PEcAn functions for cleaning up a version of the bety database

This package includes several wrapper functions for common database queries for entries that cause problems, or take up space. Please refer to the Pre-release-clean-up script located in the vignettes folder for best-practices in using these functions. See “Intended use” for more information.

Many queries and checks are net yet implemented. If you’d like to contribute to this package, look at issue #1630 and [this list of bety issues] ( to see what functions still need to be made. Add these functions to the Pre-release-clean-up vignette. See “Structure of functions” for more information.

Intended use

These functions are intended to be used interactively. The find* functions return a table of all of the entries that fit the terms provided. The write_table function then exports that table to a specific file. That file can then be manually edited in any text-editor. This is the most important step, as there will likely be entries with utility that only a person familiar with ongoing/recent projects would know.

After the editing process, the file can be fed into the cull_database_entries function. This will parse the file, and delete all the entried that are listed on the file. It will also provide a log of what was deleted.

Structure of functions

find functions

  • All find functions should have descriptive names of the form “find_TABLE_ relationship _TABLE2“. All functions will return entries from the first named table ie: find_inputs_without_formats will return input table entries.

  • All find functions need to return and object with a column “table_name” with the name of the table it’s returning entries from.

  • All find functions must return an object where there is an “id” column with “id” entries that are associated with the entries from the first table in the function

check functions

  • Not yet implemented.