fcs_insitu: Final in-situ conservation score estimation (In-situ...

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

Description

Concatenates the SRSin, GRSin, and ERSin values in a unique file, Then calculates a final priority scores as the average of the SRSin, GRSin, and ERSin values representing how well is conserved a species comparing its species distribution, germplasm buffers and occurrences files for protected areas

FCSin = mean(SRSin,GRSin,ERSin)

Usage

fcs_insitu(species, Workspace, run_version)

Arguments

species	A name species compiled using '_' to call 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 five fields:

ID	Species name
SRS	In-situ sample representativeness score
GRS	In-situ germplasm representativeness score
ERS	In-situ environmental representativeness score
FCS	In-situ final conservation score

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

fcs_insitu('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_insitu(species,Workspace,run_version)
   print(paste0(species,' DONE!'))
})

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