commits

Author: oddish3

.github/workflows/publish.yml

@@ -1,22 +1,30 @@
-name: Quarto Publish
 on:
   workflow_dispatch:
   push:
     branches:
       - main
+  pull:
+    branches:
+      - main
+
+name: Quarto Publish
+
 jobs:
-  build-deploy:
+  publish:
     runs-on: ubuntu-latest
-    permissions:
-      contents: write
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
-      - name: Set up Quarto
-        uses: quarto-dev/quarto-actions/setup@v2
-      - name: Render and Publish
-        uses: quarto-dev/quarto-actions/publish@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      - uses: quarto-dev/quarto-actions/render@v2
+
+      - name: Deploy to GitHub pages 🚀
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
-          target: gh-pages
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          folder: _site

_site/content/ons_nomis.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>rforhta</title>
+<title>R for Health Technology Assesment – rforhta</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -181,7 +181,7 @@
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title">rforhta</h1>
+<h1 class="title">R for Health Technology Assesment</h1>
 </div>
 
 
@@ -199,13 +199,42 @@ <h1 class="title">rforhta</h1>
 
 
 <p>This is a Quarto website.</p>
+<p>Quarto allows us to display code and its output</p>
 <p>To learn more about Quarto websites visit <a href="https://quarto.org/docs/websites" class="uri">https://quarto.org/docs/websites</a>.</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="dv">1</span> <span class="sc">+</span> <span class="dv">1</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>[1] 2</code></pre>
 </div>
 </div>
+<p>which wont tell automatically install the package if it is not installed for us.</p>
+<p>An example is how to plot some data, fitted with a linear model and coloured by group</p>
+<div class="cell">
+<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(</span>
+<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>  <span class="at">data =</span> penguins,</span>
+<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>  <span class="at">mapping =</span> <span class="fu">aes</span>(<span class="at">x =</span> flipper_length_mm, <span class="at">y =</span> body_mass_g)</span>
+<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a>) <span class="sc">+</span></span>
+<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a>  <span class="fu">geom_point</span>(<span class="at">mapping =</span> <span class="fu">aes</span>(<span class="at">color =</span> species)) <span class="sc">+</span></span>
+<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a>  <span class="fu">geom_smooth</span>(<span class="at">method =</span> <span class="st">"lm"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="cell-output cell-output-stderr">
+<pre><code>`geom_smooth()` using formula = 'y ~ x'</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Warning: Removed 2 rows containing non-finite outside the scale range
+(`stat_smooth()`).</code></pre>
+</div>
+<div class="cell-output cell-output-stderr">
+<pre><code>Warning: Removed 2 rows containing missing values or values outside the scale range
+(`geom_point()`).</code></pre>
+</div>
+<div class="cell-output-display">
+<div>
+<figure class="figure">
+<p><img src="index_files/figure-html/unnamed-chunk-3-1.png" class="img-fluid figure-img" width="672"></p>
+</figure>
+</div>
+</div>
+</div>
 
 
 

