Rewrite case when statements #780
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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]>
Moohan
approved these changes
Aug 3, 2023
github-merge-queue bot
pushed a commit
that referenced
this pull request
Sep 28, 2023
* Bump `{slfhelper}` version
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` (#759)
* 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]>
* Set the default reporter for `tar_outdated()` and friends
* Comment out dataset writing targets
These take a very long time to run, so were skipped at the last update. They need to be revisited.
* Make sure `year` is added as the first variable
* Correct some documentation (#769)
* Correct some documentation
This resolves a build warning.
* Style code
---------
Co-authored-by: Moohan <[email protected]>
* Make some changes suggested by lintr
Lots of layout changes, as well as lots of implicit to explicit integer / double changes.
* Document
* Fix documentation typo
* Investigate missing datazone from episode file (#773)
* 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 (#770)
* 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` (#772)
* 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]>
* Rewrite case when statements (#780)
* 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]>
* Update R-CMD-check.yaml (#781)
Co-authored-by: Jennit07 <[email protected]>
* WIP - add sc client tests
* Update documentation
* New function `create_sending_location_test_flags`
* Update documentation
* Style code
* Fix typo
* Sort the data so `lag` works as expected
* Use `""` in `select` instead of `.data$,,,`
Also, use `dplyr::last_col()` to more generically specify the range.
* Update documentation
* added solve for hscp names (#789)
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]>
* Fix locality (#802)
Tiny error and a simple fix.
Co-authored-by: Jennit07 <[email protected]>
* Add simple scripts for running targets as a workbench job (#767)
* Fix CHI duplicates of chi in individual file (#791)
* 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 NSU code for new 22/23 cohort (#784)
Update `check_year_valid` for NSUs
* Amend `get_boxi_extract_path` function for archiving DN and CMH data (#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]>
* Fix increase in total preventable beddays (#779)
* 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]>
* Add 2324 targets/workbench job file
* Use `get_source_extract_path` in homelessness (#796)
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]>
* Correct tests for NSU
* fix warning on `:=` (#797)
* 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]>
* Update script for extracting NSU from SMRA space
* Add 2324 targets/workbench job file
* Use `get_source_extract_path` in homelessness (#796)
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]>
* Correct tests for NSU
* Update year in 99_NSU extract script
* Update news for September 23 update (#811)
* 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]>
* Apply styling
* Fix issue with `case_match` types (#810)
* Fix issue with `case_match` types
It seems that `case_match()` is stricter about types than `case_when()`. See the below code:
```r
library(dplyr)
# Breaks
mutate(starwars,
new_height = case_when(
height == "172" ~ "170"),
new_height2 = case_match(
height,
"172" ~ "170"
),
.after = "height"
)
# Works
mutate(starwars,
new_height = case_when(
height == "172" ~ "170"),
new_height2 = case_match(
height,
172L ~ "170"
),
.after = "height"
)
```
Since `sending_location` is an integer, the LHS of `case_match` must be numeric. It was slightly incorrect previously but `case_when` let us get away with it!
I also updated and added to the tests.
* Style code
* Style code
---------
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Bug - Outpatients tests failing due to missing HSCP (#816)
* Update `produce_source_extract_tests`
* Update outpatients tests with hscp_var = FALSE
* Revert "Style code"
This reverts commit 8e73d4a.
* Style code
* simplify code
* Update documentation
* Rename `hscp_var` to `add_hscp_count`
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Moohan <[email protected]>
* fix read_sc_all_alarms_telecare with incorrect format in period (#814)
* fix read_sc_all_alarms_telecare with the incorrect format in period
---------
Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: James McMahon <[email protected]>
* Fix `convert_sending_location_to_lca` example
* Update script for extracting NSU from SMRA space
* Update year in 99_NSU extract script
* Update news for September 23 update (#811)
* 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]>
* Apply styling
* Fix issue with `case_match` types (#810)
* Fix issue with `case_match` types
It seems that `case_match()` is stricter about types than `case_when()`. See the below code:
```r
library(dplyr)
# Breaks
mutate(starwars,
new_height = case_when(
height == "172" ~ "170"),
new_height2 = case_match(
height,
"172" ~ "170"
),
.after = "height"
)
# Works
mutate(starwars,
new_height = case_when(
height == "172" ~ "170"),
new_height2 = case_match(
height,
172L ~ "170"
),
.after = "height"
)
```
Since `sending_location` is an integer, the LHS of `case_match` must be numeric. It was slightly incorrect previously but `case_when` let us get away with it!
