From 2d7c3d599d49ea2aa76ce21c16404e3db036f963 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Wed, 13 Sep 2023 17:09:22 +0100 Subject: [PATCH 01/29] Update the workflows so they will run on a PR to dev or development --- .github/workflows/R-CMD-check.yaml | 10 ++++++++-- .github/workflows/lint.yaml | 10 ++++++++-- .github/workflows/test-coverage.yaml | 8 ++++++-- 3 files changed, 22 insertions(+), 6 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 9fb4ca8..5b5ee01 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -2,9 +2,15 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master, dev] + branches: + - 'main' + - 'master' + - 'dev**' pull_request: - branches: [main, master, dev] + branches: + - 'main' + - 'master' + - 'dev**' name: R-CMD-check diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index c200b81..92e929b 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -2,9 +2,15 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master, dev] + branches: + - 'main' + - 'master' + - 'dev**' pull_request: - branches: [main, master, dev] + branches: + - 'main' + - 'master' + - 'dev**' name: lint diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 1365b61..6f5abde 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -2,9 +2,13 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master, dev] + branches: + - 'main' + - 'master' pull_request: - branches: [main, master, dev] + - 'main' + - 'master' + - 'dev**' name: test-coverage From afb9aeb6be285eaa72579b6cf9f57664e847af14 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Wed, 13 Sep 2023 17:44:51 +0100 Subject: [PATCH 02/29] Update the checked versions Updating these to more closely match. 1. The versions checked by CRAN. 2. The current PHS RStudio Desktop install. 3. The current PHS Post Workbench setup. --- .github/workflows/R-CMD-check.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 5b5ee01..7dc5e06 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -29,16 +29,19 @@ jobs: - {os: ubuntu-latest, r: 'release', must_pass: true} # Development and recent releases - - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release', must_pass: false} - - {os: ubuntu-latest, r: 'oldrel-1', must_pass: true} - - {os: ubuntu-latest, r: 'oldrel-2', must_pass: true} + - {os: windows-latest, r: 'devel', http-user-agent: 'release', must_pass: true} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release', must_pass: true} + - {os: ubuntu-latest, r: 'oldrel-1', must_pass: false} + - {os: ubuntu-latest, r: 'oldrel-2', must_pass: false} # An approximation for the PHS RStudio Desktop installation - {os: windows-latest, r: '3.6.1', must_pass: true} + - {os: windows-latest, r: '4.0.1', must_pass: true} - # An approximation of the PHS RStudio Server Pro setup + # An approximation of the PHS RStudio setup on Posit Workbench - {os: ubuntu-latest, r: '3.6.1', must_pass: true} - - {os: ubuntu-latest, r: '3.5.1', must_pass: false} + - {os: ubuntu-latest, r: '4.0.2', must_pass: true} + - {os: ubuntu-latest, r: '4.1.2', must_pass: true} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} From f34eac30d104497719583758b9954020696ed9c6 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Fri, 15 Sep 2023 14:57:35 +0100 Subject: [PATCH 03/29] Update render-README.yaml workflow to only open a PR on master This brings this workflow inline with style and document, and should resolve an issue where it tried to run after a release (tag) was created and it failed. --- .github/workflows/render-README.yaml | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/.github/workflows/render-README.yaml b/.github/workflows/render-README.yaml index 610b90f..61f745a 100644 --- a/.github/workflows/render-README.yaml +++ b/.github/workflows/render-README.yaml @@ -33,14 +33,20 @@ jobs: - name: Render README.Rmd run: Rscript -e 'rmarkdown::render("README.Rmd")' - - name: Commit and create a Pull Request + - name: Commit and create a Pull Request on master + if: ${{ github.ref == 'refs/heads/master' }} uses: peter-evans/create-pull-request@v4 with: - add-paths: README.md - commit-message: Render `README.md` after changes to the `.Rmd` version - branch: render_readme + commit-message: "Automated re-knit of the README" + branch: document_master delete-branch: true - title: Automated re-knit of the README + title: Re-knit README.md due to changes made to README.Rmd labels: documentation,Maintainance assignees: ${{ github.actor }} reviewers: ${{ github.actor }} + + - name: Commit and push changes on all other branches + if: ${{ github.ref != 'refs/heads/master' }} + uses: stefanzweifel/git-auto-commit-action@v4 + with: + commit_message: "Automated re-knit of the README" From 6c85d89b2122e8d99fa0c92b5f58c92950d1ef69 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Mon, 18 Sep 2023 14:53:58 +0100 Subject: [PATCH 04/29] Update test-coverage.yaml Fix typo in #107 --- .github/workflows/test-coverage.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 6f5abde..56ed12e 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -6,6 +6,7 @@ on: - 'main' - 'master' pull_request: + branches: - 'main' - 'master' - 'dev**' From 5d14b465de76ec7df063b6caefa3bebd048d46a9 Mon Sep 17 00:00:00 2001 From: Tina815 Date: Tue, 19 Sep 2023 15:52:58 +0100 Subject: [PATCH 05/29] fix title in description --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index df018e7..fe92167 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: phsmethods -Title: Standard Methods for use in Public Health Scotland +Title: Standard Methods for Use in Public Health Scotland Version: 0.2.3 Authors@R: c( person("Public Health Scotland", , , "phs.source@phs.scot", role = "cph"), From 1fe312757e81a8853754daea2afd2f42be172710 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Wed, 20 Sep 2023 09:08:45 +0100 Subject: [PATCH 06/29] Fix a typo in DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index df018e7..cb51a76 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: phsmethods Title: Standard Methods for use in Public Health Scotland Version: 0.2.3 Authors@R: c( - person("Public Health Scotland", , , "phs.source@phs.scot", role = "cph"), + person("Public Health Scotland", , , "phs.datascience@phs.scot", role = "cph"), person("David", "Caldwell", , "David.Caldwell@phs.scot", role = "aut"), person("Lucinda", "Lawrie", , "Lucinda.Lawrie@phs.scot", role = "rev"), person("Jack", "Hannah", , "jack.hannah2@phs.scot", role = "aut"), From 2ee7deb389ab9e1d97ea0d654ff7360deec3c8ad Mon Sep 17 00:00:00 2001 From: Tina815 Date: Fri, 22 Sep 2023 10:36:43 +0100 Subject: [PATCH 07/29] fix typo and add cran-comments --- .Rbuildignore | 1 + DESCRIPTION | 2 +- cran-comments.md | 5 +++++ 3 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 cran-comments.md diff --git a/.Rbuildignore b/.Rbuildignore index 0d60c6b..20be837 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -7,3 +7,4 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^cran-comments\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index fe92167..b0493f3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: phsmethods Title: Standard Methods for Use in Public Health Scotland Version: 0.2.3 Authors@R: c( - person("Public Health Scotland", , , "phs.source@phs.scot", role = "cph"), + person("Public Health Scotland", , , "phs.datascience@phs.scot", role = "cph"), person("David", "Caldwell", , "David.Caldwell@phs.scot", role = "aut"), person("Lucinda", "Lawrie", , "Lucinda.Lawrie@phs.scot", role = "rev"), person("Jack", "Hannah", , "jack.hannah2@phs.scot", role = "aut"), diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..858617d --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,5 @@ +## R CMD check results + +0 errors | 0 warnings | 1 note + +* This is a new release. From 81cc4d07f29492fc7cdec955f93785f179f445ba Mon Sep 17 00:00:00 2001 From: Tina815 Date: Fri, 22 Sep 2023 14:33:27 +0100 Subject: [PATCH 08/29] update some links after url check --- README.Rmd | 2 +- man/file_size.Rd | 2 +- man/phsmethods.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.Rmd b/README.Rmd index 9ad1ae7..25a8263 100644 --- a/README.Rmd +++ b/README.Rmd @@ -33,7 +33,7 @@ knitr::opts_chunk$set( - `dob_from_chi()` extracts Date of Birth (DoB) from the CHI number - `age_from_chi()` extracts age from the CHI number -`phsmethods` can be used on both the [PHS server](https://pwb.publichealthscotland.org/) and desktop versions of RStudio. +`phsmethods` can be used on both the PHS server and desktop versions of RStudio. ## Installation diff --git a/man/file_size.Rd b/man/file_size.Rd index db45309..172159e 100644 --- a/man/file_size.Rd +++ b/man/file_size.Rd @@ -59,7 +59,7 @@ prefixed with `Excel` Files with extensions not contained within this list will have their size returned with no prefix. To request that a certain extension be explicitly catered for, please create an issue on -\href{https://github.com/Health-SocialCare-Scotland/phsmethods/issues}{GitHub}. +\href{https://github.com/Public-Health-Scotland/phsmethods/issues}{GitHub}. File sizes are returned as the appropriate multiple of the unit byte (bytes (B), kilobytes (KB), megabytes (MB), etc.). Each multiple is taken to diff --git a/man/phsmethods.Rd b/man/phsmethods.Rd index ea38a6c..64143ac 100644 --- a/man/phsmethods.Rd +++ b/man/phsmethods.Rd @@ -9,5 +9,5 @@ Standard Methods for use in PHS. } \details{ See the README on -\href{https://github.com/Health-SocialCare-Scotland/phsmethods#readme}{GitHub}. +\href{https://github.com/Public-Health-Scotland/phsmethods#readme}{GitHub}. } From d44698ccf912f1498cf50f0ea4c464ce6e37306e Mon Sep 17 00:00:00 2001 From: Tina815 Date: Fri, 22 Sep 2023 13:36:35 +0000 Subject: [PATCH 09/29] Automated re-knit of the README --- README.html | 742 ++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 3 +- 2 files changed, 743 insertions(+), 2 deletions(-) create mode 100644 README.html diff --git a/README.html b/README.html new file mode 100644 index 0000000..c4a1a4f --- /dev/null +++ b/README.html @@ -0,0 +1,742 @@ + + + + + + + + + + + + + + + + + + + + + +

phsmethods

+

GitHub release (latest by date) Build Status codecov

+

phsmethods contains functions for commonly undertaken +analytical tasks in Public Health Scotland +(PHS):

+
    +
  • create_age_groups() categorises ages into groups
    • +
  • chi_check() assesses the validity of a CHI number
    • +
  • chi_pad() adds a leading zero to nine-digit CHI +numbers
    • +
  • sex_from_chi() extracts the sex of a person from a CHI +number
    • +
  • file_size() returns the names and sizes of files in a +directory
    • +
  • extract_fin_year() assigns a date to a financial year +in the format YYYY/YY
    • +
  • match_area() converts geography codes into area +names
    • +
  • format_postcode() formats improperly recorded +postcodes
    • +
  • qtr(), qtr_end(), qtr_next() +and qtr_prev() assign a date to a quarter
    • +
  • age_calculate() calculates age between two dates
    • +
  • dob_from_chi() extracts Date of Birth (DoB) from the +CHI number
    • +
  • age_from_chi() extracts age from the CHI number
    • +
+

phsmethods can be used on both the PHS server and +desktop versions of RStudio.

+

Installation

+

If you are using the PHS Posit Workbench the default repository is +the PHS Posit Package Manager, the benefit of this is that +phsmethods is listed there so you can install it with:

+
install.packages("phsmethods")
+

To install phsmethods directly from GitHub, the package +remotes is required, and can be installed with +install.packages("remotes").

+

You can then install phsmethods from GitHub with:

+
remotes::install_github("Public-Health-Scotland/phsmethods")
+

However, network security settings may prevent +remotes::install_github() from working on RStudio desktop. +If this is the case, phsmethods can be installed by +downloading the zip +of the repository and running the following code (replacing the +section marked <>, including the arrows +themselves):

+
remotes::install_local("<FILEPATH OF ZIPPED FILE>/phsmethods-master.zip",
+  upgrade = "never"
+)
+

Using phsmethods

+

Load phsmethods using library():

+
library(phsmethods)
+

To see the documentation for any phsmethods’ functions, +type ?function_name into the RStudio console after loading +the package:

+
?extract_fin_year
+?format_postcode
+

You can access the full list of functions and their help pages on Reference +page of pkgdown website. You will be able to see some examples of +each function.

+

There is also a very useful PHS Methods +online training course which gives you an interactive way to learn +about this package.

+

Contributing to phsmethods

+

At present, the maintainer of this package is Tina Fu.

+

This package is intended to be in continuous development and +contributions may be made by anyone within PHS. If you would like to +contribute, please first create an issue +on GitHub and assign both of the package maintainers to +it. This is to ensure that no duplication of effort occurs in the case +of multiple people having the same idea. The package maintainers will +discuss the issue and get back to you as soon as possible.

+

While the most obvious and eye-catching (as well as intimidating) way +of contributing is by writing a function, this isn’t the only way to +make a useful contribution. Fixing typos in documentation, for example, +isn’t the most glamorous way to contribute, but is of great help to the +package maintainers. Please see this blog post by +Jim Hester for more information on getting started with contributing +to open-source software.

+

When contributing, please create a branch +in this repository and carry out all work on it. Please ensure you have +linked RStudio to your GitHub account using +usethis::edit_git_config() prior to making your +contribution. When you are ready for a review, please create a pull +request and assign both of the package maintainers +as reviewers. One or both of them will conduct a review, provide +feedback and, if necessary, request changes before merging your +branch.

+

Please be mindful of information governance when contributing to this +package. No data files (aside from publicly available and downloadable +datasets or unless explicitly approved), server connection details, +passwords or person identifiable or otherwise confidential information +should be included anywhere within this package or any other repository +(whether public or private) used within PHS. This includes within code +and code commentary. For more information on security when using git and +GitHub, and on using git and GitHub for version control more generally, +please see the Transforming +Publishing Programme’s Git guide +and GitHub +guidance.

+

Please feel free to add yourself to the ‘Authors’ section of the +Description file when contributing. As a rule of thumb, +please assign your role as author ("aut") when writing an +exported function, and as contributor ("ctb") for anything +else.

+

phsmethods will, as much as possible, adhere to the tidyverse style guide and the rOpenSci package development +guide. The most pertinent points to take from these are:

+
    +
  • All function names should be in lower case, with words separated by +an underscore
    • +
  • Put a space after a comma, never before
    • +
  • Put a space before and after infix operators such as +<-, == and +
    • +
  • Limit code to 80 characters per line
    • +
  • Function documentation should be generated using roxygen2
    • +
  • All functions should be tested using testthat
    • +
  • The package should always pass devtools::check()
    • +
+

It’s not necessary to have experience with GitHub or of building an R +package to contribute to phsmethods. If you wish to +contribute code then, as long as you can write an R function, the +package maintainers can assist with error handling, writing +documentation, testing and other aspects of package development. It is +advised, however, to consult Hadley +Wickham’s R Packages book prior to making a contribution. It may +also be useful to consult the documentation +and tests +of existing functions within this package as a point of reference.

+

Please note that this README may fail to ‘Knit’ at times as a result +of network security settings. This will likely be due to the badges for +the package’s release version, continuous integration status and test +coverage at the top of the document. You should only make edits to the +.Rmd version, you can then knit yourself, or a GitHub +action should run and knit it for you when you open a pull request.

