Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ReptileAOH.R file in workstation204 #1

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

ReptileAOH.R file in workstation204 #1

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
70 changes: 70 additions & 0 deletions ReptileAOH.R
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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")