Function reference • gatoRs

Download data

Wrapper functions to download data from GBIF and iDigBio.

gators_download(): Download - Download specimen data from both iDigBio and GBIF

Clean data

Various tools to clean downloaded data produced from our download functions.

needed_records(): Identify Missing Information - Find records with redacted or missing data

need_to_georeference(): Identify Missing Information - Find records which lack coordinate information

remove_redacted(): Remove Redacted Information - Remove protected or private records prior to publication

remove_missing(): Remove Missing Information - Prepare to merge a data frame with georeferenced and retrieved records

gators_merge(): Merge Retained Data - Combined original data set with georeferenced or retained records.

remove_duplicates(): Remove Duplicates - Remove records with identical event dates and coordinates

taxa_clean(): Taxonomic Cleaning - Filter and resolve taxon names

basis_clean(): Basis Cleaning - Removes records with certain record basis

basic_locality_clean(): Locality Cleaning - Remove missing and improbable coordinates

process_flagged(): Locality Cleaning - Find possibly problematic occurrence records

thin_points(): Spatial Correction - Spatially thin records

one_point_per_pixel(): Spatial Correction - One point per pixel

full_clean(): Full Cleaning - Wrapper function to speed clean

data_chomp(): Subset Data - Get species, longitude, and latitude columns

citation_bellow(): Cite Data - Get GBIF citations

Helper functions

These functions are used within the download and cleaning functions.

get_gbif(): Used in gators_download() - Download data from the Global Biodiversity Information Facility

get_idigbio(): Used in gators_download() - Download data from Integrated Digitized Biocollections

filter_fix_names(): Used in gators_download() - Filter iDigBio results by scientific name

fix_columns(): Used in gators_download() - Fill out taxonomic name columns

fix_names(): Used in gators_download() - Fix taxonomic name capitalization

remove_skewed(): Used in basic_locality_clean() - Removed skewed locality