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Detailed Development of Ecological Niche Models

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8. Example of Projections Using CHELSA Data"

8. Example of Projections Using CHELSA Data"
In kuenm2: Detailed Development of Ecological Niche Models 

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 6
)

Summary

Description

In the vignette "Project models to multiple scenarios", we show how to project models to multiple scenarios at once using future scenarios available in WorldClim. To organize WorldClim we previously used the function (organize_future_worldclim()), and we will need to do something similar for data from other databases, for instance, from CHELSA.

We need a root directory containing folders representing different scenarios, and each of these folders stores raster variables. At the first level, inside the root, folders should correspond to distinct time periods (e.g., future years like 2070 or past periods such as LGM). Within each period folder, if applicable, sub-folders can contain data to represent emission scenarios (e.g., ssp126 and ssp585). Finally, within each emission scenario or time period folder, a separate folder for each General Circulation Model (GCM) should be included (e.g., BCC-CSM2-MR and MIROC6).

Organizing information this way can be a little tedious, but here we will show how to do it. This will make possible to project models using scenarios available in different sources. We will use variables from CHELSA representing scenarios for the Last Glacial Maximum (LGM, ~21,000 year ago).


WARNING: In November 2025, CHELSA updated its website and LGM variables have not been listed the way they were before. We keep this example because the layers are still available to download using the code below, and users can still see how the function handles past projections. Please be aware that the download links for these variables might change in the future, and the code will stop working.



Getting ready

At this point it is assumed that kuenm2 is installed (if not, see the Main guide). Load kuenm2 and any other required packages, and define a working directory (if needed).

Note: functions from other packages (i.e., not from base R or kuenm2) used in this guide will be displayed as package::function(). 

# Load packages
library(kuenm2)
library(terra)

# Current directory
getwd()

# Define new directory
#setwd("YOUR/DIRECTORY")  # uncomment and modify if setting a new directory


Naming files for projections

To start, climate variables must be saved as separate TIF files, one file per scenario. File names should follow a consistent pattern that clearly indicates the time period, GCM, and, for future scenarios, the emission scenario (SSP). In addition, variables should have the same name across all scenarios. For example:

Let’s see how to achieve this in practice.


Getting variables

Downloading LGM variables

The first step is downloading raster layers representing LGM conditions. You can download the files directly using the links we create below, or following the script.

# Define variables to download
var_to_use <- c("BIO_01", "BIO_07", "BIO_12", "BIO_15")

# Define GCMs
gcms <- c("CCSM4", "CNRM-CM5", "FGOALS-g2", "IPSL-CM5A-LR", "MIROC-ESM",
          "MPI-ESM-P", "MRI-CGCM3")

# Create a grid combining variables and GCMs
g <- expand.grid("gcm" = gcms, "var" = var_to_use)

# Create links to download
l <- do.call(paste, c(g, sep = "_"))
l <- paste0("https://os.zhdk.cloud.switch.ch/chelsav1/pmip3/bioclim/CHELSA_PMIP_",
            l, ".tif")

# See links
head(l)
#> [1] "https://os.zhdk.cloud.switch.ch/chelsav1/pmip3/bioclim/CHELSA_PMIP_CCSM4_BIO_01.tif"       
#> [2] "https://os.zhdk.cloud.switch.ch/chelsav1/pmip3/bioclim/CHELSA_PMIP_CNRM-CM5_BIO_01.tif"    
#> [3] "https://os.zhdk.cloud.switch.ch/chelsav1/pmip3/bioclim/CHELSA_PMIP_FGOALS-g2_BIO_01.tif"   
#> [4] "https://os.zhdk.cloud.switch.ch/chelsav1/pmip3/bioclim/CHELSA_PMIP_IPSL-CM5A-LR_BIO_01.tif"
#> [5] "https://os.zhdk.cloud.switch.ch/chelsav1/pmip3/bioclim/CHELSA_PMIP_MIROC-ESM_BIO_01.tif"   
#> [6] "https://os.zhdk.cloud.switch.ch/chelsav1/pmip3/bioclim/CHELSA_PMIP_MPI-ESM-P_BIO_01.tif"