I also updated and added to the tests.
* Style code
* Style code
---------
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Bug - Outpatients tests failing due to missing HSCP (#816)
* Update `produce_source_extract_tests`
* Update outpatients tests with hscp_var = FALSE
* Revert "Style code"
This reverts commit 8e73d4a.
* Style code
* simplify code
* Update documentation
* Rename `hscp_var` to `add_hscp_count`
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Moohan <[email protected]>
* fix read_sc_all_alarms_telecare with incorrect format in period (#814)
* fix read_sc_all_alarms_telecare with the incorrect format in period
---------
Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: James McMahon <[email protected]>
* Fix `convert_sending_location_to_lca` example
* Rename sheet name
Co-authored-by: James McMahon <[email protected]>
* fix warning on `:=` (#797)
* 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]>
* Add new function for counting records by sending location (#782)
* New function `create_sending_location_test_flags`
* Update R/process_tests_sc_client_lookup.R
* Update documentation
* Update ref functions for Sep23 update
* Updates target year for new `2324` file
* add homelessness flags to the episode file. (#815)
* still sorting out conflicts
* Update documentation
* Style code
* # Working code for homelessness flags
- removes applications that have a missing end date in line with the homelessness work
- `group_by` and `summarise(max)` to deal with people that have more than one application to prevent case duplication
* Update documentation
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update documentation
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update documentation
* Style code
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Style code
* Update documentation
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update documentation
* Style code
* made James' suggested changes and generally tidied up with lintR.
Replaced `anon_chi` with `chi`
* Style code
* Update documentation
* # Added homelessness flags to episode and individual files, and targets.
finishing off code to add flags to files
* Style code
* Update documentation
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Update documentation
* Style code
* Update R/process_lookup_homelessness.R
Co-authored-by: James McMahon <[email protected]>
* Style code
* Update documentation
* # Updated documentation
added homelessness params to the episode and individual file
---------
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]>
* Create HRI Variables (#778)
* New functions to determine Scottish residents and add HRI variables
* Test to check that non-Scottish residents are flagged correctly
* Style code
* use `.default =` instead of `TRUE ~`
* Make doubles specific
* Update documentation
* Pass the `slf_postcode_lookup` as data instead of the path
* Update documentation
* Use Logical `TRUE`
* Remove parameter `chi_variable`
* rename `keep_flag` to `scottish_resident`
---------
Co-authored-by: shintoLamp <[email protected]>
Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>
* Remove future from the cohorts code (#821)
Co-authored-by: Jennit07 <[email protected]>
* Use `col_select` instead of `columns` in tests
* Use `col_select` instead of `columns` in tests
* Remove `slfhelper::get_chi()`
Takes too long to process tests
* Remove `slfhelper::get_chi`
* Add demographic flags for anon chi
* Only use hscp flags if recid is NOT 00B
* Update documentation
* Remove rename of hscp - causes mismatched tests
* Include `hscp2018` in variable list
This was causing an issue in tests
* Add HRI function to individual file pipeline
* Revert "BUG - Fix for the episode file tests (#823)"
This reverts commit bf5f9b0.
* Revert "Remove rename of hscp - causes mismatched tests"
This reverts commit 628da4d.
* Update NEWS.md
* Update `check_year_valid` for 23/24 social care
* Update create_individual_file.R (#824)
* Update create_individual_file.R
* Update documentation
* Style code
---------
Co-authored-by: lizihao-anu <[email protected]>
* Lizihao anu patch 1 (#825)
* Update create_individual_file.R
* Update add_hri_variables.R
* Update documentation
* Style code
* move chi variable after `data`
* move `add_hri_variables` up list and add pipe
* Update documentation
---------
Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Add HRI last
* Add empty SC variables for 2324 - ep file
* Add SC variables for 2324 - indiv file
* add condition for aggregating ch episodes
* New function for aggregating without sc variables
* specify `chi_variable` in hri select list
This was causing an error
* Implement new aggregate for sc variables
* Remove `dplyr::everything()`
* Declare social care variables for latest year
* Style code
* Update documentation
* Include hl1 variables in aggregate
* Revert "Include hl1 variables in aggregate"
This reverts commit 562869a.
