Consolidated example data for the xsdm package

A named list containing all example datasets used in the package's documentation and examples.

Usage

example_1

Format

A list of 11 objects:

par_vec: Named numeric vector of length 9. Math-scale parameters for a 2-variable model (p = 2). Canonical names: mu1, mu2, sigltil1, sigltil2, sigrtil1, sigrtil2, ctil, pd, o_par1.
bio01: A packed SpatRaster (use terra::unwrap()) with 128 x 123 cells and 39 layers. Annual average temperature (bio1) for 1980-2018, CHELSA 2.1 data, centred on southern New Mexico, USA.
bio12: A packed SpatRaster (use terra::unwrap()) with 128 x 123 cells and 39 layers. Annual precipitation (bio12) for the same region and time period.
env_array: A 3-D numeric array with dimensions 4000 (locations) x 39 (time) x 2 (variables). Contains the environmental data (bio1 and bio12, both divided by 100) extracted from the rasters at the occ_df locations.
occ_df: A data frame with 4000 rows and 4 columns: name (character), lon (longitude), lat (latitude), presence (0/1). Occurrence records for a virtual species.
occ_vec: An integer vector of length 4000. Binary presence/absence (0/1) corresponding to occ_df$presence.
true_par_list: A list of biological-scale parameters (the "true" parameter set used to generate the virtual species). Contains mu, sigltil, sigrtil, ctil, pd, o_mat.
optim_par_list: A list of biological-scale parameters (the MLE fit for the example). Contains mu, sigltil, sigrtil, ctil, pd, o_mat.
optim_par_vec: A named numeric vector of length 9. Math-scale parameters corresponding to optim_par_list.
optim_par_vec_equivalent: A named numeric vector of length 9. A different math-scale representation that belongs to the same equivalence class as optim_par_vec. Used to test dist_between_params().
par_table: A data.frame with 9 columns (one per math-scale parameter) and 100 rows of parameter combinations.

Source

Berti et al., 2025 (doi:10.1101/2024.10.30.621023 )

Details

All rasters (bio01, bio12) are stored as packed SpatRaster objects to reduce package size. Before using them, unpack with terra::unwrap(), e.g.: bio1 <- terra::unwrap(example_1$bio01).

The environmental data are originally from CHELSA v2.1 (https://www.chelsa-climate.org/). The virtual species was generated from the parameters in true_par_list.

Examples

# Access the list
names(example_1)
#>  [1] "par_vec"                  "bio01"                   
#>  [3] "bio12"                    "env_array"               
#>  [5] "occ_df"                   "occ_vec"                 
#>  [7] "optim_par_list"           "optim_par_vec_equivalent"
#>  [9] "optim_par_vec"            "par_table"               
#> [11] "true_par_list"           

# Unpack a raster
# \donttest{
bio1 <- terra::unwrap(example_1$bio01)
# }

# Use a parameter set
math_to_bio(example_1$par_vec)
#> $mu
#> [1] 14.2  6.8
#> 
#> $sigltil
#> [1] 1.4 0.5
#> 
#> $sigrtil
#> [1] 1.35 0.10
#> 
#> $ctil
#> [1] -17.6
#> 
#> $pd
#> [1] 0.9
#> 
#> $o_mat
#>           [,1]       [,2]
#> [1,] 0.9800666 -0.1986693
#> [2,] 0.1986693  0.9800666
#>