Release v2.3.0

.github/workflows/ci.yaml

@@ -61,23 +61,22 @@ jobs:
           echo "::set-output name=tag::$imageTag"
           echo "::set-output name=repo::ghcr.io/${{ github.repository }}"
       - name: Push Dev Tag
-        if: startsWith(github.ref, 'refs/heads/dev')
         run: |
           docker tag repo ${{ steps.tagname.outputs.repo }}:${{ steps.tagname.outputs.tag }}
           docker push ${{ steps.tagname.outputs.repo }}:${{ steps.tagname.outputs.tag }}
       - name: Extract version
         if: startsWith(github.ref, 'refs/heads/main')
         id: extract_version
         run: node -pe "'::set-output name=version::' + require('./package.json').version"
-      - name: Push Version Tag Tag
-        if: startsWith(github.ref, 'refs/heads/main')
-        run: |
-          docker tag repo ${{ steps.tagname.outputs.repo }}:v{{ steps.extract_version.outputs.version }}
-          docker push ${{ steps.tagname.outputs.repo }}:v{{ steps.extract_version.outputs.version }}
       - name: Trigger Webhook
         run: |
           # trigger a webhook update
           curl -H "Authorization: Bearer ${{ secrets.DELPHI_DEPLOY_WEBHOOK_TOKEN }}" \
                -X POST ${{ secrets.DELPHI_DEPLOY_WEBHOOK_URL }} \
                -H "Content-Type: application/x-www-form-urlencoded" \
                -d "repository=${{ steps.tagname.outputs.repo }}&tag=${{ steps.tagname.outputs.tag }}"
+      - name: Push Version Tag Tag
+        if: startsWith(github.ref, 'refs/heads/main')
+        run: |
+          docker tag repo ${{ steps.tagname.outputs.repo }}:v${{ steps.extract_version.outputs.version }}
+          docker push ${{ steps.tagname.outputs.repo }}:v${{ steps.extract_version.outputs.version }}

config.toml

@@ -56,11 +56,16 @@ relativeURLs = false
     name = "Explore an Indicator"
     url = "/covidcast/indicator"
     weight = 3
+[[menu.main]]
+    parent = "covidcast"
+    name = "Explore Correlations"
+    url = "/covidcast/correlation"
+    weight = 4
 [[menu.main]]
     parent = "covidcast"
     name = "Classic Map"
     url = "/covidcast/classic"
-    weight = 4
+    weight = 30
 [[menu.main]]
     parent = "covidcast"
     name = "Forecast Evaluation"
@@ -86,6 +91,11 @@ relativeURLs = false
     name = "Export Data"
     url = "/covidcast/export"
     weight = 70
+[[menu.main]]
+    parent = "covidcast"
+    name = "Data Anomalies"
+    url = "/covidcast/data-anomalies"
+    weight = 71
 [[menu.main]]
     parent = "covidcast"
     name = "Release Log"
@@ -132,4 +142,4 @@ relativeURLs = false
     feedbackDelayMin = 45  # in sec
     feedbackDelayMax = 180 # in sec
     feedbackDuration = 60  # show it for 60sec
-    highlightLinks = "/covidcast/,/covidcast/summary,/covidcast/indicator,/covidcast/indicator-status,/forecast-eval/"
+    highlightLinks = "/covidcast/correlation,/covidcast/data-anomalies"

content/about/publications/index.md

@@ -1,6 +1,12 @@
 ---
 title: Research and White Papers
 papers:
+  - title: "Causal inference in the time of COVID-19"
+    image: causal.jpg
+    authors: Bonvini, Kennedy, Ventura, Wasserman
+    link: https://arxiv.org/abs/2103.04472
+    journal: ArXiv preprint
+    year: 2021
   - title: "Pancasting: forecasting epidemics from provisional data"
     image: pancasting.jpg
     authors: Brooks

content/blog/2020-08-28-api.Rmd

@@ -285,21 +285,20 @@ can change for _weeks_ as new data arrives:
 ```{r q-versioning, warning=FALSE, message=FALSE, cache=TRUE}
 library(covidcast)
 library(dplyr)
-# DISABLED for now since the API is not ready
 query_date <- "2020-08-01"
-# covidcast_signal(
-#   data_source = "quidel",
-#   signal = "covid_ag_raw_pct_positive",
-#   start_day = query_date,
-#   end_day = query_date,
-#   geo_type = "state",
-#   geo_value = "ny",
-#   issues = c(query_date, "2020-09-04")) %>%
-#     select(time_value, value, sample_size, issue, lag) %>%
-#     distinct(value, .keep_all=TRUE) %>%
-#     knitr::kable("html", digits = 2,
-#                  col.names = c("Test date", "Positivity rate (%)", "Sample size",
-#                                "Issued on", "Lag (days)"))
+covidcast_signal(
+  data_source = "quidel",
+  signal = "covid_ag_raw_pct_positive",
+  start_day = query_date,
+  end_day = query_date,
+  geo_type = "state",
+  geo_value = "ny",
+  issues = c(query_date, "2020-09-04")) %>%
+    select(time_value, value, sample_size, issue, lag) %>%
+    distinct(value, .keep_all=TRUE) %>%
+    knitr::kable("html", digits = 2,
+                 col.names = c("Test date", "Positivity rate (%)", "Sample size",
+                               "Issued on", "Lag (days)"))
 ```
 
