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update to R 4.4.0 #2

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Jun 9, 2024
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update to R 4.4.0 #2

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5 changes: 1 addition & 4 deletions README.Rmd
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Expand Up @@ -29,15 +29,12 @@ The project repository is structured as follows:
```
sc-policy-review
|-- .github/
|-- workflows/
|-- data/
|-- data-raw/
|-- outputs/
|-- R/
|-- reports
|-- renv
|-- library/
|-- activate.R
|-- renv.lock
|-- .Rprofile
|-- packages.R
Expand Down Expand Up @@ -70,5 +67,5 @@ sc-policy-review

### R package dependencies

This project was built using `R 4.3.3`. This project uses the `renv` framework to record R package dependencies and versions. Packages and versions used are recorded in `renv.lock` and code used to manage dependencies is in `renv/` and other files in the root project directory. On starting an R session in the working directory, run `renv::restore()` to install R package dependencies.
This project was built using `R 4.4.0`. This project uses the `renv` framework to record R package dependencies and versions. Packages and versions used are recorded in `renv.lock` and code used to manage dependencies is in `renv/` and other files in the root project directory. On starting an R session in the working directory, run `renv::restore()` to install R package dependencies.

84 changes: 41 additions & 43 deletions README.md
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# A template R workflow for general data analysis

<!-- badges: start -->

<!-- badges: end -->

This repository is a template for a
Expand All @@ -20,75 +21,72 @@ The project repository is structured as follows:

sc-policy-review
|-- .github/
|-- workflows/
|-- data/
|-- data-raw/
|-- outputs/
|-- R/
|-- reports
|-- renv
|-- library/
|-- activate.R
|-- renv.lock
|-- .Rprofile
|-- packages.R
|-- _targets.R

- `.github` contains project testing and automated deployment of outputs
workflows via continuous integration and continuous deployment (CI/CD)
using Github Actions.
- `.github` contains project testing and automated deployment of
outputs workflows via continuous integration and continuous
deployment (CI/CD) using Github Actions.

- `data/` contains intermediate and final data outputs produced by the
workflow.
- `data/` contains intermediate and final data outputs produced by the
workflow.

- `data-raw/` contains raw datasets, usually either downloaded from
source or added manually, that are used in the project. This directory
is empty given that the raw datasets used in this project are
restricted and are only distributed to eligible members of the
project. This directory is kept here to maintain reproducibility of
project directory structure and ensure that the workflow runs as
expected. Those who are collaborating on this project and who have
permissions to use the raw datasets should include their copies of the
raw dataset into this directory in their local versions of this
repository.
- `data-raw/` contains raw datasets, usually either downloaded from
source or added manually, that are used in the project. This
directory is empty given that the raw datasets used in this project
are restricted and are only distributed to eligible members of the
project. This directory is kept here to maintain reproducibility of
project directory structure and ensure that the workflow runs as
expected. Those who are collaborating on this project and who have
permissions to use the raw datasets should include their copies of
the raw dataset into this directory in their local versions of this
repository.

- `outputs/` contains compiled reports and figures produced by the
workflow.
- `outputs/` contains compiled reports and figures produced by the
workflow.

- `R/` contains functions developed/created specifically for use in this
workflow.
- `R/` contains functions developed/created specifically for use in
this workflow.

- `reports/` contains literate code for R Markdown reports rendered in
the workflow.
- `reports/` contains literate code for R Markdown reports rendered in
the workflow.

- `renv/` contains `renv` package specific files and directories used by
the package for maintaining R package dependencies within the project.
The directory `renv/library`, is a library that contains all packages
currently used by the project. This directory, and all files and
sub-directories within it, are all generated and managed by the `renv`
package. Users should not change/edit these manually.
- `renv/` contains `renv` package specific files and directories used
by the package for maintaining R package dependencies within the
project. The directory `renv/library`, is a library that contains
all packages currently used by the project. This directory, and all
files and sub-directories within it, are all generated and managed
by the `renv` package. Users should not change/edit these manually.

- `renv.lock` file is the `renv` lockfile which records enough metadata
about every package used in this project that it can be re-installed
on a new machine. This file is generated by the `renv` package and
should not be changed/edited manually.
- `renv.lock` file is the `renv` lockfile which records enough
metadata about every package used in this project that it can be
re-installed on a new machine. This file is generated by the `renv`
package and should not be changed/edited manually.

- `.Rprofile` file is a project R profile generated when initiating
`renv` for the first time. This file is run automatically every time R
is run within this project, and `renv` uses it to configure the R
session to use the `renv` project library.
- `.Rprofile` file is a project R profile generated when initiating
`renv` for the first time. This file is run automatically every time
R is run within this project, and `renv` uses it to configure the R
session to use the `renv` project library.

- `packages.R` file lists out all R package dependencies required by the
workflow.
- `packages.R` file lists out all R package dependencies required by
the workflow.

- `_targets.R` file defines the steps in the workflow’s data ingest,
data processing, data analysis, and reporting pipeline.
- `_targets.R` file defines the steps in the workflow’s data ingest,
data processing, data analysis, and reporting pipeline.

## Reproducibility

### R package dependencies

This project was built using `R 4.3.3`. This project uses the `renv`
This project was built using `R 4.4.0`. This project uses the `renv`
framework to record R package dependencies and versions. Packages and
versions used are recorded in `renv.lock` and code used to manage
dependencies is in `renv/` and other files in the root project
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2 changes: 1 addition & 1 deletion renv.lock
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@@ -1,6 +1,6 @@
{
"R": {
"Version": "4.3.1",
"Version": "4.4.0",
"Repositories": [
{
"Name": "CRAN",
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