check_spatial_outliers: This function takes a data frame of all species records,...

In HMB3/sdmgen: Rapidly estimate species ranges and habit sutiability

Description

This function takes a data frame of all species records, flags records as spatial outliers (T/F for each record in the df), and saves images of the checks for each. Manual cleaning of spatial outliers is very tedious, but automated cleaning makes mistakes, so checking is handy It uses the CoordinateCleaner package https://cran.r-project.org/web/packages/CoordinateCleaner/index.html. It assumes that the input dfs are those returned by the coord_clean_records function

Usage

check_spatial_outliers(
  all_df,
  urban_df,
  land_shp,
  clean_path,
  spatial_mult,
  prj
)

Arguments

all_df	Data.frame. DF of all species records returned by the coord_clean_records function
urban_df	Data.frame of Urban records (only used if you have urban data, e.g. I-naturalist)
land_shp	R object. Shapefile of the worlds land (e.g. https://www.naturalearthdata.com/downloads/10m-physical-vectors/10m-land/)
clean_path	Character string - The file path used for saving the checks
spatial_mult	Numeric. The multiplier of the interquartile range (method == 'quantile', see ?cc_outl)

Value

Data.frame of species records, with spatial outlier T/F flag for each record

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