fit_maxent_targ_bg_back_sel: This function takes a data frame of all species records, and...
In HMB3/sdmgen: Rapidly estimate species ranges and habit sutiability

View source: R/SDM_GEN_MAXENT_FUNCTIONS.R

This function takes a data frame of all species records, and runs a specialised maxent analysis for each species. 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

fit_maxent_targ_bg_back_sel(
  occ,
  bg,
  sdm_predictors,
  name,
  outdir,
  bsdir,
  cor_thr,
  pct_thr,
  k_thr,
  backwards_sel,
  template_raster,
  min_n,
  max_bg_size,
  background_buffer_width,
  Koppen_raster,
  shapefiles,
  features,
  replicates,
  responsecurves,
  country_shp
)

`occ`	SpatialPointsDataFrame - Spdf of all species 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
`background_buffer_width`	Numeric - The max distance (km) from occ points that BG points should be selected?
`shapefiles`	Logical - Save shapefiles of the occ and bg data (T/F)?
`features`	Character string - Which features should be used? (e.g. linear, product, quadratic 'lpq')
`replicates`	Numeric - The number of replicates to use
`responsecurves`	Logical - Save response curves of the maxent models (T/F)?
`country_shp`	.Rds object - SpatialPolygonsDataFrame of Australia for mapping maxent points
`rep_args`	RasterLayer of global koppen zones, in Mollweide54009 projection
`full_args`	Dataframe of global koppen zones, with columns : GRIDCODE, Koppen