bd-R / bdchecks

An infrastructure for biodiversity data checks

bdchecks

Managing all data checks

Install bdchecks with:

install.packages("bdchecks")

Or for development version:

devtools::install_github("bd-R/bdchecks")

Load with:

library(bdchecks)

Performing data checks

Perform data checks (not exported yet):

result <- bdchecks::perform_dc(data_bats)

Check what data checks were performed (default show method):

result

Quick glance at data check result (% of records that passed) (not exported yet):

# Nice summary
summary_dc(result)

Dealing with new data checks

This is a recommended workflow to add new data checks:

1. Load libraries

library(bdchecks)
library(devtools) # To install new version of a package
library(usethis) # To export data.checks object

2. Check if original build works

check()

3. Create new data check

3.1 Add meta information to ./inst/extdata/data_check.yaml file
3.2 Add data check function to ./R/ directory (file should be named after a data check, e.g. dc_checkthis.R). First argument to a data check function must be a vector (column) to perform data check on.
3.3 Add test data to ./inst/extdata/data_test.yaml

4. Export new dat check

install() # To have new check in `system.file("extdata/data_check.yaml")`
data.checks <- bdchecks:::datacheck_info_export() # export documentation and combines new check with old ones
use_data(data_taxonrank, data.checks, data_bats, overwrite = TRUE, internal = TRUE) # exports old (and new data checks)
document() # document new check to `Rd`
install() # install package with a new check

5. Test if everything works

perform_test_dc() # perform tests for data checks
check() # perform general check

6. Post-incorporation

6.1 Increase version (and date) in DESCRIPTON
6.2 Run git add and git commit with message: "v0.x.x Added name_of_check data check"