create_folder_structure: Creating folder and subfolder structure for a species list...

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 when an initial species list is provided

Usage

create_folder_structure(species_list, dir, run_version, initial,
  create_sp_dirs)

Arguments

species_list	A list of species to be analyzed when a species list is provided
dir	A forder to run the gap analysis including inputs and outputs
run_version	The version of the analysis used (e.g 'v1')
initial	(logical) The function will create the initial folder structure for the analysis
create_sp_dirs	(logical) The function will create folder for each species outputs in /gap_anaylsis

Value

It returns a folder structure with the following subfolder schema:

	workspace	species name as species parameter
	└───parameters	#Folder where the inputs are hosted
	│ ├───raster	# Subfolder to add mask, protected areas and ecoregions shapefile
	│ ├───occurrences	#Folder where a CSV file is used to filter species accessions occurrences
	└───gap_analysis	#Folder where results will be saved if create_sp_dirs=T

Sources used for analysis were obtained from Khoury et al., 2019 using the following download links:

	Protected area	http://dx.doi.org/10.17632/2jxj4k32m2.1#file-fc8ffd3f-8d79-481b-9ccf-4cf19b8480ec
	World mask	http://dx.doi.org/10.17632/2jxj4k32m2.1#folder-1b61c978-5753-4ab6-bbc7-11f8e4b062cf
	Terrestrial ecoregions	http://maps.tnc.org/files/shp/terr-ecoregions-TNC.zip

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

Khoury, C. K., Amariles, D., Soto, J. S., Diaz, M. V., Sotelo, S., Sosa, C. C., … Wiersema, J. H. (2019). Data for the calculation of an indicator of the comprehensiveness of conservation of useful wild plants. Data in Brief, 22, 90–97. https://doi.org/10.1016/j.dib.2018.11.125

Examples

create_folder_structure(species_list,dir,run_version,initial=F,create_sp_dirs=T)

 dir  <-  'E:/CIAT/workspace/Workspace_test'
 run_version  <- 'v1'
 species_list <- c('Cucurbita_cordata',
  'Cucurbita_digitata',
  'Cucurbita_foetidissima',
  'Cucurbita_palmata')

 x <- create_folder_structure(species,dir,run_version,initial=F,create_sp_dirs=F)

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