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Merge Dec-update-23 branch into master #890
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The new version is needed to read the SLFs now. We use this in `get_existing_data_for_tests()`
* remove unnecessary code from `get_anon_chi` `get_anon_chi` was updated in slfhelper v0.10 * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5669528966/attempts/1 Accepted in #759 (comment) Signed-off-by: check-spelling-bot <[email protected]> --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: marjom02 <[email protected]> Co-authored-by: Megan McNicol <[email protected]>
These take a very long time to run, so were skipped at the last update. They need to be revisited.
* Correct some documentation This resolves a build warning. * Style code --------- Co-authored-by: Moohan <[email protected]>
Lots of layout changes, as well as lots of implicit to explicit integer / double changes.
* Format postcode into `pc7` format * Style code * Style code * Update documentation * Update comment in R/process_extract_ae.R * Implement catch-all for PC7 format --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: James McMahon <[email protected]> Co-authored-by: Moohan <[email protected]>
* Remove some obsolete code Renaming and removing some functions. * Style code --------- Co-authored-by: Moohan <[email protected]> Co-authored-by: Zihao Li <[email protected]>
* Simplify `create_hscp_test_flags` * Update documentation * Style code * simplify `create_hb_test_flags` * implement hscp test flags into tests * Simplify `create_demog_test_flags` --------- Co-authored-by: James McMahon <[email protected]> Co-authored-by: Moohan <[email protected]>
* updated code from case_when to case_match as it's a bit easier to read * Style code * changed some more `case_when` to `case_match` * Style code * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5752014211/attempts/1 Accepted in #780 (comment) Signed-off-by: check-spelling-bot <[email protected]> * Add tests for `convert_sending_location_to_lca` --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: marjom02 <[email protected]> Co-authored-by: SwiftySalmon <[email protected]> Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
In processed extract variable is called hscp, and in final SLF it's called hscp2018. Fixed with nested if statement Co-authored-by: marjom02 <[email protected]>
Tiny error and a simple fix. Co-authored-by: Jennit07 <[email protected]>
* fix duplicated matches in chi in sc data. * Update R/create_individual_file.R * update on join_sc_client * Create a test checking if individual files have duplicated chi * add duplicated chi number to the tests in process_tests_individual_file --------- Co-authored-by: lizihao-anu <[email protected]> Co-authored-by: James McMahon <[email protected]>
Update `check_year_valid` for NSUs
…785) * Update `get_boxi_extract_path` for DN/CMH data * Remove extra function * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5856792420/attempts/1 Accepted in #785 (comment) Signed-off-by: check-spelling-bot <[email protected]> --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: James McMahon <[email protected]>
* further obsolete code change * fix the preventable_beddays Co-authored-by: James McMahon <[email protected]> --------- Co-authored-by: James McMahon <[email protected]> Co-authored-by: Jennit07 <[email protected]>
* fix warning on `:=` * Update R/aggregate_by_chi.R Co-authored-by: James McMahon <[email protected]> * Style code --------- Co-authored-by: James McMahon <[email protected]> Co-authored-by: lizihao-anu <[email protected]>
This was already set up, just not used for some reason. Note that this will switch from using a `.rds` to `.parquet` (unless you do `get_source_extract_path(year, "Homelessness", ext = "rds")`). Co-authored-by: Jennit07 <[email protected]>
* Update News for March and June updates * Update release date * WIP - update news for Sep update * Update NEWS.md Fix some typos / grammar --------- Co-authored-by: James McMahon <[email protected]>
We had a call to discuss the filter for deaths at the mid point of calendar year. This includes the changes we discussed. There was also the issue of the function `rbinom` not working correctly and selecting out whole groups rather than random samples from each group. This now works. I will run the code tomorrow to produce some of the tables but Rachel and I checked the keep population flag counts for 1819 and it seems a lot more reasonable with the figures. Great work everyone! Thanks
I have been having an issue when trying to run the episode file. I get an error with the `vctrs` package as R doesnt like when you try to do a `bind_rows()` on a list of data which has some empty data. The work around is to remove this before processing the episode file
* remove duplicate sc_send_lca * Style code * remove sc_send_lca to avoid crash in create_episode_file * undo the changes for select sc_send_lca --------- Co-authored-by: lizihao-anu <[email protected]> Co-authored-by: Jennit07 <[email protected]>
* revert back to September update * revert to september update * Style code * revert to september code * Style code * Revert to september update code --------- Co-authored-by: marjom02 <[email protected]> Co-authored-by: SwiftySalmon <[email protected]> Co-authored-by: Jennifer Thom <[email protected]>
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We have both looked over this during a call and are happy to merge into master.
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Requires more investigation as to why they are failing. Exlcuding for now
@check-spelling-bot Report🔴 Please reviewSee the 📂 files view, the 📜action log, or 📝 job summary for details. Unrecognized words (13)
To accept these unrecognized words as correct, you could run the following commands... in a clone of the [email protected]:Public-Health-Scotland/source-linkage-files.git repository curl -s -S -L 'https://raw.githubusercontent.com/check-spelling/check-spelling/main/apply.pl' |
perl - 'https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/7460784350/attempts/1' OR To have the bot accept them for you, reply quoting the following line: Available 📚 dictionaries could cover words (expected and unrecognized) not in the 📘 dictionaryThis includes both expected items (232) from .github/actions/spelling/expect.txt and unrecognized words (13)
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cspell:k8s/dict/k8s.txt
cspell:filetypes/filetypes.txt
cspell:swift/src/swift.txt
cspell:npm/dict/npm.txt
cspell:fullstack/dict/fullstack.txt To stop checking additional dictionaries, add (in check_extra_dictionaries: '' Pattern suggestions ✂️ (1)You could add these patterns to
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This looks good to merge into master at this stage, thank you for addressing the checks.
December update has been completed and now we want to bring all the branches back up to date and merge this into master