fit_maxent_targ_bg_back_sel_no_crop: Maxent Backwards selection for 'species with data' format,...

In HMB3/nenswniche: Rapidly estimate species ranges and intersect with other layers

Maxent Backwards selection for 'species with data' format, without biogeographic cropping.

Description

This function takes a data frame of all taxa records, and runs a specialised maxent analysis for each taxa. It uses the rmaxent package https://github.com/johnbaums/rmaxent It assumes that the input df is that returned by the prepare_sdm_table function

Usage

fit_maxent_targ_bg_back_sel_no_crop(
  occ,
  bg,
  sdm_predictors,
  taxa,
  outdir,
  bsdir,
  cor_thr,
  pct_thr,
  k_thr,
  backwards_sel,
  template_raster,
  min_n,
  max_bg_size,
  background_buffer_width,
  shapefiles,
  features,
  feat_save,
  replicates,
  responsecurves,
  poly
)

Arguments

occ	SpatialPointsDataFrame - Spdf of all taxa records returned by the 'prepare_sdm_table' function
bg	SpatialPointsDataFrame - Spdf of of candidate background points
sdm_predictors	Character string - Vector of enviro conditions that you want to include
outdir	Character string - The file path used for saving the maxent output
bsdir	Character string - The file path used for saving the backwards selection maxent output
cor_thr	Numeric - The max allowable pairwise correlation between predictor variables
pct_thr	Numeric - The min allowable percent variable contribution
k_thr	Numeric - The min number of variables to be kept in the model
backwards_sel	Logical - Run backwards selection using the maxent models (T/F)?
template_raster	RasterLayer - Empty raster with analysis extent (global), res (1km) and projection (Mollweide, EPSG 54009)
min_n	Numeric - The min number of records for running maxent
max_bg_size	Numeric - The max number of background points to keep
features	Character string - Which features should be used? (e.g. linear, product, quadratic 'lpq')
feat_save	Logical - Save shapefiles of the occ and bg data (T/F)?
replicates	Numeric - The number of replicates to use
responsecurves	Logical - Save response curves of the maxent models (T/F)?
poly	Character string - path to shapefile
rep_args	RasterLayer of global koppen zones, in Mollweide54009 projection
full_args	Dataframe of global koppen zones, with columns : GRIDCODE, Koppen

HMB3/nenswniche documentation built on Jan. 31, 2023, 11:46 p.m.