From 86bfc93e52adc19e719e1a7b5ca563638913af35 Mon Sep 17 00:00:00 2001
From: raphael hyde <raphaelhyd@gmail.com>
Date: Fri, 11 Dec 2020 11:53:39 -0800
Subject: [PATCH 01/12] location-solild_icon

---
 themes/delphi/assets/location-solid.svg | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 themes/delphi/assets/location-solid.svg

diff --git a/themes/delphi/assets/location-solid.svg b/themes/delphi/assets/location-solid.svg
new file mode 100644
index 000000000..e8f31f53c
--- /dev/null
+++ b/themes/delphi/assets/location-solid.svg
@@ -0,0 +1,4 @@
+<svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg">
+<rect width="24" height="24" fill="white"/>
+<path d="M19.5 11H17.9062C17.4688 8.5 15.5 6.53125 13 6.09375V4.5C13 4.25 12.75 4 12.5 4H11.5C11.2188 4 11 4.25 11 4.5V6.09375C8.46875 6.53125 6.5 8.5 6.0625 11H4.5C4.21875 11 4 11.25 4 11.5V12.5C4 12.7812 4.21875 13 4.5 13H6.0625C6.5 15.5312 8.46875 17.5 11 17.9375V19.5C11 19.7812 11.2188 20 11.5 20H12.5C12.75 20 13 19.7812 13 19.5V17.9375C15.5 17.5 17.4688 15.5312 17.9062 13H19.5C19.75 13 20 12.7812 20 12.5V11.5C20 11.25 19.75 11 19.5 11ZM12 16C9.78125 16 8 14.2188 8 12C8 9.8125 9.78125 8 12 8C14.1875 8 16 9.8125 16 12C16 14.2188 14.1875 16 12 16ZM12 9.25C10.4688 9.25 9.25 10.5 9.25 12C9.25 13.5312 10.4688 14.75 12 14.75C13.5 14.75 14.75 13.5312 14.75 12C14.75 10.5 13.5 9.25 12 9.25Z" fill="black"/>
+</svg>

From 2972ebf4a7eb9028971c975f00161143f341a30f Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Wed, 23 Dec 2020 09:33:23 -0500
Subject: [PATCH 02/12] feat: enable autoplay for slideshow

closes #196
---
 themes/delphi/layouts/partials/landing/carousel.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/themes/delphi/layouts/partials/landing/carousel.html b/themes/delphi/layouts/partials/landing/carousel.html
index 58e887add..95344bad8 100644
--- a/themes/delphi/layouts/partials/landing/carousel.html
+++ b/themes/delphi/layouts/partials/landing/carousel.html
@@ -3,7 +3,7 @@
   <div
     class="uk-position-relative uk-light uikit-main-carousel"
     tabindex="-1"
-    uk-slideshow="animation: push; ratio: false"
+    uk-slideshow="animation: push; ratio: false; autoplay: true;"
   >
     <ul class="uk-slideshow-items uk-cover-container uk-child-width-1-1 slideshow-container">
       {{ range .Params.carousel }}

From a4f2aeedf7ce3af0bc207b785f2f1b469c7bfe28 Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Mon, 28 Dec 2020 13:31:28 -0500
Subject: [PATCH 03/12] refactor: website mode menu

---
 content/covidcast/_index.md                       |  6 +++++-
 content/covidcast/export.md                       |  3 +++
 content/covidcast/single.md                       |  3 +++
 content/covidcast/survey-results.md               |  3 +++
 content/covidcast/timelapse.md                    |  3 +++
 content/covidcast/top10.md                        |  3 +++
 themes/delphi/layouts/_default/baseof.html        |  2 +-
 themes/delphi/layouts/_default/covidcast_app.html |  2 +-
 .../layouts/partials/covidcast/get-modes.html     |  5 +++++
 .../delphi/layouts/partials/covidcast/modes.html  | 15 +++++++++++++++
 themes/delphi/layouts/partials/font-awesome.html  |  9 ++++++++-
 11 files changed, 50 insertions(+), 4 deletions(-)
 create mode 100644 themes/delphi/layouts/partials/covidcast/get-modes.html
 create mode 100644 themes/delphi/layouts/partials/covidcast/modes.html

