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Merge pull request #58 from rapidsurveys/dev
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ernestguevarra authored Apr 13, 2024
2 parents 3c45644 + 2ee2650 commit 2bca0cc
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3 changes: 2 additions & 1 deletion .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ jobs:
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

Expand All @@ -47,3 +47,4 @@ jobs:
- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true
build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
48 changes: 48 additions & 0 deletions .github/workflows/pkgdown.yaml
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@@ -0,0 +1,48 @@
# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]
release:
types: [published]
workflow_dispatch:

name: pkgdown

jobs:
pkgdown:
runs-on: ubuntu-latest
# Only restrict concurrency for non-PR jobs
concurrency:
group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
permissions:
contents: write
steps:
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::pkgdown, local::.
needs: website

- name: Build site
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
shell: Rscript {0}

- name: Deploy to GitHub pages 🚀
if: github.event_name != 'pull_request'
uses: JamesIves/github-pages-deploy-action@v4.5.0
with:
clean: false
branch: gh-pages
folder: docs
95 changes: 95 additions & 0 deletions .github/workflows/rhub.yaml
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@@ -0,0 +1,95 @@
# R-hub's generic GitHub Actions workflow file. It's canonical location is at
# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
# You can update this file to a newer version using the rhub2 package:
#
# rhub::rhub_setup()
#
# It is unlikely that you need to modify this file manually.

name: R-hub
run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"

on:
workflow_dispatch:
inputs:
config:
description: 'A comma separated list of R-hub platforms to use.'
type: string
default: 'linux,windows,macos'
name:
description: 'Run name. You can leave this empty now.'
type: string
id:
description: 'Unique ID. You can leave this empty now.'
type: string

jobs:

setup:
runs-on: ubuntu-latest
outputs:
containers: ${{ steps.rhub-setup.outputs.containers }}
platforms: ${{ steps.rhub-setup.outputs.platforms }}

steps:
# NO NEED TO CHECKOUT HERE
- uses: r-hub/actions/setup@v1
with:
config: ${{ github.event.inputs.config }}
id: rhub-setup

linux-containers:
needs: setup
if: ${{ needs.setup.outputs.containers != '[]' }}
runs-on: ubuntu-latest
name: ${{ matrix.config.label }}
strategy:
fail-fast: false
matrix:
config: ${{ fromJson(needs.setup.outputs.containers) }}
container:
image: ${{ matrix.config.container }}

steps:
- uses: r-hub/actions/checkout@v1
- uses: r-hub/actions/platform-info@v1
with:
token: ${{ secrets.RHUB_TOKEN }}
job-config: ${{ matrix.config.job-config }}
- uses: r-hub/actions/setup-deps@v1
with:
token: ${{ secrets.RHUB_TOKEN }}
job-config: ${{ matrix.config.job-config }}
- uses: r-hub/actions/run-check@v1
with:
token: ${{ secrets.RHUB_TOKEN }}
job-config: ${{ matrix.config.job-config }}

other-platforms:
needs: setup
if: ${{ needs.setup.outputs.platforms != '[]' }}
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.label }}
strategy:
fail-fast: false
matrix:
config: ${{ fromJson(needs.setup.outputs.platforms) }}

steps:
- uses: r-hub/actions/checkout@v1
- uses: r-hub/actions/setup-r@v1
with:
job-config: ${{ matrix.config.job-config }}
token: ${{ secrets.RHUB_TOKEN }}
- uses: r-hub/actions/platform-info@v1
with:
token: ${{ secrets.RHUB_TOKEN }}
job-config: ${{ matrix.config.job-config }}
- uses: r-hub/actions/setup-deps@v1
with:
job-config: ${{ matrix.config.job-config }}
token: ${{ secrets.RHUB_TOKEN }}
- uses: r-hub/actions/run-check@v1
with:
job-config: ${{ matrix.config.job-config }}
token: ${{ secrets.RHUB_TOKEN }}
8 changes: 4 additions & 4 deletions .github/workflows/test-coverage.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ jobs:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-r@v2
with:
Expand All @@ -31,20 +31,20 @@ jobs:
covr::codecov(
quiet = FALSE,
clean = FALSE,
install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
)
shell: Rscript {0}