# Create a directory to save the raw variables
raw_past_chelsa <- file.path(tempdir(), "Raw_past")  # Here, in a temporary directory
dir.create(raw_past_chelsa)

# Download files and save in the Raw_past directory
options(timeout = 300)  # To avoid errors with timeout
sapply(l, function(i) {
  downfile <- file.path(raw_past_chelsa, basename(i))

  # Download only if the file has not been downloaded yet
  if(!file.exists(downfile)) {
      download.file(url = i, destfile = downfile, method = "curl")
  }
})  # It will take a while

#Check the files in the Raw_past
list.files(raw_past_chelsa)
#> [1] "CHELSA_PMIP_CCSM4_BIO_01.tif"        "CHELSA_PMIP_CCSM4_BIO_07.tif"
#> [3] "CHELSA_PMIP_CCSM4_BIO_12.tif"        "CHELSA_PMIP_CCSM4_BIO_15.tif"
#> [5] "CHELSA_PMIP_CNRM-CM5_BIO_01.tif"     "CHELSA_PMIP_CNRM-CM5_BIO_07.tif"
#> [7] "CHELSA_PMIP_CNRM-CM5_BIO_12.tif"     "CHELSA_PMIP_CNRM-CM5_BIO_15.tif"
#> [9] "CHELSA_PMIP_FGOALS-g2_BIO_01.tif"    "CHELSA_PMIP_FGOALS-g2_BIO_07.tif"
#> [11] "CHELSA_PMIP_FGOALS-g2_BIO_12.tif"    "CHELSA_PMIP_FGOALS-g2_BIO_15.tif"
#> [13] "CHELSA_PMIP_IPSL-CM5A-LR_BIO_01.tif" "CHELSA_PMIP_IPSL-CM5A-LR_BIO_07.tif"
#> [15] "CHELSA_PMIP_IPSL-CM5A-LR_BIO_12.tif" "CHELSA_PMIP_IPSL-CM5A-LR_BIO_15.tif"
#> [17] "CHELSA_PMIP_MIROC-ESM_BIO_01.tif"    "CHELSA_PMIP_MIROC-ESM_BIO_07.tif"
#> [19] "CHELSA_PMIP_MIROC-ESM_BIO_12.tif"    "CHELSA_PMIP_MIROC-ESM_BIO_15.tif"
#> [21] "CHELSA_PMIP_MPI-ESM-P_BIO_01.tif"    "CHELSA_PMIP_MPI-ESM-P_BIO_07.tif"
#> [23] "CHELSA_PMIP_MPI-ESM-P_BIO_12.tif"    "CHELSA_PMIP_MPI-ESM-P_BIO_15.tif"
#> [25] "CHELSA_PMIP_MRI-CGCM3_BIO_01.tif"    "CHELSA_PMIP_MRI-CGCM3_BIO_07.tif"
#> [27] "CHELSA_PMIP_MRI-CGCM3_BIO_12.tif"    "CHELSA_PMIP_MRI-CGCM3_BIO_15.tif"


Downloading current variables

We also need the variables representing current conditions. You can download the files directly from this link, or follow the script below:

# Create directory to save the variables
present_dir <- file.path(tempdir(), "Present_raw")
dir.create(present_dir)

# Define variables to download
var_present <-  c("bio1", "bio7", "bio12", "bio15")

# Create links, download and save in the Present_raw directory
l_present <- sapply(var_present, function(i){
  # Create link to download
  l_present_i <- paste0("https://os.zhdk.cloud.switch.ch/chelsav2/GLOBAL/climatologies/1981-2010/bio/CHELSA_", 
                        i, "_1981-2010_V.2.1.tif")

  # Donwload only if the file has not been downloaded yet
  if(!file.exists(file.path(present_dir, basename(l_present_i))))
  download.file(url = l_present_i,
                destfile = file.path(present_dir, basename(l_present_i)),
                method = "curl")
})  # This might take a while

# Check the files in the directory
list.files(present_dir)
#> [1] "CHELSA_bio1_1981-2010_V.2.1.tif"     "CHELSA_bio12_1981-2010_V.2.1.tif"
#> [3] "CHELSA_bio15_1981-2010_V.2.1.tif"    "CHELSA_bio7_1981-2010_V.2.1.tif"


Subsetting and renaming

After downloading files, we need to combine all variables for each scenario in a single TIF file. In general, past scenarios differs only in terms of GCM, while future scenarios are also separated according to different emission scenarios (i.e., SSP1-26 and SSP5-85) and GCMs.