_site/content/ons_nomis_files/figure-html/unnamed-chunk-1-1.png

@@ -2,13 +2,52 @@
   {
     "objectID": "index.html",
     "href": "index.html",
-    "title": "rforhta",
+    "title": "R for Health Technology Assesment",
     "section": "",
-    "text": "This is a Quarto website.\nTo learn more about Quarto websites visit https://quarto.org/docs/websites.\n\n1 + 1\n\n[1] 2",
+    "text": "This is a Quarto website.\nQuarto allows us to display code and its output\nTo learn more about Quarto websites visit https://quarto.org/docs/websites.\n\n1 + 1\n\n[1] 2\n\n\nwhich wont tell automatically install the package if it is not installed for us.\nAn example is how to plot some data, fitted with a linear model and coloured by group\n\nggplot(\n  data = penguins,\n  mapping = aes(x = flipper_length_mm, y = body_mass_g)\n) +\n  geom_point(mapping = aes(color = species)) +\n  geom_smooth(method = \"lm\")\n\n`geom_smooth()` using formula = 'y ~ x'\n\n\nWarning: Removed 2 rows containing non-finite outside the scale range\n(`stat_smooth()`).\n\n\nWarning: Removed 2 rows containing missing values or values outside the scale range\n(`geom_point()`).",
     "crumbs": [
       "Home"
     ]
   },
+  {
+    "objectID": "content/basicr.html",
+    "href": "content/basicr.html",
+    "title": "Base R",
+    "section": "",
+    "text": "this is your introduction to base R"
+  },
+  {
+    "objectID": "content/basicr.html#introduction",
+    "href": "content/basicr.html#introduction",
+    "title": "Base R",
+    "section": "",
+    "text": "this is your introduction to base R"
+  },
+  {
+    "objectID": "content/basicr.html#base-r",
+    "href": "content/basicr.html#base-r",
+    "title": "Base R",
+    "section": "Base R",
+    "text": "Base R"
+  },
+  {
+    "objectID": "content/basicr.html#before-r-there-was",
+    "href": "content/basicr.html#before-r-there-was",
+    "title": "Base R",
+    "section": "Before R there was?",
+    "text": "Before R there was?"
+  },
+  {
+    "objectID": "content/git.html",
+    "href": "content/git.html",
+    "title": "git and github",
+    "section": "",
+    "text": "git is a difficult but extremely helpful tool for those of us that work with data.\ngit is a tool that tracks changes to your files and enables you to share those changes with others.\nThese git configured set of files are called repositories or repos and are organised in a structured way.\nA rather large caveat is that:\n\nit is very much not advised to store data in these projects on git\nwhen working in groups, it is best to store data elsewhere and have scripts that interact with your local copy of the data\n\nIn my work, i use git to store text based code as a backup in case i make breaking changes to my analytical workflow that result in different results / different subsets of data etc.\nabcdefg",
+    "crumbs": [
+      "Basics",
+      "Git Basics"
+    ]
+  },
   {
     "objectID": "content/installr.html",
     "href": "content/installr.html",
@@ -43,42 +82,10 @@
     ]
   },
   {
-    "objectID": "content/git.html",
-    "href": "content/git.html",
-    "title": "git and github",
+    "objectID": "content/ons_nomis.html",
+    "href": "content/ons_nomis.html",
+    "title": "ONS NOMIS",
     "section": "",
-    "text": "git is a difficult but extremely helpful tool for those of us that work with data.\ngit is a tool that tracks changes to your files and enables you to share those changes with others.\nThese git configured set of files are called repositories or repos and are organised in a structured way.\nA rather large caveat is that:\n\nit is very much not advised to store data in these projects on git\nwhen working in groups, it is best to store data elsewhere and have scripts that interact with your local copy of the data\n\nIn my work, i use git to store text based code as a backup in case i make breaking changes to my analytical workflow that result in different results / different subsets of data etc.\nabcdefg",
-    "crumbs": [
-      "Basics",
-      "Git Basics"
-    ]
-  },
-  {
-    "objectID": "content/basicr.html",
-    "href": "content/basicr.html",
-    "title": "Base R",
-    "section": "",
-    "text": "this is your introduction to base R"