+ + + diff --git a/README.md b/README.md index 6ba6466..ab443a0 100644 --- a/README.md +++ b/README.md @@ -28,8 +28,7 @@ in [Public Health Scotland - `dob_from_chi()` extracts Date of Birth (DoB) from the CHI number - `age_from_chi()` extracts age from the CHI number -`phsmethods` can be used on both the [PHS -server](https://pwb.publichealthscotland.org/) and desktop versions of +`phsmethods` can be used on both the PHS server and desktop versions of RStudio. ## Installation From 816b1b5360a29111f64531c215782d852b9b3ca9 Mon Sep 17 00:00:00 2001 From: Tina815 Date: Mon, 25 Sep 2023 15:32:37 +0100 Subject: [PATCH 10/29] update links in R files --- R/file_size.R | 2 +- R/phsmethods.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/file_size.R b/R/file_size.R index 4f38bbe..99220af 100644 --- a/R/file_size.R +++ b/R/file_size.R @@ -30,7 +30,7 @@ #' Files with extensions not contained within this list will have their size #' returned with no prefix. To request that a certain extension be explicitly #' catered for, please create an issue on -#' \href{https://github.com/Health-SocialCare-Scotland/phsmethods/issues}{GitHub}. +#' \href{https://github.com/Public-Health-Scotland/phsmethods/issues}{GitHub}. #' #' File sizes are returned as the appropriate multiple of the unit byte #' (bytes (B), kilobytes (KB), megabytes (MB), etc.). Each multiple is taken to diff --git a/R/phsmethods.R b/R/phsmethods.R index 8d320e0..54453c0 100644 --- a/R/phsmethods.R +++ b/R/phsmethods.R @@ -3,7 +3,7 @@ #' Standard Methods for use in PHS. #' #' See the README on -#' \href{https://github.com/Health-SocialCare-Scotland/phsmethods#readme}{GitHub}. +#' \href{https://github.com/Public-Health-Scotland/phsmethods#readme}{GitHub}. #' #' @docType package #' @name phsmethods From e11b1324e845bf9d0e072cf835e2d3d0d286b687 Mon Sep 17 00:00:00 2001 From: Tina Fu Date: Mon, 25 Sep 2023 16:50:37 +0100 Subject: [PATCH 11/29] delete readme.html --- .Rbuildignore | 1 + .gitignore | 1 + README.html | 742 -------------------------------------------------- 3 files changed, 2 insertions(+), 742 deletions(-) delete mode 100644 README.html diff --git a/.Rbuildignore b/.Rbuildignore index 20be837..498b6f0 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,6 +1,7 @@ ^phsmethods\.Rproj$ ^\.Rproj\.user$ ^README\.Rmd$ +^README\.html$ ^README-.*\.png$ ^data-raw$ ^\.github$ diff --git a/.gitignore b/.gitignore index 234f028..e091e97 100644 --- a/.gitignore +++ b/.gitignore @@ -2,4 +2,5 @@ .Rhistory .RData .Ruserdata +*.html docs diff --git a/README.html b/README.html deleted file mode 100644 index c4a1a4f..0000000 --- a/README.html +++ /dev/null @@ -1,742 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - -

phsmethods

-

GitHub release (latest by date) Build Status codecov

-

phsmethods contains functions for commonly undertaken -analytical tasks in Public Health Scotland -(PHS):

-
    -
  • create_age_groups() categorises ages into groups
    • -
  • chi_check() assesses the validity of a CHI number
    • -
  • chi_pad() adds a leading zero to nine-digit CHI -numbers
    • -
  • sex_from_chi() extracts the sex of a person from a CHI -number
    • -
  • file_size() returns the names and sizes of files in a -directory
    • -
  • extract_fin_year() assigns a date to a financial year -in the format YYYY/YY
    • -
  • match_area() converts geography codes into area -names
    • -
  • format_postcode() formats improperly recorded -postcodes
    • -
  • qtr(), qtr_end(), qtr_next() -and qtr_prev() assign a date to a quarter
    • -
  • age_calculate() calculates age between two dates
    • -
  • dob_from_chi() extracts Date of Birth (DoB) from the -CHI number
    • -
  • age_from_chi() extracts age from the CHI number
    • -
-

phsmethods can be used on both the PHS server and -desktop versions of RStudio.

-

Installation

-

If you are using the PHS Posit Workbench the default repository is -the PHS Posit Package Manager, the benefit of this is that -phsmethods is listed there so you can install it with:

-
install.packages("phsmethods")
-

To install phsmethods directly from GitHub, the package -remotes is required, and can be installed with -install.packages("remotes").

-

You can then install phsmethods from GitHub with:

-
remotes::install_github("Public-Health-Scotland/phsmethods")
-

However, network security settings may prevent -remotes::install_github() from working on RStudio desktop. -If this is the case, phsmethods can be installed by -downloading the zip -of the repository and running the following code (replacing the -section marked <>, including the arrows -themselves):

-
remotes::install_local("<FILEPATH OF ZIPPED FILE>/phsmethods-master.zip",
-  upgrade = "never"
-)
-

Using phsmethods

-

Load phsmethods using library():

-
library(phsmethods)
-

To see the documentation for any phsmethods’ functions, -type ?function_name into the RStudio console after loading -the package:

-
?extract_fin_year
-?format_postcode
-

You can access the full list of functions and their help pages on Reference -page of pkgdown website. You will be able to see some examples of -each function.

-

There is also a very useful PHS Methods -online training course which gives you an interactive way to learn -about this package.

-

Contributing to phsmethods

-

At present, the maintainer of this package is Tina Fu.

-

This package is intended to be in continuous development and -contributions may be made by anyone within PHS. If you would like to -contribute, please first create an issue -on GitHub and assign both of the package maintainers to -it. This is to ensure that no duplication of effort occurs in the case -of multiple people having the same idea. The package maintainers will -discuss the issue and get back to you as soon as possible.

-

While the most obvious and eye-catching (as well as intimidating) way -of contributing is by writing a function, this isn’t the only way to -make a useful contribution. Fixing typos in documentation, for example, -isn’t the most glamorous way to contribute, but is of great help to the -package maintainers. Please see this blog post by -Jim Hester for more information on getting started with contributing -to open-source software.

-

When contributing, please create a branch -in this repository and carry out all work on it. Please ensure you have -linked RStudio to your GitHub account using -usethis::edit_git_config() prior to making your -contribution. When you are ready for a review, please create a pull -request and assign both of the package maintainers -as reviewers. One or both of them will conduct a review, provide -feedback and, if necessary, request changes before merging your -branch.

-

Please be mindful of information governance when contributing to this -package. No data files (aside from publicly available and downloadable -datasets or unless explicitly approved), server connection details, -passwords or person identifiable or otherwise confidential information -should be included anywhere within this package or any other repository -(whether public or private) used within PHS. This includes within code -and code commentary. For more information on security when using git and -GitHub, and on using git and GitHub for version control more generally, -please see the Transforming -Publishing Programme’s Git guide -and GitHub -guidance.

-

Please feel free to add yourself to the ‘Authors’ section of the -Description file when contributing. As a rule of thumb, -please assign your role as author ("aut") when writing an -exported function, and as contributor ("ctb") for anything -else.

-

phsmethods will, as much as possible, adhere to the tidyverse style guide and the rOpenSci package development -guide. The most pertinent points to take from these are:

-
    -
  • All function names should be in lower case, with words separated by -an underscore
    • -
  • Put a space after a comma, never before
    • -
  • Put a space before and after infix operators such as -<-, == and +
    • -
  • Limit code to 80 characters per line
    • -
  • Function documentation should be generated using roxygen2
    • -
  • All functions should be tested using testthat
    • -
  • The package should always pass devtools::check()
    • -
-

It’s not necessary to have experience with GitHub or of building an R -package to contribute to phsmethods. If you wish to -contribute code then, as long as you can write an R function, the -package maintainers can assist with error handling, writing -documentation, testing and other aspects of package development. It is -advised, however, to consult Hadley -Wickham’s R Packages book prior to making a contribution. It may -also be useful to consult the documentation -and tests -of existing functions within this package as a point of reference.

-

Please note that this README may fail to ‘Knit’ at times as a result -of network security settings. This will likely be due to the badges for -the package’s release version, continuous integration status and test -coverage at the top of the document. You should only make edits to the -.Rmd version, you can then knit yourself, or a GitHub -action should run and knit it for you when you open a pull request.

