Run GDM and return model object

Run GDM and return model object

Usage

gdm_run(
  gendist,
  coords,
  env,
  model = "full",
  sig = 0.05,
  nperm = 50,
  scale_gendist = FALSE,
  geodist_type = "Euclidean",
  distPreds = NULL,
  dist_lyr = NULL
)

Arguments

gendist

matrix of genetic distances (must range between 0 and 1 or set scale_gendist = TRUE)

coords

dataframe with x (i.e., longitude) and y (i.e., latitude) coordinates; must be in this order

env

dataframe or raster object with environmental values for each coordinate; if not provided, it will be calculated based on coords/envlayers

model

whether to fit the model with all variables ("full") or to perform variable selection to determine the best set of variables ("best"); defaults to "full"

sig

alpha value for significance threshold (defaults to 0.05); only used if model = "best"

nperm

number of permutations to use to calculate variable importance; only used if model = "best" (defaults to 50)

scale_gendist

whether to scale genetic distance data from 0 to 1 (defaults to FALSE)

geodist_type

the type of geographic distance to be calculated; options are "Euclidean" (default) for direct distance, "topographic" for topographic distances, and "resistance" for resistance distances. Note: creation and plotting of the GDM raster is only possible for "Euclidean" distances

dist_lyr

DEM raster for calculating topographic distances or resistance raster for calculating resistance distances

Value

GDM model

See also

Other GDM functions: gdm_coeffs(), gdm_df(), gdm_do_everything(), gdm_format(), gdm_map(), gdm_plot_diss(), gdm_plot_isplines(), gdm_plot_vars(), gdm_table(), gdm_var_sel(), scale01()