-  },
-  {
-    "objectID": "content/basicr.html#introduction",
-    "href": "content/basicr.html#introduction",
-    "title": "Base R",
-    "section": "",
-    "text": "this is your introduction to base R"
-  },
-  {
-    "objectID": "content/basicr.html#base-r",
-    "href": "content/basicr.html#base-r",
-    "title": "Base R",
-    "section": "Base R",
-    "text": "Base R"
-  },
-  {
-    "objectID": "content/basicr.html#before-r-there-was",
-    "href": "content/basicr.html#before-r-there-was",
-    "title": "Base R",
-    "section": "Before R there was?",
-    "text": "Before R there was?"
+    "text": "library(pacman)\np_load(here,\n       tidyverse,\n       magrittr,\n       nomisr)\n\ntblCoD <- nomisr::nomis_get_data(id        = \"NM_161_1\",\n                                 date      = 2013:2021,\n                                 geography = 2092957703,\n                                 sex       = 1:2,\n                                 age       = 1:20,\n                                 measure   = 1,\n                                 measures  = 20100,\n                                 cause_of_death = c(0,9))\n\ntblCoD <- tblCoD |> \n  dplyr::mutate(CoD = ifelse(CAUSE_OF_DEATH==9, \"CVD\", \"All\")) |> \n  dplyr::select(Year   = DATE,\n                Sex    = GENDER_NAME,\n                AgeCat = AGE_NAME,\n                AgeC   = AGE_CODE,\n                N      = OBS_VALUE,\n                CoD) |> \n  tidyr::pivot_wider(values_from = N,\n                     names_from  = CoD) |> \n  dplyr::mutate(pCVD   = CVD / All,\n                AgeLo  = c(0,1,1:18*5)[AgeC],\n                AgeHi  = c(1,1:18*5,999)[AgeC])\n\ntblCoD <- tblCoD |> \n  mutate(AgeCat = factor(AgeCat |> \n                           stringr::str_remove_all(\"Aged \") |> \n                           stringr::str_replace_all(\" to \", \"-\"),\n                         levels = c(\"under 1\", \"1-4\", paste0(1:17*5, \"-\", 1:17*5+4), \"90 and over\"),\n                         labels = c(\"<1\", \"1-4\", paste0(1:17*5, \"-\", 1:17*5+4), \"90+\")))\n\ndevtools::source_gist(\"https://gist.github.com/gbrlrgrs/fec0190eb7b5884ca713c61651476b00\")\n\nℹ Sourcing gist \"fec0190eb7b5884ca713c61651476b00\"\nℹ SHA-1 hash of file is \"96040db56263e1143fbc6ebf63038a8e2511f4f3\"\n\nts = 20\nlw = 0.5\nfnSetGGPlotThemeGR(lw = lw, ts = ts)\n\ntblCoD |> \n  ggplot2::ggplot(ggplot2::aes(x=Year, y=pCVD, Group=AgeCat)) +\n  ggplot2::geom_line(ggplot2::aes(colour=AgeCat)) +\n  ggplot2::geom_text(data = tblCoD |> dplyr::group_by(Sex, AgeCat) |> dplyr::slice_tail(n=1),\n                     aes(x=Year+0.1, label = AgeCat), hjust=0, size = ts/.pt) +\n  ggplot2::facet_grid(cols = ggplot2::vars(Sex)) +\n  viridis::scale_colour_viridis(discrete = T, name = \"Age group\") +\n  scale_y_continuous(limits = c(0, 0.35),\n                     breaks = 0:10/10,\n                     minor_breaks = 0:100/100,\n                     expand = c(0, 0),\n                     name   = \"Proportion of deaths due to CVD\") +\n  scale_x_continuous(limits = c(2013,2022),\n                     breaks = trunc(2014:2022/2)*2,\n                     minor_breaks = 2010:2025,\n                     expand = expansion(add = c(0.5, 1.5)),\n                     name   = \"Year\") +\n  theme(legend.position = \"none\",\n        plot.margin     = margin(1,1,1,1, \"cm\"))\n\n\n\n\n\n\n\n# fnSaveGG(strName = \"CVD_deaths\", cmW = 33.867, cmH = 19.05, typ = \"svg\")"
   }
 ]

_site/index.html

@@ -1,14 +1,31 @@
 ---
-title: "rforhta"
+title: "R for Health Technology Assesment"
 ---
 
 This is a Quarto website.
 
+Quarto allows us to display code and its output
+
 To learn more about Quarto websites visit
 <https://quarto.org/docs/websites>.
 
 ```{r}
 1 + 1
 ```
 
-some changes
+
+which wont tell automatically install the package if it is not installed for us.
+```{r echo=FALSE}
+library(ggplot2)
+library(palmerpenguins)
+```
+
+An example is how to plot some data, fitted with a linear model and coloured by group
+```{r}
+ggplot(
+  data = penguins,
+  mapping = aes(x = flipper_length_mm, y = body_mass_g)
+) +
+  geom_point(mapping = aes(color = species)) +
+  geom_smooth(method = "lm")
+```