- - - From a8cb3692d34eac51337ac90b75efbe5e8cc56675 Mon Sep 17 00:00:00 2001 From: Tina Fu Date: Wed, 27 Sep 2023 10:38:43 +0100 Subject: [PATCH 12/29] increment version for CRAN submission --- DESCRIPTION | 2 +- NEWS.md | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b0493f3..0d5391c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: phsmethods Title: Standard Methods for Use in Public Health Scotland -Version: 0.2.3 +Version: 1.0.0 Authors@R: c( person("Public Health Scotland", , , "phs.datascience@phs.scot", role = "cph"), person("David", "Caldwell", , "David.Caldwell@phs.scot", role = "aut"), diff --git a/NEWS.md b/NEWS.md index fb67176..fba20f2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# phsmethods 1.0.0 (2023-09-26) + +- This is the first new major release to CRAN. + # phsmethods 0.2.3 (2023-09-11) - The [{gdata}](https://github.com/r-gregmisc/gdata) import has been dropped and replaced with [{scales}](https://scales.r-lib.org/). From 1bec3bcbdc5b629c44fa5ee44dea050fbdb2761e Mon Sep 17 00:00:00 2001 From: James McMahon Date: Mon, 2 Oct 2023 18:01:54 +0100 Subject: [PATCH 13/29] Update the documentation I added return values to the documentation where it was missing - per the CRAN comments. I also converted the documentation to Markdown (using [roxygen2md](https://roxygen2md.r-lib.org/) as recommended), as it makes the documentation easier to write and maintain. I also ran `goodpractice::goodpractice()` to check if anything else was possibly missed and this led to a few more cosmetic changes and the removal of `purrr` from Imports as it's not actually being used in the package. --- DESCRIPTION | 2 +- R/age_calculate.R | 42 +++++++---- R/chi_check.R | 52 +++++++------- R/chi_pad.R | 17 +++-- R/create_age_groups.R | 28 ++++---- R/data.R | 12 ++-- R/dob_from_chi.R | 93 +++++++++++++++++-------- R/extract_fin_year.R | 12 ++-- R/file_size.R | 58 +++++++-------- R/format_postcode.R | 18 ++--- R/make_inheritance_checks.R | 18 +++-- R/match_area.R | 18 ++--- R/phsmethods.R | 4 +- R/qtr.R | 14 ++-- R/rename.R | 8 +-- R/sex_from_chi.R | 55 +++++++++------ man/age_calculate.Rd | 26 ++++--- man/age_from_chi.Rd | 27 ++++--- man/area_lookup.Rd | 8 +-- man/chi_check.Rd | 32 +++++---- man/chi_pad.Rd | 5 +- man/create_age_groups.Rd | 2 +- man/dob_from_chi.Rd | 20 +++--- man/extract_fin_year.Rd | 5 +- man/file_size.Rd | 36 +++++----- man/format_postcode.Rd | 12 ++-- man/make_inheritance_checks.Rd | 6 +- man/match_area.Rd | 8 +-- man/qtr.Rd | 7 +- man/rename.Rd | 6 +- man/sex_from_chi.Rd | 29 +++++--- tests/testthat/test-create_age_groups.R | 8 ++- 32 files changed, 407 insertions(+), 281 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cb51a76..738d351 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,7 +32,6 @@ Imports: lifecycle, lubridate, magrittr, - purrr, readr, rlang, scales (>= 1.0.0), @@ -50,3 +49,4 @@ Encoding: UTF-8 Language: en-GB LazyData: true RoxygenNote: 7.2.3 +Roxygen: list(markdown = TRUE) diff --git a/R/age_calculate.R b/R/age_calculate.R index 06a82be..6671fa8 100644 --- a/R/age_calculate.R +++ b/R/age_calculate.R @@ -1,17 +1,23 @@ #' Calculate age between two dates #' -#' @description This function calculates the age between two dates using functions in \code{lubridate}. -#' It calculates age in either years or months. +#' @description This function calculates the age between two dates using +#' functions in `lubridate`. It calculates age in either years or months. #' -#' @param start A start date (e.g. date of birth) which must be supplied with \code{Date} or \code{POSIXct} or \code{POSIXlt} -#' class. \code{\link[base:as.Date]{as.Date()}}, -#' \code{\link[lubridate:ymd]{lubridate::dmy()}} and -#' \code{\link[base:as.POSIXlt]{as.POSIXct()}} are examples of functions which +#' @param start A start date (e.g. date of birth) which must be supplied with +#' `Date` or `POSIXct` or `POSIXlt` +#' class. [base::as.Date()], +#' [`lubridate::dmy()`][lubridate::ymd] and +#' [`as.POSIXct()`][base::as.POSIXlt] are examples of functions which #' can be used to store dates as an appropriate class. -#' @param end An end date which must be supplied with \code{Date} or \code{POSIXct} or \code{POSIXlt} class. -#' Default is \code{Sys.Date()} or \code{Sys.time()} depending on the class of \code{start}. -#' @param units Type of units to be used. years and months are accepted. Default is \code{years}. -#' @param round_down Should returned ages be rounded down to the nearest whole number. Default is \code{TRUE}. +#' @param end An end date which must be supplied with `Date` or `POSIXct` or +#' `POSIXlt` class. Default is `Sys.Date()` or `Sys.time()` depending on the +#' class of `start`. +#' @param units Type of units to be used. years and months are accepted. +#' Default is `years`. +#' @param round_down Should returned ages be rounded down to the nearest whole +#' number. Default is `TRUE`. +#' +#' @return A numeric vector representing the ages in the given units. #' #' @examples #' library(lubridate) @@ -20,7 +26,8 @@ #' age_calculate(birth_date, end_date) #' age_calculate(birth_date, end_date, units = "months") #' -#' # If the start day is leap day (February 29th), age increases on 1st March every year. +#' # If the start day is leap day (February 29th), age increases on 1st March +#' # every year. #' leap1 <- lubridate::ymd("2020-02-29") #' leap2 <- lubridate::ymd("2022-02-28") #' leap3 <- lubridate::ymd("2022-03-01") @@ -28,9 +35,16 @@ #' age_calculate(leap1, leap2) #' age_calculate(leap1, leap3) #' @export -age_calculate <- function(start, end = if (lubridate::is.Date(start)) Sys.Date() else Sys.time(), - units = c("years", "months"), round_down = TRUE) { - make_inheritance_checks(list(start = start, end = end), target_classes = c("Date", "POSIXt"), ignore_null = FALSE) +age_calculate <- function( + start, + end = if (lubridate::is.Date(start)) Sys.Date() else Sys.time(), + units = c("years", "months"), + round_down = TRUE) { + make_inheritance_checks( + list(start = start, end = end), + target_classes = c("Date", "POSIXt"), + ignore_null = FALSE + ) units <- match.arg(tolower(units), c("years", "months")) diff --git a/R/chi_check.R b/R/chi_check.R index 477ce48..1f45fdd 100644 --- a/R/chi_check.R +++ b/R/chi_check.R @@ -1,7 +1,7 @@ #' @title Check the validity of a CHI number #' -#' @description \code{chi_check} takes a CHI number or a vector of CHI numbers -#' with \code{character} class. It returns feedback on the validity of the +#' @description `chi_check` takes a CHI number or a vector of CHI numbers +#' with `character` class. It returns feedback on the validity of the #' entered CHI number and, if found to be invalid, provides an explanation as #' to why. #' @@ -16,44 +16,46 @@ #' even for female. The tenth digit is a check digit, denoted `checksum`. #' #' While a CHI number is made up exclusively of numeric digits, it cannot be -#' stored with \code{numeric} class in R. This is because leading zeros in +#' stored with `numeric` class in R. This is because leading zeros in #' numeric values are silently dropped, a practice not exclusive to R. For this -#' reason, \code{chi_check} accepts input values of \code{character} class +#' reason, `chi_check` accepts input values of `character` class #' only. A leading zero can be added to a nine-digit CHI number using -#' \code{\link{chi_pad}}. +#' [chi_pad()]. #' -#' \code{chi_check} assesses whether an entered CHI number is valid by checking +#' `chi_check` assesses whether an entered CHI number is valid by checking #' whether the answer to each of the following criteria is `Yes`: #' -#' \itemize{ -#' \item Does it contain no non-numeric characters? -#' \item Is it ten digits in length? -#' \item Do the first six digits denote a valid date? -#' \item Is the checksum digit correct? -#' } +#' * Does it contain no non-numeric characters? +#' * Is it ten digits in length? +#' * Do the first six digits denote a valid date? +#' * Is the checksum digit correct? #' -#' @param x a CHI number or a vector of CHI numbers with \code{character} class. +#' @param x a CHI number or a vector of CHI numbers with `character` class. #' -#' @return \code{chi_check} returns a character string. Depending on the +#' @return `chi_check` returns a character string. Depending on the #' validity of the entered CHI number, it will return one of the following: #' -#' \itemize{ -#' \item `Valid CHI` -#' \item `Invalid character(s) present` -#' \item `Too many characters` -#' \item `Too few characters` -#' \item `Invalid date` -#' \item `Invalid checksum` -#' \item `Missing (NA)` -#' \item `Missing (Blank)` -#' } +#' * `Valid CHI` +#' * `Invalid character(s) present` +#' * `Too many characters` +#' * `Too few characters` +#' * `Invalid date` +#' * `Invalid checksum` +#' * `Missing (NA)` +#' * `Missing (Blank)` #' #' @examples #' chi_check("0101011237") #' chi_check(c("0101201234", "3201201234")) #' #' library(dplyr) -#' df <- tibble(chi = c("3213201234", "123456789", "12345678900", "010120123?", NA)) +#' df <- tibble(chi = c( +#' "3213201234", +#' "123456789", +#' "12345678900", +#' "010120123?", +#' NA +#' )) #' df %>% #' mutate(validity = chi_check(chi)) #' @export diff --git a/R/chi_pad.R b/R/chi_pad.R index 1a35609..4babb33 100644 --- a/R/chi_pad.R +++ b/R/chi_pad.R @@ -1,7 +1,7 @@ #' @title Add a leading zero to nine-digit CHI numbers #' -#' @description \code{chi_pad} takes a nine-digit CHI number with -#' \code{character} class and prefixes it with a zero. Any values provided +#' @description `chi_pad` takes a nine-digit CHI number with +#' `character` class and prefixes it with a zero. Any values provided #' which are not a string comprised of nine numeric digits remain unchanged. #' #' @details The Community Health Index (CHI) is a register of all patients in @@ -14,21 +14,24 @@ #' zero. #' #' While a CHI number is made up exclusively of numeric digits, it cannot be -#' stored with \code{numeric} class in R. This is because leading zeros in +#' stored with `numeric` class in R. This is because leading zeros in #' numeric values are silently dropped, a practice not exclusive to R. For this -#' reason, \code{chi_pad} accepts input values of \code{character} class +#' reason, `chi_pad` accepts input values of `character` class #' only, and returns values of the same class. It does not assess the validity -#' of a CHI number - please see \code{\link{chi_check}} for that. +#' of a CHI number - please see [chi_check()] for that. #' #' @inheritParams chi_check #' +#' @return The original character vector with CHI numbers padded if applicable. +#' #' @examples #' chi_pad(c("101011237", "101201234")) #' @export - chi_pad <- function(x) { if (!inherits(x, "character")) { - cli::cli_abort("The input must be a {.cls character} vector, not a {.cls {class(x)}} vector.") + cli::cli_abort( + "The input must be a {.cls character} vector, not a {.cls {class(x)}} vector." + ) } # Add a leading zero to any string comprised of nine numeric digits diff --git a/R/create_age_groups.R b/R/create_age_groups.R index 76ae9a7..4f2ef79 100644 --- a/R/create_age_groups.R +++ b/R/create_age_groups.R @@ -1,31 +1,31 @@ #' Create age groups #' #' @description -#' \code{create_age_groups()} takes a numeric vector and assigns each age to the +#' `create_age_groups()` takes a numeric vector and assigns each age to the #' appropriate age group. #' #' @param x a vector of numeric values -#' @param from the start of the smallest age group. The default is \code{0}. -#' @param to the end point of the age groups. The default is \code{90}. -#' @param by the size of the age groups. The default is \code{5}. +#' @param from the start of the smallest age group. The default is `0`. +#' @param to the end point of the age groups. The default is `90`. +#' @param by the size of the age groups. The default is `5`. #' @param as_factor The default behaviour is to return a character vector. Use -#' \code{TRUE} to return a factor vector instead. +#' `TRUE` to return a factor vector instead. #' #' @return A character vector, where each element is the age group for the -#' corresponding element in \code{x}. If \code{as_factor = TRUE}, a factor +#' corresponding element in `x`. If `as_factor = TRUE`, a factor #' vector is returned instead. #' #' @details -#' The \code{from}, \code{to} and \code{by} values are used to create distinct -#' age groups. \code{from} dictates the starting age of the lowest age group, -#' and \code{by} indicates how wide each group should be. \code{to} stipulates +#' The `from`, `to` and `by` values are used to create distinct +#' age groups. `from` dictates the starting age of the lowest age group, +#' and `by` indicates how wide each group should be. `to` stipulates #' the cut-off point at which all ages equal to or greater than this value -#' should be categorised together in a \code{to+} group. If the specified value -#' of \code{to} is not a multiple of \code{by}, the value of \code{to} is -#' rounded down to the nearest multiple of \code{by}. +#' should be categorised together in a `to+` group. If the specified value +#' of `to` is not a multiple of `by`, the value of `to` is +#' rounded down to the nearest multiple of `by`. #' -#' The default values of \code{from}, \code{to} and \code{by} correspond to the -#' \href{https://www.opendata.nhs.scot/dataset/standard-populations/resource/edee9731-daf7-4e0d-b525-e4c1469b8f69}{European Standard Population} +#' The default values of `from`, `to` and `by` correspond to the +#' [European Standard Population](https://www.opendata.nhs.scot/dataset/standard-populations/resource/edee9731-daf7-4e0d-b525-e4c1469b8f69) #' age groups. #' #' @examples diff --git a/R/data.R b/R/data.R index 52a8cdf..28715f0 100644 --- a/R/data.R +++ b/R/data.R @@ -1,22 +1,22 @@ #' Codes and names of Scottish geographical and administrative areas. #' #' A dataset containing Scotland's geography codes and associated area names. -#' It is used within \code{\link{match_area}}. +#' It is used within [match_area()]. #' -#' @details \code{geo_code} contains geography codes pertaining to Health +#' @details `geo_code` contains geography codes pertaining to Health #' Boards, Council Areas, Health and Social Care Partnerships, Intermediate #' Zones, Data Zones (2001 and 2011), Electoral Wards, Scottish Parliamentary #' Constituencies, UK Parliamentary Constituencies, Travel to work areas, #' National Parks, Community Health Partnerships, Localities (S19), #' Settlements (S20) and Scotland. #' -#' @seealso The script used to create the \code{area_lookup} dataset on -#' \href{https://github.com/Public-Health-Scotland/phsmethods/blob/master/data-raw/area_lookup.R}{GitHub}. +#' @seealso The script used to create the `area_lookup` dataset on +#' [GitHub](https://github.com/Public-Health-Scotland/phsmethods/blob/master/data-raw/area_lookup.R). #' -#' @format A \code{\link[tibble]{tibble}} with 2 variables and over 17,000 rows: +#' @format A [tibble::tibble()] with 2 variables and over 17,000 rows: #' \describe{ #' \item{geo_code}{Standard geography code - 9 characters} #' \item{area_name}{Name of the area the code represents} #' } -#' @source \url{https://statistics.gov.scot/} +#' @source "area_lookup" diff --git a/R/dob_from_chi.R b/R/dob_from_chi.R index a5e928a..b0de730 100644 --- a/R/dob_from_chi.R +++ b/R/dob_from_chi.R @@ -1,17 +1,21 @@ #' @title Extract Date of Birth (DoB) from the CHI number #' -#' @description \code{dob_from_chi} takes a CHI number or a vector of CHI numbers -#' and returns the DoB as implied by the CHI number(s). If the DoB is ambiguous -#' it will return NA +#' @description `dob_from_chi` takes a CHI number or a vector of CHI numbers +#' and returns the Date of Birth (DoB) as implied by the CHI number(s). If the +#' DoB is ambiguous it will return NA. #' -#' @param chi_number a CHI number or a vector of CHI numbers with \code{character} class. -#' @param min_date,max_date optional min and/or max dates that the Date of Birth could take as the century needs to be guessed. -#' Must be either length 1 for a 'fixed' date or the same length as \code{chi_number} for a date per CHI number. -#' min_date can be date based on common sense in the dataset, whilst max_date can be date when an event happens such as discharge date. -#' @param chi_check logical, optionally skip checking the CHI for validity which will be -#' faster but should only be used if you have previously checked the CHI(s). The default (TRUE) will check the CHI numbers. +#' @param chi_number a CHI number or a vector of CHI numbers with `character` +#' class. +#' @param min_date,max_date optional min and/or max dates that the +#' DoB could take as the century needs to be guessed. Must be either length 1 +#' for a 'fixed' date or the same length as `chi_number` for a date +#' per CHI number. `min_date` can be date based on common sense in the dataset, +#' whilst `max_date` can be date when an event happens such as discharge date. +#' @param chi_check logical, optionally skip checking the CHI for validity which +#' will be faster but should only be used if you have previously checked the +#' CHI(s). The default (TRUE) will check the CHI numbers. #' -#' @return a date vector of DoB. It will be the same length as \code{chi_number}. +#' @return a date vector of DoB. It will be the same length as `chi_number`. #' @export #' #' @examples @@ -37,18 +41,29 @@ #' min_date = as.Date("1930-01-01"), #' max_date = adm_date #' )) -dob_from_chi <- function(chi_number, min_date = NULL, max_date = NULL, chi_check = TRUE) { +dob_from_chi <- function( + chi_number, + min_date = NULL, + max_date = NULL, + chi_check = TRUE) { # Do type checking on the params if (!inherits(chi_number, "character")) { - cli::cli_abort("{.arg chi_number} must be a {.cls character} vector, not a {.cls {class(chi_number)}} vector.") + cli::cli_abort( + "{.arg chi_number} must be a {.cls character} vector, not a {.cls {class(chi_number)}} vector." + ) } - make_inheritance_checks(list(min_date = min_date, max_date = max_date), target_classes = c("Date", "POSIXct")) + make_inheritance_checks( + list(min_date = min_date, max_date = max_date), + target_classes = c("Date", "POSIXct") + ) # min and max date are in a reasonable range if (!is.null(min_date) & !is.null(max_date)) { if (any(max_date < min_date)) { - cli::cli_abort("{.arg max_date}, must always be greater than or equal to {.arg min_date}.") + cli::cli_abort( + "{.arg max_date}, must always be greater than or equal to {.arg min_date}." + ) } } @@ -62,7 +77,9 @@ dob_from_chi <- function(chi_number, min_date = NULL, max_date = NULL, chi_check if (any(max_date > Sys.Date())) { to_replace <- max_date > Sys.Date() max_date[to_replace] <- Sys.Date() - cli::cli_warn(c("!" = "Any {.arg max_date} values which are in the future will be set to today: {.val {Sys.Date()}}.")) + cli::cli_warn( + c("!" = "Any {.arg max_date} values which are in the future will be set to today: {.val {Sys.Date()}}.") + ) } # Default the min_date to 1 Jan 1900 @@ -77,7 +94,9 @@ dob_from_chi <- function(chi_number, min_date = NULL, max_date = NULL, chi_check new_na_count <- sum(is.na(chi_number)) - na_count if (new_na_count > 0) { - cli::cli_alert_warning(("{format(new_na_count, big.mark = ',')}{cli::qty(new_na_count)} CHI number{?s} {?is/are} invalid and will be given {.val NA} for {?its/their} Date{?s} of Birth.")) + cli::cli_alert_warning( + ("{format(new_na_count, big.mark = ',')}{cli::qty(new_na_count)} CHI number{?s} {?is/are} invalid and will be given {.val NA} for {?its/their} Date{?s} of Birth.") + ) } } @@ -105,10 +124,12 @@ dob_from_chi <- function(chi_number, min_date = NULL, max_date = NULL, chi_check is.na(date_1900) ~ date_2000, # Invalid leap year date in 20XX. is.na(date_2000) ~ date_1900, - # When 20XX date is in the valid range and the 19XX date isn't, 20XX is guessed. + # When 20XX date is in the valid range and the 19XX date isn't, + # 20XX is guessed. (date_2000 >= min_date & date_2000 <= max_date) & !