- name: Show testthat output
if: always()
run: |
## --------------------------------------------------------------------
find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash

- name: Upload test results
if: failure()
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: coverage-test-failures
path: ${{ runner.temp }}/package
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@
packrat/lib*/
inst/ramOP/rsconnect/
inst/doc
docs
2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ Encoding: UTF-8
LazyData: true
Language: en-GB
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
RoxygenNote: 7.3.1
VignetteBuilder: knitr
URL: https://rapidsurveys.io/oldr/, https://github.com/rapidsurveys/oldr
BugReports: https://github.com/rapidsurveys/oldr/issues
14 changes: 3 additions & 11 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -18,19 +18,15 @@ knitr::opts_chunk$set(
# oldr: An Implementation of the Rapid Assessment Method for Older People (RAM-OP) <img src="man/figures/logo.png" width="200" align="right" />

<!-- Badges start here-->
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![CRAN](https://img.shields.io/cran/l/oldr.svg)](https://CRAN.R-project.org/package=oldr)
[![CRAN](https://img.shields.io/cran/v/oldr.svg)](https://cran.r-project.org/package=oldr)
[![CRAN](http://cranlogs.r-pkg.org/badges/oldr)](https://CRAN.R-project.org/package=oldr)
[![R-CMD-check](https://github.com/rapidsurveys/oldr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rapidsurveys/oldr/actions/workflows/R-CMD-check.yaml)
[![test-coverage](https://github.com/rapidsurveys/oldr/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/rapidsurveys/oldr/actions/workflows/test-coverage.yaml)
[![codecov](https://codecov.io/gh/rapidsurveys/oldr/branch/main/graph/badge.svg)](https://codecov.io/gh/rapidsurveys/oldr)
[![CodeFactor](https://www.codefactor.io/repository/github/rapidsurveys/oldr/badge)](https://www.codefactor.io/repository/github/rapidsurveys/oldr)
[![DOI](https://zenodo.org/badge/105472081.svg)](https://zenodo.org/badge/latestdoi/105472081)
<!-- Badges end here-->

<!-- [![cran checks](https://cranchecks.info/badges/summary/oldr)](https://cran.r-project.org/web/checks/check_results_oldr.html) -->

[HelpAge International](http://www.helpage.org), [VALID International](http://www.validinternational.org), and [Brixton Health](http://www.brixtonhealth.com), with financial assistance from the [Humanitarian Innovation Fund (HIF)](http://www.elrha.org/hif/home/), have developed a **Rapid Assessment Method for Older People (RAM-OP)** that provides accurate and reliable estimates of the needs of older people. The method uses simple procedures, in a short time frame (i.e. about two weeks including training, data collection, data entry, and data analysis), and at considerably lower cost than other methods. The **RAM-OP** method is based on the following principles:

* Use of a familiar *“household survey”* design employing a two-stage cluster sample design optimised to allow the use of a small primary sample (*m ≥ 16 clusters*) and a small overall (*n ≥ 192*) sample.
Expand All @@ -41,15 +37,11 @@ knitr::opts_chunk$set(

## Installation

<!---
You can install `oldr` from [CRAN](https://cran.r-project.org) with:

```{r install-cran, echo = TRUE, eval = FALSE}
install.packages("oldr")
```
--->

The `oldr` package is still in active development and not yet available on [CRAN](https://cran.r-project.org/).

You can install the development version of `oldr` from [GitHub](https://github.com/rapidsurveys/oldr) with:

Expand Down Expand Up @@ -188,4 +180,4 @@ citation("oldr")

Feedback, bug reports, and feature requests are welcome; file issues or seek support [here](https://github.com/rapidsurveys/oldr/issues). If you would like to contribute to the package, please see our [contributing guidelines](https://rapidsurveys.io/oldr/CONTRIBUTING.html).