* Fix aggregation_by_chi (#829)
* test commit push
* Revert "test commit push"
This reverts commit ff51536.
* combine aggregate_by_chi with sc and without sc
* Style code
* Update documentation
---------
Co-authored-by: lizihao-anu <[email protected]>
* Update NEWS.md
* Only use hscp test flags if NOT 00B
* BUG - Fix episode file tests (#830)
* add anon chi parameter in `get_existing_data..`
* remove `slfhelper::get_chi()`
* Use `anon_chi` parameter
* declare `anon_chi` tests
* Update documentation
* update documentation
* Style code
* remove hscp count for now
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
* Add tests for `compute_mid_year_age` (#809)
* Add tests for `compute_mid_year_age`
* Remove redundant code
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Add a new function to set up keyring (#800)
* Add a new function to set up keyring
I've tested this by deleting my `.Renviron` and deleting my keyring `keyring::keyring_delete("createslf")` and it seems to work. Would be great to have someone with an existing set-up (Jen) test it, and to have someone who doesn't have it set up to test it.
The code looks complicated but I've just tried to catch every scenario, so the process should be smooth and clear (from the user's point of view).
I've also expanded the code relating to the username, which will now hopefully work in more cases.
* [check-spelling] Update metadata
Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5824423711/attempts/1
Accepted in #800 (comment)
Signed-off-by: check-spelling-bot <[email protected]>
* Update documentation
---------
Signed-off-by: check-spelling-bot <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Add additional tests for `get_file_path` (#808)
* Add additional tests for `get_file_path`
* Style code
---------
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Rename `run_episode_file()` -> `create_episode_file()` (#803)
* Rename `run_episode_file()` -> `create_episode_file()`
This improves consistency! When speaking to Megan we noted that having the two 'main' functions with different names was needlessly confusing!
* Delete run_targets_tests.R
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
* Remove incorrect references to rds (#798)
* Remove incorrect references to rds
Since we (mostly) don't use rds anymore these references are incorrect and potentially confusing.
I've updated lots of documentation to remove the reference to rds.
I've also updated many comments that mentioned rds (these were probably the most confusing).
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
* Make targets and tarchetypes required packages (#799)
Co-authored-by: Megan McNicol <[email protected]>
* Update episode file functions to pass data through (#754)
* Update `read_file` to return an empty tibble if passed the dummy path
This is needed for some other bits, notably NSUs
* Update SPARRA and HHG paths to return dummy if the year is invalid
* Extract all data as a parameter
* Style code
* Update documentation
* Style code
* Update documentation
* rename `run` to `create_episode_file`
* Update documentation
---------
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Tests/it extract path (#807)
* Add additional tests for `check_it_reference()`
* Make the check on the IT reference stricter
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Update workflow to run against the development branch (#795)
* Make test-coverage.yaml run against development
* Make lint-changed-files.yaml run against development
---------
Co-authored-by: Jennit07 <[email protected]>
* Update `create_episode_file`
* remove `run_episode_file`
* Update documentation
* new function for `client_lookup_path`
* rename to `get_sc_lookup_paths`
* Update documentation
* Use `get_sc_client_lookup_path`
* Update client tests
* Update documentation
* Style code
* add sc client tests to targets
* remove client path from `get_source_extract_path`
* Update documentation
---------
Signed-off-by: check-spelling-bot <[email protected]>
Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
Co-authored-by: marjom02 <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Zihao Li <[email protected]>
Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: Bateman McBride <[email protected]>
Co-authored-by: shintoLamp <[email protected]>
github-merge-queue bot
pushed a commit
that referenced
this pull request
Oct 2, 2023
* Bump `{slfhelper}` version
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` (#759)
* 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]>
* Set the default reporter for `tar_outdated()` and friends
* Comment out dataset writing targets
These take a very long time to run, so were skipped at the last update. They need to be revisited.
* Make sure `year` is added as the first variable
* Correct some documentation (#769)
* Correct some documentation
This resolves a build warning.
* Style code
---------
Co-authored-by: Moohan <[email protected]>
* Make some changes suggested by lintr
Lots of layout changes, as well as lots of implicit to explicit integer / double changes.
