combine_records_extract: This function combines occurrence files from ALA and GBIF...

Description Usage Arguments Value

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

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combine_records_extract(
  ala_df,
  gbif_df,
  urban_df,
  add_urban,
  species_list,
  template_raster,
  thin_records,
  world_raster,
  prj,
  biocl_vars,
  env_vars,
  worldclim_grids,
  save_data,
  data_path,
  save_run
)

Arguments

ala_df

Data frame of ALA records

gbif_df

Data frame of GBIF records

urban_df

Data frame of Urban records (only used if you have urban data, e.g. I-naturalist)

species_list

List of species analysed, used to cut the dataframe down

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

prj

The projection system used. Currently, needs to be WGS84

biocl_vars

The variables used - eg the standard bioclim names (https://www.worldclim.org/).

env_vars

The actual variable names (e.g. bio1 = rainfall, etc.) Only needed for worldlcim

worldclim_grids

Are you using worldclim stored as long intergers? If so, divide by 10.

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 species, etc.). Useful for multiple runs.

Value

Data frame of all ALA/GBIF records, with global enviro conditions for each record location (i.e. lat/lon)


HMB3/sdmgen documentation built on April 16, 2021, 7:29 p.m.