Simulated example landscape

Loads the example shipped with the package: a simulated 60 x 40 km mountain range modeled loosely on the central Sierra Nevada, with 80 snowmelt meadows in four lineages. A long, gradual western slope rises to a crest near the eastern edge; east of it a steep escarpment lies in a rain shadow; two steep-walled canyons cut the western slope. Migrants leave water-stressed meadows for wetter neighbors. Under warming (+4.2 C) snowpack shrinks by a share that falls with elevation, from about 90% in the foothills to under 20% at the crest, so the push uphill grows most at low elevation. The script that builds the example is in the package source (data-raw/make_example.R).

Usage

corridor_example(acc = FALSE)

Arguments

acc

Also compute the accumulated cost surfaces.

Value

A list with

dem, resistance

Elevation (m) and movement resistance SpatRasters; ridgelines have resistance 1e6.

env, env_future

Environmental layers now and under warming: snowpack (mm), runoff (mm), a meadow moisture index (log scale), summer temperature (C), slope (degrees) and forest cover (0-1).

sites

The 80 meadows as sf points with site, elevation and lineage.

lineage_tmrca

Time since each pair of lineages split (thousand years), for lineage_cross().

resistance_slope, resistance_cover

The two components blended 80:20 into resistance, for comparing path hypotheses.

acc

Accumulated cost surfaces for every meadow, from accumulated_cost(). Only with acc = TRUE; they take a few seconds to compute and are cached for the rest of the session.

files

Paths to the genotypes (about 1,300 SNPs, 8 individuals per meadow) in STRUCTURE (structure), GENEPOP (genepop) and VCF (vcf) format, the VCF population map (popmap), and a small GENEPOP sample of six meadows and 100 SNPs (small) for quick tests.

Examples

ex <- corridor_example()
terra::plot(ex$dem, col = hcl.colors(100, "viridis"))
plot(sf::st_geometry(ex$sites), add = TRUE, pch = 19)