improve build and fixes for latest blogdown

.github/workflows/ci.yaml

@@ -46,14 +46,22 @@ jobs:
         with:
           path: |
             ./blogdown
-          key: ${{ runner.os }}-blogdown2-${{ hashFiles('content/blog/**.Rmd') }}
+          key: ${{ runner.os }}-blogdown2-${{ hashFiles('environment.yml') }}-${{ hashFiles('content/blog/**.Rmd') }}
           restore-keys: |
+            ${{ runner.os }}-blogdown2-${{ hashFiles('environment.yml') }}-
             ${{ runner.os }}-blogdown2-
       - name: Build site
         shell: bash -l {0}
         run: |
           npm run build:blog
 
+      - uses: actions/upload-artifact@v2
+        with:
+          name: blog
+          path: |
+            ./content/blog
+            ./static/blog
+
       - uses: actions/setup-node@v1
         with:
           node-version: "12"

.prettierignore

@@ -29,4 +29,6 @@
 *.md
 *.jpeg
 *.ico
-/themes/delphi/layouts/partials/webp-image.html
+/themes/delphi/layouts/partials/webp-image.html
+/themes/delphi/layouts/shortcodes/apireflink.html
+/themes/delphi/layouts/shortcodes/reflink.html

README.md

@@ -86,6 +86,7 @@ In order to convert the Rmd files to HTML files for Hugo you also need to:
    - `local=TRUE` similar to `-D` to process draft files
    - `run_hugo=FALSE` to manually run hugo
    - `build_rmd=TRUE` force a (re)build of the Rmd pages
+1. Run blogdown to convert a single file to HTML: `Rscript -e 'blogdown::build_site(local=TRUE, run_hugo=FALSE, build_rmd="content/blog/<NAME>.Rmd")'`
 1. Alternatively, run `npm run build:blog`
 1. Run Hugo server as usual
 

content/blog/2015-07-23-template-post.Rmd

@@ -110,12 +110,12 @@ suggest we consider the following tags as base tags:
 
 ### Linking to other pages and blog posts:
 
-using the file name and the Hugo shortcodes, e.g.: [Facebook Post](`r blogdown::shortcode_html("relref", "2020-08-26-fb-survey")`).
+using the file name and the Hugo shortcodes, e.g.: `r blogdown::shortcode_html("reflink", "2020-08-26-fb-survey", "Facebook Post")`.
 Jumping to a specific section/anchor is supported too: 
-[previous exploratory investigations](`r blogdown::shortcode_html("relref", "2020-08-26-fb-survey#some-interesting-examples")`)
+`r blogdown::shortcode_html("reflink", "2020-08-26-fb-survey#some-interesting-examples", "previous exploratory investigations")`
 
 ### Linking to the API doc:
 
 there is another shortcode for creating an api link, e.g. 
-[public API](`r blogdown::shortcode_html("apiref", "/")`) or
-[Doctor's Visits signal](`r blogdown::shortcode_html("apiref", "api/covidcast-signals/doctor-visits.html")`) 
+`r blogdown::shortcode_html("apireflink", "/", "public API")` or
+`r blogdown::shortcode_html("apireflink", "api/covidcast-signals/doctor-visits.html", "Doctor's Visits signal")` 

content/blog/2015-07-23-template-post.html

@@ -23,8 +23,6 @@
 ---
 
 <script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
-<link href="/rmarkdown-libs/anchor-sections/anchor-sections.css" rel="stylesheet" />
-<script src="/rmarkdown-libs/anchor-sections/anchor-sections.js"></script>
 
