strategy_tol)
.testParam_notInValues.m("mat.PFG.tol$strategy_tol", mat.PFG.tol$strategy_tol
, c("full_light", "pioneer", "ubiquist", "semi_shade", "undergrowth"))
}
}
}
## CHECK parameter opt.folder.name
opt.folder.name = .getParam_opt.folder.name(opt.folder.name
, paste0(name.simulation, "/DATA/PFGS/SOIL/"))
#############################################################################
no.PFG = nrow(mat.PFG.soil)
## GET PFG NAME
NAME = as.character(mat.PFG.soil$PFG)
#############################################################################
## GET GERMINATION RATE depending on soil conditions
## = these rates should express a deviation from the
## germination rate in optimal conditions (=100%)
## = for each soil condition (Low, Medium, High)
## 11 levels : 0 = 0 %
## 1 = 10 %
## 2 = 20 %
## 3 = 30 %
## 4 = 40 %
## 5 = 50 %
## 6 = 60 %
## 7 = 70 %
## 8 = 80 %
## 9 = 90 %
## 10 = 100 %
ACTIVE_GERM = matrix(10, nrow = 3, ncol = no.PFG)
if (sum(colnames(mat.PFG.soil) == "type") == 1)
{
## woody species have little variation in germination rate depending on soil conditions
ACTIVE_GERM[c(1,3), which(mat.PFG.soil$type %in% c("C", "P"))] = 9
## herbaceous germinate less in richer soil
ACTIVE_GERM[1, which(mat.PFG.soil$type == "H")] = 8 ## low soil conditions
ACTIVE_GERM[3, which(mat.PFG.soil$type == "H")] = 5 ## high soil conditions
} else if (sum(colnames(mat.PFG.soil) == "active_germ_low") == 1 ||
sum(colnames(mat.PFG.soil) == "active_germ_medium") == 1 ||
sum(colnames(mat.PFG.soil) == "active_germ_high") == 1)
{
if (sum(colnames(mat.PFG.soil) == "active_germ_low") == 1)
{
ACTIVE_GERM[1, ] = mat.PFG.soil$active_germ_low
}
if (sum(colnames(mat.PFG.soil) == "active_germ_medium") == 1)
{
ACTIVE_GERM[2, ] = mat.PFG.soil$active_germ_medium
}
if (sum(colnames(mat.PFG.soil) == "active_germ_high") == 1)
{
ACTIVE_GERM[3, ] = mat.PFG.soil$active_germ_high
}
} else if (sum(colnames(mat.PFG.soil) == "strategy_ag") == 1)
{
for (i in 1:no.PFG){
ACTIVE_GERM[, i] = switch(mat.PFG.soil$strategy_ag[i]
, poor_lover = c(8, 9, 5)
, indifferent = c(9, 9, 9)
, rich_lover = c(5, 9, 8)
)
}
} else
{
warning(paste0("Missing data! The `ACTIVE_GERM` parameter has not been set. "
, "Please check."))
}
#############################################################################
if (sum(colnames(mat.PFG.soil) == "soil_contrib") == 1)
{
## GET SOIL CONTRIBUTION
SOIL_CONTRIB = as.numeric(mat.PFG.soil$soil_contrib)
## GET SOIL TOLERANCE LIMITS
SOIL_LOW = as.numeric(mat.PFG.soil$soil_tol_min)
SOIL_HIGH = as.numeric(mat.PFG.soil$soil_tol_max)
} else if (sum(colnames(mat.PFG.soil) == "strategy_contrib") == 1)
{
SOIL_CONTRIB = SOIL_LOW = SOIL_HIGH = vector(length = no.PFG)
for (i in 1:no.PFG){
tmp = switch(mat.PFG.soil$strategy_contrib[i]
# , full_light = c(1,1,1,0,0,1,0,0,1)
# , pioneer = c(1,1,1,0,1,1,0,1,1)
, ubiquist = c(2.5, 1, 4)
# , semi_shade = c(1,1,0,1,1,0,1,1,1)
# , undergrowth = c(1,1,0,1,1,0,1,1,0)
)
SOIL_CONTRIB[i] = tmp[1]
SOIL_LOW[i] = tmp[2]
SOIL_HIGH[i] = tmp[3]
}
} else
{
warning(paste0("Missing data! The `SOIL_CONTRIB`, `SOIL_LOW` and "
, "`SOIL_HIGH` parameters have not been set. "
, "Please check."))
