Merge pull request #22 from nutriverse:dev

add tests and setup new website workflow; fix #19; fix #20; fix #21
nutriverse · Dec 18, 2024 · 1c87877 · 1c87877
2 parents 402f5d1 + 76aba3f
commit 1c87877
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diff --git a/.github/workflows/netlify.yaml b/.github/workflows/netlify.yaml
@@ -0,0 +1,53 @@
+on:
+  pull_request:
+    branches: [main, master]
+
+name: pkgdown-pr
+
+jobs:
+  netlify:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-tinytex@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: Install package
+        run: R CMD INSTALL .
+
+      - name: Create website
+        run: |
+          pkgdown::build_site()
+        shell: Rscript {0}
+
+      - name: Create index file
+        run: |
+          echo '<!DOCTYPE html><html><head><meta http-equiv="refresh" content="0;URL=/dev/index.html" />  <script language="javascript"> window.location.replace('/dev/index.html')</script></head></html>' > ./docs/index.html
+
+      - name: Deploy to Netlify
+        uses: nwtgck/[email protected]
+        with:
+          publish-dir: './docs'
+          production-branch: main
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message:
+            'Deploy from GHA: ${{ github.event.pull_request.title || github.event.head_commit.message }} (${{ github.sha }})'
+          # these default to 'true'
+          enable-commit-comment: false
+          enable-github-deployment: false
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
diff --git a/README.Rmd b/README.Rmd
@@ -25,11 +25,26 @@ knitr::opts_chunk$set(
 
 Ensuring the precision and accuracy of measurements is critical when collecting anthropometric data. Anthropometrists are usually tested for precision and accuracy of measurement through standardisation tests performed prior to anthropometric data collection. This package provides functions to calculate inter- and intra-observer technical error of measurement (TEM) to assess precision of measurements.
 
-## What does `anthrocheckr` do?
+## What does the package do?
+
+`{anthrocheckr}` provides functions for:
+
+1. Calculating standard summaries for intra-observer or inter-observer measurements;
+
+2. Calculating intra-observer or inter-observer technical error of measurement (TEM) for multiple subjects and for multiple measurers/observers;
+
+3. Calculating multiple measurers/observers relative technical error of measurement (relative TEM);
+
+4. Calculating intra-observer total technical error of measurement (total TEM);
+
+5. Calculating coefficient of reliability; and,
+
+6. Calculating bias in measurements/observation against a gold standard.
+
 
 ## Installation
 
-`anthrocheckr` is not yet on [CRAN](https://cran.r-project.org) but can be installed from the [nutriverse R universe](https://nutriverse.r-universe.dev) as follows:
+`{anthrocheckr}` is not yet on [CRAN](https://cran.r-project.org) but can be installed from the [nutriverse R Universe](https://nutriverse.r-universe.dev) as follows:
 
 ```{r install-r-universe, eval = FALSE}
 install.packages(
@@ -38,13 +53,15 @@ install.packages(
 )
 ```
 
+
 ## Usage
 
 
 
+
 ## Citation
 
-If you find the `anthrocheckr` package useful please cite using the suggested citation provided by a call to the `citation()` function as follows:
+If you find the `{anthrocheckr}` package useful please cite using the suggested citation provided by a call to the `citation()` function as follows:
 
 ```{r citation}
 citation("anthrocheckr")

diff --git a/README.md b/README.md
@@ -25,13 +25,33 @@ performed prior to anthropometric data collection. This package provides
 functions to calculate inter- and intra-observer technical error of
 measurement (TEM) to assess precision of measurements.
 
-## What does `anthrocheckr` do?
+## What does the package do?
+
+`{anthrocheckr}` provides functions for:
+
+1.  Calculating standard summaries for intra-observer or inter-observer
+    measurements;
+
+2.  Calculating intra-observer or inter-observer technical error of
+    measurement (TEM) for multiple subjects and for multiple
+    measurers/observers;
+
+3.  Calculating multiple measurers/observers relative technical error of
+    measurement (relative TEM);
+
+4.  Calculating intra-observer total technical error of measurement
+    (total TEM);
+
+5.  Calculating coefficient of reliability; and,
+
+6.  Calculating bias in measurements/observation against a gold
+    standard.
 
 ## Installation
 
-`anthrocheckr` is not yet on [CRAN](https://cran.r-project.org) but can
-be installed from the [nutriverse R
-universe](https://nutriverse.r-universe.dev) as follows:
+`{anthrocheckr}` is not yet on [CRAN](https://cran.r-project.org) but
+can be installed from the [nutriverse R
+Universe](https://nutriverse.r-universe.dev) as follows:
 
