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speciesTable.R
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speciesTable.R
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#' Customize species trait table values
#'
#' @template speciesTable
#' @param params A named list (of parameters) of named lists (by species), with species
#' traits overrides (e.g., `list(seeddistance_eff = list(Abie_sp = 25))`).
#'
#' @author Alex Chubaty and Ceres Barros
#' @export
updateSpeciesTable <- function(speciesTable, params) {
## checks:
traits <- names(params)
missingTraits <- traits[!traits %in% names(speciesTable)]
if (length(missingTraits))
stop("The traits: ", paste(missingTraits, collapse = ", "), "\ndo not exist in `speciesTable`")
for (trt in traits) {
subParams <- params[[trt]]
## checks:
spp <- names(subParams)
missingSpp <- spp[!spp %in% speciesTable$species]
if (length(missingSpp)) {
stop("The species: ", paste(missingSpp, collapse = ", "),
"\ndo not exist in `speciesTable$species`")
}
## this is sub ideal to convert classes, but the only solution I found.
## neither class(...) <- class(..) nor as(..., class(...)) were changing integer to numeric.
## only as.numeric(...) worked
if (class(unlist(subParams)) != class(speciesTable[[trt]])) {
asFUN <- get(paste0("as.", class(unlist(subParams))))
if (!is.function(asFUN))
stop("Can't find an `as.` method to convert class to '", class(unlist(subParams)), "'")
speciesTable <- speciesTable[, (trt) := lapply(.SD, asFUN), .SDcols = trt]
}
for (sp in spp) {
set(speciesTable, which(speciesTable$species == sp), trt, subParams[[sp]])
}
}
return(speciesTable)
}