# @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
########################################## Start Functions ###############################################
# This function calculates the FCSex. It loads srs.csv, grs.csv, ers.csv and
# calculates FCS. It saves output in summary.csv
# @param (string) species: species ID
# @return (data.frame): This function returns a data frame with ID, SRS, GRS, ERS, FCS
# for a given species.
insituGapAnalysis <- function(species_list, occurrenceData, raster_list){
# call SRSin
srsIn <- gapAnalysisR::srs_insitu(species_list = species_list,
occurrenceData = occurrenceData,
raster_list = raster_list)
# call GRSin
grsIn <- gapAnalysisR::insitu_grs(species_list = species_list,
occurrenceData = occurrenceData,
raster_list = raster_list)
# call ERSin
ersIn <- gapAnalysisR::ers_insitu(species_list = species_list,
occurrenceData =occurrenceData,
raster_list = raster_list)
# call FCSex
fcsIn <- gapAnalysisR::fcs_insitu(srsIn,grsIn,ersIn)
# return dataframe from FCSex
return(fcsIn)
}
#importFrom("methods", "as")
#importFrom("stats", "complete.cases", "filter", "median")
#importFrom("utils", "data", "memory.limit", "read.csv", "write.csv")
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