Integrate_gap_analysis_function: Run a combined gap analysis combining all the functions of...

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

Description

Allows calculate all indicators provided by GapAnalysisR R package. Please use the Pre_analysis_function function before run this pipeline

Usage

Integrate_gap_analysis_function(dir, run_version, Workspace, species,
  buff_dist, species_csv, pre_analysis, insitu, exsitu, eooAoo)

Arguments

dir	A forder to run the gap analysis including inputs and outputs
run_version	The version of the analysis used (e.g 'v1')
Workspace	A forder where the pipeline will be executed
species	Species name provided by user or the get_sp_names function
buff_dist	Distance around germplasm accessions geographical coordinates in km^2
species_csv	CSV file name located at /Workspace/parameters/input to be splitted
pre_analysis	(logical) This option allows to run the set of pre-analysis functions: create_buffers
insitu	(logical) This option allows to calculate In-situ indicators: srs_insitu grs_insitu ers_insitu fcs_insitu
exsitu	(logical) This option allows to calculate Ex-situ indicators: srs_exsitu grs_exsitu ers_exsitu fcs_exsitu gap_map_exsitu
eooAoo	(logical) This option allows to calculate EOO and AOO to get IUCN conservation status

Value

This function run the complete GapAnalysisR pipeline in one unique function

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

Integrate_gap_analysis_function(dir,run_version,Workspace,buff_dist,pre_analysis,insitu,exsitu,eooAoo)

 dir  <-  'E:/CIAT/workspace/Workspace_test'
 run_version  <- 'v1'
 species_csv <- 'Cucurbita_CWR_2019_09_30.csv'
 Workspace  <-  'E:/CIAT/workspace/Workspace_test/workspace'
 buff_dist <- 50000 #50km radius
 pre_analysis <- T
 insitu <- T
 exsitu <- T
 eooAoo <- T

 Integrate_gap_analysis_function(dir,run_version,Workspace,species,buff_dist,species_csv,pre_analysis,insitu,exsitu,eooAoo)
 #INCLUDE INPUT FILES BEFORE RUN THE NEXT FUNCTION

 species_list <- get_sp_names(Workspace,species_csv)

 lapply(1:length(species_list),function(i){
  species <- species_list[[i]]
  x <- Integrate_gap_analysis_function(dir,run_version,Workspace,species,buff_dist,species_csv,pre_analysis,insitu,exsitu,eooAoo)
  cat(paste0(species,"| status:",x),"\n")
 })

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