Fix error with empty excluded_data tables
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…king for new version, waiting for austraits.build update
…rough the internal data subsets for version 3.0.2 and version 4.0.0. Pivot_ needs austraits.build fixes to implenment. Some minor fix to pivot_wider for dependencies #60
Some packages needed to make plots are included in suggests. This means that core functions of package may not work.
- reuse outputs from previous function calls to reduce runtime - reduce dataset sizes for slow functions (summarise_trait_means, trait_pivot_wider, plot_locations) - silence some outputs closes #62
- As documented in #79 , the Zenodo API has changed, breaking our download feature. - This commit updates the internals to work with the latest changes. Specifically: - the way to access json for all versions has changed (changed url structure, and for id we now use one of the record ids, rather than the conceptid) - the call to download file has changed - format of the API json has changed Also - added record id to the table of versions - put a check in to remove "v" from any version entered by user
* changes required for v5 austraits.build * Removed original_name for trait_pivot_wider3 for v5.0.0 * Added trait_pivot_wider for v4.x.x and code for what_version * Making new switches for join and as_wide_table based on new versioning * Sub switch for extract_ and recreated internal data * Sub switches for trait_pivot_longer * Minor fix in join_methods * Added vars a global vars * Removed .data calls when not needed * Update to work with latest zenodo API (#81) - As documented in #79 , the Zenodo API has changed, breaking our download feature. - This commit updates the internals to work with the latest changes. Specifically: - the way to access json for all versions has changed (changed url structure, and for id we now use one of the record ids, rather than the conceptid) - the call to download file has changed - format of the API json has changed Also - added record id to the table of versions - put a check in to remove "v" from any version entered by user * Recreated data so extract is passing * Update `treatment_id` with `treatment_context_id` * Revert "Update `treatment_id` with `treatment_context_id`" This reverts commit 3fc6717. * minor column name changes Changes column names, reflecting recent changes to traits.build output. * Update as_wide_table.R add `any_of` to column selection within `as_wide_table` to accommodate other traits.build databases that don't have the same columns in taxon_list.csv * Fixed getting versions and load austraits with zenodo updates and minor update with as_wide_table with removal of variable * Fixed minor bug in get_version_latest --------- Co-authored-by: Elizabeth Wenk <[email protected]> Co-authored-by: Daniel Falster <[email protected]> Co-authored-by: yangsophieee <[email protected]>
* Created lites for all main versions of AusTraits * Passing for as_wide_table * Passing for as_wide_table and for extract_ * expanding test suite to all 3 majors, switches for method id adjusted * expanding test suite to all 3 majors for summarise_D * Expanding these for all 3 versions * Added PR trigger for dev branch
* bug fix for `extract_data` so it works even after you have joined other columns * edit `plot_trait_distribution_beeswarm` to work with a single table and for its message to accurately reflect which grouping variables are allowed
* Renamed file and integrated check compatability in print funciton
Revert to original format of `bind_databases` arguments - required for traits.build to work using furrr method
* Update README.Rmd * Returning tibble for flatten_database * Minor updates to dependnencies to pass R CMD check Remove reference to `summarise_trait_means` * Extract_data missing S3 class assign * Updated bootswatch --------- Co-authored-by: ehwenk <[email protected]>
* Export print function so it works and available for testing * More tests for plot_locations * Used cli for error message for and more test for plot_trait_ * Snapshotting the output of print.traits.build * Testing functions in utils file and removing what_version * Testing for get_versions_latest
Add tests for parts of functions not being tested
* Function to test database structure * Adding new test function where appropriate * Rebuilt embedded lite data layers so that they have the proper class attached to them --------- Co-authored-by: Daniel Falster <[email protected]>
* Add missing cheatsheet * Ignore from RBuild
- join_location_properties(format = "single_column_json") was not retaining location_name as its own column.
* Both fixed this and added tests
- Also, value_type was being lost during separate_trait_values - and probably has been for a long time.
fix error - due to excluded_data table being a completely empty tibble rather than having empty columns if there is no excluded_data. Caused a problem with back-to-back extract_ function uses
Forgot I also needed a column "error" and added test.
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If there was no data in the excluded_data table, the
extract_functions were returning an empty tibble, not a tibble of empty named, columns. In addition to being the wrong output, this was leading to warnings when running multipleextract_functions.A change at the end of the main
extract_datafunction fixes this