}
no.class = seq(min(round(SOIL_CONTRIB))
, max(round(SOIL_CONTRIB))
, 1)
cat("\n ---------- INFORMATION : SOIL \n")
cat("\n Classes : ", no.class)
cat("\n Number of classes : ", max(no.class))
cat("\n Number of PFG within each class (contribution) : "
, table(cut(SOIL_CONTRIB, breaks = 1:max(no.class))))
cat("\n")
#############################################################################
## GET SOIL TOLERANCE
## = for each life stage (Germinant, Immature, Mature)
## = for each soil condition (Low, Medium, High)
## 11 levels : 0 = 0 %
## 1 = 10 %
## 2 = 20 %
## 3 = 30 %
## 4 = 40 %
## 5 = 50 %
## 6 = 60 %
## 7 = 70 %
## 8 = 80 %
## 9 = 90 %
## 10 = 100 %
SOIL_TOL = matrix(10, nrow = 3 * 3, ncol = no.PFG)
if (is.null(mat.PFG.tol))
{
SOIL_TOL[1, ] = 1 ## Germinant - Low soil conditions
SOIL_TOL[3, ] = 3 ## Germinant - High soil conditions
SOIL_TOL[4, ] = 4 ## Immature - Low soil conditions
SOIL_TOL[6, ] = 6 ## Immature - High soil conditions
SOIL_TOL[7, ] = 7 ## Mature - Low soil conditions
SOIL_TOL[9, ] = 9 ## Mature - High soil conditions
} else
{
if (sum(colnames(mat.PFG.tol) == "lifeStage") == 1)
{
for (ii in 1:nrow(mat.PFG.tol))
{
LS_res = paste0(mat.PFG.tol$lifeStage[ii], "_", mat.PFG.tol$resources[ii])
ind_ii = switch(LS_res
, Germinant_Low = 1
, Germinant_Medium = 2
, Germinant_High = 3
, Immature_Low = 4
, Immature_Medium = 5
, Immature_High = 6
, Mature_Low = 7
, Mature_Medium = 8
, Mature_High = 9
)
SOIL_TOL[ind_ii, which(NAME == mat.PFG.tol$PFG[ii])] = mat.PFG.tol$tolerance[ii]
}
} else if (sum(colnames(mat.PFG.tol) == "strategy_tol") == 1)
{
for (i in 1:no.PFG){
SOIL_TOL[, i] = switch(mat.PFG.tol$strategy_tol[i]
# , full_light = c(1,1,1,0,0,1,0,0,1)
# , pioneer = c(1,1,1,0,1,1,0,1,1)
, ubiquist = c(9,10,9,9,10,9,9,10,9)
# , semi_shade = c(1,1,0,1,1,0,1,1,1)
# , undergrowth = c(1,1,0,1,1,0,1,1,0)
)
}
} else
{
warning("Missing data! The `SOIL_TOL` parameter has not been set. Please check.")
}
}
#############################################################################
names.params.list = mat.PFG.soil$PFG
names.params.list.sub = c("NAME", "SOIL_CONTRIB"
, "SOIL_LOW", "SOIL_HIGH"
, "ACTIVE_GERM", "SOIL_TOL")
params.list = lapply(names.params.list.sub, function(x) { return(get(x)) })
params.csv = t(do.call(rbind, params.list))
colnames(params.csv) = c("NAME"
, "SOIL_CONTRIB"
, "SOIL_LOW"
, "SOIL_HIGH"
, paste0("ACTIVE_GERM_for_", c("L", "M", "H"))
, paste0("SOIL_TOL_for_",
c("GeL", "GeM", "GeH"
, "ImL", "ImM", "ImH"
, "MaL", "MaM", "MaH"))
)
write.table(params.csv
, file = paste0(name.simulation
, "/DATA/PFGS/"
, ifelse(opt.folder.name == ""
, ""
, sub("/$", "_", opt.folder.name))
, "SOIL_COMPLETE_TABLE.csv")
, row.names = FALSE
, col.names = TRUE)
#############################################################################
params.list = lapply(1:no.PFG, function(x) {
lapply(names.params.list.sub, function(y) {
val = get(y)
if (is.null(nrow(val))){
val = val[x]
} else {
val = val[, x]
}
return(val)
})
})
for (i in 1:length(params.list)) {
params = params.list[[i]]
names(params) = names.params.list.sub
.createParams(params.file = paste0(name.simulation
, "/DATA/PFGS/SOIL/"
, opt.folder.name
, "SOIL_"
, names.params.list[i],
".txt")
, params.list = params)
}
cat("\n> Done!\n")
cat("\n Complete table of information about PFG soil parameters can be find in "
, paste0(name.simulation, "/DATA/PFGS/"), "folder.")
cat("\n")
}
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