class(v)
nrow(v)
vor = st_set_geometry(sf0, v)
head(vor)
st_write(vor,"c:/tmp/vor.gpkg")
st_write(vor,"c:/tmp/vor2.gpkg")
pov=fasterize(vor,mask,field="pover")
plot(pov)
pov=pov*mask
plot(pov)
hist(pov)
(q95=quantile(pov[],probs=0.95,na.rm=T))
(q90=quantile(pov[],probs=0.90,na.rm=T))
(q95=quantile(pov[],probs=0.95,na.rm=T))
(q99=quantile(pov[],probs=0.99,na.rm=T))
pov_st=(pov/q99*100)
pov_st=ifel(pov>100,100,pov_st)
pov_st=100-pov_st
pov_st=rast(pov/q99*100)
pov_st=ifel(pov>100,100,pov_st)
pov_st=100-pov_st
plot(pov_st)
pov_st$pov_st*mask
plot(pov_st)
pov_st=rast(pov/q99*100)
pov_st=ifel(pov>100,100,pov_st)
hist(pov_st)
pov_st=ifel(pov_st>100,100,pov_st)
hist(pov_st)
pov_st=100-pov_st
pov_st$pov_st*mask
plot(pov_st)
hist(pov_st)
plot(pov_st)
pov_st$pov_st*mask
plot(pov_st)
plot(mask)
pov_st=rast(pov/q99*100)
pov_st=ifel(pov_st>100,100,pov_st)
pov_st=100-pov_st
pov_st=pov_st*mask
plot(pov_st)
pov_st=pov_st*mask
pov_st=rast(pov/q99*100)
pov_st=ifel(pov_st>100,100,pov_st)
pov_st=100-pov_st
pov_st
mask
pov_st=pov_st*rast(mask)
plot(pov_st)
hist(pov_st)
f_out=paste0(path_out,"/poverty.tif")
writeRaster(pov_st,f_out)
writeRaster(pov_st,f_out,overwrite=T)
f1=paste0(path_out,"/conflict.tif")
confl=rast(f1)
f1=paste0(path_out,"/elevation.tif")
elev=rast(f1)
elev=resample(elev,mask)
f1=paste0(path_out,"/pop_density.tif")
pop=rast(f1)
f1=paste0(path_out,"/d2road.tif")
road=rast(f1)
f1=paste0(path_out,"/poverty.tif")
poverty=rast(f1)
res0
f_mask=paste0(path_in,"/mask_", res0,"m.tif")
mask=rast(f_mask)
stack=c(confl,elev,pop,road,poverty)
risk=mean(stack)
risk=risk*mask
plot(risk)
hist(risk)
f_mask=paste0(path_in,"/mask_", res0,"m.tif")
mask=rast(f_mask)
stack=c(confl,elev,pop,road,poverty)
bbox(confl)
st_bbox(confl)
st_bbox(elev)
elev=rast(f1)
elev=resample(elev,mask)
mask
elev
f_out=paste0(path_out,"/elevation.tif")
elev=rast(f_out)
elev
elev=terra::resample(elev,mask)
mask
elev=terra::resample(elev,rast(mask))
writeRaster(elev,f_out,overwrite=T)
f1=paste0(path_out,"/conflict.tif")
confl=rast(f1)
f1=paste0(path_out,"/elevation.tif")
elev=rast(f1)
f1=paste0(path_out,"/pop_density.tif")
pop=rast(f1)
f1=paste0(path_out,"/d2road.tif")
road=rast(f1)
f1=paste0(path_out,"/poverty.tif")
poverty=rast(f1)
res0
st_bbox(confl)
st_bbox(elev)
st_bbox(pop)
st_bbox(road)
st_bbox(poverty)
f_mask=paste0(path_in,"/mask_", res0,"m.tif")
mask=rast(f_mask)
stack=c(confl,elev,pop,road,poverty)
risk=mean(stack)
risk=risk*mask
plot(risk)
f_out=paste0(path_out,"/risk_noweight.tif")
st_write(risk,f_out)
writeRaster(risk,f_out)
df_xy=as.points(mask)
df_xy=as.points(rast(mask))
nrow(df_xy)
path1="D:/waleol2022"
path0="C:/PL/03_PUBLI/2022/linchant_simul"
f2=passte0(path0,"/result_antelope_roset.csv")
t2=read.table(f2,header=T,sep=";")
f2=paste0(path0,"/result_antelope_roset.csv")
t2=read.table(f2,header=T,sep=";")
t2
names(t2)
f1=paste0(path0,"/result_antelope_transect.csv")
t1=read.table(f1,header=T,sep=";")