diff --git a/content/covidcast/_index.md b/content/covidcast/_index.md
index b3dffc6cc..653b02f38 100644
--- a/content/covidcast/_index.md
+++ b/content/covidcast/_index.md
@@ -1,5 +1,9 @@
 ---
 title: COVIDcast
-layout: covidcast_app
 description: COVIDcast tracks and forecasts the spread of COVID-19. By Carnegie Mellon's Delphi Research Group.
+layout: covidcast_app
+app_mode: overview
+order: 1
+modeTitle: Map Overview
+icon: solid/map
 ---
diff --git a/content/covidcast/export.md b/content/covidcast/export.md
index c46ba78d1..cd8fb04c5 100644
--- a/content/covidcast/export.md
+++ b/content/covidcast/export.md
@@ -3,4 +3,7 @@ title: COVIDCast Export Data
 linkTitle: Export Data
 description: Use COVIDcast data in your own analysis
 layout: covidcast_app
+app_mode: export
+order: 6
+icon: solid/download
 ---
diff --git a/content/covidcast/single.md b/content/covidcast/single.md
index bd92dbcfb..03b6e525e 100644
--- a/content/covidcast/single.md
+++ b/content/covidcast/single.md
@@ -3,4 +3,7 @@ title: COVIDCast Region Details
 linkTitle: Region Details
 description: COVIDcast tracks and forecasts the spread of COVID-19. By Carnegie Mellon's Delphi Research Group.
 layout: covidcast_app
+app_mode: single
+order: 4
+icon: location-solid
 ---
diff --git a/content/covidcast/survey-results.md b/content/covidcast/survey-results.md
index 84c2c1840..3474a1ccb 100644
--- a/content/covidcast/survey-results.md
+++ b/content/covidcast/survey-results.md
@@ -4,4 +4,7 @@ linkTitle: Survey Results
 description: |
   In collaboration with Facebook Data for Good, along with a consortium of universities and public health officials, the Delphi Group at Carnegie Mellon University conducts research surveys to monitor the spread and impact of the COVID-19 pandemic in the United States. This survey is advertised through Facebook. It has run continuously since early April 2020.
 layout: covidcast_app
+app_mode: survey-results
+order: 5
+icon: solid/poll
 ---
diff --git a/content/covidcast/timelapse.md b/content/covidcast/timelapse.md
index e63535034..ce2af8b26 100644
--- a/content/covidcast/timelapse.md
+++ b/content/covidcast/timelapse.md
@@ -2,4 +2,7 @@
 title: COVIDCast Timelapse
 linkTitle: Timelapse
 layout: covidcast_app
+app_mode: timelapse
+order: 2
+icon: solid/clock
 ---
diff --git a/content/covidcast/top10.md b/content/covidcast/top10.md
index e94682409..515946dee 100644
--- a/content/covidcast/top10.md
+++ b/content/covidcast/top10.md
@@ -2,4 +2,7 @@
 title: COVIDCast Top 10
 linkTitle: Top 10
 layout: covidcast_app
+app_mode: top10
+order: 3
+icon: solid/list
 ---
diff --git a/themes/delphi/layouts/_default/baseof.html b/themes/delphi/layouts/_default/baseof.html
index f2389b0a8..f70a407fa 100644
--- a/themes/delphi/layouts/_default/baseof.html
+++ b/themes/delphi/layouts/_default/baseof.html
@@ -8,7 +8,7 @@
   </head>
   <body class="{{ block "body_class" . }}{{ end }}">
     {{ partial "nav.html" . }}
-    {{ block "breadcrumb" . }}{{ partial "menu/breadcrumb.html" . }}{{ end }}
+    {{ partial "menu/breadcrumb.html" . }}
     {{ block "main" . }} {{ end }}
     {{ partial "footer.html" . }}
     {{ partial "scripts.html" . }}
diff --git a/themes/delphi/layouts/_default/covidcast_app.html b/themes/delphi/layouts/_default/covidcast_app.html
index 1e4cbfd4b..bebdcceb4 100644
--- a/themes/delphi/layouts/_default/covidcast_app.html
+++ b/themes/delphi/layouts/_default/covidcast_app.html
@@ -7,9 +7,9 @@
   <script src="{{ "./covidcast/styles.js" | relURL }}"></script>
   <script src="{{ "./covidcast/bundle.js" | relURL }}"></script>
 {{ end }}
-{{ define "breadcrumb" }}<!--no breadcrumb -->{{ end }}
 {{ define "body_class" }}covidcast_wrapper{{ end }}
 {{ define "main" }}
+  {{partial "covidcast/modes.html" . }}
   <div id="vizbox">
     <div class="ie-banner" style="display: none">
       <div>
diff --git a/themes/delphi/layouts/partials/covidcast/get-modes.html b/themes/delphi/layouts/partials/covidcast/get-modes.html
new file mode 100644
index 000000000..8026bdd11
--- /dev/null
+++ b/themes/delphi/layouts/partials/covidcast/get-modes.html
@@ -0,0 +1,5 @@
+{{- $mainPage := $.GetPage "/covidcast" -}}
+{{- $pages := where $mainPage.Pages ".Params.layout" "eq" "covidcast_app" -}}
+{{- $pages = append (slice $mainPage) $pages -}}
+{{- $pages = sort $pages ".Params.order" -}}
+{{- return $pages -}}
\ No newline at end of file
diff --git a/themes/delphi/layouts/partials/covidcast/modes.html b/themes/delphi/layouts/partials/covidcast/modes.html
new file mode 100644
index 000000000..fb5c53502
--- /dev/null
+++ b/themes/delphi/layouts/partials/covidcast/modes.html
@@ -0,0 +1,15 @@
+<div class="uk-visible@s covidcast-modes">
+  <div class="uk-container uk-margin-remove-vertical">
+      {{$currentPage := .}}
+    <ul class="uk-tab">
+        {{range (partial "covidcast/get-modes.html" .)}}
+        <li data-mode="{{.Params.app_mode}}" class="covidcast-mode {{if eq $currentPage.Permalink .Permalink}}uk-active{{end}}">
+            <a href="{{.RelPermalink}}">
+                {{partial "font-awesome.html" .Params.icon }}
+                {{.Params.modeTitle | default .LinkTitle}}
+            </a>
+        </li>
+        {{end}}
+    </ul>
+  </div>
+</div>
diff --git a/themes/delphi/layouts/partials/font-awesome.html b/themes/delphi/layouts/partials/font-awesome.html
index ca31eb1fa..ecf915735 100644
--- a/themes/delphi/layouts/partials/font-awesome.html
+++ b/themes/delphi/layouts/partials/font-awesome.html
@@ -1,3 +1,10 @@
 <span class="inline-svg-icon">
-  {{ readFile (print "./node_modules/@fortawesome/fontawesome-free/svgs/" . ".svg" ) | safeHTML }}
+  {{- $fileName := (print . ".svg" ) -}}
+  {{- $faPath := path.Join "./node_modules/@fortawesome/fontawesome-free/svgs/" $fileName -}}
+  {{- $localPath := path.Join "./themes/delphi/assets/" $fileName -}}
+  {{- if fileExists $localPath -}}
+    {{ readFile $localPath | safeHTML }}
+  {{- else -}}
+    {{ readFile $faPath | safeHTML }}
+  {{- end -}}
 </span>