(date_1900 >= min_date & date_1900 <= max_date) ~ date_2000, - # When 19XX date is in the valid range and the 20XX date isn't, 19XX is guessed. + # When 19XX date is in the valid range and the 20XX date isn't, + # 19XX is guessed. (date_1900 >= min_date & date_1900 <= max_date) & !(date_2000 >= min_date & date_2000 <= max_date) ~ date_1900 )) @@ -127,19 +148,26 @@ dob_from_chi <- function(chi_number, min_date = NULL, max_date = NULL, chi_check #' @title Extract age from the CHI number #' -#' @description \code{age_from_chi} takes a CHI number or a vector of CHI numbers -#' and returns the age as implied by the CHI number(s). If the DoB is ambiguous -#' it will return NA. It uses \code{dob_from_chi}. +#' @description `age_from_chi` takes a CHI number or a vector of CHI numbers +#' and returns the age as implied by the CHI number(s). If the Date of Birth +#' (DoB) is ambiguous it will return NA. It uses [dob_from_chi()]. #' -#' @param chi_number a CHI number or a vector of CHI numbers with \code{character} class. -#' @param ref_date calculate the age at this date, default is to use \code{Sys.Date()} i.e. today. -#' @param min_age,max_age optional min and/or max dates that the Date of Birth could take as the century needs to be guessed. -#' Must be either length 1 for a 'fixed' age or the same length as \code{chi_number} for an age per CHI number. -#' min_age can be age based on common sense in the dataset, whilst max_age can be age when an event happens such as the age at discharge. -#' @param chi_check logical, optionally skip checking the CHI for validity which will be -#' faster but should only be used if you have previously checked the CHI(s), the default (TRUE) will to check the CHI numbers. +#' @param chi_number a CHI number or a vector of CHI numbers with `character` +#' class. +#' @param ref_date calculate the age at this date, default is to use +#' `Sys.Date()` i.e. today. +#' @param min_age,max_age optional min and/or max dates that the DoB could take +#' as the century needs to be guessed. +#' Must be either length 1 for a 'fixed' age or the same length as `chi_number` +#' for an age per CHI number. +#' `min_age` can be age based on common sense in the dataset, whilst `max_age` +#' can be age when an event happens such as the age at discharge. +#' @param chi_check logical, optionally skip checking the CHI for validity which +#' will be faster but should only be used if you have previously checked the +#' CHI(s), the default (TRUE) will to check the CHI numbers. #' -#' @return an integer vector of ages in years truncated to the nearest year. It will be the same length as \code{chi_number}. +#' @return an integer vector of ages in years truncated to the nearest year. +#' It will be the same length as `chi_number`. #' @export #' #' @examples @@ -167,7 +195,12 @@ dob_from_chi <- function(chi_number, min_date = NULL, max_date = NULL, chi_check #' mutate(chi_age = age_from_chi(chi, #' ref_date = dis_date #' )) -age_from_chi <- function(chi_number, ref_date = NULL, min_age = 0, max_age = NULL, chi_check = TRUE) { +age_from_chi <- function( + chi_number, + ref_date = NULL, + min_age = 0, + max_age = NULL, + chi_check = TRUE) { # Do type checking on the params if (!inherits(chi_number, "character")) { cli::cli_abort("{.arg chi_number} must be a {.cls character} vector, not a {.cls {class(chi_number)}} vector.") diff --git a/R/extract_fin_year.R b/R/extract_fin_year.R index 2a74537..a8d7676 100644 --- a/R/extract_fin_year.R +++ b/R/extract_fin_year.R @@ -1,16 +1,18 @@ #' @title Extract the formatted financial year from a date #' -#' @description \code{extract_fin_year} takes a date and extracts the +#' @description `extract_fin_year` takes a date and extracts the #' correct financial year in the PHS specified format from it. #' #' @details The PHS accepted format for financial year is YYYY/YY e.g. 2017/18. #' -#' @param date A date which must be supplied with \code{Date} or \code{POSIXct} -#' class. \code{\link[base:as.Date]{as.Date()}}, -#' \code{\link[lubridate:ymd]{lubridate::dmy()}} and -#' \code{\link[base:as.POSIXlt]{as.POSIXct()}} are examples of functions which +#' @param date A date which must be supplied with `Date` or `POSIXct` +#' class. [base::as.Date()], +#' [`lubridate::dmy()`][lubridate::ymd] and +#' [`as.POSIXct()`][base::as.POSIXlt] are examples of functions which #' can be used to store dates as an appropriate class. #' +#' @return A character vector of financial years in the form '2017/18'. +#' #' @examples #' x <- lubridate::dmy(c(21012017, 04042017, 17112017)) #' extract_fin_year(x) diff --git a/R/file_size.R b/R/file_size.R index 4f38bbe..2336dca 100644 --- a/R/file_size.R +++ b/R/file_size.R @@ -1,58 +1,58 @@ #' @title Calculate file size #' -#' @description \code{file_size} takes a filepath and an optional regular +#' @description `file_size` takes a filepath and an optional regular #' expression pattern. It returns the size of all files within that directory #' which match the given pattern. #' #' @details The sizes of files with certain extensions are returned with the -#' type of file prefixed. For example, the size of a 12 KB \code{.xlsx} file is +#' type of file prefixed. For example, the size of a 12 KB `.xlsx` file is #' returned as `Excel 12 KB`. The complete list of explicitly catered-for file #' extensions and their prefixes are as follows: #' #' \itemize{ -#' \item \code{.xls}, \code{.xlsb}, \code{.xlsm} and \code{.xlsx} files are +#' \item `.xls`, `.xlsb`, `.xlsm` and `.xlsx` files are #' prefixed with `Excel` -#' \item \code{.csv} files are prefixed with `CSV` -#' \item \code{.sav} and \code{.zsav} files are prefixed with `SPSS` -#' \item \code{.doc}, \code{.docm} and \code{.docx} files are prefixed with +#' \item `.csv` files are prefixed with `CSV` +#' \item `.sav` and `.zsav` files are prefixed with `SPSS` +#' \item `.doc`, `.docm` and `.docx` files are prefixed with #' `Word` -#' \item \code{.rds} files are prefixed with `RDS` -#' \item \code{.txt} files are prefixed with `Text`, -#' \item \code{.fst} files are prefixed with `FST`, -#' \item \code{.pdf} files are prefixed with `PDF`, -#' \item \code{.tsv} files are prefixed with `TSV`, -#' \item \code{.html} files are prefixed with `HTML`, -#' \item \code{.ppt}, \code{.pptm} and \code{.pptx} files are prefixed with +#' \item `.rds` files are prefixed with `RDS` +#' \item `.txt` files are prefixed with `Text`, +#' \item `.fst` files are prefixed with `FST`, +#' \item `.pdf` files are prefixed with `PDF`, +#' \item `.tsv` files are prefixed with `TSV`, +#' \item `.html` files are prefixed with `HTML`, +#' \item `.ppt`, `.pptm` and `.pptx` files are prefixed with #' `PowerPoint`, -#' \item \code{.md} files are prefixed with `Markdown` +#' \item `.md` files are prefixed with `Markdown` #' } #' #' Files with extensions not contained within this list will have their size #' returned with no prefix. To request that a certain extension be explicitly #' catered for, please create an issue on -#' \href{https://github.com/Health-SocialCare-Scotland/phsmethods/issues}{GitHub}. +#' [GitHub](https://github.com/Health-SocialCare-Scotland/phsmethods/issues). #' #' File sizes are returned as the appropriate multiple of the unit byte #' (bytes (B), kilobytes (KB), megabytes (MB), etc.). Each multiple is taken to #' be 1,024 units of the preceding denomination. #' #' @param filepath A character string denoting a filepath. Defaults to the -#' working directory, \code{getwd()}. +#' working directory, `getwd()`. #' @param pattern An optional character string denoting a -#' \code{\link[base:regex]{regular expression}} pattern. Only file names which -#' match the regular expression will be returned. See the \strong{See Also} +#' [`regular expression()`][base::regex] pattern. Only file names which +#' match the regular expression will be returned. See the **See Also** #' section for resources regarding how to write regular expressions. #' -#' @return A \code{\link[tibble]{tibble}} listing the names of files within -#' \code{filepath} which match \code{pattern} and their respective sizes. The -#' column names of this tibble are `name` and `size`. If no \code{pattern} is -#' specified, \code{file_size} returns the names and sizes of all files within -#' \code{filepath}. File names and sizes are returned in alphabetical order of -#' file name. Sub-folders contained within \code{filepath} will return a file +#' @return A [tibble::tibble()] listing the names of files within +#' `filepath` which match `pattern` and their respective sizes. The +#' column names of this tibble are `name` and `size`. If no `pattern` is +#' specified, `file_size` returns the names and sizes of all files within +#' `filepath`. File names and sizes are returned in alphabetical order of +#' file name. Sub-folders contained within `filepath` will return a file #' size of `0 B`. #' -#' If \code{filepath} is an empty folder, or \code{pattern} matches no files -#' within \code{filepath}, \code{file_size} returns \code{NULL}. +#' If `filepath` is an empty folder, or `pattern` matches no files +#' within `filepath`, `file_size` returns `NULL`. #' #' @examples #' # Name and size of all files in working directory @@ -68,10 +68,10 @@ #' extract(1) #' #' @seealso For more information on using regular expressions, see this -#' \href{https://www.jumpingrivers.com/blog/regular-expressions-every-r-programmer-should-know/}{Jumping Rivers blog post} +#' [Jumping Rivers blog post](https://www.jumpingrivers.com/blog/regular-expressions-every-r-programmer-should-know/) #' and this -#' \href{https://stringr.tidyverse.org/articles/regular-expressions.html}{vignette} -#' from the \code{\link[stringr:stringr-package]{stringr}} package. +#' [vignette](https://stringr.tidyverse.org/articles/regular-expressions.html) +#' from the [`stringr()`][stringr::stringr-package] package. #' #' @export diff --git a/R/format_postcode.R b/R/format_postcode.R index d242fd5..112f383 100644 --- a/R/format_postcode.R +++ b/R/format_postcode.R @@ -1,8 +1,8 @@ #' @title Format a postcode #' -#' @description \code{format_postcode} takes a character string or vector of character -#' strings. It extracts the input values which adhere to the standard UK -#' postcode format (with or without spaces), assigns the appropriate amount +#' @description `format_postcode` takes a character string or vector of +#' character strings. It extracts the input values which adhere to the standard +#' UK postcode format (with or without spaces), assigns the appropriate amount #' of spacing to them (for both pc7 and pc8 formats) and ensures all letters #' are capitalised. #' @@ -16,10 +16,10 @@ #' \item 2 letters #' } #' -#' \href{https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/283357/ILRSpecification2013_14Appendix_C_Dec2012_v1.pdf}{UK government regulations} +#' [UK government regulations](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/283357/ILRSpecification2013_14Appendix_C_Dec2012_v1.pdf) #' mandate which letters and numbers can be used in specific sections of a #' postcode. However, these regulations are liable to change over time. For -#' this reason, \code{format_postcode} does not validate whether a given +#' this reason, `format_postcode` does not validate whether a given #' postcode actually exists, or whether specific numbers and letters are being #' used in the appropriate places. It only assesses whether the given input is #' consistent with the above format and, if so, assigns the appropriate amount @@ -29,9 +29,9 @@ #' which adhere to the standard UK postcode format may be upper or lower case #' and will be formatted regardless of existing spacing. Any input values which #' do not adhere to the standard UK postcode format will generate an NA and a -#' warning message - see \strong{Value} section for more information. +#' warning message - see **Value** section for more information. #' @param format A character string denoting the desired output format. Valid -#' options are `pc7` and `pc8`. The default is `pc7`. See \strong{Value} +#' options are `pc7` and `pc8`. The default is `pc7`. See **Value** #' section for more information on the string length of output values. #' @param quiet (optional) If quiet is `TRUE` all messages and warnings will be #' suppressed. This is useful in a production context and when you are sure of @@ -39,12 +39,12 @@ #' postcodes. This will also make the function a bit quicker as fewer checks #' are performed. #' -#' @return When \code{format} is set equal to \code{pc7}, \code{format_postcode} +#' @return When `format` is set equal to `pc7`, `format_postcode` #' returns a character string of length 7. 5 character postcodes have two #' spaces after the 2nd character; 6 character postcodes have 1 space after the #' 3rd character; and 7 character postcodes have no spaces. #' -#' When \code{format} is set equal to \code{pc8}, \code{format_postcode} returns +#' When `format` is set equal to `pc8`, `format_postcode` returns #' a character string with maximum length 8. All postcodes, whether 5, 6 or 7 #' characters, have one space before the last 3 characters. #' diff --git a/R/make_inheritance_checks.R b/R/make_inheritance_checks.R index 9ebcc42..f89372c 100644 --- a/R/make_inheritance_checks.R +++ b/R/make_inheritance_checks.R @@ -1,11 +1,15 @@ #' Check that a set of arguments inherits from a set of classes #' Throws an exception if one argument does not pass the checks. #' Argument must have AT LEAST ONE of the specified classes to pass. -#' @param arguments a list object containing argument_name=argument pairs for each argument. Argument names must be provided or else they will be ignored. +#' @param arguments a list object containing argument_name=argument pairs for +#' each argument. Argument names must be provided or else they will be ignored. #' @param target_classes character vector of the classes to check for. -#' @param ignore_null boolean. Indicates whether to ignore arguments with value NULL (TRUE) or to throw an exception (FALSE). Default = TRUE. +#' @param ignore_null boolean. Indicates whether to ignore arguments with value +#' NULL (TRUE) or to throw an exception (FALSE). Default = TRUE. -make_inheritance_checks <- function(arguments, target_classes, ignore_null = TRUE) { +make_inheritance_checks <- function(arguments, + target_classes, + ignore_null = TRUE) { caller_func <- ifelse(length(sys.calls()) > 1, deparse(sys.calls()[[sys.nframe() - 1]]), NA @@ -22,7 +26,13 @@ make_inheritance_checks <- function(arguments, target_classes, ignore_null = TRU if (ignore_null) { return(NULL) } else { - return(stringr::str_glue("{.arg {% argument %}} is {.val NULL} but must be {cli::qty(target_classes)} {?any of }{.cls {target_classes}}.", .open = "{%", .close = "%}")) + return( + stringr::str_glue( + "{.arg {% argument %}} is {.val NULL} but must be {cli::qty(target_classes)} {?any of }{.cls {target_classes}}.", + .open = "{%", + .close = "%}" + ) + ) } } if (!inherits(arguments[[argument]], target_classes) & !is.null(arguments[[argument]])) { diff --git a/R/match_area.R b/R/match_area.R index 896c272..15929b9 100644 --- a/R/match_area.R +++ b/R/match_area.R @@ -1,10 +1,10 @@ #' @title Translate geography codes into area names #' -#' @description \code{match_area} takes a geography code or vector of geography +#' @description `match_area` takes a geography code or vector of geography #' codes. It matches the input to the corresponding value in the -#' \code{\link{area_lookup}} dataset and returns the corresponding area name. +#' [area_lookup()] dataset and returns the corresponding area name. #' -#' @details \code{match_area} relies predominantly on the standard 9 digit +#' @details `match_area` relies predominantly on the standard 9 digit #' geography codes. The only exceptions are: #' \itemize{ #' \item RA2701: No Fixed Abode @@ -13,7 +13,7 @@ #' \item RA2704: Unknown Residency #' } #' -#' \code{match_area} caters for both current and previous versions of geography +#' `match_area` caters for both current and previous versions of geography #' codes (e.g 2014 and 2019 Health Boards). #' #' It can account for geography codes pertaining to Health Boards, Council @@ -23,10 +23,10 @@ #' Community Health Partnerships, Localities (S19), Settlements (S20) and #' Scotland. #' -#' \code{match_area} returns a non-NA value only when an exact match is present +#' `match_area` returns a non-NA value only when an exact match is present #' between the input value and the corresponding variable in the -#' \code{\link{area_lookup}} dataset. These exact matches are sensitive to both -#' case and spacing. It is advised to inspect \code{\link{area_lookup}} in the +#' [area_lookup()] dataset. These exact matches are sensitive to both +#' case and spacing. It is advised to inspect [area_lookup()] in the #' case of unexpected results, as these may be explained by subtle differences #' in transcription between the input value and the corresponding value in the #' lookup dataset. @@ -34,10 +34,10 @@ #' @param x A geography code or vector of geography codes. #' @return Each geography code within Scotland is unique, and consequently -#' \code{match_area} returns a single area name for each input value. +#' `match_area` returns a single area name for each input value. #' Any input value without a corresponding value in the -#' \code{\link{area_lookup}} dataset will return an NA output value. +#' [area_lookup()] dataset will return an NA output value. #' #' @examples #' match_area("S20000010") diff --git a/R/phsmethods.R b/R/phsmethods.R index 8d320e0..9e929de 100644 --- a/R/phsmethods.R +++ b/R/phsmethods.R @@ -1,9 +1,9 @@ -#' \code{phsmethods} package +#' `phsmethods` package #' #' Standard Methods for use in PHS. #' #' See the README on -#' \href{https://github.com/Health-SocialCare-Scotland/phsmethods#readme}{GitHub}. +#' [GitHub](https://github.com/Health-SocialCare-Scotland/phsmethods#readme). #' #' @docType package #' @name phsmethods diff --git a/R/qtr.R b/R/qtr.R index 68c7ea6..57ec4be 100644 --- a/R/qtr.R +++ b/R/qtr.R @@ -7,13 +7,13 @@ #' value. #' #' \itemize{ -#' \item \code{qtr} returns the current quarter +#' \item `qtr` returns the current quarter #' -#' \item \code{qtr_end} returns the last month in the quarter +#' \item `qtr_end` returns the last month in the quarter #' -#' \item \code{qtr_next} returns the next quarter +#' \item `qtr_next` returns the next quarter #' -#' \item \code{qtr_prev} returns the previous quarter +#' \item `qtr_prev` returns the previous quarter #' } #' #' @details Quarters are defined as: @@ -25,11 +25,13 @@ #' \item October to December (Oct-Dec) #' } #' -#' @param date A date which must be supplied with \code{Date} or \code{POSIXct} -#' @param format A \code{character} string specifying the format the quarter +#' @param date A date which must be supplied with `Date` or `POSIXct` +#' @param format A `character` string specifying the format the quarter #' should be displayed in. Valid options are `long` (January to March 2018) and #' `short` (Jan-Mar 2018). The default is `long`. #' +#' @return A character vector of financial quarters in the specified format. +#' #' @examples #' x <- lubridate::dmy(c(26032012, 04052012, 23092012)) #' qtr(x) diff --git a/R/rename.R b/R/rename.R index b4f053e..561badf 100644 --- a/R/rename.R +++ b/R/rename.R @@ -8,14 +8,14 @@ #' work and will error. At the next update they will be #' removed completely. #' -#' * `postcode()` -> `format_postcode()` -#' * `age_group()` -> `create_age_groups()` -#' * `fin_year()` -> `extract_fin_year()` +#' * `postcode()` → `format_postcode()` +#' * `age_group()` → `create_age_groups()` +#' * `fin_year()` → `extract_fin_year()` #' #' @keywords internal #' @name rename #' @aliases NULL -#' @md +#' @return NULL NULL #' @rdname rename diff --git a/R/sex_from_chi.R b/R/sex_from_chi.R index cb4c1e9..c9706cd 100644 --- a/R/sex_from_chi.R +++ b/R/sex_from_chi.R @@ -1,8 +1,8 @@ #' @title Extract sex from the CHI number #' -#' @description \code{sex_from_chi} takes a CHI number or a vector of CHI numbers -#' and returns the sex as implied by the CHI number(s). The default return type is -#' an integer but this can be modified. +#' @description `sex_from_chi` takes a CHI number or a vector of CHI numbers +#' and returns the sex as implied by the CHI number(s). The default return type +#' is an integer but this can be modified. #' #' @details The Community Health Index (CHI) is a register of all patients in #' NHS Scotland. A CHI number is a unique, ten-digit identifier assigned to @@ -11,35 +11,46 @@ #' The ninth digit of a CHI number identifies a patient's sex: odd for men, #' even for women. #' -#' The default behaviour for \code{sex_from_chi} is to first check the CHI number is -#' valid using \code{check_chi} and then to return 1 for male and 2 for female. +#' The default behaviour for `sex_from_chi` is to first check the CHI number is +#' valid using `check_chi` and then to return 1 for male and 2 for female. #' -#' There are options to return custom values e.g. \code{'M'} and \code{'F'} or to return -#' a factor which will have labels \code{'Male'} and \code{'Female')} +#' There are options to return custom values e.g. `'M'` and `'F'` or to return +#' a factor which will have labels `'Male'` and `'Female')` #' -#' @param chi_number a CHI number or a vector of CHI numbers with \code{character} class. -#' @param male_value,female_value optionally supply custom values for Male and Female. Note -#' that that these must be of the same class. -#' @param as_factor logical, optionally return as a factor with labels \code{'Male'} -#' and \code{'Female'}. Note that this will override any custom values supplied with -#' \code{male_value} or \code{female_value}. -#' @param chi_check logical, optionally skip checking the CHI for validity which will be -#' faster but should only be used if you have previously checked the CHI(s). +#' @param chi_number a CHI number or a vector of CHI numbers with `character` +#' class. +#' @param male_value,female_value optionally supply custom values for Male and +#' Female. Note that that these must be of the same class. +#' @param as_factor logical, optionally return as a factor with labels `'Male'` +#' and `'Female'`. Note that this will override any custom values supplied with +#' `male_value` or `female_value`. +#' @param chi_check logical, optionally skip checking the CHI for validity which +#' will be faster but should only be used if you have previously checked the +#' CHI(s). #' -#' @return a vector with the same class as \code{male_value} and \code{female_value}, (integer -#' by default) unless \code{as_factor} is \code{TRUE} in which case a factor will be returned. +#' @return a vector with the same class as `male_value` and `female_value`, +#' (integer by default) unless `as_factor` is `TRUE` in which case a factor will +#' be returned. #' @export #' #' @examples #' sex_from_chi("0101011237") #' sex_from_chi(c("0101011237", "0101336489", NA)) -#' sex_from_chi(c("0101011237", "0101336489", NA), male_value = "M", female_value = "F") +#' sex_from_chi( +#' c("0101011237", "0101336489", NA), +#' male_value = "M", +#' female_value = "F" +#' ) #' sex_from_chi(c("0101011237", "0101336489", NA), as_factor = TRUE) #' #' library(dplyr) #' df <- tibble(chi = c("0101011237", "0101336489", NA)) #' df %>% mutate(chi_sex = sex_from_chi(chi)) -sex_from_chi <- function(chi_number, male_value = 1L, female_value = 2L, as_factor = FALSE, chi_check = TRUE) { +sex_from_chi <- function(chi_number, + male_value = 1L, + female_value = 2L, + as_factor = FALSE, + chi_check = TRUE) { # Do type checking on male/female values male_class <- class(male_value) female_class <- class(female_value) @@ -74,7 +85,11 @@ sex_from_chi <- function(chi_number, male_value = 1L, female_value = 2L, as_fact # Convert to a factor if required if (as_factor) { - sex <- factor(sex, levels = c(male_value, female_value), labels = c("Male", "Female")) + sex <- factor( + x = sex, + levels = c(male_value, female_value), + labels = c("Male", "Female") + ) } return(sex) diff --git a/man/age_calculate.Rd b/man/age_calculate.Rd index 0181d7f..4970a03 100644 --- a/man/age_calculate.Rd +++ b/man/age_calculate.Rd @@ -12,22 +12,29 @@ age_calculate( ) } \arguments{ -\item{start}{A start date (e.g. date of birth) which must be supplied with \code{Date} or \code{POSIXct} or \code{POSIXlt} -class. \code{\link[base:as.Date]{as.Date()}}, +\item{start}{A start date (e.g. date of birth) which must be supplied with +\code{Date} or \code{POSIXct} or \code{POSIXlt} +class. \code{\link[base:as.Date]{base::as.Date()}}, \code{\link[lubridate:ymd]{lubridate::dmy()}} and \code{\link[base:as.POSIXlt]{as.POSIXct()}} are examples of functions which can be used to store dates as an appropriate class.} -\item{end}{An end date which must be supplied with \code{Date} or \code{POSIXct} or \code{POSIXlt} class. -Default is \code{Sys.Date()} or \code{Sys.time()} depending on the class of \code{start}.} +\item{end}{An end date which must be supplied with \code{Date} or \code{POSIXct} or +\code{POSIXlt} class. Default is \code{Sys.Date()} or \code{Sys.time()} depending on the +class of \code{start}.} -\item{units}{Type of units to be used. years and months are accepted. Default is \code{years}.} +\item{units}{Type of units to be used. years and months are accepted. +Default is \code{years}.} -\item{round_down}{Should returned ages be rounded down to the nearest whole number. Default is \code{TRUE}.} +\item{round_down}{Should returned ages be rounded down to the nearest whole +number. Default is \code{TRUE}.} +} +\value{ +A numeric vector representing the ages in the given units. } \description{ -This function calculates the age between two dates using functions in \code{lubridate}. -It calculates age in either years or months. +This function calculates the age between two dates using +functions in \code{lubridate}. It calculates age in either years or months. } \examples{ library(lubridate) @@ -36,7 +43,8 @@ end_date <- lubridate::ymd("2022-02-21") age_calculate(birth_date, end_date) age_calculate(birth_date, end_date, units = "months") -# If the start day is leap day (February 29th), age increases on 1st March every year. +# If the start day is leap day (February 29th), age increases on 1st March +# every year. leap1 <- lubridate::ymd("2020-02-29") leap2 <- lubridate::ymd("2022-02-28") leap3 <- lubridate::ymd("2022-03-01") diff --git a/man/age_from_chi.Rd b/man/age_from_chi.Rd index b4892c0..e6e0967 100644 --- a/man/age_from_chi.Rd +++ b/man/age_from_chi.Rd @@ -13,24 +13,31 @@ age_from_chi( ) } \arguments{ -\item{chi_number}{a CHI number or a vector of CHI numbers with \code{character} class.} +\item{chi_number}{a CHI number or a vector of CHI numbers with \code{character} +class.} -\item{ref_date}{calculate the age at this date, default is to use \code{Sys.Date()} i.e. today.} +\item{ref_date}{calculate the age at this date, default is to use +\code{Sys.Date()} i.e. today.} -\item{min_age, max_age}{optional min and/or max dates that the Date of Birth could take as the century needs to be guessed. -Must be either length 1 for a 'fixed' age or the same length as \code{chi_number} for an age per CHI number. -min_age can be age based on common sense in the dataset, whilst max_age can be age when an event happens such as the age at discharge.} +\item{min_age, max_age}{optional min and/or max dates that the DoB could take +as the century needs to be guessed. +Must be either length 1 for a 'fixed' age or the same length as \code{chi_number} +for an age per CHI number. +\code{min_age} can be age based on common sense in the dataset, whilst \code{max_age} +can be age when an event happens such as the age at discharge.} -\item{chi_check}{logical, optionally skip checking the CHI for validity which will be -faster but should only be used if you have previously checked the CHI(s), the default (TRUE) will to check the CHI numbers.} +\item{chi_check}{logical, optionally skip checking the CHI for validity which +will be faster but should only be used if you have previously checked the +CHI(s), the default (TRUE) will to check the CHI numbers.} } \value{ -an integer vector of ages in years truncated to the nearest year. It will be the same length as \code{chi_number}. +an integer vector of ages in years truncated to the nearest year. +It will be the same length as \code{chi_number}. } \description{ \code{age_from_chi} takes a CHI number or a vector of CHI numbers -and returns the age as implied by the CHI number(s). If the DoB is ambiguous -it will return NA. It uses \code{dob_from_chi}. +and returns the age as implied by the CHI number(s). If the Date of Birth +(DoB) is ambiguous it will return NA. It uses \code{\link[=dob_from_chi]{dob_from_chi()}}. } \examples{ age_from_chi("0101336489") diff --git a/man/area_lookup.Rd b/man/area_lookup.Rd index 9986703..e232eec 100644 --- a/man/area_lookup.Rd +++ b/man/area_lookup.Rd @@ -5,10 +5,10 @@ \alias{area_lookup} \title{Codes and names of Scottish geographical and administrative areas.} \format{ -A \code{\link[tibble]{tibble}} with 2 variables and over 17,000 rows: +A \code{\link[tibble:tibble]{tibble::tibble()}} with 2 variables and over 17,000 rows: \describe{ - \item{geo_code}{Standard geography code - 9 characters} - \item{area_name}{Name of the area the code represents} +\item{geo_code}{Standard geography code - 9 characters} +\item{area_name}{Name of the area the code represents} } } \source{ @@ -19,7 +19,7 @@ area_lookup } \description{ A dataset containing Scotland's geography codes and associated area names. -It is used within \code{\link{match_area}}. +It is used within \code{\link[=match_area]{match_area()}}. } \details{ \code{geo_code} contains geography codes pertaining to Health diff --git a/man/chi_check.Rd b/man/chi_check.Rd index 95d577f..e042552 100644 --- a/man/chi_check.Rd +++ b/man/chi_check.Rd @@ -12,16 +12,15 @@ chi_check(x) \value{ \code{chi_check} returns a character string. Depending on the validity of the entered CHI number, it will return one of the following: - \itemize{ -\item `Valid CHI` -\item `Invalid character(s) present` -\item `Too many characters` -\item `Too few characters` -\item `Invalid date` -\item `Invalid checksum` -\item `Missing (NA)` -\item `Missing (Blank)` +\item \verb{Valid CHI} +\item \verb{Invalid character(s) present} +\item \verb{Too many characters} +\item \verb{Too few characters} +\item \verb{Invalid date} +\item \verb{Invalid checksum} +\item \code{Missing (NA)} +\item \code{Missing (Blank)} } } \description{ @@ -39,18 +38,17 @@ The first six digits of a CHI number are a patient's date of birth in DD/MM/YY format. The ninth digit of a CHI number identifies a patient's sex: odd for male, -even for female. The tenth digit is a check digit, denoted `checksum`. +even for female. The tenth digit is a check digit, denoted \code{checksum}. While a CHI number is made up exclusively of numeric digits, it cannot be stored with \code{numeric} class in R. This is because leading zeros in numeric values are silently dropped, a practice not exclusive to R. For this reason, \code{chi_check} accepts input values of \code{character} class only. A leading zero can be added to a nine-digit CHI number using -\code{\link{chi_pad}}. +\code{\link[=chi_pad]{chi_pad()}}. \code{chi_check} assesses whether an entered CHI number is valid by checking -whether the answer to each of the following criteria is `Yes`: - +whether the answer to each of the following criteria is \code{Yes}: \itemize{ \item Does it contain no non-numeric characters? \item Is it ten digits in length? @@ -63,7 +61,13 @@ chi_check("0101011237") chi_check(c("0101201234", "3201201234")) library(dplyr) -df <- tibble(chi = c("3213201234", "123456789", "12345678900", "010120123?", NA)) +df <- tibble(chi = c( + "3213201234", + "123456789", + "12345678900", + "010120123?", + NA +)) df \%>\% mutate(validity = chi_check(chi)) } diff --git a/man/chi_pad.Rd b/man/chi_pad.Rd index d7bb3da..68b7d04 100644 --- a/man/chi_pad.Rd +++ b/man/chi_pad.Rd @@ -9,6 +9,9 @@ chi_pad(x) \arguments{ \item{x}{a CHI number or a vector of CHI numbers with \code{character} class.} } +\value{ +The original character vector with CHI numbers padded if applicable. +} \description{ \code{chi_pad} takes a nine-digit CHI number with \code{character} class and prefixes it with a zero. Any values provided @@ -29,7 +32,7 @@ stored with \code{numeric} class in R. This is because leading zeros in numeric values are silently dropped, a practice not exclusive to R. For this reason, \code{chi_pad} accepts input values of \code{character} class only, and returns values of the same class. It does not assess the validity -of a CHI number - please see \code{\link{chi_check}} for that. +of a CHI number - please see \code{\link[=chi_check]{chi_check()}} for that. } \examples{ chi_pad(c("101011237", "101201234")) diff --git a/man/create_age_groups.Rd b/man/create_age_groups.Rd index ef46d0c..735a67b 100644 --- a/man/create_age_groups.Rd +++ b/man/create_age_groups.Rd @@ -32,7 +32,7 @@ The \code{from}, \code{to} and \code{by} values are used to create distinct age groups. \code{from} dictates the starting age of the lowest age group, and \code{by} indicates how wide each group should be. \code{to} stipulates the cut-off point at which all ages equal to or greater than this value -should be categorised together in a \code{to+} group. If the specified value +should be categorised together in a \verb{to+} group. If the specified value of \code{to} is not a multiple of \code{by}, the value of \code{to} is rounded down to the nearest multiple of \code{by}. diff --git a/man/dob_from_chi.Rd b/man/dob_from_chi.Rd index 3b8e8ff..809e12e 100644 --- a/man/dob_from_chi.Rd +++ b/man/dob_from_chi.Rd @@ -7,22 +7,26 @@ dob_from_chi(chi_number, min_date = NULL, max_date = NULL, chi_check = TRUE) } \arguments{ -\item{chi_number}{a CHI number or a vector of CHI numbers with \code{character} class.} +\item{chi_number}{a CHI number or a vector of CHI numbers with \code{character} +class.} -\item{min_date, max_date}{optional min and/or max dates that the Date of Birth could take as the century needs to be guessed. -Must be either length 1 for a 'fixed' date or the same length as \code{chi_number} for a date per CHI number. -min_date can be date based on common sense in the dataset, whilst max_date can be date when an event happens such as discharge date.} +\item{min_date, max_date}{optional min and/or max dates that the +DoB could take as the century needs to be guessed. Must be either length 1 +for a 'fixed' date or the same length as \code{chi_number} for a date +per CHI number. \code{min_date} can be date based on common sense in the dataset, +whilst \code{max_date} can be date when an event happens such as discharge date.