* Document
* Fix documentation typo
* Investigate missing datazone from episode file (#773)
* 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 (#770)
* 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` (#772)
* 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]>
* Rewrite case when statements (#780)
* 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]>
* Update R-CMD-check.yaml (#781)
Co-authored-by: Jennit07 <[email protected]>
* added solve for hscp names (#789)
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]>
* Fix locality (#802)
Tiny error and a simple fix.
Co-authored-by: Jennit07 <[email protected]>
* Add simple scripts for running targets as a workbench job (#767)
* Fix CHI duplicates of chi in individual file (#791)
* 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 NSU code for new 22/23 cohort (#784)
Update `check_year_valid` for NSUs
* Amend `get_boxi_extract_path` function for archiving DN and CMH data (#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]>
* Fix increase in total preventable beddays (#779)
* 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 `:=` (#797)
* 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]>
* Add 2324 targets/workbench job file
* Use `get_source_extract_path` in homelessness (#796)
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]>
* Correct tests for NSU
* Update script for extracting NSU from SMRA space
* Update year in 99_NSU extract script
* Update news for September 23 update (#811)
* 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]>
* Apply styling
* Fix issue with `case_match` types (#810)
* Fix issue with `case_match` types
It seems that `case_match()` is stricter about types than `case_when()`. See the below code:
```r
library(dplyr)
# Breaks
mutate(starwars,
new_height = case_when(
height == "172" ~ "170"),
new_height2 = case_match(
height,
"172" ~ "170"
),
.after = "height"
)
# Works
mutate(starwars,
new_height = case_when(
height == "172" ~ "170"),
new_height2 = case_match(
height,
172L ~ "170"
),
.after = "height"
)
```
Since `sending_location` is an integer, the LHS of `case_match` must be numeric. It was slightly incorrect previously but `case_when` let us get away with it!
I also updated and added to the tests.
* Style code
* Style code
---------
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Bug - Outpatients tests failing due to missing HSCP (#816)
* Update `produce_source_extract_tests`
* Update outpatients tests with hscp_var = FALSE
* Revert "Style code"
This reverts commit 8e73d4a.
* Style code
* simplify code
* Update documentation
* Rename `hscp_var` to `add_hscp_count`
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Moohan <[email protected]>
* fix read_sc_all_alarms_telecare with incorrect format in period (#814)
* fix read_sc_all_alarms_telecare with the incorrect format in period
---------
Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: James McMahon <[email protected]>
* Fix `convert_sending_location_to_lca` example
* Use `col_select` instead of `columns` in tests
* Add tests for `compute_mid_year_age` (#809)
* Add tests for `compute_mid_year_age`
* Remove redundant code
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Add a new function to set up keyring (#800)
* Add a new function to set up keyring
I've tested this by deleting my `.Renviron` and deleting my keyring `keyring::keyring_delete("createslf")` and it seems to work. Would be great to have someone with an existing set-up (Jen) test it, and to have someone who doesn't have it set up to test it.
The code looks complicated but I've just tried to catch every scenario, so the process should be smooth and clear (from the user's point of view).
I've also expanded the code relating to the username, which will now hopefully work in more cases.
* [check-spelling] Update metadata
Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5824423711/attempts/1
Accepted in #800 (comment)
Signed-off-by: check-spelling-bot <[email protected]>
* Update documentation
---------
Signed-off-by: check-spelling-bot <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Add additional tests for `get_file_path` (#808)
* Add additional tests for `get_file_path`
* Style code
---------
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Rename `run_episode_file()` -> `create_episode_file()` (#803)
* Rename `run_episode_file()` -> `create_episode_file()`
This improves consistency! When speaking to Megan we noted that having the two 'main' functions with different names was needlessly confusing!
* Delete run_targets_tests.R
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
* Remove incorrect references to rds (#798)
* Remove incorrect references to rds
Since we (mostly) don't use rds anymore these references are incorrect and potentially confusing.
I've updated lots of documentation to remove the reference to rds.
I've also updated many comments that mentioned rds (these were probably the most confusing).