First, let's combine the variables from the present scenario. To speed up the analysis in this example, we will also resample the raster layers from 30 arc-seconds to 10 arc-minutes, and crop the variables using a calibration area (provided as example data with the package). We will also rename the variables as follows "bio1", "bio12", "bio15", and "bio7".

# Import are for model calibration (M)
m <- vect(system.file("extdata", "m.gpkg", 
                        package = "kuenm2"))

# Import present variables
present_files <- list.files(present_dir, full.names = TRUE)  # List files
present_var <- rast(present_files)

# Mask variables using the calibration area (m)
present_m <- crop(present_var, m, mask = TRUE)

# Check variables names
names(present_m)
#> [1] "CHELSA_bio1_1981-2010_V.2.1"  "CHELSA_bio12_1981-2010_V.2.1"
#> [3] "CHELSA_bio15_1981-2010_V.2.1" "CHELSA_bio7_1981-2010_V.2.1"

# Rename variables
names(present_m) <- c("bio1", "bio12", "bio15", "bio7")
names(present_m)
#> [1] "bio1"  "bio12" "bio15" "bio7"

# Check current resolution (30arc-sec)
res(present_m)
#> [1] 0.008333333 0.008333333

# Decrease resolution to 10arc-min
present_chelsa <- aggregate(present_m, fact = 20, fun = "mean")

# Save processed raster
dir_current <- file.path(tempdir(), "Current_CHELSA")
dir.create(dir_current)

writeRaster(present_chelsa, 
            filename = file.path(dir_current, "Current_CHELSA.tif"))


Now, let's do the same with variables representing LGM conditions:

# Import LGM variables
lgm_files <- list.files(raw_past_chelsa, full.names = TRUE)  # List files
lgm_var <- rast(lgm_files)

# Mask variables using the calibration area (m)
lgm_m <- crop(lgm_var, m, mask = TRUE)

# Decrease resolution to 10arc-min
lgm_chelsa <- aggregate(lgm_m, fact = 20, fun = "mean")

# Check variables names
names(lgm_chelsa)
#>  [1] "CHELSA_PMIP_CCSM4_BIO_01"        "CHELSA_PMIP_CCSM4_BIO_07"       
#>  [3] "CHELSA_PMIP_CCSM4_BIO_12"        "CHELSA_PMIP_CCSM4_BIO_15"       
#>  [5] "CHELSA_PMIP_CNRM-CM5_BIO_01"     "CHELSA_PMIP_CNRM-CM5_BIO_07"    
#>  [7] "CHELSA_PMIP_CNRM-CM5_BIO_12"     "CHELSA_PMIP_CNRM-CM5_BIO_15"    
#>  [9] "CHELSA_PMIP_FGOALS-g2_BIO_01"    "CHELSA_PMIP_FGOALS-g2_BIO_07"   
#> [11] "CHELSA_PMIP_FGOALS-g2_BIO_12"    "CHELSA_PMIP_FGOALS-g2_BIO_15"   
#> [13] "CHELSA_PMIP_IPSL-CM5A-LR_BIO_01" "CHELSA_PMIP_IPSL-CM5A-LR_BIO_07"
#> [15] "CHELSA_PMIP_IPSL-CM5A-LR_BIO_12" "CHELSA_PMIP_IPSL-CM5A-LR_BIO_15"
#> [17] "CHELSA_PMIP_MIROC-ESM_BIO_01"    "CHELSA_PMIP_MIROC-ESM_BIO_07"   
#> [19] "CHELSA_PMIP_MIROC-ESM_BIO_12"    "CHELSA_PMIP_MIROC-ESM_BIO_15"   
#> [21] "CHELSA_PMIP_MPI-ESM-P_BIO_01"    "CHELSA_PMIP_MPI-ESM-P_BIO_07"   
#> [23] "CHELSA_PMIP_MPI-ESM-P_BIO_12"    "CHELSA_PMIP_MPI-ESM-P_BIO_15"   
#> [25] "CHELSA_PMIP_MRI-CGCM3_BIO_01"    "CHELSA_PMIP_MRI-CGCM3_BIO_07"   
#> [27] "CHELSA_PMIP_MRI-CGCM3_BIO_12"    "CHELSA_PMIP_MRI-CGCM3_BIO_15"


