se agrego paquete

Se agrego mvtnorm en el step de camptrap_format

.gitignore

@@ -5,6 +5,9 @@ runner.env
 **/.cache
 **/.config
 .server
+<<<<<<< Updated upstream
 /output/
 /scripts/00_auk_filter/input/original/
-scripts/00_auk_filter_v2/input/original/
+scripts/00_auk_filter_v2/input/original/
+=======
+>>>>>>> Stashed changes

runners/conda-dockerfile

@@ -0,0 +1,50 @@
+FROM  condaforge/mambaforge
+
+ADD ./r-environment.yml /data/r-environment.yml
+
+WORKDIR /data
+
+RUN mamba init
+
+# Since we are using the user from the client computer to run the scripts,
+# we need to create and open the permissions of a few files/directories.
+RUN chmod a+w /data
+
+COPY .condarc /.condarc
+RUN chmod 777 /.condarc
+
+# Conda cache and environments folder will be replaced by a virtual volume, but we want them to be writable by the runtime user.
+# Permissions cannot be defined at mount time, hence we create empty folder with the appropriate permissions.
+RUN mkdir /.cache && mkdir /.cache/conda && chmod a+w /.cache/conda
+RUN mkdir /.conda && chmod a+w /.conda
+RUN mkdir /r-libs-user && chmod a+w /r-libs-user
+RUN mkdir /conda-env-yml && chmod a+w /conda-env-yml
+
+# Initialize mamba when logging in with bash
+RUN echo 'eval "$(conda shell.bash hook)"; source /opt/conda/etc/profile.d/mamba.sh' > /.bashrc && chmod a+x /.bashrc
+
+# Allow to read bashrc to execute mamba init when using docker exec
+# See https://stackoverflow.com/a/74017557/3519951
+RUN sed -e '/[ -z "$PS1" ] && return/s/^/#/g' -i /root/.bashrc
+
+RUN mamba env create -f /data/r-environment.yml
+
+# Hide "error libmamba Could not open lockfile '/opt/conda/pkgs/cache/cache.lock'" when installing manually with non-root user
+# That error would not prevent the correct installation, but it looked like it to the user.
+RUN chmod -R 777 /opt/conda/pkgs/cache
+
+
+# These packages are not in conda-forge
+# ADD CRAN PACKAGES HERE
+RUN bash --login -c "mamba activate rbase; R -e 'install.packages(c(\"CoordinateCleaner\", \
+        \"geodata\", \
+        \"OpenStreetMap\"\
+    ), repos=\"https://cloud.r-project.org/\")'"
+
+
+
+# ADD GITHUB PACKAGES HERE
+RUN bash --login -c "mamba activate rbase; R -e 'devtools::install_github(\"ReseauBiodiversiteQuebec/stac-catalogue\")'"
+RUN bash --login -c "mamba activate rbase; R -e 'devtools::install_github(\"connectscape/Makurhini\")'"
+
+RUN date +"%Y-%m-%d %R" > /version.txt

runners/r-environment.yml

@@ -0,0 +1,34 @@
+name: rbase
+channels:
+  - conda-forge
+  - r
+dependencies:
+  - conda-build
+  - libgdal
+  - r-abind
+  - r-base
+  - r-curl
+  - r-devtools
+  - r-dismo
+  - r-downloader
+  - r-enmeval
+  - r-essentials
+  - r-gdalcubes
+  - r-gdalutilities
+  - r-gdalutils
+  - r-ggsci
+  - r-rjava
+  - r-jpeg
+  - r-landscapemetrics
+  - r-png
+  - r-rcurl
+  - r-rgbif
+  - r-rjson
+  - r-rredlist
+  - r-rstac
+  - r-sf
+  - r-stars
+  - r-terra
+  - r-tidyselect
+  - r-unmarked
+  - r-magrittr

scripts/CamTrap_format2/CamTrap_format2.R

@@ -2,7 +2,7 @@
 
 # Install necessary libraries - packages  
 packagesPrev<- installed.packages()[,"Package"] # Check and get a list of installed packages in this machine and R version
-packagesNeed<- c("magrittr", "data.table", "terra", "raster", "sf", "pbapply", "this.path", "rjson", "tools", "unmarked", "reshape2", "Rcpp" , "RcppEigen", "RcppParallel", "RcppNumerical", "secr", "camtrapR") # Define the list of required packages to run the script
+packagesNeed<- c("magrittr", "data.table", "terra", "raster", "sf", "pbapply", "this.path", "rjson", "tools", "unmarked", "reshape2", "Rcpp" , "RcppEigen", "RcppParallel", "RcppNumerical", "secr", "camtrapR", "mvtnorm") # Define the list of required packages to run the script
 new.packages <- packagesNeed[!(packagesNeed %in% packagesPrev)]; if(length(new.packages)) {install.packages(new.packages, binary=T, force=T, dependencies = F, repos= "https://packagemanager.posit.co/cran/__linux__/jammy/latest")} # Check and install required packages that are not previously installed
 
 # Load libraries

scripts/SHI/scpSHI_Jetz_complete.R

@@ -67,7 +67,10 @@ v_time_steps <- seq(t_0,t_n,time_step)
 
 #credentials
 token <- Sys.getenv("IUCN_TOKEN")
+<<<<<<< Updated upstream
 print(token)
+=======
+>>>>>>> Stashed changes
 
 #Filter source for land cover, global or colombia
 # LC_source <- input$lc_source
@@ -205,7 +208,11 @@ print("========== Map of suitable area generated ==========")
 #3.1 GFW data-------------------------------------------------------------------
 #forest base map
 cube_GFW_TC <-
+<<<<<<< Updated upstream
   load_cube(stac_path = "https://io.biodiversite-quebec.ca/stac/",
+=======
+  load_cube(stac_path = "https://stac.geobon.org/",
+>>>>>>> Stashed changes
             limit = 1000,
             collections = c("gfw-treecover2000"),
             bbox = sf_ext_srs,
@@ -232,7 +239,11 @@ print("========== Base forest layer downloaded ==========")
 
 # Download forest loss maps and create different layers for each year to remove from forest
 cube_GFW_loss <-
+<<<<<<< Updated upstream
   load_cube(stac_path = "https://io.biodiversite-quebec.ca/stac/",
+=======
+  load_cube(stac_path = "https://stac.geobon.org/",
+>>>>>>> Stashed changes
             limit = 1000,
             collections = c("gfw-lossyear"),
             bbox = sf_ext_srs,
@@ -262,7 +273,11 @@ if(t_0!=2000){
 r_year_loss_mask_plot <- terra::classify(s_year_loss_mask[[length(l_r_year_loss)]],rcl=cbind(0,NA)) # turn 0 to NA
 
 cube_GFW_gain <-
+<<<<<<< Updated upstream
   load_cube(stac_path = "https://io.biodiversite-quebec.ca/stac",
+=======
+  load_cube(stac_path = "https://stac.geobon.org/",
+>>>>>>> Stashed changes
             limit = 1000,
             collections = c("gfw-gain"),
             bbox = sf_ext_srs,

scripts/data/loadFromStac.yml

@@ -53,3 +53,18 @@ outputs:
     label: Weight matrix with layers
     description: Weight matrix used for Bon optimization. Vector of layer linkes followed by weights.
     type: text
+<<<<<<< Updated upstream
+=======
+conda:
+  channels:
+    - r
+    - conda-forge
+  dependencies:
+    - libgdal
+    - proj
+    - r-proj
+    - r-gdalcubes
+    - r-rstac
+    - r-dplyr
+    - r-rcurl
+>>>>>>> Stashed changes