Vignettes

.Rbuildignore

@@ -10,3 +10,9 @@
 ^doc$
 ^Meta$
 ^data-raw$
+^README\.qmd$
+^README_files$
+^mwana\.Rproj$
+^vignettes/plausibility_files$
+^vignettes/prevalence_files$
+^vignettes/sample_size_files$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,53 @@
+# 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.yaml
+
+permissions: read-all
+
+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
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - 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

.gitignore

@@ -9,3 +9,9 @@ inst/doc
 docs
 /doc/
 /Meta/
+
+/README_files/
+
+/vignettes/plausibility_files/
+/vignettes/prevalence_files/
+/vignettes/sample_size_files/

DESCRIPTION

@@ -14,7 +14,7 @@ Description: A streamlined and comprehensive implementation of the Standardized
   prevalence estimation, with enhanced programmable process particularly when 
   handling large multiple datasets.
 License: GPL (>= 3)
-URL: https://github.com/nutriverse/mwana, https://nutriverse.io/mwana
+URL: https://github.com/nutriverse/mwana, https://nutriverse.io/mwana, http://nutriverse.io/mwana/
 BugReports: https://github.com/nutriverse/mwana/issues
 Imports: 
     dplyr (>= 1.1.4),
@@ -29,6 +29,7 @@ Imports:
 Suggests:
     knitr,
     rmarkdown,
+    quarto,
     spelling,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
@@ -39,4 +40,5 @@ RoxygenNote: 7.3.2
 Depends: 
     R (>= 4.1)
 LazyData: true
-VignetteBuilder: knitr
+VignetteBuilder:
+    quarto

R/age.R

@@ -38,10 +38,10 @@ compute_age_in_months <- function (surv_date, birth_date) {
 
 
 #'
-#' Wrangle child's age
+#' Process child's age
 #'
 #' @description
-#' Wrangle child's age for downstream analysis. This includes calculating age
+#' Process child's age for downstream analysis. This includes calculating age
 #' in months based on the date of data collection and child's date of birth and
 #' setting to `NA` the age values that are less than 6.0 and greater than or equal
 #' to 60.0 months old.
@@ -66,6 +66,7 @@ compute_age_in_months <- function (surv_date, birth_date) {
 #' @examples
 #'
 #' ## A sample data ----
+#'
 #' df <- data.frame(
 #' survy_date = as.Date(c(
 #' "2023-01-01", "2023-01-01", "2023-01-01", "2023-01-01", "2023-01-01")),

README.md

@@ -2,18 +2,18 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# `mwana`: Utilities for Analysing Children’s Nutritional Status
+# `mwana`: Utilities for analysing children’s nutritional status
 
 <!-- badges: start -->
 
+[![R-CMD-check](https://github.com/nutriverse/mwana/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tomaszaba/ipccheckr/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/nutriverse/mwana/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tomaszaba/ipccheckr?branch=main)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![Project Status: WIP – Initial development is in progress, but there
 has not yet been a stable, usable release suitable for the
 public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
-[![R-CMD-check](https://github.com/nutriverse/mwana/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tomaszaba/ipccheckr/actions/workflows/R-CMD-check.yaml)
-[![Codecov test
-coverage](https://codecov.io/gh/nutriverse/mwana/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tomaszaba/ipccheckr?branch=main)
 <!-- badges: end -->
 
 Child anthropometric assessments, implemented routinely in most
@@ -82,7 +82,8 @@ summaries of the outputs.
 
 #### A useful workflow for plausibility check using `mwana`
 
-<img src="man/figures/README-worflow-1.png" data-fig-align="center" />
+<img src="README_files/figure-commonmark/worflow-1.png"
+data-fig-align="center" />
 
 ### Prevalence analysis
 
@@ -157,23 +158,24 @@ function as follows:
 
 ``` r
 citation("ipccheckr")
-#> To cite ipccheckr: in publications use:
-#> 
-#>   Tomás Zaba, Ernest Guevarra (2024). _ipccheckr: Toolkit for
-#>   Performing IPC Acute Malnutrition-related Data Checks_. R package
-#>   version 0.0.0.9000, <https://github.com/tomaszaba/ipccheckr>.
-#> 
-#> A BibTeX entry for LaTeX users is
-#> 
-#>   @Manual{,
-#>     title = {ipccheckr: Toolkit for Performing IPC Acute Malnutrition-related Data Checks},
-#>     author = {{Tomás Zaba} and {Ernest Guevarra}},
-#>     year = {2024},
-#>     note = {R package version 0.0.0.9000},
-#>     url = {https://github.com/tomaszaba/ipccheckr},
-#>   }
 ```
 
+    To cite ipccheckr: in publications use:
+
+      Tomás Zaba, Ernest Guevarra (2024). _ipccheckr: Toolkit for
+      Performing IPC Acute Malnutrition-related Data Checks_. R package
+      version 0.0.0.9000, <https://github.com/tomaszaba/ipccheckr>.
+
+    A BibTeX entry for LaTeX users is
+
+      @Manual{,
+        title = {ipccheckr: Toolkit for Performing IPC Acute Malnutrition-related Data Checks},
+        author = {{Tomás Zaba} and {Ernest Guevarra}},
+        year = {2024},
+        note = {R package version 0.0.0.9000},
+        url = {https://github.com/tomaszaba/ipccheckr},
+      }
+
 # Community guidelines
 
 Feedback, bug reports and feature requests are welcome; file issues or