From 10ca63a1978c0bfe092ad1d87879f4a8daf606ec Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Mon, 28 Dec 2020 14:06:14 -0500
Subject: [PATCH 04/12] feat: add modes to menu

---
 config.toml | 30 +++++++++++++++++++++++++-----
 1 file changed, 25 insertions(+), 5 deletions(-)

diff --git a/config.toml b/config.toml
index 91cf26117..c63b3f4cd 100644
--- a/config.toml
+++ b/config.toml
@@ -38,29 +38,49 @@ relativeURLs = false
     weight = 2
 [[menu.main]]
     parent = "covidcast"
-    name = "Map"
+    name = "Map Overview"
     url = "/covidcast"
     weight = 1
+[[menu.main]]
+    parent = "covidcast"
+    name = "Timelapse"
+    url = "/covidcast/timelapse"
+    weight = 2
+[[menu.main]]
+    parent = "covidcast"
+    name = "Top 10"
+    url = "/covidcast/top10"
+    weight = 3
+[[menu.main]]
+    parent = "covidcast"
+    name = "Single Region"
+    url = "/covidcast/single"
+    weight = 4
 [[menu.main]]
     parent = "covidcast"
     name = "Surveys"
     url = "/covidcast/surveys"
-    weight = 2
+    weight = 5
 [[menu.main]]
     parent = "covidcast"
     name = "Survey Results"
     url = "/covidcast/survey-results"
-    weight = 3
+    weight = 6
+[[menu.main]]
+    parent = "covidcast"
+    name = "Export Data"
+    url = "/covidcast/export"
+    weight = 7
 [[menu.main]]
     parent = "covidcast"
     name = "Release Log"
     url = "/covidcast/release-log"
-    weight = 4
+    weight = 8
 [[menu.main]]
     parent = "covidcast"
     name = "Terms Of Use"
     url = "/covidcast/terms-of-use"
-    weight = 5
+    weight = 9
 [[menu.main]]
     identifier = "flu"
     name = "Flu and Other Diseases"

From 919ce8e058b6ffdd089fb26b50b0b48ae608e7a7 Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Mon, 28 Dec 2020 14:12:22 -0500
Subject: [PATCH 05/12] fix: format

---
 .../layouts/_default/covidcast_app.html       |  2 +-
 .../layouts/partials/covidcast/get-modes.html |  2 +-
 .../layouts/partials/covidcast/modes.html     | 19 +++++++++++--------
 .../delphi/layouts/partials/font-awesome.html |  2 +-
 4 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/themes/delphi/layouts/_default/covidcast_app.html b/themes/delphi/layouts/_default/covidcast_app.html
index bebdcceb4..a11b96586 100644
--- a/themes/delphi/layouts/_default/covidcast_app.html
+++ b/themes/delphi/layouts/_default/covidcast_app.html
@@ -9,7 +9,7 @@
 {{ end }}
 {{ define "body_class" }}covidcast_wrapper{{ end }}
 {{ define "main" }}
-  {{partial "covidcast/modes.html" . }}
+  {{ partial "covidcast/modes.html" . }}
   <div id="vizbox">
     <div class="ie-banner" style="display: none">
       <div>
diff --git a/themes/delphi/layouts/partials/covidcast/get-modes.html b/themes/delphi/layouts/partials/covidcast/get-modes.html
index 8026bdd11..ce34f294f 100644
--- a/themes/delphi/layouts/partials/covidcast/get-modes.html
+++ b/themes/delphi/layouts/partials/covidcast/get-modes.html
@@ -2,4 +2,4 @@
 {{- $pages := where $mainPage.Pages ".Params.layout" "eq" "covidcast_app" -}}
 {{- $pages = append (slice $mainPage) $pages -}}
 {{- $pages = sort $pages ".Params.order" -}}
-{{- return $pages -}}
\ No newline at end of file
+{{- return $pages -}}
diff --git a/themes/delphi/layouts/partials/covidcast/modes.html b/themes/delphi/layouts/partials/covidcast/modes.html
index fb5c53502..75d4ed6b5 100644
--- a/themes/delphi/layouts/partials/covidcast/modes.html
+++ b/themes/delphi/layouts/partials/covidcast/modes.html
@@ -1,15 +1,18 @@
 <div class="uk-visible@s covidcast-modes">
   <div class="uk-container uk-margin-remove-vertical">
-      {{$currentPage := .}}
+    {{ $currentPage := . }}
     <ul class="uk-tab">
-        {{range (partial "covidcast/get-modes.html" .)}}
-        <li data-mode="{{.Params.app_mode}}" class="covidcast-mode {{if eq $currentPage.Permalink .Permalink}}uk-active{{end}}">
-            <a href="{{.RelPermalink}}">
-                {{partial "font-awesome.html" .Params.icon }}
-                {{.Params.modeTitle | default .LinkTitle}}
-            </a>
+      {{ range (partial "covidcast/get-modes.html" .) }}
+        <li
+          data-mode="{{ .Params.app_mode }}"
+          class="covidcast-mode {{ if eq $currentPage.Permalink .Permalink }}uk-active{{ end }}"
+        >
+          <a href="{{ .RelPermalink }}">
+            {{ partial "font-awesome.html" .Params.icon }}
+            {{ .Params.modeTitle | default .LinkTitle }}
+          </a>
         </li>
-        {{end}}
+      {{ end }}
     </ul>
   </div>
 </div>
diff --git a/themes/delphi/layouts/partials/font-awesome.html b/themes/delphi/layouts/partials/font-awesome.html
index ecf915735..e79719aa5 100644
--- a/themes/delphi/layouts/partials/font-awesome.html
+++ b/themes/delphi/layouts/partials/font-awesome.html
@@ -4,7 +4,7 @@
   {{- $localPath := path.Join "./themes/delphi/assets/" $fileName -}}
   {{- if fileExists $localPath -}}
     {{ readFile $localPath | safeHTML }}
-  {{- else -}}
+    {{- else -}}
     {{ readFile $faPath | safeHTML }}
   {{- end -}}
 </span>