This project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
This project is released with a [Contributor Code of Conduct](https://rapidsurveys.io/oldr/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
32 changes: 12 additions & 20 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,20 +7,16 @@

[![Project Status: Active – The project has reached a stable, usable
state and is being actively
developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![Lifecycle:
stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![CRAN](https://img.shields.io/cran/l/oldr.svg)](https://CRAN.R-project.org/package=oldr)
[![CRAN](https://img.shields.io/cran/v/oldr.svg)](https://cran.r-project.org/package=oldr)
[![CRAN](http://cranlogs.r-pkg.org/badges/oldr)](https://CRAN.R-project.org/package=oldr)
[![R-CMD-check](https://github.com/rapidsurveys/oldr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rapidsurveys/oldr/actions/workflows/R-CMD-check.yaml)
[![test-coverage](https://github.com/rapidsurveys/oldr/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/rapidsurveys/oldr/actions/workflows/test-coverage.yaml)
[![codecov](https://codecov.io/gh/rapidsurveys/oldr/branch/main/graph/badge.svg)](https://codecov.io/gh/rapidsurveys/oldr)
[![CodeFactor](https://www.codefactor.io/repository/github/rapidsurveys/oldr/badge)](https://www.codefactor.io/repository/github/rapidsurveys/oldr)
[![DOI](https://zenodo.org/badge/105472081.svg)](https://zenodo.org/badge/latestdoi/105472081)
<!-- Badges end here-->

<!-- [![cran checks](https://cranchecks.info/badges/summary/oldr)](https://cran.r-project.org/web/checks/check_results_oldr.html) -->

[HelpAge International](http://www.helpage.org), [VALID
International](http://www.validinternational.org), and [Brixton
Health](http://www.brixtonhealth.com), with financial assistance from
Expand Down Expand Up @@ -48,17 +44,11 @@ based on the following principles:

## Installation

<!---
You can install `oldr` from [CRAN](https://cran.r-project.org) with:

```r
``` r
install.packages("oldr")
```
--->

The `oldr` package is still in active development and not yet available
on [CRAN](https://cran.r-project.org/).

You can install the development version of `oldr` from
[GitHub](https://github.com/rapidsurveys/oldr) with:
Expand Down Expand Up @@ -90,21 +80,23 @@ citation provided by a call to the `citation` function as follows:

``` r
citation("oldr")
#>
#> To cite oldr in publications use:
#>
#> Ernest Guevarra (2023). oldr: An Implementation of Rapid Assessment
#> Method for Older People R package version 0.1.0.9000 URL
#> https://rapidsurveys.io/oldr/
#> Mark Myatt, Ernest Guevarra, Pascale Fritsch, Katja Siling (2024).
#> _oldr: An Implementation of Rapid Assessment Method for Older
#> People_. doi:10.5281/zenodo.7505731
#> <https://doi.org/10.5281/zenodo.7505731>, R package version
#> 0.1.0.9000, <https://rapidsurveys.io/oldr/>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {oldr: An Implementation of Rapid Assessment Method for Older People},
#> author = {{Mark Myatt} and {Ernest Guevarra} and {Pascale Fritsch} and {Katja Siling}},
#> year = {2023},
#> year = {2024},
#> note = {R package version 0.1.0.9000},
#> url = {https://rapidsurveys.io/oldr/},
#> doi = {10.5281/zenodo.7505731},
#> }
```

Expand All @@ -116,5 +108,5 @@ would like to contribute to the package, please see our [contributing
guidelines](https://rapidsurveys.io/oldr/CONTRIBUTING.html).

This project is released with a [Contributor Code of
Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.
Conduct](https://rapidsurveys.io/oldr/CODE_OF_CONDUCT.html). By
contributing to this project, you agree to abide by its terms.
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