Note that file names contain the information on the GCM. The trick here is using these patterns for grouping the variables:

# In each iteration, 'i' is a GCM
lgm_by_gcm <- lapply(gcms, function(i){
  # Subset variables that belong to GCM i
  lgm_gcm_i <- lgm_chelsa[[grepl(i, names(lgm_chelsa))]]

  # Rename variables
  names(lgm_gcm_i) <- c("bio1", "bio7", "bio12", "bio15")
  return(lgm_gcm_i)
})

names(lgm_by_gcm) <- gcms


One important thing to note is that variables from LGM have different units compared to the current ones. In the current time, bio_1 have values in ºC, while in the LGM it has values in K * 10. bio_7 have values in ºC in the current time and in ºC * 10 in LGM. The current precipitation variables are in millimeters (mm) or percentage of variation (bio_15), while in the LGM they are in mm * 10 or % * 10. 

# Check values of variables in present
#> minmax(present_chelsa[[c("bio1", "bio7", "bio12", "bio15")]])
#>         bio1     bio7    bio12    bio15
#> min 12.87700 10.11300 1211.605 10.32925
#> max 24.70025 21.06125 3063.049 70.45125

# Check values of variables in LGM (CCSM4)
minmax(lgm_by_gcm$CCSM4)
#>         bio1     bio7    bio12    bio15
#> min 2822.425 173.5125 10710.62  86.9125
#> max 2946.758 219.7700 23159.20 659.0025


We need to convert these variables so they have the same units as the current variables:

# Fixing units in loop
lgm_fixed_units <- lapply(lgm_by_gcm, function(x) {
  x$bio1 <- (x$bio1 / 10) - 273  # Divide by 10 and subtracts -273
  x$bio7 <- x$bio7 / 10  # Divide by 10
  x$bio12 <- x$bio12 / 10  # Divide by 10
  x$bio15 <- x$bio15 / 10  # Divide by 10
  return(x)
})

# Check units
minmax(lgm_fixed_units$CCSM4)
#>         bio1     bio7    bio12    bio15
#> min  9.24250 17.35125 1071.062  8.69125
#> max 21.67575 21.97700 2315.920 65.90025


Now that we have the variables for LGM grouped by GCMs, with names and units fixed accordingly, we can write the files to disk. Remember that file names must include the time period (LGM) and the GCM of each scenario:

# Create directory to save processed lgm variables
dir_lgm <- file.path(tempdir(), "LGM_CHELSA")
dir.create(dir_lgm)

# Processing in loop
lapply(names(lgm_fixed_units), function(i) {
  # Subset SpatRaster from GCM i
  r_i <- lgm_fixed_units[[i]]

  # Name the file with the Period (LGM) and GCM (i)
  filename_i <- paste0("CHELSA_LGM_", i, ".tif") 

  # Write Raster
  writeRaster(r_i, filename = file.path(dir_lgm, filename_i))
})


Organizing variables

At this points we have:

Now, we can use the function organize_for_projection() to organize the files in the specific hierarchical manner compatible with kuenm2. The function requires:

The function also allows to use a spatial object (SpatVector, SpatRaster, or SpatExtent) to mask the variables, and append names of static variables (i.e., topographic variables) to the climatic variables.

