grs_insitu: Germplasm representativeness score estimation (In-situ...

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

Description

Performs an estimation of germplasm representativeness score for in-situ gap analysis (GRSin) using Khoury et al., (2019) methodology This function uses a germplasm buffer raster file (e.g. CA50), a thresholded species distribution model, and a raster file of protected areas

GRSin = min(100,(Germplasm buffer area into protected area/species distribution area in protected areas)*100)

Usage

insitu_grs(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 raster file with the species distribution model restricted to the protected areas raster file provided. Also, this function returns a data frame file saved at gap_analysis folder with four columns:

ID	Species name
SPP_AREA_km2	Area occupied by the species using as input a SDM thresholded file in tiff format
SPP_WITHIN_PA_AREA_km2	Area occupied by the germplasm accessions in a species distribution model
GRS	GRSex 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

grs_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 <- grs_insitu(species,Workspace,run_version)
    print(paste0(species,' DONE!'))
 

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