 <div id="TOC">
 <ul>
@@ -49,21 +47,21 @@
 see <a href="http://rmarkdown.rstudio.com" class="uri">http://rmarkdown.rstudio.com</a>.</p>
 <p>You can embed an R code chunk like this:</p>
 <pre class="r"><code>summary(cars)
-##      speed           dist
-##  Min.   : 4.0   Min.   :  2.00
-##  1st Qu.:12.0   1st Qu.: 26.00
-##  Median :15.0   Median : 36.00
-##  Mean   :15.4   Mean   : 42.98
-##  3rd Qu.:19.0   3rd Qu.: 56.00
+##      speed           dist       
+##  Min.   : 4.0   Min.   :  2.00  
+##  1st Qu.:12.0   1st Qu.: 26.00  
+##  Median :15.0   Median : 36.00  
+##  Mean   :15.4   Mean   : 42.98  
+##  3rd Qu.:19.0   3rd Qu.: 56.00  
 ##  Max.   :25.0   Max.   :120.00
 fit &lt;- lm(dist ~ speed, data = cars)
 fit
-##
+## 
 ## Call:
 ## lm(formula = dist ~ speed, data = cars)
-##
+## 
 ## Coefficients:
-## (Intercept)        speed
+## (Intercept)        speed  
 ##     -17.579        3.932</code></pre>
 <div id="including-plots" class="section level2">
 <h2>Including Plots</h2>
@@ -142,14 +140,14 @@ <h3>Tags</h3>
 <h2>Linking</h2>
 <div id="linking-to-other-pages-and-blog-posts" class="section level3">
 <h3>Linking to other pages and blog posts:</h3>
-<p>using the file name and the Hugo shortcodes, e.g.: <a href="{{< relref "2020-08-26-fb-survey" >}}">Facebook Post</a>.
+<p>using the file name and the Hugo shortcodes, e.g.: {{< reflink "2020-08-26-fb-survey" "Facebook Post" >}}.
 Jumping to a specific section/anchor is supported too:
-<a href="{{< relref "2020-08-26-fb-survey#some-interesting-examples" >}}">previous exploratory investigations</a></p>
+{{< reflink "2020-08-26-fb-survey#some-interesting-examples" "previous exploratory investigations" >}}</p>
 </div>
 <div id="linking-to-the-api-doc" class="section level3">
 <h3>Linking to the API doc:</h3>
 <p>there is another shortcode for creating an api link, e.g. 
-<a href="{{< apiref "/" >}}">public API</a> or
-<a href="{{< apiref "api/covidcast-signals/doctor-visits.html" >}}">Doctor’s Visits signal</a></p>
+{{< apireflink "/" "public API" >}} or
+{{< apireflink "api/covidcast-signals/doctor-visits.html" "Doctor's Visits signal" >}}</p>
 </div>
 </div>

content/blog/2020-08-10-hello-world.Rmd

@@ -59,7 +59,7 @@ and making headway into dengue and norovirus.
 To learn about the work our group has done in the past,
 including some papers we've written, software tools we've built,
 and the real-time epidemiological data server we've been deploying since 2016,
-check out [our website](`r blogdown::shortcode("ref", "/")`).
+check out `r blogdown::shortcode_html("reflink", "/", "our website")`.
 
 When the COVID-19 pandemic arrived, we focused all our attention on it.
 Our Delphi team
@@ -70,7 +70,7 @@ including Stanford, UC Davis, and USC, and also from industry.
 The pace has been intense and dizzying at times,
 and we're infinitely grateful for the contributions
 and commitment of all our new members---we'd be nowhere without them.
-See [here](`r blogdown::shortcode("ref", "team")`)
+See `r blogdown::shortcode_html("reflink", "team", "here")`
 for a list of the Delphi team members.
 
 With new members comes a new breadth of expertise:
@@ -145,14 +145,12 @@ Here's a quick summary:
   aggregated counts from massive medical claims data sets through partners like
   Change Healthcare.
 
-- We've built a [public
-  API](`r blogdown::shortcode_html("apiref", "api/covidcast.html")`),
-  and [R and Python
-  packages](`r blogdown::shortcode_html("apiref", "api/covidcast_clients.html")`),
+- We've built a `r blogdown::shortcode_html("apireflink", "api/covidcast.html", "public API")`,
+  and `r blogdown::shortcode_html("apireflink", "api/covidcast_clients.html", "R and Python packages")`,
   to serve our indicators to researchers and the public. This API provides new
   data daily.
 
-- We've built [interactive maps and graphics](`r blogdown::shortcode("ref", "covidcast")`) to
+- We've built `r blogdown::shortcode_html("reflink", "covidcast", "interactive maps and graphics")` to
   display our indicators, and better inform the public and decision-makers.
 