From 2e60f0ce369583f5266d7ed1e23595149cbb4dcc Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Mon, 28 Dec 2020 14:12:31 -0500
Subject: [PATCH 06/12] feat: use new covidcast branch

---
 package-lock.json | 4 ++--
 package.json      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index d0c12d7f6..cf531d5cd 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -4267,8 +4267,8 @@
    "dev": true
   },
   "www-covidcast": {
-   "version": "github:cmu-delphi/www-covidcast#40034c7e0f4996fdabbc15692148571aed41e3dc",
-   "from": "github:cmu-delphi/www-covidcast#40034c7e0f4996fdabbc15692148571aed41e3dc",
+   "version": "github:cmu-delphi/www-covidcast#62f085de193a4f1e5b817d3ba20b680860b6a24d",
+   "from": "github:cmu-delphi/www-covidcast#62f085de193a4f1e5b817d3ba20b680860b6a24d",
    "requires": {
     "uikit": "^3.5.10"
    },
diff --git a/package.json b/package.json
index a1b8e55b0..f6e2bbd16 100644
--- a/package.json
+++ b/package.json
@@ -7,7 +7,7 @@
     "highlight.js": "^10.4.1",
     "katex": "^0.12.0",
     "uikit": "^3.5.9",
-    "www-covidcast": "github:cmu-delphi/www-covidcast#40034c7e0f4996fdabbc15692148571aed41e3dc"
+    "www-covidcast": "github:cmu-delphi/www-covidcast#62f085de193a4f1e5b817d3ba20b680860b6a24d"
   },
   "devDependencies": {
     "cpx": "^1.5.0",

From 1d814cea4dbb0baf298ea265347063524138e459 Mon Sep 17 00:00:00 2001
From: Ryan Tibshirani <ryantibs@gmail.com>
Date: Mon, 28 Dec 2020 21:56:39 -0500
Subject: [PATCH 07/12] Improve model eqn and text

---
 content/blog/2020-09-21-forecast-demo.Rmd | 39 +++++++++++------------
 1 file changed, 18 insertions(+), 21 deletions(-)

diff --git a/content/blog/2020-09-21-forecast-demo.Rmd b/content/blog/2020-09-21-forecast-demo.Rmd
index d10b13a81..b26c4315a 100644
--- a/content/blog/2020-09-21-forecast-demo.Rmd
+++ b/content/blog/2020-09-21-forecast-demo.Rmd
@@ -111,20 +111,16 @@ We evaluate the following four models:
 
 $$
 \begin{aligned}
-&\text{Cases:} \\
-& h(Y_{\ell,t+d})
-\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) \\
-&\text{Cases + Facebook:} \\
-& h(Y_{\ell,t+d})
-\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
+h(Y_{\ell,t+d})
+&\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) \\
+h(Y_{\ell,t+d})
+&\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
 \sum_{j=0}^2 \gamma_j h(F_{\ell,t-7j}) \\
-&\text{Cases + Google:} \\
-& h(Y_{\ell,t+d})
-\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
+h(Y_{\ell,t+d})
+&\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
 \sum_{j=0}^2 \gamma_j h(G_{\ell,t-7j}) \\
-&\text{Cases + Facebook + Google:} \\
-& h(Y_{\ell,t+d})
-\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
+h(Y_{\ell,t+d})
+&\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
 \sum_{j=0}^2 \gamma_j h(F_{\ell,t-7j}) +
 \sum_{j=0}^2 \tau_j h(G_{\ell,t-7j}).
 \end{aligned}
@@ -134,14 +130,15 @@ Here $d=7$ or $d=14$, depending on the target value
 (number of days we predict ahead),
 and $h$ is a transformation to be specified later.
 
