User-friendly data cleaning pipeline for the inexperienced R user
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README.md

Build Status codecov

bdclean

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.

Install

Development version, from GitHub

library("devtools")
devtools::install_github("bd-R/bdclean")
library("bdclean")

Download some data from GBIF

library(rgbif)
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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