Description Usage Arguments Value References Examples
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
ERSin = min(100,(Number of ecoregions where germplasm accessions in protected areas/ Number of ecoregions where species distribution is intersected with protected areas)*100)
1 | ers_insitu(species, Workspace, run_version)
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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') |
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_N_ECO | Number of ecosystems where species distribution model is within protected areas |
SPP_WITHIN_PA_N_ECO | Number of ecosystems where germplasm accessions are within protected areas |
ERS | ERSex result |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ers_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 <- ers_insitu(species,Workspace,run_version)
print(paste0(species,' DONE!'))
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