first step is using list.files(path, full.names = TRUE) to list the path to the files representing present and LGM conditions. Remember, we save the processed current variables in the present_dir directory and the LGM variables in dir_lgm:

dir_current <- system.file("extdata", package = "kuenm2")
dir_lgm <- system.file("extdata", package = "kuenm2")

# Listing files in directories
present_list <- list.files(path = dir_current, pattern = "Current_CHELSA",
                           full.names = TRUE)

lgm_list <- list.files(path = dir_lgm, pattern = "LGM", full.names = TRUE)


Let's check the listed files to ensure they are storing the full path to the variables of each scenario:

# Check list of files with full paths
## Present
present_list  # Paths can be different in distinct computers
#> "Local\\Temp\\Current_CHELSA.tif"

# Past
lgm_list  # Paths can be different in distinct computers
#> [1] "Local\\Temp\\CHELSA_LGM_CCSM4.tif"       
#> [2] "Local\\Temp\\CHELSA_LGM_CNRM-CM5.tif"    
#> [3] "Local\\Temp\\CHELSA_LGM_FGOALS-g2.tif"   
#> [4] "Local\\Temp\\CHELSA_LGM_IPSL-CM5A-LR.tif"
#> [5] "Local\\Temp\\CHELSA_LGM_MIROC-ESM.tif"   
#> [6] "Local\\Temp\\CHELSA_LGM_MPI-ESM-P.tif"   
#> [7] "Local\\Temp\\CHELSA_LGM_MRI-CGCM3.tif"


After checking files, we are ready to organize them:

# Create a directory to save the variables
# Here, in a temporary directory. Change to your work directory in your computer
out_dir <- file.path(tempdir(), "Projection_variables")

# Organizing files the way it is needed
organize_for_projection(output_dir = out_dir, 
                        variable_names = c("bio1", "bio7", "bio12", "bio15"), 
                        present_file = present_list, 
                        past_files = lgm_list, 
                        past_period = "LGM", 
                        past_gcm = c("CCSM4", "CNRM-CM5", "FGOALS-g2", 
                                     "IPSL-CM5A-LR", "MIROC-ESM", "MPI-ESM-P",
                                     "MRI-CGCM3"),
                        resample_to_present = TRUE,
                        overwrite = TRUE)


We can check the files structured hierarchically in nested folders using the dir_tree() function from the fs package:

# Install package if necessary
if(!require("fs")) {
  install.packages("fs")
}

fs::dir_tree(out_dir)
#> Local\Temp\Projection_variables
#> ├── Past
#> │   └── LGM
#> │       ├── CCSM4
#> │       │   └── Variables.tif
#> │       ├── CNRM-CM5
#> │       │   └── Variables.tif
#> │       ├── FGOALS-g2
#> │       │   └── Variables.tif
#> │       ├── IPSL-CM5A-LR
#> │       │   └── Variables.tif
#> │       ├── MIROC-ESM
#> │       │   └── Variables.tif
#> │       ├── MPI-ESM-P
#> │       │   └── Variables.tif
#> │       └── MRI-CGCM3
#> │           └── Variables.tif
#> └── Present
#>     └── Variables.tif


After organizing variables, the next step is to create the prepared_projection object.

But before this, let's import a fitted_model object provided as example data in kuenm2. This object was created in a process that used current variables from CHELSA. For more information check the vignettes about data preparation, model calibration and model exploration. 

d_chelsa <- prepare_data(algorithm = "maxnet", occ = occ_data, x = "x", y = "y",
                         raster_variables = present_chelsa, 
                         species = "Myrcia hatschbachii", partition_method = "kfolds", 
                         n_partitions = 4,
                         n_background = 1000,
                         features = c("l", "q", "lq", "lqp"),
                         r_multiplier = c(0.1, 1, 2))

m_chelsa <- calibration(data = d_chelsa, 
                        error_considered = c(5, 10),
                        omission_rate = 10,
                        parallel = TRUE,  # Set TRUE to run in parallel
                        ncores = 8)

fitted_model_chelsa <- fit_selected(m_chelsa, n_replicates = 4)

# Load the object with fitted models
data(fitted_model_chelsa, package = "kuenm2")


Data preparation for model projections

Now, let's prepare data for model projections to multiple scenarios. We need the paths to the folders where the raster files are stored.