names(t1)
names(t2)
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t12=rbind(t1b,t2b)
t12
t12=t12[order(t12$i_date)]
t12=t12[order(t12$i_date),]
t12
f1=paste0(path0,"/result_buffalo_transect.csv")
t1=read.table(f1,header=T,sep=";")
names(t2)f2=paste0(path0,"/result_buffalo_roset.csv")
t2=read.table(f2,header=T,sep=";")
t_ant=t12[order(t12$i_date),]
t_ant
f1=paste0(path0,"/result_buffalo_transect.csv")
t1=read.table(f1,header=T,sep=";")
names(t2)f2=paste0(path0,"/result_buffalo_roset.csv")
t2=read.table(f2,header=T,sep=";")
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t_buff=rbind(t1b,t2b)
t_buff=t12[order(t12$i_date),]
f1=paste0(path0,"/result_buffalo_transect.csv")
t1=read.table(f1,header=T,sep=";")
names(t2)f2=paste0(path0,"/result_buffalo_roset.csv")
t2=read.table(f2,header=T,sep=";")
f2=paste0(path0,"/result_buffalo_roset.csv")
t2=read.table(f2,header=T,sep=";")
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t_buff=rbind(t1b,t2b)
t_buff=t12[order(t12$i_date),]
names(t1)
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2$i_date=1
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t1$i_date=1
t2$i_date=1
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2$rate=0
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t_buff=rbind(t1b,t2b)
t_12=rbind(t1b,t2b)
t_buff=t12[order(t12$i_date),]
t_buff
f1=paste0(path0,"/result_buffalo_transect.csv")
t1=read.table(f1,header=T,sep=";")
f2=paste0(path0,"/result_buffalo_roset.csv")
t2=read.table(f2,header=T,sep=";")
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t2$rate=0
t1$i_date=1
t2$i_date=1
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t_12=rbind(t1b,t2b)
t_buff=t12[order(t12$i_date),]
t_buff
path0="C:/PL/03_PUBLI/2022/linchant_simul"
f1=paste0(path0,"/result_antelope_transect.csv")
t1=read.table(f1,header=T,sep=";")
names(t2)f2=paste0(path0,"/result_antelope_roset.csv")
t2=read.table(f2,header=T,sep=";")
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t12=rbind(t1b,t2b)
t_ant=t12[order(t12$i_date),]
t_ant
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
names(t2)
t2$i_date=1
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t12=rbind(t1b,t2b)
names(t2)
path0="C:/PL/03_PUBLI/2022/linchant_simul"
f1=paste0(path0,"/result_antelope_transect.csv")
t1=read.table(f1,header=T,sep=";")
names(t2)f2=paste0(path0,"/result_antelope_roset.csv")
t2=read.table(f2,header=T,sep=";")
names(t1)
names(t2)
t2$rate=0
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t2$rate=0
t2$i_date=1
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t12=rbind(t1b,t2b)
t_ant=t12[order(t12$i_date),]
t_ant
names(t2)f2=paste0(path0,"/result_antelope_roset.csv")
t2=read.table(f2,header=T,sep=";")
path0="C:/PL/03_PUBLI/2022/linchant_simul"
f1=paste0(path0,"/result_antelope_transect.csv")
t1=read.table(f1,header=T,sep=";")
f2=paste0(path0,"/result_antelope_roset.csv")
