combine_records_extract: Extract environmental records for occurrence data.
In HMB3/nenswniche: Rapidly estimate species ranges and intersect with other layers

combine_records_extract

R Documentation

Extract environmental records for occurrence data.

Description

This function combines occurrence files from ALA and GBIF into one table, and extracts enviro values. It assumes that both files come from the previous GBIF/ALA combine function.

Usage

combine_records_extract(
  records_df,
  add_sites,
  site_df,
  add_site,
  filter_taxo,
  taxa_list,
  taxa_level,
  template_raster,
  thin_records,
  world_raster,
  epsg,
  complete_var,
  raster_divide,
  env_variables,
  save_data,
  data_path,
  save_run
)

Arguments

`records_df`	Data frame of ALA records
`site_df`	Data frame of site records (only used if you have site data, e.g. I-naturalist)
`taxa_list`	List of taxa analyzed, used to cut the dataframe down
`taxa_level`	What taxonomic level to analyze at?
`template_raster`	A global R Raster used to thin records to 1 record per 1km grid cell
`thin_records`	Do you want to thin the records out? If so, it will be 1 record per 1km*1km grid cell
`world_raster`	An global R Raster of the enviro conditions used to extract values for all records
`epsg`	The projection system used. Currently, needs to be WGS84
`save_data`	Do you want to save the data frame?
`data_path`	The file path used for saving the data frame
`save_run`	A run name to append to the data frame (e.g. bat taxa, etc.). Useful for multiple runs.
`env_vars`	The actual variable names (e.g. bio1 = rainfall, etc.) Only needed for worldlcim
`worldclim_divide`	Are you using worldclim stored as long intergers? If so, divide by 10.