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 × 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 × 123 cells and 39 layers. Annual precipitation (bio12) for the same region and time period.
env_array: A 3‑D numeric array with dimensions `2000 (locations) × 39 (time) × 2 (variables)`. Contains the environmental data (bio1 and bio12) extracted from the rasters for all locations.
occ_df: A data frame with 1000 rows and 4 columns: `name` (character), `x` (longitude), `y` (latitude), `presence` (0/1). Occurrence records for the virtual species *Mus virtualis*.
occ_vec: An integer vector of length 2000. Binary presence/absence (0/1) for the same locations as `env_array`.
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_list: A list of biological‑scale parameters (a “true” parameter set, not necessarily the MLE). Used in examples of `interpret_parameters()`, `vsp()`, etc.
par_vec_vsp: A named numeric vector of length 9, math‑scale parameters. Currently an alias for `par_vec` (retained for backward compatibility).
par_table: A data.frame with 9 columns corresponding to a parameter in math scale and 100 rows corresponding to 100 combinations.

Source

Berti e al, 2024 (<https://doi.org/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 `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_list"                
#> [11] "par_vec_vsp"              "par_table"               

# 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
#>