Create generalised extract_data function
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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
Specific context tables might be empty (null) if a series of extract functions are used in tandem. Was fixing tests for austraits_lite5.0.0 and came across another issue... Unlike the old extract functions the new one doesn't work with vectors of values - line 123 in `extract_data`
The tests to do with extract_data are generally working, but there is a weird, oscillating bug with the order of tables in the database list that I can't work out. And also there is a test on line 198 (expect_equal(trait_subset$traits %>% dplyr::distinct(dataset_id) %>% nrow(), 5)) alternates between giving 5 & 8 as output. But bugs fixed: - works with empty tibbles - works with vectors of values to match
series of small errors causing tests to fail: - needed to reorder tables in some of the austraits_lite versions - recreated the austraits_lite for versions 3 & 4 that are empty, other than having the structure required to test compatibility - plot_data needed an `as.numeric` - the function `summarise_trait_means` was still being tests on v3.0 and indeed looking at the code, isn't going to summarise, because it is only searching for replicates within a single observation_id
The function `join_context_properties` was not being exported
…raitecoevo/austraits into generalise_extract_off_develop
…dding links in roxygen
…raitecoevo/austraits into generalise_extract_off_develop
…raitecoevo/austraits into generalise_extract_off_develop
…raitecoevo/austraits into generalise_extract_off_develop
Write tests for bind_databases (issue #114)
…raitecoevo/austraits into generalise_extract_off_develop
…raitecoevo/austraits into generalise_extract_off_develop
changed `plant_trait_name` to `trait_name` in the function `plot_trait_distribution_beeswarm` to generalise it to all traits.build databases. Towards Issue #111
…raitecoevo/austraits into generalise_extract_off_develop
…raitecoevo/austraits into generalise_extract_off_develop
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Hi @ehwenk, I think the PR has incorrectly been directed to |
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extract_datafunction that makes it possible to subset a traits.build database using any column in any table.traits.buildthat is used to bind together datasets has been moved to austraits, allowing one to extract multiple pieces of a database, then bind them back together into a single database