-Informally, the first model bases its predictions of future case rates
-on the following three features:
+Informally, the first model, which we'll call the "Cases" model, 
+bases its predictions of future case rates on the following three features:
 current COVID-19 case rates, and those 1 and 2 weeks back.
-The second model additionally incorporates the current Facebook signal,
-and the Facebook signal from 1 and 2 weeks back.
-The third model is exactly same but substitutes the Google signal
-instead of the Facebook one.
-Finally, the fourth model uses both Facebook and Google signals.
+The second model, "Cases + Facebook", additionally incorporates the 
+current Facebook signal, and the Facebook signal from 1 and 2 weeks back.
+The third model, "Cases + Google", is exactly the same but substitutes the 
+Google signal instead of the Facebook one.
+Finally, the fourth model, "Cases + Facebook + Google", 
+uses both Facebook and Google signals.
 For each model, in order to make a forecast at time $t_0$
 (to predict case rates at time $t_0+d$),
 we fit a linear model using least absolute deviations (LAD) regression,
@@ -293,8 +290,8 @@ is much bigger but still below 0.01.
     test](https://en.wikipedia.org/wiki/Wilcoxon_signed-rank_test)
     (for paired data, as we have here) is more popular,
     because it tends to be more powerful than the sign test.
-    Applied here, it does indeed give smaller p-values pretty much across the board.
-    However, it assumes symmetry of the distribution in question
+    Applied here, it does indeed give smaller p-values pretty much across the 
+    board. However, it assumes symmetry of the distribution in question
     (in our case, the difference in scaled errors),
     whereas the sign test does not, and thus we show results from the latter.
 

From e5bf6adb872113bff0ceaad699d300bad6e7eb00 Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Tue, 29 Dec 2020 08:13:30 -0500
Subject: [PATCH 08/12] feat: recompile Rmd

---
 content/blog/2020-09-21-forecast-demo.html | 123 ++++++++++-----------
 1 file changed, 60 insertions(+), 63 deletions(-)

diff --git a/content/blog/2020-09-21-forecast-demo.html b/content/blog/2020-09-21-forecast-demo.html
index 632638cf3..265b19e13 100644
--- a/content/blog/2020-09-21-forecast-demo.html
+++ b/content/blog/2020-09-21-forecast-demo.html
@@ -14,14 +14,14 @@
 summary: |
   Building on our previous two posts (on our COVID-19 symptom surveys through
   Facebook and Google)
-  this post offers a deeper dive into empirical analysis, examining whether the
-  % CLI-in-community indicators from our two surveys can be used to improve
+  this post offers a deeper dive into empirical analysis, examining whether the 
+  % CLI-in-community indicators from our two surveys can be used to improve 
   the accuracy of short-term forecasts of county-level COVID-19 case rates.
 acknowledgements: |
   Delphi's forecasting effort involves many people from our
-  modeling team, from forecaster design, to implementation, to evaluation. The
+  modeling team, from forecaster design, to implementation, to evaluation. The 
   broader insights on forecasting shared in this post certainly cannot be
-  attributable to Ryan's work alone, and are a reflection of the work carried out
+  attributable to Ryan's work alone, and are a reflection of the work carried out 
   by all these team members.
 related:
   - 2020-09-18-google-survey
@@ -120,20 +120,16 @@ <h2>Problem Setup</h2>
 We evaluate the following four models:</p>
 <p><span class="math display">\[
 \begin{aligned}
-&amp;\text{Cases:} \\
-&amp; h(Y_{\ell,t+d})
-\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) \\
-&amp;\text{Cases + Facebook:} \\
-&amp; h(Y_{\ell,t+d})
-\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
+h(Y_{\ell,t+d})
+&amp;\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) \\
+h(Y_{\ell,t+d})
+&amp;\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
 \sum_{j=0}^2 \gamma_j h(F_{\ell,t-7j}) \\
-&amp;\text{Cases + Google:} \\
-&amp; h(Y_{\ell,t+d})
-\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
+h(Y_{\ell,t+d})
+&amp;\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
 \sum_{j=0}^2 \gamma_j h(G_{\ell,t-7j}) \\
-&amp;\text{Cases + Facebook + Google:} \\
-&amp; h(Y_{\ell,t+d})
-\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
+h(Y_{\ell,t+d})
+&amp;\approx \alpha + \sum_{j=0}^2 \beta_j h(Y_{\ell,t-7j}) +
 \sum_{j=0}^2 \gamma_j h(F_{\ell,t-7j}) +
 \sum_{j=0}^2 \tau_j h(G_{\ell,t-7j}).
 \end{aligned}
@@ -141,14 +137,15 @@ <h2>Problem Setup</h2>
 <p>Here <span class="math inline">\(d=7\)</span> or <span class="math inline">\(d=14\)</span>, depending on the target value
 (number of days we predict ahead),
 and <span class="math inline">\(h\)</span> is a transformation to be specified later.</p>
-<p>Informally, the first model bases its predictions of future case rates
-on the following three features:
+<p>Informally, the first model, which we’ll call the “Cases” model,
+bases its predictions of future case rates on the following three features:
 current COVID-19 case rates, and those 1 and 2 weeks back.
-The second model additionally incorporates the current Facebook signal,
-and the Facebook signal from 1 and 2 weeks back.
-The third model is exactly same but substitutes the Google signal
-instead of the Facebook one.
-Finally, the fourth model uses both Facebook and Google signals.
+The second model, “Cases + Facebook”, additionally incorporates the
+current Facebook signal, and the Facebook signal from 1 and 2 weeks back.
+The third model, “Cases + Google”, is exactly the same but substitutes the
+Google signal instead of the Facebook one.
+Finally, the fourth model, “Cases + Facebook + Google”,
+uses both Facebook and Google signals.
 For each model, in order to make a forecast at time <span class="math inline">\(t_0\)</span>
 (to predict case rates at time <span class="math inline">\(t_0+d\)</span>),
 we fit a linear model using least absolute deviations (LAD) regression,
@@ -217,17 +214,17 @@ <h2>Forecasting Code</h2>
                                     as.Date(max(time_value)),
                                     by = &quot;day&quot;)) %&gt;% ungroup()
   df = full_join(df, df_all, by = c(&quot;geo_value&quot;, &quot;time_value&quot;))
-
+  
   # Group by geo value, sort rows by increasing time
-  df = df %&gt;% group_by(geo_value) %&gt;% arrange(time_value)
-
+  df = df %&gt;% group_by(geo_value) %&gt;% arrange(time_value) 
+  
   # Load over shifts, and add lag value or lead value
   for (shift in shifts) {
     fun = ifelse(shift &lt; 0, lag, lead)
     varname = sprintf(&quot;value%+d&quot;, shift)
     df = mutate(df, !!varname := fun(value, n = abs(shift)))
   }
-
+  
   # Ungroup and return
   return(ungroup(df))
 }
@@ -261,40 +258,40 @@ <h2>Forecasting Code</h2>
 case_num = 200
 geo_values = covidcast_signal(&quot;jhu-csse&quot;, &quot;confirmed_cumulative_num&quot;,
                               &quot;2020-05-14&quot;, &quot;2020-05-14&quot;) %&gt;%
-  filter(value &gt;= case_num) %&gt;% pull(geo_value)
+  filter(value &gt;= case_num) %&gt;% pull(geo_value) 
 
