srs_insitu: Sample representativeness score estimation (In-situ...

Description Usage Arguments Value References Examples

View source: R/srsIn.R

Description

Performs an estimation of sample representativeness score for in-situ gap analysis (SRSin) using Khoury et al., (2019) methodology This function uses counts from herbarium an germplasm accessions and calculate the SRS in-situ score as:

SRSin = Number of germplasm accessions in protected areas / Number of herbarium accessions in protected areas

Usage

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srs_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 eight fields:

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

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

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

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