run_sdm_analysis_crop: Run SDM analyses for 'species with data' format, with...

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

Run SDM analyses for 'species with data' format, with bio-geographic cropping.

Description

This function takes a data frame of all taxa records, and runs a specialised maxent analysis for each taxa. It uses the dismo package https://github.com/johnbaums/rmaxent

Usage

run_sdm_analysis_crop(
  taxa_list,
  taxa_level,
  sdm_df,
  sdm_predictors,
  maxent_dir,
  bs_dir,
  backwards_sel,
  template_raster,
  cor_thr,
  pct_thr,
  k_thr,
  min_n,
  max_bg_size,
  background_buffer_width,
  shapefiles,
  features,
  replicates,
  responsecurves,
  crop_Koppen,
  Koppen_raster,
  Koppen_zones,
  country_shp
)

Arguments

taxa_list	Character string - the taxa to run maxent models for
taxa_level	Character string - the taxnomic level to run maxent models for
sdm_df	SpatialPointsDataFrame. Spdf of all taxa records returned by the 'prepare_sdm_table' function
sdm_predictors	Character string - Vector of enviro conditions that you want to include
maxent_dir	Character string - The file path used for saving the maxent output
bs_dir	Character string - The file path used for saving the backwards selection maxent output
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)
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
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)?
Koppen_raster	RasterLayer of global koppen zones, in Mollweide54009 projection
Koppen_zones	Dataframe of global koppen zones, with columns : GRIDCODE, Koppen
country_shp	.Rds object - SpatialPolygonsDataFrame of Australia for mapping maxent points
koppen_crop	Logical - Should we use a koppen zone raster to select background points?

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