create_sp_dirs: Creating folder and subfolder structure of gap analysis...

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

Description

Creates the output folders structure for each species to host results obtained by the gap analysis pipeline This function is used internally in the create_folder_structure function

Usage

create_sp_dirs(species, gap_dir, run_version)

Arguments

species	A name species compiled using '_' to call occurrences files from Workspace/parameter/occurrences folder
run_version	The version of the analysis used (e.g 'v1')
Workspace	A forder where the pipeline will be executed

Value

It returns a folder structure with the following subfolder schema:

	species name	species name as species parameter
	└───v1	#Run version
	│ ├───gap_analysis	# Gap analysis results
	│ ├───combined	#Folder where results of fcs_combine.R are saved
	│ ├───exsitu	#Folder where Ex-situ indicators results will be saved
	│ └───insitu	#Folder where In-situ indicators results will be saved
	└───redList	#Folder where results of eooAoo function will be saved

References

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

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

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