 - We've developed forecasts of the future spread of the pandemic,

content/blog/2020-08-10-hello-world.html

@@ -13,21 +13,19 @@
   Hello from the Delphi research group at Carnegie Mellon University!
   We're a group of faculty, students, and staff, based primarily out of CMU
   together with strong collaborators from other universities and industry.
-  Our group was founded in 2012 to advance the theory and practice of epidemic
-  forecasting. Since March 2020, we have refocused efforts towards helping combat
+  Our group was founded in 2012 to advance the theory and practice of epidemic 
+  forecasting. Since March 2020, we have refocused efforts towards helping combat 
   the COVID-19 pandemic, by supporting informed decision-making at federal, state,
   and local levels of government and in the healthcare sector. Until now, we've
-  been pretty “heads down” with our work, and slow to communicate what we've been
-  up to. But at last ... Delphi finally has a blog! This first post serves as an
+  been pretty “heads down” with our work, and slow to communicate what we've been 
+  up to. But at last ... Delphi finally has a blog! This first post serves as an 
   introduction of sorts. Future posts will dive deeper into our various projects.
 output:
   blogdown::html_page:
     toc: true
 ---
 
 <script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
-<link href="/rmarkdown-libs/anchor-sections/anchor-sections.css" rel="stylesheet" />
-<script src="/rmarkdown-libs/anchor-sections/anchor-sections.js"></script>
 
 <div id="TOC">
 <ul>
@@ -69,7 +67,7 @@ <h2>A Little Bit About Us</h2>
 To learn about the work our group has done in the past,
 including some papers we’ve written, software tools we’ve built,
 and the real-time epidemiological data server we’ve been deploying since 2016,
-check out <a href="{{% ref "/" %}}">our website</a>.</p>
+check out {{< reflink "/" "our website" >}}.</p>
 <p>When the COVID-19 pandemic arrived, we focused all our attention on it.
 Our Delphi team
 quickly grew to 30+ members, and is still growing.
@@ -79,7 +77,7 @@ <h2>A Little Bit About Us</h2>
 The pace has been intense and dizzying at times,
 and we’re infinitely grateful for the contributions
 and commitment of all our new members—we’d be nowhere without them.
-See <a href="{{% ref "team" %}}">here</a>
+See {{< reflink "team" "here" >}}
 for a list of the Delphi team members.</p>
 <p>With new members comes a new breadth of expertise:
 our expertise now covers statistical modeling, computation,
@@ -146,13 +144,11 @@ <h2>What We’ve Been Up To</h2>
 through partnerships with Facebook and Google, and others are based on
 aggregated counts from massive medical claims data sets through partners like
 Change Healthcare.</p></li>
-<li><p>We’ve built a <a href="{{< apiref "api/covidcast.html" >}}">public
-API</a>,
-and <a href="{{< apiref "api/covidcast_clients.html" >}}">R and Python
-packages</a>,
+<li><p>We’ve built a {{< apireflink "api/covidcast.html" "public API" >}},
+and {{< apireflink "api/covidcast_clients.html" "R and Python packages" >}},
 to serve our indicators to researchers and the public. This API provides new
 data daily.</p></li>
-<li><p>We’ve built <a href="{{% ref "covidcast" %}}">interactive maps and graphics</a> to
+<li><p>We’ve built {{< reflink "covidcast" "interactive maps and graphics" >}} to
 display our indicators, and better inform the public and decision-makers.</p></li>
 <li><p>We’ve developed forecasts of the future spread of the pandemic,
 validated them prospectively, and started submitting them to CDC.</p></li>

content/blog/2020-08-26-fb-survey.Rmd

@@ -61,8 +61,8 @@ We believe that this combination of _detail_ and _scale_
 has never before been available in a public health emergency.
 
 We make aggregated data publicly available daily through our
-[COVIDcast API](`r blogdown::shortcode_html("apiref", "api/covidcast.html")`),
-and visualize it on our [COVIDcast interactive map](`r blogdown::shortcode_html("ref", "covidcast")`).
+`r blogdown::shortcode_html("apireflink", "api/covidcast.html", "COVIDcast API")`,
+and visualize it on our `r blogdown::shortcode_html("reflink", "covidcast", "COVIDcast interactive map")`.
 We also make (fully de-identified) individual survey responses available
 to researchers who agree to
 [data use terms](https://dataforgood.fb.com/docs/covid-19-symptom-survey-request-for-data-access/).
@@ -174,8 +174,7 @@ package](https://cmu-delphi.github.io/covidcast/covidcastR/).
 In all, fetching the data from our API and producing the heatmaps
 requires only 15 lines of code.
 If you're interested, click the "Code" button to reveal the source.
-We'll cover our [R and Python covidcast
-packages](`r blogdown::shortcode_html("apiref", "api/covidcast_clients.html")`)
+We'll cover our `r blogdown::shortcode_html("apireflink", "api/covidcast_clients.html", "R and Python covidcast packages")`
 in a future blog post.
 