 # Fetch county-level Google and Facebook % CLI-in-community signals, and JHU
 # confirmed case incidence proportion
 start_day = &quot;2020-04-11&quot;
 end_day = &quot;2020-09-01&quot;
 g = covidcast_signal(&quot;google-survey&quot;, &quot;smoothed_cli&quot;) %&gt;%
-  filter(geo_value %in% geo_values) %&gt;%
-  select(geo_value, time_value, value)
-f = covidcast_signal(&quot;fb-survey&quot;, &quot;smoothed_hh_cmnty_cli&quot;,
+  filter(geo_value %in% geo_values) %&gt;% 
+  select(geo_value, time_value, value) 
+f = covidcast_signal(&quot;fb-survey&quot;, &quot;smoothed_hh_cmnty_cli&quot;, 
                      start_day, end_day) %&gt;%
-  filter(geo_value %in% geo_values) %&gt;%
-  select(geo_value, time_value, value)
+  filter(geo_value %in% geo_values) %&gt;% 
+  select(geo_value, time_value, value) 
 c = covidcast_signal(&quot;jhu-csse&quot;, &quot;confirmed_7dav_incidence_prop&quot;,
                      start_day, end_day) %&gt;%
-  filter(geo_value %in% geo_values) %&gt;%
+  filter(geo_value %in% geo_values) %&gt;% 
   select(geo_value, time_value, value)
 
-# Find &quot;complete&quot; counties, present in all three data signals at all times
+# Find &quot;complete&quot; counties, present in all three data signals at all times 
 geo_values_complete = intersect(intersect(g$geo_value, f$geo_value),
                                 c$geo_value)
 
-# Filter to complete counties, transform the signals, append 1-2 week lags to
+# Filter to complete counties, transform the signals, append 1-2 week lags to 
 # all three, and also 1-2 week leads to case rates
-lags = 1:2 * -7
+lags = 1:2 * -7 
 leads = 1:2 * 7
-g = g %&gt;% filter(geo_value %in% geo_values_complete) %&gt;%
-  mutate(value = trans(value * rescale_g)) %&gt;%
-  append_shifts(shifts = lags)
-f = f %&gt;% filter(geo_value %in% geo_values_complete) %&gt;%
-  mutate(value = trans(value * rescale_f)) %&gt;%
-  append_shifts(shifts = lags)
+g = g %&gt;% filter(geo_value %in% geo_values_complete) %&gt;% 
+  mutate(value = trans(value * rescale_g)) %&gt;% 
+  append_shifts(shifts = lags) 
+f = f %&gt;% filter(geo_value %in% geo_values_complete) %&gt;% 
+  mutate(value = trans(value * rescale_f)) %&gt;% 
+  append_shifts(shifts = lags) 
 c = c %&gt;% filter(geo_value %in% geo_values_complete) %&gt;%
-  mutate(value = trans(value * rescale_c)) %&gt;%
+  mutate(value = trans(value * rescale_c)) %&gt;% 
   append_shifts(shifts = c(lags, leads))
 
 # Rename columns
@@ -310,47 +307,47 @@ <h2>Forecasting Code</h2>
 
 # Use quantgen for LAD regression (this package supports quantile regression and
 # more; you can find it on GitHub here: https://github.com/ryantibs/quantgen)
-library(quantgen)
+library(quantgen) 
 
 res_list = vector(&quot;list&quot;, length = length(leads))
 