In addition to storing the paths to the variables for each scenario, the function verifies if all variables used to fit the final models are present across all scenarios. To perform this check, you need to provide either the fitted_models object you intend to use for projection or simply the variable names. We strongly suggest using the fitted_models object to minimize errors.

We also need to provide information so the function can identify time periods, SSPs, and GCMs (no SSPs in this example).

# Define present_dir and past_dir
in_dir_present <- file.path(out_dir, "Present")
in_dir_past <- file.path(out_dir, "Past")

# Prepare projections using fitted models to check variables
pr <- prepare_projection(models = fitted_model_chelsa,
                         present_dir = in_dir_present,  # Directory with present variables
                         past_dir = in_dir_past, 
                         past_period = "LGM", 
                         past_gcm = c("CCSM4", "CNRM-CM5", "FGOALS-g2", 
                                      "IPSL-CM5A-LR", "MIROC-ESM", "MPI-ESM-P",
                                      "MRI-CGCM3"), 
                         future_dir = NULL,  # NULL because we won't project to the Future
                         future_period = NULL, 
                         future_pscen = NULL,  
                         future_gcm = NULL)


When we print the projection_data object, it summarizes all scenarios we will predict to, and shows the root directory where the files are stored:

pr
#> projection_data object summary
#> ==============================
#> Variables prepared to project models for Present and Past 
#> Past projections contain the following periods and GCMs:
#>   - Periods: LGM 
#>   - GCMs: CCSM4 | CNRM-CM5 | FGOALS-g2 | IPSL-CM5A-LR | MIROC-ESM | MPI-ESM-P | MRI-CGCM3 
#> All variables are located in the following root directory:
#> Local/Temp/Projection_variables


Projecting models

After preparing the data, we can use the project_selected() function to project selected models across the scenarios specified before. For a comprehensive explanation of this step, please see the Project models to multiple scenarios vignette.

# Create a folder to save projection results
# Here, in a temporary directory
out_dir_projections <- file.path(tempdir(), "Projection_results/chelsa")
dir.create(out_dir_projections, recursive = TRUE)

# Project selected models to multiple scenarios
p <- project_selected(models = fitted_model_chelsa, 
                      projection_data = pr,
                      out_dir = out_dir_projections, 
                      write_replicates = TRUE,
                      progress_bar = FALSE,  # Do not print progress bar
                      overwrite = TRUE)

# Import mean of each projected scenario
p_mean <- import_results(projection = p, consensus = "mean")

# Plot all scenarios
terra::plot(p_mean, cex.main = 0.8)


Detecting changes: Past vs present

When projecting a model to different temporal scenarios (past or future), changes in suitable areas can be classified into three categories relative to the current baseline: gain, loss and stability. The interpretation of these categories depends on the temporal direction of the projection.

When projecting to future scenarios:

When projecting to past scenarios:

These outcomes may vary across different General Circulation Models (GCMs) within each time scenario (e.g., various Shared Socioeconomic Pathways (SSPs) for the same period).

The projection_changes() function summarizes the number of GCMs predicting gain, loss, and stability for each time scenario.

By default, this function writes the summary results to disk (unless write_results is set to FALSE), but it does not save binary layers for individual GCMs. In the example below, we demonstrate how to configure the function to return the raster layers with changes and write the binary results to disk.

Here, we present an example of detected changes from LGM to current conditions. 

# Run function to detect changes
changes <- projection_changes(model_projections = p, consensus = "mean",
                              output_dir = out_dir_projections, 
                              write_bin_models = TRUE,  # Write individual binary results
                              return_raster = TRUE, overwrite = TRUE)

# Set colors
summary_with_colors <- colors_for_changes(changes_projections = changes)

# Plot
terra::plot(summary_with_colors$Summary_changes)


In this example, we can see that the species has lost a lot of its suitable area when comparing LGM to present-day conditions. This is supported by the high agreement among GCMs.



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kuenm2 documentation built on April 21, 2026, 1:07 a.m.

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