 ## Why Run These Surveys?
@@ -211,8 +210,7 @@ surveys:
   which may be a sizeable fraction of the US population, but certainly not all of
   it. We'll also likely see bias because some people on Facebook are more inclined
   to take surveys than others. We attempt to correct for both of these biases
-  using a [statistical reweighting
-  scheme](`r blogdown::shortcode_html("apiref", "api/covidcast-signals/fb-survey.html#survey-weighting")`),
+  using a `r blogdown::shortcode_html("apireflink", "api/covidcast-signals/fb-survey.html#survey-weighting", "statistical reweighting scheme")`,
   but these corrections aren't perfect.
 
 - Our symptom data is entirely self-reported, in contrast to data
@@ -249,8 +247,7 @@ quantities, in a given location, on a given day:
   community_ with COVID-like illness.
 
 Details on how we compute the % CLI and % CLI-in-community estimates can be
-found in our [COVIDcast signals
-documentation](`r blogdown::shortcode_html("apiref", "api/covidcast-signals/fb-survey.html")`).
+found in our `r blogdown::shortcode_html("apireflink", "api/covidcast-signals/fb-survey.html", "COVIDcast signals documentation")`.
 
 The % CLI-in-community indicator has an interesting backstory: it was sort of a
 "happy accident" from an experiment we tried with surveys we were running in
@@ -272,10 +269,8 @@ public health. They assured us that lengthening the survey wouldn't hurt the
 completion rate too much, and they were right: of the people who complete the
 first section, over 85% go on to finish the full survey!
 
-Our [survey documentation
-site](`r blogdown::shortcode_html("apiref", "symptom-survey/")`) includes more
-details about the survey, including the [full text of every survey
-version](`r blogdown::shortcode_html("apiref", "symptom-survey/coding.html")`).
+Our `r blogdown::shortcode_html("apireflink", "symptom-survey/", "survey documentation site")` includes more
+details about the survey, including the `r blogdown::shortcode_html("apireflink", "symptom-survey/coding.html", "full text of every survey version")`.
 And yes, researchers can [request
 access](https://dataforgood.fb.com/docs/covid-19-symptom-survey-request-for-data-access/)
 to (fully de-identified) individual survey responses for research purposes,
@@ -605,6 +600,5 @@ This new survey is currently being deployed,
 and data should become available in the next few weeks.
 Detailed data will be available to researchers,
 while new aggregates---such as of mask-wearing---will
-be made public, as usual, through our [COVIDcast
-API](`r blogdown::shortcode_html("apiref", "api/covidcast.html")`)
-and [COVIDcast interactive map](`r blogdown::shortcode_html("ref", "covidcast")`).
+be made public, as usual, through our `r blogdown::shortcode_html("apireflink", "api/covidcast.html", "COVIDcast API")`
+and `r blogdown::shortcode_html("reflink", "covidcast", "COVIDcast interactive map")`.

content/blog/2020-08-26-fb-survey.html

@@ -47,16 +47,16 @@
     toc: true
 ---
 
-<link href="/rmarkdown-libs/anchor-sections/anchor-sections.css" rel="stylesheet" />
-<script src="/rmarkdown-libs/anchor-sections/anchor-sections.js"></script>
+<script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
 