 Many data sources are subject to revisions:

content/covidcast/correlation.md

@@ -0,0 +1,10 @@
+---
+title: COVIDcast | Indicator Correlation
+linkTitle: Indicator Correlation
+description: COVIDcast tracks and forecasts the spread of COVID-19. By Carnegie Mellon's Delphi Research Group.
+layout: covidcast_app
+app_mode: correlation
+order: 4
+heroImage: /images/landing-page/hero-images/covidcast_v2.jpg
+feedback: true
+---

content/covidcast/data-anomalies.md

@@ -0,0 +1,10 @@
+---
+title: COVIDcast | Data Anomalies
+linkTitle: Data Anomalies
+description: COVIDcast tracks and forecasts the spread of COVID-19. By Carnegie Mellon's Delphi Research Group.
+layout: covidcast_app
+app_mode: data-anomalies
+order: 7
+heroImage: /images/landing-page/hero-images/covidcast_v2.jpg
+feedback: true
+---

content/covidcast/export.md

@@ -5,7 +5,6 @@ description: Use COVIDcast data in your own analysis
 layout: covidcast_app
 app_mode: export
 order: 6
-icon: solid/download
 heroImage: /images/landing-page/hero-images/covidcast_v2.jpg
 feedback: true
 ---

content/covidcast/release-log/headless/v2.2.0.md

@@ -0,0 +1,10 @@
+---
+title: v2.2.0
+date: 2021-04-01
+---
+
+### New Features
+ * Indicator Status Overview dashboard: Explore the status of API indicators and their coverages
+
+
+More information: https://github.com/cmu-delphi/www-covidcast/releases/tag/v2.2.0

content/covidcast/release-log/headless/v2.3.0.md

@@ -0,0 +1,13 @@
+---
+title: v2.3.0
+date: 2021-04-15
+---
+
+### New Features
+ * Explore Correlations: Explore correlations between different indicators
+ * Annotation Overview: Show all data anomalies recorded in COVIDcast in a central place
+ * Expandable Line Charts: Expand the line chart of indicators to show the full historic range
+ * HHS and Nation Support: The classic map now supports displaying HHS region and national level data
+
+
+More information: https://github.com/cmu-delphi/www-covidcast/releases/tag/v2.3.0

content/covidcast/surveys.md

@@ -42,6 +42,7 @@ Our [National COVID Survey Dashboard]({{< relref "covidcast/survey-results" >}})
 
 ### Blog posts and presentations
 
+- Alejandra Arrieta, Emmanuela Gakidou, Heidi Larson, Erin Mullany, and Christopher Troeger, April 1, 2021. [Through Understanding and Empathy, We Can Convince Women to Get the COVID-19 Vaccine](https://www.thinkglobalhealth.org/article/through-understanding-and-empathy-we-can-convince-women-get-covid-19-vaccine). Think Global Health.
 - Joseph Friedman, Silvia Montoya and Emmanuela Gakidou, March 8, 2021. [Gender Equality in the Global Return to School](https://www.thinkglobalhealth.org/article/gender-equality-global-return-school). Think Global Health.
 - Leanna Morinishi, Kris Barkume, Esther Kim, and Alex Reinhart, February 2, 2021. [Home for the Holidays? The Impact of US Holidays on Social Behaviors and Preventative Measures]({{< relref "2021-01-22-holiday-surveys" >}}). Delphi blog.
 - Alex Reinhart, Esther Kim, Andy Garcia, and Sarah LaRocca, January 28, 2021. [Using the COVID-19 Symptom Survey to Track Vaccination Uptake and Sentiment in the United States]({{< relref "2021-01-28-survey-vaccines" >}}). Delphi blog.

package.json

@@ -1,13 +1,13 @@
 {
   "name": "www-main",
-  "version": "2.2.0",
+  "version": "2.3.0",
   "private": true,
   "dependencies": {
     "@fortawesome/fontawesome-free": "^5.15.3",
     "highlight.js": "^10.6.0",
     "katex": "^0.13.0",
     "uikit": "^3.6.18",
-    "www-covidcast": "https://github.com/cmu-delphi/www-covidcast/releases/download/v2.2.0/www-covidcast-2.2.0.tgz"
+    "www-covidcast": "https://github.com/cmu-delphi/www-covidcast/releases/download/v2.3.1/www-covidcast-2.3.1.tgz"
   },
   "devDependencies": {
     "hugo-bin": "^0.69.0",