 # Loop over lead, forecast dates, build models and record errors (warning: this
 # computation takes a while)
-for (i in 1:length(leads)) {
+for (i in 1:length(leads)) { 
   lead = leads[i]; if (verbose) cat(&quot;***&quot;, lead, &quot;***\n&quot;)
-
+  
   # Create a data frame to store our forecast results. Code below populates its
-  # rows in a way that breaks from typical dplyr operations, done for efficiency
-  res_list[[i]] = z %&gt;%
-    filter(between(time_value, as.Date(start_day) - min(lags) + lead,
+  # rows in a way that breaks from typical dplyr operations, done for efficiency 
+  res_list[[i]] = z %&gt;% 
+    filter(between(time_value, as.Date(start_day) - min(lags) + lead, 
                    as.Date(end_day) - lead)) %&gt;%
     select(geo_value, time_value) %&gt;%
-    mutate(err0 = as.double(NA), err1 = as.double(NA), err2 = as.double(NA),
-           err3 = as.double(NA), err4 = as.double(NA), lead = lead)
+    mutate(err0 = as.double(NA), err1 = as.double(NA), err2 = as.double(NA), 
+           err3 = as.double(NA), err4 = as.double(NA), lead = lead) 
   valid_dates = unique(res_list[[i]]$time_value)
-
+  
   for (k in 1:length(valid_dates)) {
     date = valid_dates[k]; if (verbose) cat(format(date), &quot;... &quot;)
-
+    
     # Filter down to training set and test set
     z_tr = z %&gt;% filter(between(time_value, date - lead - n, date - lead))
     z_te = z %&gt;% filter(time_value == date)
     inds = which(res_list[[i]]$time_value == date)
-
+    
     # Create training and test responses
     y_tr = z_tr %&gt;% pull(paste0(&quot;case+&quot;, lead))
     y_te = z_te %&gt;% pull(paste0(&quot;case+&quot;, lead))
-
+    
     # Strawman model
     if (verbose) cat(&quot;0&quot;)
     y_hat = z_te %&gt;% pull(case)
     res_list[[i]][inds,]$err0 = abs(inv_trans(y_hat) - inv_trans(y_te))
-
+    
     # Cases only model
     if (verbose) cat(&quot;1&quot;)
     x_tr_case = z_tr %&gt;% select(starts_with(&quot;case&quot;) &amp; !contains(&quot;+&quot;))
     x_te_case = z_te %&gt;% select(starts_with(&quot;case&quot;) &amp; !contains(&quot;+&quot;))
-    x_tr = x_tr_case; x_te = x_te_case # For symmetry wrt what follows
+    x_tr = x_tr_case; x_te = x_te_case # For symmetry wrt what follows 
     ok = complete.cases(x_tr, y_tr)
     if (sum(ok) &gt; 0) {
       obj = quantile_lasso(as.matrix(x_tr[ok,]), y_tr[ok], tau = 0.5,
@@ -358,7 +355,7 @@ <h2>Forecasting Code</h2>
       y_hat = as.numeric(predict(obj, newx = as.matrix(x_te)))
       res_list[[i]][inds,]$err1 = abs(inv_trans(y_hat) - inv_trans(y_te))
     }
-
+    
     # Cases and Facebook model
     if (verbose) cat(&quot;2&quot;)
     x_tr_fb = z_tr %&gt;% select(starts_with(&quot;fb&quot;))
@@ -386,7 +383,7 @@ <h2>Forecasting Code</h2>
       y_hat = as.numeric(predict(obj, newx = as.matrix(x_te)))
       res_list[[i]][inds,]$err3 = abs(inv_trans(y_hat) - inv_trans(y_te))
     }
-
+    
     # Cases, Facebook, and Google model
     if (verbose) cat(&quot;4\n&quot;)
     x_tr = cbind(x_tr_case, x_tr_fb, x_tr_goog)
@@ -401,7 +398,7 @@ <h2>Forecasting Code</h2>
   }
 }
 
-# Bind results over different leads into one big data frame, and save
+# Bind results over different leads into one big data frame, and save 
 res = do.call(rbind, res_list)
 save(list = ls(), file = &quot;demo.rda&quot;)</code></pre>
 </div>
@@ -1036,8 +1033,8 @@ <h2>Wrap-Up</h2>
 test</a>
 (for paired data, as we have here) is more popular,
 because it tends to be more powerful than the sign test.
-Applied here, it does indeed give smaller p-values pretty much across the board.
-However, it assumes symmetry of the distribution in question
+Applied here, it does indeed give smaller p-values pretty much across the
+board. However, it assumes symmetry of the distribution in question
 (in our case, the difference in scaled errors),
 whereas the sign test does not, and thus we show results from the latter.<a href="#fnref2" class="footnote-back">↩︎</a></p></li>
 <li id="fn3"><p>Delphi’s “production” forecasters are still based on relatively simple

From 34182820745c37ee0e1539c0286a9f0509e4b0e1 Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Tue, 29 Dec 2020 10:23:54 -0500
Subject: [PATCH 09/12] feat: update covidcast

---
 package-lock.json | 4 ++--
 package.json      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index e4e75bfdc..1d7086cb0 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -4267,8 +4267,8 @@
    "dev": true
   },
   "www-covidcast": {
-   "version": "github:cmu-delphi/www-covidcast#62f085de193a4f1e5b817d3ba20b680860b6a24d",
-   "from": "github:cmu-delphi/www-covidcast#62f085de193a4f1e5b817d3ba20b680860b6a24d",
+   "version": "github:cmu-delphi/www-covidcast#e7f0a2c6041859683649124152bf7a17654419cb",
+   "from": "github:cmu-delphi/www-covidcast#e7f0a2c6041859683649124152bf7a17654419cb",
    "requires": {
     "uikit": "^3.5.10"
    },
diff --git a/package.json b/package.json
index ca4e2c1cf..bed3708b6 100644
--- a/package.json
+++ b/package.json
@@ -7,7 +7,7 @@
     "highlight.js": "^10.4.1",
     "katex": "^0.12.0",
     "uikit": "^3.5.9",
-    "www-covidcast": "github:cmu-delphi/www-covidcast#62f085de193a4f1e5b817d3ba20b680860b6a24d"
+    "www-covidcast": "github:cmu-delphi/www-covidcast#e7f0a2c6041859683649124152bf7a17654419cb"
   },
   "devDependencies": {
     "cpx": "^1.5.0",

