From d44698ccf912f1498cf50f0ea4c464ce6e37306e Mon Sep 17 00:00:00 2001 From: Tina815 Date: Fri, 22 Sep 2023 13:36:35 +0000 Subject: [PATCH] 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):

+ +

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:

+ +

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