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
* Make targets and tarchetypes required packages (#799)
Co-authored-by: Megan McNicol <[email protected]>
* Update episode file functions to pass data through (#754)
* Update `read_file` to return an empty tibble if passed the dummy path
This is needed for some other bits, notably NSUs
* Update SPARRA and HHG paths to return dummy if the year is invalid
* Extract all data as a parameter
* Style code
* Update documentation
* Style code
* Update documentation
* rename `run` to `create_episode_file`
* Update documentation
---------
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Tests/it extract path (#807)
* Add additional tests for `check_it_reference()`
* Make the check on the IT reference stricter
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Update workflow to run against the development branch (#795)
* Make test-coverage.yaml run against development
* Make lint-changed-files.yaml run against development
---------
Co-authored-by: Jennit07 <[email protected]>
* Remove package wide imports of `readr` (#792)
* Update documentation
* Use `readr::` where possible
* Update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
* Handle OpenData extracts better (#794)
* Refactor the LA Code OpenData
This should now run as its own target and then be passed to the homelessness data.
I also added some tests.
* Also add some tests for the GP prac clusters OpenData
* Update documentation
---------
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Fix the pkgdown site/job (#804)
* Fix the pkgdown site/job
It generates this site: https://public-health-scotland.github.io/source-linkage-files/ although it hasn't been working for a while since any new function needs to be added to (or captured by) the `_pkgdown.yml` file.
This PR is a pretty minimal fix to get the site working again.
* Update documentation
* Update documentation
* Update `create_episode_file`
* Remove `run_episode_file`
* update documentation
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>
* Add new 'final' file path functions (#787)
* New function for SLF final file paths
* Implement final file path functions
* Style code
* Update documentation
* Update final file paths to use `...`
* fixing conflicts with `run episode file` getting renamed to `create episode file`
* Update documentation
* Update documentation
* Style code
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: marjom02 <[email protected]>
Co-authored-by: SwiftySalmon <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
* Check scripts are in snake case (#793)
* Update `get_boxi_extract_path` for DN/CMH data
* Remove extra function
* Update documentation
* change `get_boxi_extract_path` to snake_case
* change `get_source_extract_path` to snake_case
* Update documentation
* Update targets with snake_case
* Fix typo
* Style code
---------
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
Co-authored-by: SwiftySalmon <[email protected]>
* transform the python script for sorting BI extracts to R (#833)
* transform the python script for sorting BI extracts to R
* Style code
* Delete 00-Sort_BI_Extracts.py
---------
Co-authored-by: lizihao-anu <[email protected]>
* Use `get_slf_episode_path` in right place
* fix pipe
* Fix typo in string
* Update documentation
* Rename to `convert_sc_sending_location_to_lca`
* Update documentation
* Style code
* Update documentation
---------
Signed-off-by: check-spelling-bot <[email protected]>
Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
Co-authored-by: marjom02 <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Zihao Li <[email protected]>
Co-authored-by: lizihao-anu <[email protected]>
Jennit07
added a commit
that referenced
this pull request
Nov 21, 2023
* Rename function to `convert_sc_sending_location_to_lca` (#839) * Bump `{slfhelper}` version 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` (#759) * 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]> * Set the default reporter for `tar_outdated()` and friends * Comment out dataset writing targets These take a very long time to run, so were skipped at the last update. They need to be revisited. * Make sure `year` is added as the first variable * Correct some documentation (#769) * Correct some documentation This resolves a build warning. * Style code --------- Co-authored-by: Moohan <[email protected]> * Make some changes suggested by lintr Lots of layout changes, as well as lots of implicit to explicit integer / double changes. * Document * Fix documentation typo * Investigate missing datazone from episode file (#773) * 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 (#770) * 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` (#772) * 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]> * Rewrite case when statements (#780) * 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]> * Update R-CMD-check.yaml (#781) Co-authored-by: Jennit07 <[email protected]> * added solve for hscp names (#789) 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]> * Fix locality (#802) Tiny error and a simple fix. Co-authored-by: Jennit07 <[email protected]> * Add simple scripts for running targets as a workbench job (#767) * Fix CHI duplicates of chi in individual file (#791) * 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 