t2=read.table(f2,header=T,sep=";")
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t2$rate=0
t2$i_date=1
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t12=rbind(t1b,t2b)
t_ant=t12[order(t12$i_date),]
t_ant
f1=paste0(path0,"/result_buffalo_transect.csv")
t1=read.table(f1,header=T,sep=";")
f2=paste0(path0,"/result_buffalo_roset.csv")
t2=read.table(f2,header=T,sep=";")
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t2$rate=0
t1$i_date=1
t2$i_date=1
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t_12=rbind(t1b,t2b)
t_buff=t12[order(t12$i_date),]
t_buff
f1=paste0(path0,"/result_buffalo_transect.csv")
t1=read.table(f1,header=T,sep=";")
f2=paste0(path0,"/result_buffalo_roset.csv")
t2=read.table(f2,header=T,sep=";")
t1
t2
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t2$rate=0
t1$i_date=1
t2$i_date=1
t1b=dplyr::select(t1,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t1b
t_12=rbind(t1b,t2b)
t_12
t12=rbind(t1b,t2b)
t_buff=t12[order(t12$i_date),]
t_buff
t_ant
t_ant$sp="ant"
tab=rbind(t_ant,t_buff)
tab
t_buff$sp="buff"
t_ant$sp="ant"
tab=rbind(t_ant,t_buff)
tab
tab$rate=rate
rate=c(20.04,10.11,2.95,5.9,8.85,11.8)
tab$rate=rate
tab
tab=dplyr::select(sp,i_date:cv_Jolly)
tab=dplyr::select(tab,sp,i_date:cv_Jolly)
tab
rate=c(20.04,10.11,2.95,5.9,8.85,11.8)
path0="C:/PL/03_PUBLI/2022/linchant_simul"
f1=paste0(path0,"/result_antelope_transect.csv")
t1=read.table(f1,header=T,sep=";")
f2=paste0(path0,"/result_antelope_roset.csv")
t2=read.table(f2,header=T,sep=";")
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t1$rate=0
t2$rate=0
t1$rate=rate
t2$rate=rate
t1$sp="ANT"
t2$sp="ANT"
t1b=dplyr::select(t1,sp,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,sp,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t12=rbind(t1b,t2b)
t_ant=t12[order(t12$i_date),]
t_ant
f1=paste0(path0,"/result_buffalo_transect.csv")
t1=read.table(f1,header=T,sep=";")
f2=paste0(path0,"/result_buffalo_roset.csv")
t2=read.table(f2,header=T,sep=";")
t1
t2
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t2$rate=0
t1$i_date=1
t2$i_date=1
t2$rate=rate
t1$sp="BUF"
t2$sp="BUF"
t1b=dplyr::select(t1,sp,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,sp,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t12=rbind(t1b,t2b)
t_buff=t12[order(t12$i_date),]
t_buff
names(t1)
names(t2)
t1$type="TR"
t2$type="ROS"
t1$cover=t1$id_dist
t2$cover=t2$nb_flight
t2$rate=rate
t1$i_date=1
t2$i_date=1
t2$rate=rate
t1$sp="BUF"
t2$sp="BUF"
t1b=dplyr::select(t1,sp,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t2b=dplyr::select(t2,sp,i_date,type,rate,mean_d,std_d,cv_d,bias,pvalue,cv_Jolly)
t12=rbind(t1b,t2b)
t_buff=t12[order(t12$i_date),]
t_buff
t2
rate
t2$rate=rate
t12$rate=rate
t_buff=t12[order(t12$i_date),]
t_buff
t_ant
(tab=rbind(t_ant,t_buff))
tab=rbind(t_ant,t_buff)
tab$raste=rate
tab
tab=rbind(t_ant,t_buff)
tab$rate=rate
tab
write.table(tab,"table_1_2_7sept2022.csv")