} -\item{chi_check}{logical, optionally skip checking the CHI for validity which will be -faster but should only be used if you have previously checked the CHI(s). The default (TRUE) will check the CHI numbers.} +\item{chi_check}{logical, optionally skip checking the CHI for validity which +will be faster but should only be used if you have previously checked the +CHI(s). The default (TRUE) will check the CHI numbers.} } \value{ a date vector of DoB. It will be the same length as \code{chi_number}. } \description{ \code{dob_from_chi} takes a CHI number or a vector of CHI numbers -and returns the DoB as implied by the CHI number(s). If the DoB is ambiguous -it will return NA +and returns the Date of Birth (DoB) as implied by the CHI number(s). If the +DoB is ambiguous it will return NA. } \examples{ dob_from_chi("0101336489") diff --git a/man/extract_fin_year.Rd b/man/extract_fin_year.Rd index d3e083e..361d044 100644 --- a/man/extract_fin_year.Rd +++ b/man/extract_fin_year.Rd @@ -8,11 +8,14 @@ extract_fin_year(date) } \arguments{ \item{date}{A date which must be supplied with \code{Date} or \code{POSIXct} -class. \code{\link[base:as.Date]{as.Date()}}, +class. \code{\link[base:as.Date]{base::as.Date()}}, \code{\link[lubridate:ymd]{lubridate::dmy()}} and \code{\link[base:as.POSIXlt]{as.POSIXct()}} are examples of functions which can be used to store dates as an appropriate class.} } +\value{ +A character vector of financial years in the form '2017/18'. +} \description{ \code{extract_fin_year} takes a date and extracts the correct financial year in the PHS specified format from it. diff --git a/man/file_size.Rd b/man/file_size.Rd index db45309..9a2a062 100644 --- a/man/file_size.Rd +++ b/man/file_size.Rd @@ -11,18 +11,18 @@ file_size(filepath = getwd(), pattern = NULL) working directory, \code{getwd()}.} \item{pattern}{An optional character string denoting a -\code{\link[base:regex]{regular expression}} pattern. Only file names which +\code{\link[base:regex]{regular expression()}} pattern. Only file names which match the regular expression will be returned. See the \strong{See Also} section for resources regarding how to write regular expressions.} } \value{ -A \code{\link[tibble]{tibble}} listing the names of files within +A \code{\link[tibble:tibble]{tibble::tibble()}} listing the names of files within \code{filepath} which match \code{pattern} and their respective sizes. The -column names of this tibble are `name` and `size`. If no \code{pattern} is +column names of this tibble are \code{name} and \code{size}. If no \code{pattern} is specified, \code{file_size} returns the names and sizes of all files within \code{filepath}. File names and sizes are returned in alphabetical order of file name. Sub-folders contained within \code{filepath} will return a file -size of `0 B`. +size of \verb{0 B}. If \code{filepath} is an empty folder, or \code{pattern} matches no files within \code{filepath}, \code{file_size} returns \code{NULL}. @@ -35,25 +35,25 @@ which match the given pattern. \details{ The sizes of files with certain extensions are returned with the type of file prefixed. For example, the size of a 12 KB \code{.xlsx} file is -returned as `Excel 12 KB`. The complete list of explicitly catered-for file +returned as \verb{Excel 12 KB}. The complete list of explicitly catered-for file extensions and their prefixes are as follows: \itemize{ \item \code{.xls}, \code{.xlsb}, \code{.xlsm} and \code{.xlsx} files are -prefixed with `Excel` -\item \code{.csv} files are prefixed with `CSV` -\item \code{.sav} and \code{.zsav} files are prefixed with `SPSS` +prefixed with \code{Excel} +\item \code{.csv} files are prefixed with \code{CSV} +\item \code{.sav} and \code{.zsav} files are prefixed with \code{SPSS} \item \code{.doc}, \code{.docm} and \code{.docx} files are prefixed with -`Word` -\item \code{.rds} files are prefixed with `RDS` -\item \code{.txt} files are prefixed with `Text`, -\item \code{.fst} files are prefixed with `FST`, -\item \code{.pdf} files are prefixed with `PDF`, -\item \code{.tsv} files are prefixed with `TSV`, -\item \code{.html} files are prefixed with `HTML`, +\code{Word} +\item \code{.rds} files are prefixed with \code{RDS} +\item \code{.txt} files are prefixed with \code{Text}, +\item \code{.fst} files are prefixed with \code{FST}, +\item \code{.pdf} files are prefixed with \code{PDF}, +\item \code{.tsv} files are prefixed with \code{TSV}, +\item \code{.html} files are prefixed with \code{HTML}, \item \code{.ppt}, \code{.pptm} and \code{.pptx} files are prefixed with -`PowerPoint`, -\item \code{.md} files are prefixed with `Markdown` +\code{PowerPoint}, +\item \code{.md} files are prefixed with \code{Markdown} } Files with extensions not contained within this list will have their size @@ -84,5 +84,5 @@ For more information on using regular expressions, see this \href{https://www.jumpingrivers.com/blog/regular-expressions-every-r-programmer-should-know/}{Jumping Rivers blog post} and this \href{https://stringr.tidyverse.org/articles/regular-expressions.html}{vignette} -from the \code{\link[stringr:stringr-package]{stringr}} package. +from the \code{\link[stringr:stringr-package]{stringr()}} package. } diff --git a/man/format_postcode.Rd b/man/format_postcode.Rd index b3c6b09..0dcc45f 100644 --- a/man/format_postcode.Rd +++ b/man/format_postcode.Rd @@ -14,10 +14,10 @@ do not adhere to the standard UK postcode format will generate an NA and a warning message - see \strong{Value} section for more information.} \item{format}{A character string denoting the desired output format. Valid -options are `pc7` and `pc8`. The default is `pc7`. See \strong{Value} +options are \code{pc7} and \code{pc8}. The default is \code{pc7}. See \strong{Value} section for more information on the string length of output values.} -\item{quiet}{(optional) If quiet is `TRUE` all messages and warnings will be +\item{quiet}{(optional) If quiet is \code{TRUE} all messages and warnings will be suppressed. This is useful in a production context and when you are sure of the data or you are specifically using this function to remove invalid postcodes. This will also make the function a bit quicker as fewer checks @@ -30,7 +30,7 @@ spaces after the 2nd character; 6 character postcodes have 1 space after the 3rd character; and 7 character postcodes have no spaces. When \code{format} is set equal to \code{pc8}, \code{format_postcode} returns - a character string with maximum length 8. All postcodes, whether 5, 6 or 7 +a character string with maximum length 8. All postcodes, whether 5, 6 or 7 characters, have one space before the last 3 characters. Any input values which do not adhere to the standard UK postcode format will @@ -44,9 +44,9 @@ contain lower case letters will generate a warning message explaining that these letters will be capitalised. } \description{ -\code{format_postcode} takes a character string or vector of character -strings. It extracts the input values which adhere to the standard UK -postcode format (with or without spaces), assigns the appropriate amount +\code{format_postcode} takes a character string or vector of +character strings. It extracts the input values which adhere to the standard +UK postcode format (with or without spaces), assigns the appropriate amount of spacing to them (for both pc7 and pc8 formats) and ensures all letters are capitalised. } diff --git a/man/make_inheritance_checks.Rd b/man/make_inheritance_checks.Rd index eb50fb0..be8e295 100644 --- a/man/make_inheritance_checks.Rd +++ b/man/make_inheritance_checks.Rd @@ -9,11 +9,13 @@ Argument must have AT LEAST ONE of the specified classes to pass.} make_inheritance_checks(arguments, target_classes, ignore_null = TRUE) } \arguments{ -\item{arguments}{a list object containing argument_name=argument pairs for each argument. Argument names must be provided or else they will be ignored.} +\item{arguments}{a list object containing argument_name=argument pairs for +each argument. Argument names must be provided or else they will be ignored.} \item{target_classes}{character vector of the classes to check for.} -\item{ignore_null}{boolean. Indicates whether to ignore arguments with value NULL (TRUE) or to throw an exception (FALSE). Default = TRUE.} +\item{ignore_null}{boolean. Indicates whether to ignore arguments with value +NULL (TRUE) or to throw an exception (FALSE). Default = TRUE.} } \description{ Check that a set of arguments inherits from a set of classes diff --git a/man/match_area.Rd b/man/match_area.Rd index 807e638..79bee65 100644 --- a/man/match_area.Rd +++ b/man/match_area.Rd @@ -13,12 +13,12 @@ match_area(x) Each geography code within Scotland is unique, and consequently \code{match_area} returns a single area name for each input value. Any input value without a corresponding value in the -\code{\link{area_lookup}} dataset will return an NA output value. +\code{\link[=area_lookup]{area_lookup()}} dataset will return an NA output value. } \description{ \code{match_area} takes a geography code or vector of geography codes. It matches the input to the corresponding value in the -\code{\link{area_lookup}} dataset and returns the corresponding area name. +\code{\link[=area_lookup]{area_lookup()}} dataset and returns the corresponding area name. } \details{ \code{match_area} relies predominantly on the standard 9 digit @@ -42,8 +42,8 @@ Scotland. \code{match_area} returns a non-NA value only when an exact match is present between the input value and the corresponding variable in the -\code{\link{area_lookup}} dataset. These exact matches are sensitive to both -case and spacing. It is advised to inspect \code{\link{area_lookup}} in the +\code{\link[=area_lookup]{area_lookup()}} dataset. These exact matches are sensitive to both +case and spacing. It is advised to inspect \code{\link[=area_lookup]{area_lookup()}} in the case of unexpected results, as these may be explained by subtle differences in transcription between the input value and the corresponding value in the lookup dataset. diff --git a/man/qtr.Rd b/man/qtr.Rd index 4f966e1..c74b617 100644 --- a/man/qtr.Rd +++ b/man/qtr.Rd @@ -19,8 +19,11 @@ qtr_prev(date, format = c("long", "short")) \item{date}{A date which must be supplied with \code{Date} or \code{POSIXct}} \item{format}{A \code{character} string specifying the format the quarter -should be displayed in. Valid options are `long` (January to March 2018) and -`short` (Jan-Mar 2018). The default is `long`.} +should be displayed in. Valid options are \code{long} (January to March 2018) and +\code{short} (Jan-Mar 2018). The default is \code{long}.} +} +\value{ +A character vector of financial quarters in the specified format. } \description{ The qtr functions take a date input and calculate the relevant diff --git a/man/rename.Rd b/man/rename.Rd index a0e14f0..a6276c6 100644 --- a/man/rename.Rd +++ b/man/rename.Rd @@ -20,9 +20,9 @@ to improve code clarity. The old functions no longer work and will error. At the next update they will be removed completely. \itemize{ -\item \code{postcode()} -> \code{format_postcode()} -\item \code{age_group()} -> \code{create_age_groups()} -\item \code{fin_year()} -> \code{extract_fin_year()} +\item \code{postcode()} → \code{format_postcode()} +\item \code{age_group()} → \code{create_age_groups()} +\item \code{fin_year()} → \code{extract_fin_year()} } } \keyword{internal} diff --git a/man/sex_from_chi.Rd b/man/sex_from_chi.Rd index 4dc3798..c7e4071 100644 --- a/man/sex_from_chi.Rd +++ b/man/sex_from_chi.Rd @@ -13,26 +13,29 @@ sex_from_chi( ) } \arguments{ -\item{chi_number}{a CHI number or a vector of CHI numbers with \code{character} class.} +\item{chi_number}{a CHI number or a vector of CHI numbers with \code{character} +class.} -\item{male_value, female_value}{optionally supply custom values for Male and Female. Note -that that these must be of the same class.} +\item{male_value, female_value}{optionally supply custom values for Male and +Female. Note that that these must be of the same class.} \item{as_factor}{logical, optionally return as a factor with labels \code{'Male'} and \code{'Female'}. Note that this will override any custom values supplied with \code{male_value} or \code{female_value}.} -\item{chi_check}{logical, optionally skip checking the CHI for validity which will be -faster but should only be used if you have previously checked the CHI(s).} +\item{chi_check}{logical, optionally skip checking the CHI for validity which +will be faster but should only be used if you have previously checked the +CHI(s).} } \value{ -a vector with the same class as \code{male_value} and \code{female_value}, (integer -by default) unless \code{as_factor} is \code{TRUE} in which case a factor will be returned. +a vector with the same class as \code{male_value} and \code{female_value}, +(integer by default) unless \code{as_factor} is \code{TRUE} in which case a factor will +be returned. } \description{ \code{sex_from_chi} takes a CHI number or a vector of CHI numbers -and returns the sex as implied by the CHI number(s). The default return type is -an integer but this can be modified. +and returns the sex as implied by the CHI number(s). The default return type +is an integer but this can be modified. } \details{ The Community Health Index (CHI) is a register of all patients in @@ -46,12 +49,16 @@ The default behaviour for \code{sex_from_chi} is to first check the CHI number i valid using \code{check_chi} and then to return 1 for male and 2 for female. There are options to return custom values e.g. \code{'M'} and \code{'F'} or to return -a factor which will have labels \code{'Male'} and \code{'Female')} +a factor which will have labels \code{'Male'} and \verb{'Female')} } \examples{ sex_from_chi("0101011237") sex_from_chi(c("0101011237", "0101336489", NA)) -sex_from_chi(c("0101011237", "0101336489", NA), male_value = "M", female_value = "F") +sex_from_chi( + c("0101011237", "0101336489", NA), + male_value = "M", + female_value = "F" +) sex_from_chi(c("0101011237", "0101336489", NA), as_factor = TRUE) library(dplyr) diff --git a/tests/testthat/test-create_age_groups.R b/tests/testthat/test-create_age_groups.R index e08866e..a15155c 100644 --- a/tests/testthat/test-create_age_groups.R +++ b/tests/testthat/test-create_age_groups.R @@ -56,8 +56,12 @@ test_that("Default value for age groups", { test_that("Handling of non-numeric values for x", { # If x is not numeric cut will error - expect_error(create_age_groups(c("1", "57", "apple", "12"), as_factor = FALSE)) + expect_error( + create_age_groups(c("1", "57", "apple", "12"), as_factor = FALSE) + ) # This is true even if all elements are numbers stored as character - expect_error(create_age_groups(c("26", "9", "78", "81"), as_factor = FALSE)) + expect_error( + create_age_groups(c("26", "9", "78", "81"), as_factor = FALSE) + ) }) From 815b5e9373d9241171b96a8f5a24ff66ffa57f1f Mon Sep 17 00:00:00 2001 From: James McMahon Date: Tue, 3 Oct 2023 10:21:05 +0100 Subject: [PATCH 14/29] Update the pacakge description. The notes from the CRAN maintainer were: > The Description field is intended to be a (one paragraph) description of what the package does and why it may be useful. Please add more details about the package functionality and implemented methods in your Description text. The only guidelines I found otherwise were: * It is a single paragraph. * It is informative and concise, and it clearly describes what the package does and why it is useful. * It does not include the package name. * It does not start with "A package for ..." or "This package does ...". * It is written in plain text, with no markup. * It is indented correctly, with each line no more than 80 characters wide. * It includes relevant citations, formatted in the correct style. * It is free of errors in grammar and spelling. --- DESCRIPTION | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0d5391c..0e9fd4d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,13 +17,15 @@ Authors@R: c( comment = c(ORCID = "0000-0002-5380-2029")), person("Nicolaos", "Christofidis", , "nicolaos.christofidis@phs.scot", role = "aut") ) -Description: Bespoke functions for commonly undertaken analytical tasks in - Public Health Scotland. +Description: A collection of methods, primarily developed for Public + Health Scoltand (PHS) analysts, but the package is generally useful to + others working in the healthcare space, particularly since it has + functions for working with CHI numbers. The package can help to make + data manipulation and analysis more efficient and reproducible. License: GPL (>= 2) URL: https://github.com/Public-Health-Scotland/phsmethods, https://public-health-scotland.github.io/phsmethods/ -BugReports: - https://github.com/Public-Health-Scotland/phsmethods/issues +BugReports: https://github.com/Public-Health-Scotland/phsmethods/issues Depends: R (>= 2.10) Imports: From a9d2a2cd40bcc0d677a8379d357e95188a66589d Mon Sep 17 00:00:00 2001 From: TinaFu <31853064+Tina815@users.noreply.github.com> Date: Mon, 23 Oct 2023 14:10:39 +0100 Subject: [PATCH 15/29] Update DESCRIPTION --- DESCRIPTION | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0e9fd4d..9455d67 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,11 +17,12 @@ Authors@R: c( comment = c(ORCID = "0000-0002-5380-2029")), person("Nicolaos", "Christofidis", , "nicolaos.christofidis@phs.scot", role = "aut") ) -Description: A collection of methods, primarily developed for Public - Health Scoltand (PHS) analysts, but the package is generally useful to - others working in the healthcare space, particularly since it has - functions for working with CHI numbers. The package can help to make - data manipulation and analysis more efficient and reproducible. +Description: A collection of methods for commonly undertaken analytical tasks, + primarily developed for Public Health Scoltand (PHS) analysts, but the package is also + generally useful to others working in the healthcare space, particularly since it has + functions for working with Community Health Index (CHI) numbers. + The package can help to make data manipulation and analysis more + efficient and reproducible. License: GPL (>= 2) URL: https://github.com/Public-Health-Scotland/phsmethods, https://public-health-scotland.github.io/phsmethods/ From c7c6856eab64221f48ceb3ab1834e39d1a341ac4 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Mon, 30 Oct 2023 