 <div id="TOC">
 <ul>
 <li><a href="#short-background">Short Background</a></li>
 <li><a href="#why-run-these-surveys">Why Run These Surveys?</a></li>
 <li><a href="#whats-in-the-survey">What’s in the Survey?</a></li>
 <li><a href="#some-interesting-examples">Some Interesting Examples</a></li>
-<li><a href="#basic-correlation-analysis">Basic Correlation Analysis</a><ul>
+<li><a href="#basic-correlation-analysis">Basic Correlation Analysis</a>
+<ul>
 <li><a href="#correlations-sliced-by-time">Correlations Sliced by Time</a></li>
 <li><a href="#correlations-sliced-by-county">Correlations Sliced by County</a></li>
 </ul></li>
@@ -77,8 +77,8 @@
 We believe that this combination of <em>detail</em> and <em>scale</em>
 has never before been available in a public health emergency.</p>
 <p>We make aggregated data publicly available daily through our
-<a href="{{< apiref "api/covidcast.html" >}}">COVIDcast API</a>,
-and visualize it on our <a href="{{< ref "covidcast" >}}">COVIDcast interactive map</a>.
+{{< apireflink "api/covidcast.html" "COVIDcast API" >}},
+and visualize it on our {{< reflink "covidcast" "COVIDcast interactive map" >}}.
 We also make (fully de-identified) individual survey responses available
 to researchers who agree to
 <a href="https://dataforgood.fb.com/docs/covid-19-symptom-survey-request-for-data-access/">data use terms</a>.</p>
@@ -178,8 +178,7 @@ <h2>Short Background</h2>
 In all, fetching the data from our API and producing the heatmaps
 requires only 15 lines of code.
 If you’re interested, click the “Code” button to reveal the source.
-We’ll cover our <a href="{{< apiref "api/covidcast_clients.html" >}}">R and Python covidcast
-packages</a>
+We’ll cover our {{< apireflink "api/covidcast_clients.html" "R and Python covidcast packages" >}}
 in a future blog post.</p>
 </div>
 <div id="why-run-these-surveys" class="section level2">
@@ -213,8 +212,7 @@ <h2>Why Run These Surveys?</h2>
 which may be a sizeable fraction of the US population, but certainly not all of
 it. We’ll also likely see bias because some people on Facebook are more inclined
 to take surveys than others. We attempt to correct for both of these biases
-using a <a href="{{< apiref "api/covidcast-signals/fb-survey.html#survey-weighting" >}}">statistical reweighting
-scheme</a>,
+using a {{< apireflink "api/covidcast-signals/fb-survey.html#survey-weighting" "statistical reweighting scheme" >}},
 but these corrections aren’t perfect.</p></li>
 <li><p>Our symptom data is entirely self-reported, in contrast to data
 reported by medical professionals. Some fraction of the responses could be
@@ -248,8 +246,7 @@ <h2>What’s in the Survey?</h2>
 community</em> with COVID-like illness.</p></li>
 </ul>
 <p>Details on how we compute the % CLI and % CLI-in-community estimates can be
-found in our <a href="{{< apiref "api/covidcast-signals/fb-survey.html" >}}">COVIDcast signals
-documentation</a>.</p>
+found in our {{< apireflink "api/covidcast-signals/fb-survey.html" "COVIDcast signals documentation" >}}.</p>
 <p>The % CLI-in-community indicator has an interesting backstory: it was sort of a
 “happy accident” from an experiment we tried with surveys we were running in
 partnership with Google. (We’ll cover our Google survey in a future blog post.)
@@ -268,10 +265,8 @@ <h2>What’s in the Survey?</h2>
 public health. They assured us that lengthening the survey wouldn’t hurt the
 completion rate too much, and they were right: of the people who complete the
 first section, over 85% go on to finish the full survey!</p>
-<p>Our <a href="{{< apiref "symptom-survey/" >}}">survey documentation
-site</a> includes more
-details about the survey, including the <a href="{{< apiref "symptom-survey/coding.html" >}}">full text of every survey
-version</a>.
+<p>Our {{< apireflink "symptom-survey/" "survey documentation site" >}} includes more
+details about the survey, including the {{< apireflink "symptom-survey/coding.html" "full text of every survey version" >}}.
 And yes, researchers can <a href="https://dataforgood.fb.com/docs/covid-19-symptom-survey-request-for-data-access/">request
 access</a>
 to (fully de-identified) individual survey responses for research purposes,
@@ -579,7 +574,6 @@ <h2>What’s Next with the Surveys</h2>
 and data should become available in the next few weeks.
 Detailed data will be available to researchers,
 while new aggregates—such as of mask-wearing—will
-be made public, as usual, through our <a href="{{< apiref "api/covidcast.html" >}}">COVIDcast
-API</a>
-and <a href="{{< ref "covidcast" >}}">COVIDcast interactive map</a>.</p>
+be made public, as usual, through our {{< apireflink "api/covidcast.html" "COVIDcast API" >}}
+and {{< reflink "covidcast" "COVIDcast interactive map" >}}.</p>
 </div>