NSU code for new 22/23 cohort (#784) Update `check_year_valid` for NSUs * Amend `get_boxi_extract_path` function for archiving DN and CMH data (#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]> * Fix increase in total preventable beddays (#779) * 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 `:=` (#797) * 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]> * Add 2324 targets/workbench job file * Use `get_source_extract_path` in homelessness (#796) 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]> * Correct tests for NSU * Update script for extracting NSU from SMRA space * Update year in 99_NSU extract script * Update news for September 23 update (#811) * 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]> * Apply styling * Fix issue with `case_match` types (#810) * Fix issue with `case_match` types It seems that `case_match()` is stricter about types than `case_when()`. See the below code: ```r library(dplyr) # Breaks mutate(starwars, new_height = case_when( height == "172" ~ "170"), new_height2 = case_match( height, "172" ~ "170" ), .after = "height" ) # Works mutate(starwars, new_height = case_when( height == "172" ~ "170"), new_height2 = case_match( height, 172L ~ "170" ), .after = "height" ) ``` Since `sending_location` is an integer, the LHS of `case_match` must be numeric. It was slightly incorrect previously but `case_when` let us get away with it! I also updated and added to the tests. * Style code * Style code --------- Co-authored-by: Moohan <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Jennit07 <[email protected]> * Bug - Outpatients tests failing due to missing HSCP (#816) * Update `produce_source_extract_tests` * Update outpatients tests with hscp_var = FALSE * Revert "Style code" This reverts commit 8e73d4a. * Style code * simplify code * Update documentation * Rename `hscp_var` to `add_hscp_count` * Update documentation --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: James McMahon <[email protected]> Co-authored-by: Moohan <[email protected]> * fix read_sc_all_alarms_telecare with incorrect format in period (#814) * fix read_sc_all_alarms_telecare with the incorrect format in period --------- Co-authored-by: lizihao-anu <[email protected]> Co-authored-by: James McMahon <[email protected]> * Fix `convert_sending_location_to_lca` example * Use `col_select` instead of `columns` in tests * Add tests for `compute_mid_year_age` (#809) * Add tests for `compute_mid_year_age` * Remove redundant code * Update documentation --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Jennit07 <[email protected]> * Add a new function to set up keyring (#800) * Add a new function to set up keyring I've tested this by deleting my `.Renviron` and deleting my keyring `keyring::keyring_delete("createslf")` and it seems to work. Would be great to have someone with an existing set-up (Jen) test it, and to have someone who doesn't have it set up to test it. The code looks complicated but I've just tried to catch every scenario, so the process should be smooth and clear (from the user's point of view). I've also expanded the code relating to the username, which will now hopefully work in more cases. * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5824423711/attempts/1 Accepted in #800 (comment) Signed-off-by: check-spelling-bot <[email protected]> * Update documentation --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Jennit07 <[email protected]> * Add additional tests for `get_file_path` (#808) * Add additional tests for `get_file_path` * Style code --------- Co-authored-by: Moohan <[email protected]> Co-authored-by: Jennit07 <[email protected]> * Rename `run_episode_file()` -> `create_episode_file()` (#803) * Rename `run_episode_file()` -> `create_episode_file()` This improves consistency! When speaking to Megan we noted that having the two 'main' functions with different names was needlessly confusing! * Delete run_targets_tests.R * Update documentation --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Megan McNicol <[email protected]> * Remove incorrect references to rds (#798) * Remove incorrect references to rds Since we (mostly) don't use rds anymore these references are incorrect and potentially confusing. I've updated lots of documentation to remove the reference to rds. I've also updated many comments that mentioned rds (these were probably the most confusing). * Update documentation --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Megan McNicol <[email protected]> * Make targets and tarchetypes required packages (#799) Co-authored-by: Megan McNicol <[email protected]> * Update episode file functions to pass data through (#754) * Update `read_file` to return an empty tibble if passed the dummy path This is needed for some other bits, notably NSUs * Update SPARRA and HHG paths to return dummy if the year is invalid * Extract all data as a parameter * Style code * Update documentation * Style code * Update documentation * rename `run` to `create_episode_file` * Update documentation --------- Co-authored-by: Moohan <[email protected]> Co-authored-by: Jennifer Thom <[email protected]> Co-authored-by: Jennit07 <[email protected]> * Tests/it extract path (#807) * Add additional tests for `check_it_reference()` * Make the