 ``` r
 install.packages(
@@ -44,7 +64,7 @@ install.packages(
 
 ## Citation
 
-If you find the `anthrocheckr` package useful please cite using the
+If you find the `{anthrocheckr}` package useful please cite using the
 suggested citation provided by a call to the `citation()` function as
 follows:
 
@@ -53,8 +73,9 @@ citation("anthrocheckr")
 #> To cite anthrocheckr in publications use:
 #> 
 #>   Ernest Guevarra (2024). _anthrocheckr: An Implementation of
-#>   Anthropometric Measurement Standardisation Tests_. R package
-#>   version 0.0.9000, <https://nutriverse.io/anthrocheckr/>.
+#>   Anthropometric Measurement Standardisation Tests_. R
+#>   package version 0.0.9000,
+#>   <https://nutriverse.io/anthrocheckr/>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 

diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -7,16 +7,19 @@ development:
 
 template:
   bootstrap: 5
-  bootswatch: cosmo
-  theme: haddock
-  ganalytics: #
+  theme: breeze-light
+  ganalytics: "G-83YFE32VFQ"
+  bslib:
+    bootswatch: pulse
+    pkgdown-nav-height: 100px
+    success: "#004225"
 
 navbar:
   bg: success
-  type: light
+  type: dark
   structure:
     left:  [home, intro, reference, articles, news]
-    right: [mastodon, linkedin, github]
+    right: [search, mastodon, github]
 
   components:
     articles:
@@ -26,10 +29,8 @@ navbar:
         href: articles/tem.html
     mastodon:
       icon: "fab fa-mastodon fa-lg"
-      href: https://fosstodon.org/@katilingban
-    linkedin:
-      icon: "fab fa-linkedin fa-lg"
-      href: https://www.linkedin.com/company/katilingban
+      aria-label: Mastodon
+      href: https://fosstodon.org/@nutriverse
 
 home:
   links:

diff --git a/tests/testthat/test-01_summary_measure.R b/tests/testthat/test-01_summary_measure.R
@@ -0,0 +1,31 @@
+# Tests for summary measures function ------------------------------------------
+
+test_that("calculate_* works as expected", {
+  expect_type(
+    calculate_mean(
+      c(
+        smartStd[smartStd$observer == 0 , "weight1"], 
+        smartStd[smartStd$observer == 0 , "weight2"]
+      )
+    ),
+    "double"
+  )
+  expect_type(
+    calculate_sd(
+      c(
+        smartStd[smartStd$observer == 0 , "weight1"], 
+        smartStd[smartStd$observer == 0 , "weight2"]
+      )
+    ),
+    "double"
+  )
+  expect_type(
+    calculate_max(
+      c(
+        smartStd[smartStd$observer == 0 , "weight1"], 
+        smartStd[smartStd$observer == 0 , "weight2"]
+      )
+    ),
+    "double"
+  )
+})
diff --git a/tests/testthat/test-04_calculate_team_tem.R b/tests/testthat/test-04_calculate_team_tem.R
@@ -0,0 +1,3 @@
+# Tests for calculate_team_tem -------------------------------------------------
+
+
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/anthrocheckr.Rmd b/vignettes/anthrocheckr.Rmd
@@ -0,0 +1,51 @@
+---
+title: "Anthropometric measurement standardisation tests"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Anthropometric measurement standardisation tests}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup, echo = FALSE}
+library(anthrocheckr)
+```
+
+Ensuring the precision and accuracy of measurements is critical when collecting anthropometric data. Anthropometrists are usually tested for precision and accuracy of measurement through standardisation tests performed prior to anthropometric data collection. This package provides functions to calculate inter- and intra-observer technical error of measurement (TEM) to assess precision of measurements.
+
+## What does anthrocheckr do?
+
+`{anthrocheckr}` provides functions for:
+
+1. Calculating standard summaries for intra-observer or inter-observer measurements;
+
+2. Calculating intra-observer or inter-observer technical error of measurement (TEM) for multiple subjects and for multiple measurers/observers;
+
+3. Calculating multiple measurers/observers relative technical error of measurement (relative TEM);
+
+4. Calculating intra-observer total technical error of measurement (total TEM);
+
+5. Calculating coefficient of reliability; and,
+
+6. Calculating bias in measurements/observation against a gold standard.
+
+
+## Installation
+
+`{anthrocheckr}` is not yet on [CRAN](https://cran.r-project.org) but can be installed from the [nutriverse R Universe](https://nutriverse.r-universe.dev) as follows:
+
+```{r install-r-universe, eval = FALSE}
+install.packages(
+  "anthrocheckr",
+  repos = c('https://nutriverse.r-universe.dev', 'https://cloud.r-project.org')
+)
+```
+
+## Usage
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		# Tests for calculate_team_tem -------------------------------------------------