#' @title Combining Ex-situ and In-situ gap analysis results in one comprehensive score
#' @name fcs_combine
#' @description Concatenates the SRSin, GRSin, ERSin, SRSex, GRSex, ERSex and Final conservation scores
#' in one unique CSV file with a combined conservation score using the minimun, average and maximum values between FCSin and FCSex scores
#' and provides final conservation categories based on the scores above mentioned.
#'
#' @param species A name species compiled using '_' to call occurrences files from Workspace/parameter/occurrences folder
#' @param Workspace A forder where the pipeline will be executed
#' @param run_version The version of the analysis used (e.g 'v1')
#'
#' @return It returns a data frame file saved at gap_analysis folder with nive fields:
#'
#' \tabular{lcc}{
#' ID \tab Species name \cr
#' FCSex \tab Ex-situ final conservation score \cr
#' FCSin \tab In-situ final conservation score \cr
#' FCSc_min \tab Final conservation score mininum value between FCSin and FCSex \cr
#' FCSc_max \tab Final conservation score maximum value between FCSin and FCSex \cr
#' FCSc_mean \tab Final conservation score average value between FCSin and FCSex \cr
#' FCSc_min_class \tab Final conservation category using FCSc_min value \cr
#' FCSc_max_class \tab Final conservation category using FCSc_max value \cr
#' FCSc_mean_class \tab Final conservation category using FCSc_mean value \cr
#' }
#'
#' @examples fcs_combine('Cucurbita_digitata',Workspace,'v1')
#'
#' Workspace <- 'E:/CIAT/workspace/Workspace_test/workspace'
#' run_version <- 'v1'
#' species_list <- c('Cucurbita_cordata',
#' 'Cucurbita_digitata',
#' 'Cucurbita_foetidissima',
#' 'Cucurbita_palmata')
#'
#' run_version <-'v1'
#
#' lapply(1:length(species_list),function(i){
#' species <- species_list[[i]]
#' x <- fcs_combine(species,Workspace,run_version)
#' print(paste0(species,' DONE!'))
#' })
#'
#'@references
#'
#' Khoury, C. K., Amariles, D., Soto, J. S., Diaz, M. V., Sotelo, S., Sosa, C. C., … Jarvis, A. (2019).
#' Comprehensiveness of conservation of useful wild plants: An operational indicator for biodiversity
#' and sustainable development targets. Ecological Indicators. https://doi.org/10.1016/j.ecolind.2018.11.016
#'
#' @export
fcs_combine <- function(fcsEx, fcsIn) {
#importFrom("methods", "as")
#importFrom("stats", "complete.cases", "filter", "median")
#importFrom("utils", "data", "memory.limit", "read.csv", "write.csv")
#join datasets and select necessary Columns
df <- dplyr::left_join(x = fcsEx, y = fcsIn, by = "species") %>%
dplyr::select("species", "FCSex", "FCSin")
for(i in 1:nrow(df)){
#compute FCSc_min and FCSc_max
df$FCSc_min[i] <- min(c(df$FCSex[i],df$FCSin[i]),na.rm=T)
df$FCSc_max[i] <- max(c(df$FCSex[i],df$FCSin[i]),na.rm=T)
df$FCSc_mean[i] <- mean(c(df$FCSex[i],df$FCSin[i]),na.rm=T)
#assign classes (min)
if (df$FCSc_min[i] < 25) {
df$FCSc_min_class[i] <- "HP"
} else if (df$FCSc_min[i] >= 25 & df$FCSc_min[i] < 50) {
df$FCSc_min_class[i] <- "MP"
} else if (df$FCSc_min[i] >= 50 & df$FCSc_min[i] < 75) {
df$FCSc_min_class[i] <- "LP"
} else {
df$FCSc_min_class[i] <- "SC"
}
#assign classes (max)
if (df$FCSc_max[i] < 25) {
df$FCSc_max_class[i] <- "HP"
} else if (df$FCSc_max[i] >= 25 & df$FCSc_max[i] < 50) {
df$FCSc_max_class[i] <- "MP"
} else if (df$FCSc_max[i] >= 50 & df$FCSc_max[i] < 75) {
df$FCSc_max_class[i] <- "LP"
} else {
df$FCSc_max_class[i] <- "SC"
}
#assign classes (mean)
if (df$FCSc_mean[i] < 25) {
df$FCSc_mean_class[i] <- "HP"
} else if (df$FCSc_mean[i] >= 25 & df$FCSc_mean[i] < 50) {
df$FCSc_mean_class[i] <- "MP"
} else if (df$FCSc_mean[i] >= 50 & df$FCSc_mean[i] < 75) {
df$FCSc_mean_class[i] <- "LP"
} else {
df$FCSc_mean_class[i] <- "SC"
}
}
return(df)
}
# Workspace = "E:/CIAT/workspace/Workspace_test/workspace"
# run_version="v1"
# species_list <- c(
# "Cucurbita_cordata",
# "Cucurbita_digitata",
# "Cucurbita_foetidissima",
# "Cucurbita_palmata"
# )
# run_version <-"v1"
#
# lapply(1:length(species_list),function(i){
# species <- species_list[[i]]
# x <- fcs_combine(species,Workspace,run_version)
# cat(paste0(species," DONE!"),"\n")
# })
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