srs_exsitu: Sample representativeness score estimation (Ex-situ...

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

Description

Performs an estimation of sample representativeness score for ex-situ gap analysis (SRSex) using Ramirez-Villegas et al., (2010) methodology This function uses counts from herbarium an germplasm accessions and calculate the SRS ex-situ score as:

SRSex = Number of germplasm accessions / Number of herbarium accessions

Usage

srs_exsitu(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 eight columns:

ID	Species name
NTOTAL	Number of records available for a given species
NTOTAL_COORDS	Number of records with geographical coordinates available for a given species
NG	Number of germplasm accessions available for a given species
NG_COORDS	Number of germplasm accessions with geographical coordinates Savailable for a given species
NH	Number of herbarium accessions available for a given species
NH_COORDS	Number of herbarium accessions with geographical coordinates Savailable for a given species
SRS	SRSex score calculated from a CSV file summarizing the number of records for a given species

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

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

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