User-friendly data cleaning pipeline for the inexperienced R user
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User-friendly biodiversity data cleaning pipeline

bdclean will provide features to manage complete pipeline for biodiversity data cleaning. A modular approach to plug in data checking and cleaning functions would make this package one stop shop for many biodiversity data cleaning needs.


Development version, from GitHub


Download some data from GBIF

occdat <- occ_data(
  country = "AU",     # Country code for australia
  classKey= 359,      # Class code for mammalia
  limit = 5000,         # Get only 5000 records

Taking just the species occurrence dataframe

myData <- occdat$data

Using bdclean

Getting your input: generating input questions and saving your answers

myConfig <- get_config()

Cleaning your data based on your answers

cleanData <- clean_data(myData, myConfig)

Cleaning reports should be created in Your-Working-Directory\CleaningReports

Package release

bdclean is still under development, a CRAN release with many package upgrades is expected in July 2018.

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🌳 πŸ„ 🐚 🐟 🐸 🐝 🐒 πŸ“ πŸ‹ πŸ’ :octocat: