Conda dependencies for other scripts

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scripts/IUCN_redlist_historyAssesment/IUCN_redlist_historyAssesment.R

@@ -2,9 +2,9 @@
 #### Load required packages - libraries to run the script ####
 
 # 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", "dplyr", "plyr", "ggplot2", "tibble", "pbapply", "rredlist", "plyr", "reshape2") # 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
+# packagesPrev<- installed.packages()[,"Package"] # Check and get a list of installed packages in this machine and R version
+# packagesNeed<- c("magrittr", "dplyr", "plyr", "ggplot2", "tibble", "pbapply", "rredlist", "plyr", "reshape2") # 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
 packagesList<-list("magrittr", "rredlist", "ggplot2") # Explicitly list the required packages throughout the entire routine. Explicitly listing the required packages throughout the routine ensures that only the necessary packages are listed. Unlike 'packagesNeed', this list includes packages with functions that cannot be directly called using the '::' syntax. By using '::', specific functions or objects from a package can be accessed directly without loading the entire package. Loading an entire package involves loading all the functions and objects

scripts/IUCN_redlist_historyAssesment/IUCN_redlist_historyAssesment.yml

@@ -7,6 +7,22 @@ author:
  - name: Victor Julio Rincon
    email: [email protected]
 external_link: https://github.com/GEO-BON/biab-2.0
+conda:
+  channels:
+    - r
+    - conda-forge
+  dependencies:
+    - r-magrittr
+    - r-data.table
+    - r-dplyr
+    - r-plyr
+    - r-ggplot2
+    - r-tibble
+    - r-pbapply
+    - r-rredlist
+    - r-plyr
+    - r-reshape2
+
 inputs:
   species_data:
     label: Species data

scripts/RedListIndex/RedListIndex.yml

@@ -3,8 +3,75 @@ name: Red List Index
 description: "Estimates the Red List Index (RLI) for a group of species, reflecting trends in the overall extinction risk for that group."
 external_link: https://nrl.iucnredlist.org/assessment/red-list-index
 author:
- - name: Maria Camila diaz ([email protected])
- - name: Victor Julio Rincon ([email protected])
+ - name: Maria Camila diaz
+   email: [email protected]
+ - name: Victor Julio Rincon
+   email: [email protected]
+conda:
+  channels:
+    - r
+    - conda-forge
+  dependencies:
+    - r-magrittr
+    - r-data.table
+    - r-reshape2
+    - r-dplyr
+    - r-plyr
+    - r-ggplot2
+    - r-tibble
+    - r-pbapply
+    - r-rredlist
+    - r-plyr
+    # - r-red (not in channels)
+    - r-gdistance
+    - r-BAT
+    - r-ape
+    - r-geometry
+    - r-magic
+    - r-hypervolume
+    - r-ks
+    - r-mclust
+    - r-mvtnorm
+    - r-pracma
+    - r-fastcluster
+    - r-pdist
+    - r-palmerpenguins
+    - r-caret
+    - r-recipes
+    - r-timeDate
+    - r-gower
+    - r-hardhat
+    - r-ipred
+    - r-prodlim
+    - r-lava
+    - r-future.apply
+    - r-future
+    - r-globals
+    - r-listenv
+    - r-parallelly
+    - r-ModelMetrics
+    - r-pROC
+    - r-nls2
+    - r-proto
+    - r-vegan
+    - r-permute
+    - r-phytools
+    - r-combinat
+    - r-clusterGeneration
+    - r-DEoptim
+    - r-expm
+    - r-optimParallel
+    - r-phangorn
+    - r-fastmatch
+    - r-scatterplot3d
+    - r-predicts
+    - r-coda
+    - r-mnormt
+    - r-numDeriv
+    - r-quadprog
+    - r-dismo
+    - r-geosphere
+
 inputs:
   history_assessment_data:
     label: History assessment data