check on the IT reference stricter * Update documentation --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Jennit07 <[email protected]> * Update workflow to run against the development branch (#795) * Make test-coverage.yaml run against development * Make lint-changed-files.yaml run against development --------- Co-authored-by: Jennit07 <[email protected]> * Remove package wide imports of `readr` (#792) * Update documentation * Use `readr::` where possible * Update documentation --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Megan McNicol <[email protected]> * Handle OpenData extracts better (#794) * Refactor the LA Code OpenData This should now run as its own target and then be passed to the homelessness data. I also added some tests. * Also add some tests for the GP prac clusters OpenData * Update documentation --------- Co-authored-by: Moohan <[email protected]> Co-authored-by: Jennit07 <[email protected]> * Fix the pkgdown site/job (#804) * Fix the pkgdown site/job It generates this site: https://public-health-scotland.github.io/source-linkage-files/ although it hasn't been working for a while since any new function needs to be added to (or captured by) the `_pkgdown.yml` file. This PR is a pretty minimal fix to get the site working again. * Update documentation * Update documentation * Update `create_episode_file` * Remove `run_episode_file` * update documentation --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Jennifer Thom <[email protected]> * Add new 'final' file path functions (#787) * New function for SLF final file paths * Implement final file path functions * Style code * Update documentation * Update final file paths to use `...` * fixing conflicts with `run episode file` getting renamed to `create episode file` * Update documentation * Update documentation * Style code --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: marjom02 <[email protected]> Co-authored-by: SwiftySalmon <[email protected]> Co-authored-by: Megan McNicol <[email protected]> * Check scripts are in snake case (#793) * Update `get_boxi_extract_path` for DN/CMH data * Remove extra function * Update documentation * change `get_boxi_extract_path` to snake_case * change `get_source_extract_path` to snake_case * Update documentation * Update targets with snake_case * Fix typo * Style code --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: James McMahon <[email protected]> Co-authored-by: Megan McNicol <[email protected]> Co-authored-by: SwiftySalmon <[email protected]> * transform the python script for sorting BI extracts to R (#833) * transform the python script for sorting BI extracts to R * Style code * Delete 00-Sort_BI_Extracts.py --------- Co-authored-by: lizihao-anu <[email protected]> * Use `get_slf_episode_path` in right place * fix pipe * Fix typo in string * Update documentation * Rename to `convert_sc_sending_location_to_lca` * Update documentation * Style code * Update documentation --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: James McMahon <[email protected]> Co-authored-by: Megan McNicol <[email protected]> Co-authored-by: marjom02 <[email protected]> Co-authored-by: Megan McNicol <[email protected]> Co-authored-by: Moohan <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Zihao Li <[email protected]> Co-authored-by: lizihao-anu <[email protected]> * Rename function `add_smrtype` (#840) * rename to `add_smrtype` * Rename script to `add_smrtype` * update documentation * Remove TODO comment * Style code * Update documentation --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Megan McNicol <[email protected]> * add_keep_population_flag for create_individual_file * fix homelessness path * Update documentation * Style code * change boxi file names back to capitals (#845) A previous pull request changed all capitals to lowercase - however boxi file names have capitals so it was no longer reading in files. This is a fix Co-authored-by: marjom02 <[email protected]> Co-authored-by: Jennit07 <[email protected]> * Bump stefanzweifel/git-auto-commit-action from 4 to 5 (#846) Bumps [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action) from 4 to 5. - [Release notes](https://github.com/stefanzweifel/git-auto-commit-action/releases) - [Changelog](https://github.com/stefanzweifel/git-auto-commit-action/blob/master/CHANGELOG.md) - [Commits](stefanzweifel/git-auto-commit-action@v4...v5) --- updated-dependencies: - dependency-name: stefanzweifel/git-auto-commit-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Jennit07 <[email protected]> * Style code * some changes to add_keep_population_flag * Style code * Update documentation * some changes to add_keep_population_flag * Style code * minor changes * Update documentation --------- Signed-off-by: check-spelling-bot <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: James McMahon <[email protected]> Co-authored-by: Megan McNicol <[email protected]> Co-authored-by: marjom02 <[email protected]> Co-authored-by: Megan McNicol <[email protected]> Co-authored-by: Moohan <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: lizihao-anu <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jennifer Thom <[email protected]>
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changed
case_whentocase_matchas it's easier to read