17:53:11 +0000 Subject: [PATCH 16/29] Accept new snapshots Due to minor changes in testthat --- tests/testthat/_snaps/format_postcode.md | 15 +- tests/testthat/_snaps/rename.md | 190 ++++++++++++++--------- 2 files changed, 125 insertions(+), 80 deletions(-) diff --git a/tests/testthat/_snaps/format_postcode.md b/tests/testthat/_snaps/format_postcode.md index ae6814a..a66d72f 100644 --- a/tests/testthat/_snaps/format_postcode.md +++ b/tests/testthat/_snaps/format_postcode.md @@ -2,8 +2,10 @@ Code format_postcode("g2") - Warning + Condition + Warning: 1 value has lower case letters these will be converted to upper case. + Warning: 1 non-NA input value does not adhere to the standard UK postcode format (with or without spaces) and will be coded as NA. The standard format is: * 1 or 2 letters, followed by @@ -18,8 +20,10 @@ Code format_postcode(c("DG98BS", "dg98b")) - Warning + Condition + Warning: 1 value has lower case letters these will be converted to upper case. + Warning: 1 non-NA input value does not adhere to the standard UK postcode format (with or without spaces) and will be coded as NA. The standard format is: * 1 or 2 letters, followed by @@ -34,7 +38,8 @@ Code format_postcode(c("ML53RB", NA, "ML5", "???", 53, as.factor("ML53RB"))) - Warning + Condition + Warning: 4 non-NA input values do not adhere to the standard UK postcode format (with or without spaces) and will be coded as NA. The standard format is: * 1 or 2 letters, followed by @@ -53,8 +58,10 @@ [1] "KY1 1RZ" NA NA NA Code format_postcode(c("KY1 1RZ", "ky1rz", "KY11 R", "KY11R!"), quiet = FALSE) - Warning + Condition + Warning: 1 value has lower case letters these will be converted to upper case. + Warning: 3 non-NA input values do not adhere to the standard UK postcode format (with or without spaces) and will be coded as NA. The standard format is: * 1 or 2 letters, followed by diff --git a/tests/testthat/_snaps/rename.md b/tests/testthat/_snaps/rename.md index 8ddf50b..1907066 100644 --- a/tests/testthat/_snaps/rename.md +++ b/tests/testthat/_snaps/rename.md @@ -2,126 +2,150 @@ Code expect_equal(stringr::str_length(postcode("G26QE", format = "pc7")), 7) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(stringr::str_length(postcode("G26QE", format = "pc8")), 6) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(stringr::str_length(postcode(c("KA89NB", "PA152TY"), format = "pc7")), c(7, 7)) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(stringr::str_length(postcode(c("KA89NB", "PA152TY"), format = "pc8")), c(7, 8)) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(postcode("G36RB"), "G3 6RB") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(postcode("G432XR"), "G43 2XR") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(postcode("DG29BA"), "DG2 9BA") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(postcode("FK101RY"), "FK101RY") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(postcode("E1W3TJ"), "E1W 3TJ") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(postcode("EC1Y8SE"), "EC1Y8SE") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code input_hampden <- c("G429BA", "g429ba", "G42 9BA", "G 4 2 9 B A", "G429b a") formatted_hampden <- suppressWarnings(postcode(input_hampden)) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_true(length(unique(formatted_hampden)) == 1) - Error - object 'formatted_hampden' not found + Condition + Error in `unique()`: + ! object 'formatted_hampden' not found Code expect_equal(unique(formatted_hampden), "G42 9BA") - Error - object 'formatted_hampden' not found + Condition + Error in `unique()`: + ! object 'formatted_hampden' not found Code expect_true(is.na(suppressWarnings(postcode("G2?QE")))) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_warning(postcode(c("G207AL", "G2O07AL"))) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_equal(suppressWarnings(postcode(c("EH7 5QG", NA, "EH11 2NL", "EH5 2HF*"))), c("EH7 5QG", NA, "EH112NL", NA)) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code input_dens <- c("Dd37Jy", "DD37JY", "D d 337JY") warnings_dens <- capture_warnings(postcode(input_dens)) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_length(warnings_dens, 2) - Error - object 'warnings_dens' not found + Condition + Error in `eval_bare()`: + ! object 'warnings_dens' not found Code input_pittodrie <- c("ab245qh", NA, "ab245q", "A B245QH") warnings_pittodrie <- capture_warnings(postcode(input_pittodrie)) - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_length(warnings_pittodrie, 3) - Error - object 'warnings_pittodrie' not found + Condition + Error in `eval_bare()`: + ! object 'warnings_pittodrie' not found Code expect_warning(postcode("g2"), "^1") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_warning(postcode(c("DG98BS", "dg98b")), "^1") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_warning(postcode(c("KY1 1RZ", "ky1rz", "KY11 R", "KY11R!")), "^3") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code expect_warning(postcode(c("ML53RB", NA, "ML5", "???", 53, as.factor("ML53RB"))), "^4") - Error - `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. # age_group is deprecated @@ -129,8 +153,9 @@ Code expect_identical(age_group(c(4, 51, 21, 89), 0, 80, 10, as_factor = FALSE), c( "0-9", "50-59", "20-29", "80+")) - Error - `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `create_age_groups()` instead. Code expect_identical(age_group(c(8, 94, 44, 55, 14), 0, 90, 5, as_factor = TRUE), @@ -138,28 +163,32 @@ "10-14", "15-19", "20-24", "25-29", "30-34", "35-39", "40-44", "45-49", "50-54", "55-59", "60-64", "65-69", "70-74", "75-79", "80-84", "85-89", "90+"), ordered = TRUE)) - Error - `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `create_age_groups()` instead. Code expect_identical(age_group(c(81, 86, 33, 11), 4, 84, 3, as_factor = FALSE), c( "79-81", "82+", "31-33", "10-12")) - Error - `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `create_age_groups()` instead. Code expect_identical(age_group(c(0, 99, 1000, 5, 5), 5, 90, 5, as_factor = FALSE), c(NA, "90+", "90+", "5-9", "5-9")) - Error - `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `create_age_groups()` instead. Code expect_identical(age_group(10, as_factor = TRUE), factor(c("10-14"), levels = c( "0-4", "5-9", "10-14", "15-19", "20-24", "25-29", "30-34", "35-39", "40-44", "45-49", "50-54", "55-59", "60-64", "65-69", "70-74", "75-79", "80-84", "85-89", "90+"), ordered = TRUE)) - Error - `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `age_group()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `create_age_groups()` instead. Code expect_error(age_group(c("1", "57", "apple", "12"), as_factor = FALSE)) @@ -169,43 +198,51 @@ Code expect_equal(fin_year(as.Date("20120331", "%Y%m%d")), "2011/12") - Error - `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `extract_fin_year()` instead. Code expect_equal(fin_year(as.Date("20120401", "%Y%m%d")), "2012/13") - Error - `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `extract_fin_year()` instead. Code expect_equal(fin_year(as.POSIXct("20190104", format = "%Y%m%d")), "2018/19") - Error - `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `extract_fin_year()` instead. Code expect_equal(fin_year(as.Date("17111993", "%d%m%Y")), "1993/94") - Error - `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `extract_fin_year()` instead. Code expect_equal(fin_year(as.Date("19980404", "%Y%m%d")), "1998/99") - Error - `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `extract_fin_year()` instead. Code expect_equal(fin_year(as.Date("21-Jan-2017", "%d-%B-%Y")), "2016/17") - Error - `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `extract_fin_year()` instead. Code expect_equal(fin_year(as.POSIXct("20181401", format = "%Y%d%m")), "2017/18") - Error - `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `extract_fin_year()` instead. Code expect_equal(fin_year(lubridate::dmy(29102019)), "2019/20") - Error - `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `extract_fin_year()` instead. Code expect_error(fin_year("28102019")) @@ -213,7 +250,8 @@ expect_error(fin_year(as.numeric("28102019"))) expect_error(fin_year(as.factor("28-Oct-2019"))) expect_equal(fin_year(c(lubridate::dmy(5012020), NA)), c("2019/20", NA)) - Error - `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. + Condition + Error: + ! `fin_year()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `extract_fin_year()` instead. From 5e4060c0b05789353eb989c70b03b58b29d1f742 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Tue, 31 Oct 2023 08:39:42 +0000 Subject: [PATCH 17/29] Update spelling WORDLIST --- inst/WORDLIST | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 inst/WORDLIST diff --git a/inst/WORDLIST b/inst/WORDLIST new file mode 100644 index 0000000..221d9ef --- /dev/null +++ b/inst/WORDLIST @@ -0,0 +1,25 @@ +Authors’ +DD +DoB +FST +Knit’ +Maechler +RStudio +TSV +YY +YYYY +blogpost +cli +codecov +etc +filepath +gdata +nd +pkgdown +qtr +rOpenSci +rd +tibble +tidyverse +’ +’s From 9895fcbb6aeaad28656b2134ce1a5238d132839f Mon Sep 17 00:00:00 2001 From: James McMahon Date: Tue, 31 Oct 2023 09:12:16 +0000 Subject: [PATCH 18/29] Refactor lines causing issues in rename tests --- tests/testthat/_snaps/rename.md | 28 +++++++--------------------- tests/testthat/test-rename.R | 11 ++++------- 2 files changed, 11 insertions(+), 28 deletions(-) diff --git a/tests/testthat/_snaps/rename.md b/tests/testthat/_snaps/rename.md index 1907066..897392d 100644 --- a/tests/testthat/_snaps/rename.md +++ b/tests/testthat/_snaps/rename.md @@ -64,21 +64,17 @@ i Please use `format_postcode()` instead. Code input_hampden <- c("G429BA", "g429ba", "G42 9BA", "G 4 2 9 B A", "G429b a") - formatted_hampden <- suppressWarnings(postcode(input_hampden)) + expect_true(length(unique(postcode(input_hampden))) == 1) Condition Error: ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. Code - expect_true(length(unique(formatted_hampden)) == 1) + expect_equal(unique(postcode(input_hampden)), "G42 9BA") Condition - Error in `unique()`: - ! object 'formatted_hampden' not found - Code - expect_equal(unique(formatted_hampden), "G42 9BA") - Condition - Error in `unique()`: - ! object 'formatted_hampden' not found + Error: + ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. + i Please use `format_postcode()` instead. Code expect_true(is.na(suppressWarnings(postcode("G2?QE")))) Condition @@ -100,28 +96,18 @@ i Please use `format_postcode()` instead. Code input_dens <- c("Dd37Jy", "DD37JY", "D d 337JY") - warnings_dens <- capture_warnings(postcode(input_dens)) + expect_length(capture_warnings(postcode(input_dens)), 2) Condition Error: ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. - Code - expect_length(warnings_dens, 2) - Condition - Error in `eval_bare()`: - ! object 'warnings_dens' not found Code input_pittodrie <- c("ab245qh", NA, "ab245q", "A B245QH") - warnings_pittodrie <- capture_warnings(postcode(input_pittodrie)) + expect_length(capture_warnings(postcode(input_pittodrie)), 3) Condition Error: ! `postcode()` was deprecated in phsmethods 0.2.1 and is now defunct. i Please use `format_postcode()` instead. - Code - expect_length(warnings_pittodrie, 3) - Condition - Error in `eval_bare()`: - ! object 'warnings_pittodrie' not found Code expect_warning(postcode("g2"), "^1") Condition diff --git a/tests/testthat/test-rename.R b/tests/testthat/test-rename.R index f9c00a3..bd9272c 100644 --- a/tests/testthat/test-rename.R +++ b/tests/testthat/test-rename.R @@ -18,10 +18,9 @@ test_that("postcode is deprecated", { expect_equal(postcode("EC1Y8SE"), "EC1Y8SE") input_hampden <- c("G429BA", "g429ba", "G42 9BA", "G 4 2 9 B A", "G429b a") - formatted_hampden <- suppressWarnings(postcode(input_hampden)) - expect_true(length(unique(formatted_hampden)) == 1) - expect_equal(unique(formatted_hampden), "G42 9BA") + expect_true(length(unique(postcode(input_hampden))) == 1) + expect_equal(unique(postcode(input_hampden)), "G42 9BA") expect_true(is.na(suppressWarnings(postcode("G2?QE")))) expect_warning(postcode(c("G207AL", "G2O07AL"))) @@ -34,12 +33,10 @@ test_that("postcode is deprecated", { ) input_dens <- c("Dd37Jy", "DD37JY", "D d 337JY") - warnings_dens <- capture_warnings(postcode(input_dens)) - expect_length(warnings_dens, 2) + expect_length(capture_warnings(postcode(input_dens)), 2) input_pittodrie <- c("ab245qh", NA, "ab245q", "A B245QH") - warnings_pittodrie <- capture_warnings(postcode(input_pittodrie)) - expect_length(warnings_pittodrie, 3) + expect_length(capture_warnings(postcode(input_pittodrie)), 3) expect_warning(postcode("g2"), "^1") expect_warning(postcode(c("DG98BS", "dg98b")), "^1") From 9c25925d3a0bc122edc6880c39d1394e0d9141f0 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Wed, 1 Nov 2023 10:26:18 +0000 Subject: [PATCH 19/29] Fix a typo in the DESCRIPTION Scoltand -> Scotland --- DESCRIPTION | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e65343d..f5c2d52 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,12 +17,12 @@ Authors@R: c( comment = c(ORCID = "0000-0002-5380-2029")), person("Nicolaos", "Christofidis", , "nicolaos.christofidis@phs.scot", role = "aut") ) -Description: A collection of methods for commonly undertaken analytical tasks, - primarily developed for Public Health Scoltand (PHS) analysts, but the package is also - generally useful to others working in the healthcare space, particularly since it has - functions for working with Community Health Index (CHI) numbers. - The package can help to make data manipulation and analysis more - efficient and reproducible. +Description: A collection of methods for commonly undertaken analytical + tasks, primarily developed for Public Health Scotland (PHS) analysts, + but the package is also generally useful to others working in the + healthcare space, particularly since it has functions for working with + Community Health Index (CHI) numbers. The package can help to make + data manipulation and analysis more efficient and reproducible. License: GPL (>= 2) URL: https://github.com/Public-Health-Scotland/phsmethods, https://public-health-scotland.github.io/phsmethods/ @@ -51,5 +51,5 @@ Config/testthat/edition: 3 Encoding: UTF-8 Language: en-GB LazyData: true -RoxygenNote: 7.2.3 Roxygen: list(markdown = TRUE) +RoxygenNote: 7.2.3 From cf888c19952a1b7511763c7f3da5e788790a8974 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Wed, 1 Nov 2023 11:47:42 +0000 Subject: [PATCH 20/29] Add a `\value` to rename.Rd I don't really like this as it doesn't make any sense. It's also not consistent with the tidyverse advice: https://lifecycle.r-lib.org/articles/communicate.html#rename-a-function or the example they show (rvest) - https://github.com/tidyverse/rvest/blob/HEAD/R/rename.R https://github.com/tidyverse/rvest/blob/0cda79b4671bab46ba5717c8658ff81030091281/man/rename.Rd However, I'm pretty sure it should satisfy CRAN's requirements. --- R/rename.R | 2 +- man/rename.Rd | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/R/rename.R b/R/rename.R index 561badf..0a481e1 100644 --- a/R/rename.R +++ b/R/rename.R @@ -15,7 +15,7 @@ #' @keywords internal #' @name rename #' @aliases NULL -#' @return NULL +#' @returns `r lifecycle::badge('deprecated')` NULL #' @rdname rename diff --git a/man/rename.Rd b/man/rename.Rd index a6276c6..ad1e445 100644 --- a/man/rename.Rd +++ b/man/rename.Rd @@ -12,6 +12,9 @@ age_group(x, from = 0, to = 90, by = 5, as_factor = FALSE) fin_year(date) } +\value{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} +} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} From baec35a5ae56ae655d7c48ca6ff2bf11fb57e089 Mon Sep 17 00:00:00 2001 From: Nick Christofides Date: Mon, 20 Nov 2023 14:44:27 +0000 Subject: [PATCH 21/29] Updated extract_fin_year. --- R/extract_fin_year.R | 28 ++++----- tests/testthat/test-extract_fin_year.R | 82 ++++++++++++++++++++++++++ 2 files changed, 94 insertions(+), 16 deletions(-) diff --git a/R/extract_fin_year.R b/R/extract_fin_year.R index a8d7676..f0eddc2 100644 --- a/R/extract_fin_year.R +++ b/R/extract_fin_year.R @@ -18,8 +18,8 @@ #' extract_fin_year(x) #' @export extract_fin_year <- function(date) { - if (!inherits(date, c("Date", "POSIXct"))) { - cli::cli_abort("{.arg date} must be a {.cls Date} or {.cls POSIXct} vector, + if (!inherits(date, c("Date", "POSIXt"))) { + cli::cli_abort("{.arg date} must be a {.cls Date} or {.cls POSIXt} vector, not a {.cls {class(date)}} vector.") } @@ -29,18 +29,14 @@ extract_fin_year <- function(date) { # and then match them back on to the original input. This vastly improves # performance for large inputs. - unique_date <- unique(date) - - unique_fy_q <- - lubridate::year(unique_date) - (lubridate::month(unique_date) %in% 1:3) - - unique_fy <- ifelse( - is.na(unique_date), - NA_character_, - paste0(unique_fy_q, "/", (unique_fy_q %% 100L) + 1L) - ) - - fin_years <- unique_fy[match(date, unique_date)] - - return(fin_years) + # Note: lubridate year and month coerce to double + # We only need integers for our purposes + posix <- as.POSIXlt(date, tz = lubridate::tz(date)) + y <- posix$year + 1900L + m <- posix$mon + 1L + fy <- y - ( (m - 3L) %/% 1L <= 0L ) + next_fy <- (fy + 1L) %% 100L + out <- sprintf("%.4d/%02d", fy, next_fy) + out[is.na(date)] <- NA_character_ + out } diff --git a/tests/testthat/test-extract_fin_year.R b/tests/testthat/test-extract_fin_year.R index 46cd8d5..7467ac6 100644 --- a/tests/testthat/test-extract_fin_year.R +++ b/tests/testthat/test-extract_fin_year.R @@ -22,3 +22,85 @@ test_that("Non-date formats produce an error", { test_that("NAs are handled correctly", { expect_equal(extract_fin_year(c(lubridate::dmy(05012020), NA)), c("2019/20", NA)) }) + +test_that("YYYY/YY format applied