diff --git a/ReptileAOH.R b/ReptileAOH.R new file mode 100644 index 0000000..d69c555 --- /dev/null +++ b/ReptileAOH.R @@ -0,0 +1,70 @@ +# install packages +# remotes::install_github("prioritizr/aoh@osgeo4w") + +# load packages +library(aoh) +library(terra) +library(rappdirs) +library(ggplot2) + +# IUCN Red List key +# usethis::edit_r_environ() +# IUCN_REDLIST_KEY="074f76c8df75a1575489ddab78d7df8a24e7e47476d53beb783829ac0da2362b" +# is_iucn_rl_api_available() +# TRUE + +# set environmental variables +Sys.setenv("GDAL_PYTHON" = "python") +Sys.setenv("GDAL_CALC" = "C:\\OSGeo4W\\apps\\Python39\\Scripts\\gdal_calc.py") +Sys.setenv("GDAL_ESCAPE" = "false") + +# import species range data +# download data from https://www.iucnredlist.org/resources/spatial-data-download +# dir.create("E:/Priority program/Re-PriorityProgram20220903/ReAOH") +path <- "G:/Priority program/Re-PriorityProgram20220903/ReAOH/REPTILES.zip" +reptl_range_data <- read_spp_range_data(path) +# print(reptl_range_data) +reptl_range_data2.1 <- reptl_range_data[1001:1500,] +# create cache directory +# dir.create("G:/Priority program/Re-PriorityProgram20220903/ReAOH/cache") +cache_dir<-"G:/Priority program/Re-PriorityProgram20220903/ReAOH/cache" + +# prepare information +reptl_info_data2.1 <- create_spp_info_data(reptl_range_data2.1, cache_dir = cache_dir) + +print(reptl_info_data2.1) + +## Generate area of habitat +# specify a folder to save area of habitat +# dir.create("G:/Priority program/Re-PriorityProgram20220903/ReAOH/REPTILES") +output_dir <- "G:/Priority program/Re-PriorityProgram20220903/ReAOH/REPTILES" +n_threads <- parallel::detectCores() - 1 +reptl_aoh_data2.1 <- create_spp_aoh_data(reptl_info_data2.1, output_dir = output_dir, cache_dir = cache_dir, n_threads = n_threads) + +saveRDS(reptl_aoh_data2.1,"G:/Priority program/Re-PriorityProgram20220903/ReAOH/reptl_aoh_data2.1.rds") +library(dplyr) +reptl_spp_list2.1 <- reptl_aoh_data2.1 %>% + mutate(filename=paste0(id_no,"_",seasonal)) %>% + select(filename,id_no,seasonal,binomial,category,path) +reptl_spp_list2.1 <- as.data.frame(reptl_spp_list2.1) +reptl_spp_list2.1<-reptl_spp_list2.1[,-ncol(reptl_spp_list2.1)] +write.csv(reptl_spp_list2.1,"G:/Priority program/Re-PriorityProgram20220903/ReAOH/reptl_spp_list2.1.csv",row.names=F) + + +# Group2.2.1 +reptl_range_data2.2.1 <- reptl_range_data[1501:1600,] +reptl_info_data2.2.1 <- create_spp_info_data(reptl_range_data2.2.1, cache_dir = cache_dir) +reptl_aoh_data2.2.1 <- create_spp_aoh_data(reptl_info_data2.2.1, output_dir = output_dir, cache_dir = cache_dir, n_threads = n_threads) + +reptl_spp_list2.2.1 <- reptl_aoh_data2.2.1 %>% + mutate(filename=paste0(id_no,"_",seasonal)) %>% + select(filename,id_no,seasonal,binomial,category,path) +reptl_spp_list2.2.1 <- as.data.frame(reptl_spp_list2.2.1) +reptl_spp_list2.2.1<-reptl_spp_list2.2.1[,-ncol(reptl_spp_list2.2.1)] +write.csv(reptl_spp_list2.2.1,"G:/Priority program/Re-PriorityProgram20220903/ReAOH/reptl_spp_list2.2.1.csv",row.names=F) +# Group 2.2.2 and so on +source("G:/Priority program/Re-PriorityProgram20220903/ReAOH/FUNCTION-group_generate_aoh.R") +group_generate_aoh("REPTILES",1601,1700,"2.2.2") +group_generate_aoh("REPTILES",1701,1800,"2.2.3") +group_generate_aoh("REPTILES",1801,1900,"2.2.4") +group_generate_aoh("REPTILES",1901,2000,"2.2.5")