ers_exsitu: Environmental representativeness score estimation (Ex-situ...

In dcarver1/gapAnalysisR: An R package to calculate conservation indicators using species distribution models

Description

Performs an estimation of enviromental representativeness score for ex-situ gap analysis (ERSex) using Ramirez-Villegas et al., (2010) methodology, this function uses a csv with coordinates, a germplasm buffer raster file and a vectorial file of eccoregions

ERSex = min(100,(Number of ecoregions where germplasm accessions are available/ Number of ecoregions where species is available)*100)

Usage

ers_exsitu(species, Workspace, run_version)

Arguments

species	A name species compiled using '_' to call the raster files (SDM and germplasm buffer) from Workspace/parameters/inputs folder and occurrences files from Workspace/parameter/occurrences folder
Workspace	A forder where the pipeline will be executed
run_version	The version of the analysis used (e.g 'v1')

Value

It returns a data frame file saved at gap_analysis folder with four columns:

#'

ID	Species name
SPP_N_ECO	Number of ecosystems where the species was located
G_N_ECO	Number of ecosystems where germplasm accessions were available
ERS	ERSex result

References

Ramírez-Villegas, J., Khoury, C., Jarvis, A., Debouck, D. G., & Guarino, L. (2010). A Gap Analysis Methodology for Collecting Crop Genepools: A Case Study with Phaseolus Beans. PLOS ONE, 5(10), e13497. Retrieved from https://doi.org/10.1371/journal.pone.0013497

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

Examples

ers_exsitu('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 <- ers_exsitu(species,Workspace,run_version)
   print(paste0(species,' DONE!'))
})

dcarver1/gapAnalysisR documentation built on Feb. 29, 2020, 12:13 p.m.