From 8328bd79d2992ddc384fd5f66185730d069a0015 Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Tue, 29 Dec 2020 12:58:36 -0500
Subject: [PATCH 10/12] feat: prepare release v1.12.1

---
 content/covidcast/release-log/headless/v1.12.1.md | 10 ++++++++++
 package-lock.json                                 |  4 ++--
 package.json                                      |  2 +-
 3 files changed, 13 insertions(+), 3 deletions(-)
 create mode 100644 content/covidcast/release-log/headless/v1.12.1.md

diff --git a/content/covidcast/release-log/headless/v1.12.1.md b/content/covidcast/release-log/headless/v1.12.1.md
new file mode 100644
index 000000000..493d5cf5c
--- /dev/null
+++ b/content/covidcast/release-log/headless/v1.12.1.md
@@ -0,0 +1,10 @@
+---
+title: v1.12.1
+date: 2020-12-29
+---
+
+Bugfix release for improved mobile experience
+
+#### Improvements
+
+- [#700](https://github.com/cmu-delphi/www-covidcast/pull/700) Improve mobile experience
diff --git a/package-lock.json b/package-lock.json
index 1d7086cb0..26e3bd2e6 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -4267,8 +4267,8 @@
    "dev": true
   },
   "www-covidcast": {
-   "version": "github:cmu-delphi/www-covidcast#e7f0a2c6041859683649124152bf7a17654419cb",
-   "from": "github:cmu-delphi/www-covidcast#e7f0a2c6041859683649124152bf7a17654419cb",
+   "version": "github:cmu-delphi/www-covidcast#a4f828cf30eed46671c694ef3002acbfbc00369b",
+   "from": "github:cmu-delphi/www-covidcast#a4f828cf30eed46671c694ef3002acbfbc00369b",
    "requires": {
     "uikit": "^3.5.10"
    },
diff --git a/package.json b/package.json
index bed3708b6..aa16125fb 100644
--- a/package.json
+++ b/package.json
@@ -7,7 +7,7 @@
     "highlight.js": "^10.4.1",
     "katex": "^0.12.0",
     "uikit": "^3.5.9",
-    "www-covidcast": "github:cmu-delphi/www-covidcast#e7f0a2c6041859683649124152bf7a17654419cb"
+    "www-covidcast": "github:cmu-delphi/www-covidcast#a4f828cf30eed46671c694ef3002acbfbc00369b"
   },
   "devDependencies": {
     "cpx": "^1.5.0",

From 96ac3c65bec1dfa35207a2b82ff962b65408be43 Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Tue, 29 Dec 2020 13:03:40 -0500
Subject: [PATCH 11/12] feat: upgrade to covidcast v1.12.1

---
 package-lock.json | 4 ++--
 package.json      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 26e3bd2e6..9799fb814 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -4267,8 +4267,8 @@
    "dev": true
   },
   "www-covidcast": {
-   "version": "github:cmu-delphi/www-covidcast#a4f828cf30eed46671c694ef3002acbfbc00369b",
-   "from": "github:cmu-delphi/www-covidcast#a4f828cf30eed46671c694ef3002acbfbc00369b",
+   "version": "https://github.com/cmu-delphi/www-covidcast/releases/download/v1.12.1/www-covidcast-1.12.1.tgz",
+   "integrity": "sha512-mWV4WVcfCRpLct+gHkCCuw5NfuNVcJfhZ4Kr8jQczRtARRGm2xmUzGi9pDTdpo6mbrdyhXjOMx5icytjgLx7KA==",
    "requires": {
     "uikit": "^3.5.10"
    },
diff --git a/package.json b/package.json
index aa16125fb..a77e4e421 100644
--- a/package.json
+++ b/package.json
@@ -7,7 +7,7 @@
     "highlight.js": "^10.4.1",
     "katex": "^0.12.0",
     "uikit": "^3.5.9",
-    "www-covidcast": "github:cmu-delphi/www-covidcast#a4f828cf30eed46671c694ef3002acbfbc00369b"
+    "www-covidcast": "https://github.com/cmu-delphi/www-covidcast/releases/download/v1.12.1/www-covidcast-1.12.1.tgz"
   },
   "devDependencies": {
     "cpx": "^1.5.0",

From 38e87760f874c0d4c7540aa22a71a87a7e145f21 Mon Sep 17 00:00:00 2001
From: Samuel Gratzl <sam@sgratzl.com>
Date: Tue, 29 Dec 2020 13:07:22 -0500
Subject: [PATCH 12/12] build: prepare release

---
 package-lock.json | 2 +-
 package.json      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 9799fb814..535aa2224 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
 {
  "name": "www-main",
- "version": "1.12.0",
+ "version": "1.12.1",
  "lockfileVersion": 1,
  "requires": true,
  "dependencies": {
diff --git a/package.json b/package.json
index a77e4e421..c216af964 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "www-main",
-  "version": "1.12.0",
+  "version": "1.12.1",
   "private": true,
   "dependencies": {
     "@fortawesome/fontawesome-free": "^5.15.1",