correctly", { + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/April/1999"), NA)), + c(NA, "1999/00", NA)) + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/April/2000"), NA)), + c(NA, "2000/01", NA)) + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/April/2001"), NA)), + c(NA, "2001/02", NA)) + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "31/March/1999"), NA)), + c(NA, "1998/99", NA)) + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "31/March/2000"), NA)), + c(NA, "1999/00", NA)) + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "31/March/2001"), NA)), + c(NA, "2000/01", NA)) + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/December/1999"), NA)), + c(NA, "1999/00", NA)) + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/December/2000"), NA)), + c(NA, "2000/01", NA)) + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/December/2999"), NA)), + c(NA, "2999/00", NA)) + expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/December/3000"), NA)), + c(NA, "3000/01", NA)) + + expect_equal(extract_fin_year( + lubridate::as_datetime( + c(lubridate::dmy(NA, "01/April/1999"), NA) + ) + ), + c(NA, "1999/00", NA)) + + expect_equal(extract_fin_year( + lubridate::as_datetime( + c(lubridate::dmy(NA, "01/December/2000"), NA) + ) + ), + c(NA, "2000/01", NA)) + + expect_equal(extract_fin_year( + lubridate::as_datetime( + c(lubridate::dmy(NA, "01/April/0001"), NA) + ) + ), + c(NA, "0001/02", NA)) +}) + +test_that("Correct outputs", { + start <- lubridate::dmy("01/04/1999") + end <- lubridate::dmy("31/03/2024") + x <- seq(start, end, by = "day") + year_breaks <- start + lubridate::years(0:25) + fin_years <- extract_fin_year(x) + + df <- dplyr::tibble(x = x, fin_years = fin_years) + out <- dplyr::summarise(df, + start = min(x), + end = max(x), + n = dplyr::n(), + .by = fin_years) + + # We'll compare the above output by first creating an expected result + # This will be a tibble of start and end dates for each financial year + # We then use that find the number of days that lie between + # each pair + + start_end_df <- dplyr::tibble(start = seq(start, end, by = "year")) + start_end_df$end <- start_end_df$start + lubridate::years(1) - lubridate::days(1) + + start_end_df <- start_end_df %>% + dplyr::group_by(start, end) %>% + dplyr::mutate(n = sum(dplyr::between(x, start, end))) + + expected_years <- lubridate::year(start_end_df$start) + expected_years2 <- lubridate::year(start_end_df$end) %% 100 + expected_years2_padded <- stringr::str_pad(expected_years2, width = 2, + side = "left", pad = "0") + expected_fin_years <- paste0(expected_years, "/", expected_years2_padded) + + expect_equal(out$fin_years, expected_fin_years) + expect_equal(out$start, start_end_df$start) + expect_equal(out$end, start_end_df$end) + expect_equal(out$n, start_end_df$n) +}) From 507d94a19d92b77fcbc15b3f19aa62c4092ed506 Mon Sep 17 00:00:00 2001 From: Nick Christofides <74770457+Nic-Chr@users.noreply.github.com> Date: Mon, 20 Nov 2023 16:27:30 +0000 Subject: [PATCH 22/29] Update test-extract_fin_year.R Simplified tests with snapshot. --- tests/testthat/test-extract_fin_year.R | 29 +++----------------------- 1 file changed, 3 insertions(+), 26 deletions(-) diff --git a/tests/testthat/test-extract_fin_year.R b/tests/testthat/test-extract_fin_year.R index 7467ac6..a234d87 100644 --- a/tests/testthat/test-extract_fin_year.R +++ b/tests/testthat/test-extract_fin_year.R @@ -69,38 +69,15 @@ test_that("YYYY/YY format applied correctly", { test_that("Correct outputs", { start <- lubridate::dmy("01/04/1999") - end <- lubridate::dmy("31/03/2024") + end <- lubridate::dmy("31/03/2011") x <- seq(start, end, by = "day") - year_breaks <- start + lubridate::years(0:25) fin_years <- extract_fin_year(x) - df <- dplyr::tibble(x = x, fin_years = fin_years) + df <- data.frame(x = x, fin_years = fin_years) out <- dplyr::summarise(df, start = min(x), end = max(x), n = dplyr::n(), .by = fin_years) - - # We'll compare the above output by first creating an expected result - # This will be a tibble of start and end dates for each financial year - # We then use that find the number of days that lie between - # each pair - - start_end_df <- dplyr::tibble(start = seq(start, end, by = "year")) - start_end_df$end <- start_end_df$start + lubridate::years(1) - lubridate::days(1) - - start_end_df <- start_end_df %>% - dplyr::group_by(start, end) %>% - dplyr::mutate(n = sum(dplyr::between(x, start, end))) - - expected_years <- lubridate::year(start_end_df$start) - expected_years2 <- lubridate::year(start_end_df$end) %% 100 - expected_years2_padded <- stringr::str_pad(expected_years2, width = 2, - side = "left", pad = "0") - expected_fin_years <- paste0(expected_years, "/", expected_years2_padded) - - expect_equal(out$fin_years, expected_fin_years) - expect_equal(out$start, start_end_df$start) - expect_equal(out$end, start_end_df$end) - expect_equal(out$n, start_end_df$n) + expect_snapshot(out) }) From b3cd8e7f80dda7605d018192aa9d57988759187f Mon Sep 17 00:00:00 2001 From: Nick Christofides <74770457+Nic-Chr@users.noreply.github.com> Date: Mon, 20 Nov 2023 16:30:42 +0000 Subject: [PATCH 23/29] Update extract_fin_year.R Simplified code. --- R/extract_fin_year.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/extract_fin_year.R b/R/extract_fin_year.R index f0eddc2..704a7c6 100644 --- a/R/extract_fin_year.R +++ b/R/extract_fin_year.R @@ -33,8 +33,8 @@ extract_fin_year <- function(date) { # We only need integers for our purposes posix <- as.POSIXlt(date, tz = lubridate::tz(date)) y <- posix$year + 1900L - m <- posix$mon + 1L - fy <- y - ( (m - 3L) %/% 1L <= 0L ) + m <- posix$mon + fy <- y - (m < 3L) next_fy <- (fy + 1L) %% 100L out <- sprintf("%.4d/%02d", fy, next_fy) out[is.na(date)] <- NA_character_ From 1808d1de2c24ccdae3ab79db1fa8dd55711473ce Mon Sep 17 00:00:00 2001 From: James McMahon Date: Mon, 20 Nov 2023 16:41:56 +0000 Subject: [PATCH 24/29] Style code --- tests/testthat/test-extract_fin_year.R | 111 +++++++++++++++---------- 1 file changed, 69 insertions(+), 42 deletions(-) diff --git a/tests/testthat/test-extract_fin_year.R b/tests/testthat/test-extract_fin_year.R index a234d87..0d5ab81 100644 --- a/tests/testthat/test-extract_fin_year.R +++ b/tests/testthat/test-extract_fin_year.R @@ -24,47 +24,73 @@ test_that("NAs are handled correctly", { }) test_that("YYYY/YY format applied correctly", { - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/April/1999"), NA)), - c(NA, "1999/00", NA)) - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/April/2000"), NA)), - c(NA, "2000/01", NA)) - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/April/2001"), NA)), - c(NA, "2001/02", NA)) - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "31/March/1999"), NA)), - c(NA, "1998/99", NA)) - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "31/March/2000"), NA)), - c(NA, "1999/00", NA)) - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "31/March/2001"), NA)), - c(NA, "2000/01", NA)) - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/December/1999"), NA)), - c(NA, "1999/00", NA)) - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/December/2000"), NA)), - c(NA, "2000/01", NA)) - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/December/2999"), NA)), - c(NA, "2999/00", NA)) - expect_equal(extract_fin_year(c(lubridate::dmy(NA, "01/December/3000"), NA)), - c(NA, "3000/01", NA)) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "01/April/1999"), NA)), + c(NA, "1999/00", NA) + ) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "01/April/2000"), NA)), + c(NA, "2000/01", NA) + ) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "01/April/2001"), NA)), + c(NA, "2001/02", NA) + ) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "31/March/1999"), NA)), + c(NA, "1998/99", NA) + ) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "31/March/2000"), NA)), + c(NA, "1999/00", NA) + ) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "31/March/2001"), NA)), + c(NA, "2000/01", NA) + ) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "01/December/1999"), NA)), + c(NA, "1999/00", NA) + ) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "01/December/2000"), NA)), + c(NA, "2000/01", NA) + ) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "01/December/2999"), NA)), + c(NA, "2999/00", NA) + ) + expect_equal( + extract_fin_year(c(lubridate::dmy(NA, "01/December/3000"), NA)), + c(NA, "3000/01", NA) + ) - expect_equal(extract_fin_year( - lubridate::as_datetime( - c(lubridate::dmy(NA, "01/April/1999"), NA) - ) - ), - c(NA, "1999/00", NA)) + expect_equal( + extract_fin_year( + lubridate::as_datetime( + c(lubridate::dmy(NA, "01/April/1999"), NA) + ) + ), + c(NA, "1999/00", NA) + ) - expect_equal(extract_fin_year( - lubridate::as_datetime( - c(lubridate::dmy(NA, "01/December/2000"), NA) - ) - ), - c(NA, "2000/01", NA)) + expect_equal( + extract_fin_year( + lubridate::as_datetime( + c(lubridate::dmy(NA, "01/December/2000"), NA) + ) + ), + c(NA, "2000/01", NA) + ) - expect_equal(extract_fin_year( - lubridate::as_datetime( - c(lubridate::dmy(NA, "01/April/0001"), NA) - ) - ), - c(NA, "0001/02", NA)) + expect_equal( + extract_fin_year( + lubridate::as_datetime( + c(lubridate::dmy(NA, "01/April/0001"), NA) + ) + ), + c(NA, "0001/02", NA) + ) }) test_that("Correct outputs", { @@ -75,9 +101,10 @@ test_that("Correct outputs", { df <- data.frame(x = x, fin_years = fin_years) out <- dplyr::summarise(df, - start = min(x), - end = max(x), - n = dplyr::n(), - .by = fin_years) + start = min(x), + end = max(x), + n = dplyr::n(), + .by = fin_years + ) expect_snapshot(out) }) From 80063f15274d1eb3e483d59bb3df9e7fafd19023 Mon Sep 17 00:00:00 2001 From: James McMahon Date: Mon, 20 Nov 2023 16:55:23 +0000 Subject: [PATCH 25/29] Accept and add the snapshot Also add the code to the snapshot, which will hopefully make it easier to check. I expanded the date range, because why not, and it might pick up an issue one day... --- tests/testthat/_snaps/extract_fin_year.md | 113 ++++++++++++++++++++++ tests/testthat/test-extract_fin_year.R | 28 +++--- 2 files changed, 129 insertions(+), 12 deletions(-) create mode 100644 tests/testthat/_snaps/extract_fin_year.md diff --git a/tests/testthat/_snaps/extract_fin_year.md b/tests/testthat/_snaps/extract_fin_year.md new file mode 100644 index 0000000..1c006e6 --- /dev/null +++ b/tests/testthat/_snaps/extract_fin_year.md @@ -0,0 +1,113 @@ +# Correct outputs + + Code + start <- lubridate::make_date(1999, 4, 1) + end <- lubridate::make_date(2100, 3, 31) + dates <- seq(start, end, by = "day") + df <- data.frame(date = dates, fin_year = extract_fin_year(dates)) + dplyr::summarise(df, first_date = min(date), last_date = max(date), days = dplyr::n(), + .by = fin_year) + Output + fin_year first_date last_date days + 1 1999/00 1999-04-01 2000-03-31 366 + 2 2000/01 2000-04-01 2001-03-31 365 + 3 2001/02 2001-04-01 2002-03-31 365 + 4 2002/03 2002-04-01 2003-03-31 365 + 5 2003/04 2003-04-01 2004-03-31 366 + 6 2004/05 2004-04-01 2005-03-31 365 + 7 2005/06 2005-04-01 2006-03-31 365 + 8 2006/07 2006-04-01 2007-03-31 365 + 9 2007/08 2007-04-01 2008-03-31 366 + 10 2008/09 2008-04-01 2009-03-31 365 + 11 2009/10 2009-04-01 2010-03-31 365 + 12 2010/11 2010-04-01 2011-03-31 365 + 13 2011/12 2011-04-01 2012-03-31 366 + 14 2012/13 2012-04-01 2013-03-31 365 + 15 2013/14 2013-04-01 2014-03-31 365 + 16 2014/15 2014-04-01 2015-03-31 365 + 17 2015/16 2015-04-01 2016-03-31 366 + 18 2016/17 2016-04-01 2017-03-31 365 + 19 2017/18 2017-04-01 2018-03-31 365 + 20 2018/19 2018-04-01 2019-03-31 365 + 21 2019/20 2019-04-01 2020-03-31 366 + 22 2020/21 2020-04-01 2021-03-31 365 + 23 2021/22 2021-04-01 2022-03-31 365 + 24 2022/23 2022-04-01 2023-03-31 365 + 25 2023/24 2023-04-01 2024-03-31 366 + 26 2024/25 2024-04-01 2025-03-31 365 + 27 2025/26 2025-04-01 2026-03-31 365 + 28 2026/27 2026-04-01 2027-03-31 365 + 29 2027/28 2027-04-01 2028-03-31 366 + 30 2028/29 2028-04-01 2029-03-31 365 + 31 2029/30 2029-04-01 2030-03-31 365 + 32 2030/31 2030-04-01 2031-03-31 365 + 33 2031/32 2031-04-01 2032-03-31 366 + 34 2032/33 2032-04-01 2033-03-31 365 + 35 2033/34 2033-04-01 2034-03-31 365 + 36 2034/35 2034-04-01 2035-03-31 365 + 37 2035/36 2035-04-01 2036-03-31 366 + 38 2036/37 2036-04-01 2037-03-31 365 + 39 2037/38 2037-04-01 2038-03-31 365 + 40 2038/39 2038-04-01 2039-03-31 365 + 41 2039/40 2039-04-01 2040-03-31 366 + 42 2040/41 2040-04-01 2041-03-31 365 + 43 2041/42 2041-04-01 2042-03-31 365 + 44 2042/43 2042-04-01 2043-03-31 365 + 45 2043/44 2043-04-01 2044-03-31 366 + 46 2044/45 2044-04-01 2045-03-31 365 + 47 2045/46 2045-04-01 2046-03-31 365 + 48 2046/47 2046-04-01 2047-03-31 365 + 49 2047/48 2047-04-01 2048-03-31 366 + 50 2048/49 2048-04-01 2049-03-31 365 + 51 2049/50 2049-04-01 2050-03-31 365 + 52 2050/51 2050-04-01 2051-03-31 365 + 53 2051/52 2051-04-01 2052-03-31 366 + 54 2052/53 2052-04-01 2053-03-31 365 + 55 2053/54 2053-04-01 2054-03-31 365 + 56 2054/55 2054-04-01 2055-03-31 365 + 57 2055/56 2055-04-01 2056-03-31 366 + 58 2056/57 2056-04-01 2057-03-31 365 + 59 2057/58 2057-04-01 2058-03-31 365 + 60 2058/59 2058-04-01 2059-03-31 365 + 61 2059/60 2059-04-01 2060-03-31 366 + 62 2060/61 2060-04-01 2061-03-31 365 + 63 2061/62 2061-04-01 2062-03-31 365 + 64 2062/63 2062-04-01 2063-03-31 365 + 65 2063/64 2063-04-01 2064-03-31 366 + 66 2064/65 2064-04-01 2065-03-31 365 + 67 2065/66 2065-04-01 2066-03-31 365 + 68 2066/67 2066-04-01 2067-03-31 365 + 69 2067/68 2067-04-01 2068-03-31 366 + 70 2068/69 2068-04-01 2069-03-31 365 + 71 2069/70 2069-04-01 2070-03-31 365 + 72 2070/71 2070-04-01 2071-03-31 365 + 73 2071/72 2071-04-01 2072-03-31 366 + 74 2072/73 2072-04-01 2073-03-31 365 + 75 2073/74 2073-04-01 2074-03-31 365 + 76 2074/75 2074-04-01 2075-03-31 365 + 77 2075/76 2075-04-01 2076-03-31 366 + 78 2076/77 2076-04-01 2077-03-31 365 + 79 2077/78 2077-04-01 2078-03-31 365 + 80 2078/79 2078-04-01 2079-03-31 365 + 81 2079/80 2079-04-01 2080-03-31 366 + 82 2080/81 2080-04-01 2081-03-31 365 + 83 2081/82 2081-04-01 2082-03-31 365 + 84 2082/83 2082-04-01 2083-03-31 365 + 85 2083/84 2083-04-01 2084-03-31 366 + 86 2084/85 2084-04-01 2085-03-31 365 + 87 2085/86 2085-04-01 2086-03-31 365 + 88 2086/87 2086-04-01 2087-03-31 365 + 89 2087/88 2087-04-01 2088-03-31 366 + 90 2088/89 2088-04-01 2089-03-31 365 + 91 2089/90 2089-04-01 2090-03-31 365 + 92 2090/91 2090-04-01 2091-03-31 365 + 93 2091/92 2091-04-01 2092-03-31 366 + 94 2092/93 2092-04-01 2093-03-31 365 + 95 2093/94 2093-04-01 2094-03-31 365 + 96 2094/95 2094-04-01 2095-03-31 365 + 97 2095/96 2095-04-01 2096-03-31 366 + 98 2096/97 2096-04-01 2097-03-31 365 + 99 2097/98 2097-04-01 2098-03-31 365 + 100 2098/99 2098-04-01 2099-03-31 365 + 101 2099/00 2099-04-01 2100-03-31 365 + diff --git a/tests/testthat/test-extract_fin_year.R b/tests/testthat/test-extract_fin_year.R index 0d5ab81..5bc5cff 100644 --- a/tests/testthat/test-extract_fin_year.R +++ b/tests/testthat/test-extract_fin_year.R @@ -94,17 +94,21 @@ test_that("YYYY/YY format applied correctly", { }) test_that("Correct outputs", { - start <- lubridate::dmy("01/04/1999") - end <- lubridate::dmy("31/03/2011") - x <- seq(start, end, by = "day") - fin_years <- extract_fin_year(x) + expect_snapshot({ + start <- lubridate::make_date(1999, 4, 1) + end <- lubridate::make_date(2100, 3, 31) + dates <- seq(start, end, by = "day") - df <- data.frame(x = x, fin_years = fin_years) - out <- dplyr::summarise(df, - start = min(x), - end = max(x), - n = dplyr::n(), - .by = fin_years - ) - expect_snapshot(out) + df <- data.frame( + date = dates, + fin_year = extract_fin_year(dates) + ) + + dplyr::summarise(df, + first_date = min(date), + last_date = max(date), + days = dplyr::n(), + .by = fin_year + ) + }) }) From 561742137deecc3d62a160d55d3cab332afe182f Mon Sep 17 00:00:00 2001 From: Tina Fu Date: Tue, 21 Nov 2023 15:11:14 +0000 Subject: [PATCH 26/29] add CRAN-SUBMISSION to buildignore --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index 498b6f0..d5786df 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -9,3 +9,4 @@ ^docs$ ^pkgdown$ ^cran-comments\.md$ +^CRAN-SUBMISSION$ From d9ccf46f13b52fdca10edbaab40d419a8e0dc2e3 Mon Sep 17 00:00:00 2001 From: TinaFu <31853064+Tina815@users.noreply.github.com> Date: Tue, 21 Nov 2023 16:17:49 +0000 Subject: [PATCH 27/29] Update comments --- R/extract_fin_year.R | 6 ------ 1 file changed, 6 deletions(-) diff --git a/R/extract_fin_year.R b/R/extract_fin_year.R index 704a7c6..13d0a1d 100644 --- a/R/extract_fin_year.R +++ b/R/extract_fin_year.R @@ -23,12 +23,6 @@ extract_fin_year <- function(date) { not a {.cls {class(date)}} vector.") } - # Simply converting all elements of the input vector resulted in poor - # performance for large vectors. The function was rewritten to extract - # a vector of unique elements from the input, convert those to financial year - # and then match them back on to the original input. This vastly improves - # performance for large inputs. - # Note: lubridate year and month coerce to double # We only need integers for our purposes posix <- as.POSIXlt(date, tz = lubridate::tz(date)) From 106aaa6853fe8ce305bcc83751794bac2f30cb62 Mon Sep 17 00:00:00 2001 From: TinaFu <31853064+Tina815@users.noreply.github.com> Date: Tue, 21 Nov 2023 16:25:20 +0000 Subject: [PATCH 28/29] Update @param text --- R/extract_fin_year.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/extract_fin_year.R b/R/extract_fin_year.R index 13d0a1d..69be46a 100644 --- a/R/extract_fin_year.R +++ b/R/extract_fin_year.R @@ -5,8 +5,8 @@ #' #' @details The PHS accepted format for financial year is YYYY/YY e.g. 2017/18. #' -#' @param date A date which must be supplied with `Date` or `POSIXct` -#' class. [base::as.Date()], +#' @param date A date which must be supplied with `Date`, `POSIXct`, `POSIXlt` or +#' `POSIXt` class. [base::as.Date()], #' [`lubridate::dmy()`][lubridate::ymd] and #' [`as.POSIXct()`][base::as.POSIXlt] are examples of functions which #' can be used to store dates as an appropriate class. From c6eb8825f42130c13ca5750784f23d82fe929d37 Mon Sep 17 00:00:00 2001 From: Tina815 Date: Tue, 21 Nov 2023 16:33:52 +0000 Subject: [PATCH 29/29] Update documentation --- man/extract_fin_year.Rd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/man/extract_fin_year.Rd b/man/extract_fin_year.Rd index 361d044..5c06015 100644 --- a/man/extract_fin_year.Rd +++ b/man/extract_fin_year.Rd @@ -7,8 +7,8 @@ extract_fin_year(date) } \arguments{ -\item{date}{A date which must be supplied with \code{Date} or \code{POSIXct} -class. \code{\link[base:as.Date]{base::as.Date()}}, +\item{date}{A date which must be supplied with \code{Date}, \code{POSIXct}, \code{POSIXlt} or +\code{POSIXt} class. \code{\link[base:as.Date]{base::as.Date()}}, \code{\link[lubridate:ymd]{lubridate::dmy()}} and \code{\link[base:as.POSIXlt]{as.POSIXct()}} are examples of functions which can be used to store dates as an appropriate class.}