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]>

Also, use `dplyr::last_col()` to more generically specify the range.

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]>

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]>

* 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]>

* 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]>

* 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 the incorrect format in period

---------

Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: James McMahon <[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]>

* 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]>

* 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 the incorrect format in period

---------

Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: James McMahon <[email protected]>

Co-authored-by: James McMahon <[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]>

* New function `create_sending_location_test_flags`

* 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]>

* 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]>

Co-authored-by: Jennit07 <[email protected]>

Takes too long to process tests

The episode file tests were taking far too long to process the tests due
to `slfhelper::get_chi()`. I have changed the tests to check for
`anon_chi` instead of `chi`. This will show how many unique `anon_chi`
we have and how many missing. The only difference from the `chi` checks
before is that we cant test for `valid chi` using `phs_methods::`. I
have tested this against 1718 and it is able to produce the tests.

Once this has merged back in we will be able to run targets again as due
to tests failing this was unable to create the individual file.

This was causing an issue in tests

This reverts commit bf5f9b0.

This reverts commit 628da4d.

* Update create_individual_file.R

* Update documentation

* Style code

---------

Co-authored-by: lizihao-anu <[email protected]>

* 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]>

This was causing an error