write.table(tab,"table_1_2_7sept2022.csv",col.names = T,row.names = F,sep=";")
write.table(tab,"table_1_2_7sept2022.csv",col.names = T,row.names = F,sep=";")
getwd()
write.table(tab,paste0(path0,"/table_1_2_7sept2022.csv"),col.names = T,row.names = F,sep=";")
# 3.1. Install packages, load libraries and clear workspace --------
# install missing packages
pkgs = c("sf","sp","raster","rgdal","dplyr","units","purrr",
"lwgeom","gdalUtils","fasterize")
to_install = !pkgs %in% installed.packages()
if(any(to_install)) {
install.packages(pkgs[to_install])
}
# load libraries
library(sp)
library(sf)
library(raster)
library(gdalUtils)
library(dplyr)
library(units)
library(purrr)
library(lwgeom)
library(xlsx)
# Clear workspace
rm(list=ls())
# define working directory (to adapt)
setwd("C:/tmp/R_GIS_01/data")
setwd("C:/PL/01_COURS/R_01_GIS_with_R/data")
# Read a vector layer (-> sf object)
comm=st_read("communes.shp",stringsAsFactors = F)
setwd("C:/PL/01_COURS/tthr_2022/R01_2022")
path0="C:/PL/01_COURS/tthr_2022/R01_2022"
setwd(paste0(path0,"/data"))
#path0="C:/tmp/R_GIS_01/data"
#path0="C:/PL/01_COURS/R_01_GIS_with_R/data"
file_in=paste0(path0,"/data/communes.shp")
# Read a vector layer (-> sf object)
comm=st_read("communes.shp",stringsAsFactors = F)
# !!!! use "/" in place of  "\" !!!!
# define working directory (to adapt)
setwd("C:/tmp/R_GIS_01/data")
setwd("C:/PL/01_COURS/tthr_2022/R01_2022/data")
# Read a vector layer (-> sf object)
comm=st_read("communes.shp",stringsAsFactors = F)
setwd("C:/PL/01_COURS/tthr_2022/R01_2022/data")
# !!!! use "/" in place of  "\" !!!!
# define working directory (to adapt)
setwd("C:/tmp/R_GIS_01/data")
library(sp)
library(sf)
library(raster)
library(gdalUtils)
library(dplyr)
library(units)
library(purrr)
library(lwgeom)
setwd("C:/PL/01_COURS/tthr_2022/R01_2022/data")
# Read a vector layer (-> sf object)
comm=st_read("communes.shp",stringsAsFactors = F)
getwd()
setwd("C:/PL/01_COURS/tthr_2022/R01_2022/data")
# !!!! use "/" in place of  "\" !!!!
# define working directory (to adapt)
setwd("C:/tmp/R_GIS_01/data_in")
# Clear workspace
rm(list=ls())
setwd("C:/PL/01_COURS/tthr_2022/R01_2022/data_in")
# Read a vector layer (-> sf object)
comm=st_read("communes.shp",stringsAsFactors = F)
plot(comm$geometry)
f_out=paste0(path0,"/output/communes.shp")
st_write(comm,f_out,delete_layer=TRUE)
# Save sf object -> shapefile
# delete_layer=TRUE : this option overwrite existing files
f_out=paste0(path0,"/output/communes.shp")
path0="C:/PL/01_COURS/tthr_2022/R01_2022"
path_in=paste0(path0,"/data_in")
path_out=paste0(path0,"/output")
# Read a vector layer (-> sf object)
file_in=paste0(path_in,"/communes.shp")
comm=st_read(file_in,stringsAsFactors = F)
st_write(comm,f_out,delete_layer=TRUE)
f_out=paste0(path_out,"/communes.shp")
st_write(comm,f_out,delete_layer=TRUE)
# Display warnings
# it means that some numerical attributes have been rounded
warnings()
