R/exsituGapAnalysis.R

Defines functions exsituGapAnalysis

#@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.

exsituGapAnalysis <- function(countsData, species_list, occurrenceData, raster_list, bufferDistance){
  # call SRSex
  srsEx <- gapAnalysisR::srs_exsitu(countsData = countsData,
      species_list = speciesList)
  # call GRSex
  grsEx <- gapAnalysisR::grs_exsitu(occurrenceData = occurrenceData,
    species_list = speciesList,
    raster_list = raster_list,
    bufferDistance = bufferDistance)
  # call ERSex
  ersEx <- gapAnalysisR::ers_exsitu(species_list = species_list,
    occurrenceData = occurrenceData,
    raster_list = raster_list,
    bufferDistance = bufferDistance)

  # call FCSex
  fcsEx <- fcs_exsitu(srsEx,grsEx,ersEx)

  # return dataframe from FCSex
  return(fcsEx)
}
    #importFrom("methods", "as")
  #importFrom("stats", "complete.cases", "filter", "median")
  #importFrom("utils", "data", "memory.limit", "read.csv", "write.csv")
dcarver1/gapAnalysisR documentation built on Feb. 29, 2020, 12:13 p.m.