Release v2.6.0

.github/workflows/blog.yaml

@@ -5,18 +5,19 @@ on:
     paths: # run only when an Rmd file changes
       - "**.Rmd"
       - "environment.yml"
+      - "dependencies.R"
       - ".github/workflows/blog.yaml"
 
 jobs:
-  build:
+  blog:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
         with:
           # submodules: true  # Fetch Hugo themes (true OR recursive)
           fetch-depth: 3
       - name: Cache Conda
-        uses: actions/[email protected].5
+        uses: actions/[email protected].6
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda6-${{ hashFiles('environment.yml') }}
@@ -42,7 +43,7 @@ jobs:
         run: |
           Rscript ./dependencies.R
       - name: Restore Blogdown Cache
-        uses: actions/[email protected].5
+        uses: actions/[email protected].6
         with:
           path: |
             ./blogdown
@@ -65,7 +66,7 @@ jobs:
       - uses: actions/[email protected]
         with:
           node-version: "12"
-      - uses: actions/[email protected].5
+      - uses: actions/[email protected].6
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}

.github/workflows/ci.yaml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/[email protected]
         with:
           node-version: "14"
-      - uses: actions/[email protected].5
+      - uses: actions/[email protected].6
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node3-${{ hashFiles('**/package-lock.json') }}

.github/workflows/release_main.yml

@@ -47,7 +47,7 @@ jobs:
         with:
           node-version: "14"
       - name: Cache Node.js modules
-        uses: actions/[email protected].5
+        uses: actions/[email protected].6
         with:
           path: ~/.npm # npm cache files are stored in `~/.npm` on Linux/macOS
           key: ${{ runner.OS }}-node2-${{ hashFiles('**/package-lock.json') }}

.vscode/settings.json

@@ -2,6 +2,7 @@
   "editor.formatOnSave": true,
   "editor.formatOnPaste": true,
   "editor.formatOnSaveMode": "modifications",
+  "prettier.prettierPath": "./node_modules/prettier",
   "[scss]": {
     "files.trimTrailingWhitespace": true,
     "editor.formatOnSave": true,
@@ -16,5 +17,6 @@
     "files.trimTrailingWhitespace": true,
     "editor.formatOnSave": true,
     "editor.defaultFormatter": "esbenp.prettier-vscode"
-  }
+  },
+  "prettier.enableDebugLogs": true
 }

README.md

@@ -79,6 +79,8 @@ In order to convert the Rmd files to HTML files for Hugo you also need to:
 1. Activate the environment: `conda activate www-main`
 1. Install extra R dependencies: `Rscript ./dependencies.R`
 
+As an alternative you can use Docker and Docker Compose. Then it reduces to `docker-compose up -d` to create a docker container for the current environment. In the following you would need to jump into the container to execute the upcoming command via `docker-compose exec r bash`.
+
 #### Commands
 
 1. Activate the environment: `conda activate www-main`
@@ -93,15 +95,88 @@ In order to convert the Rmd files to HTML files for Hugo you also need to:
 blogdown also has an integrated server `blogdown::serve_site()` which will render RMarkdown files on the fly and does a similar thing as `hugo server -D`.
 A shortcut is available through `npm run start:blog`.
 
-#### Adding a new blog post
+## Adding a new blog post
+
+*Prerequisite*: Installed Blog Editor environment from the previous section
+
+### Create new blog file
+
+Create a new file `content/blog` with a naming convention of `YYYY-MM-DD-short-title.Rmd`. The date is the creation date. Copy the template post or another example to start with. *Note*: Starting the file with an underscore (e.g. `_2021-04-20-jj-vaccine.Rmd`), will stop this file from being automatically checked by the Github Action CI. Only do this when the public CI cannot build this post, if for example private data is used.
 
 In case you use new dependencies don't forget to either edit `environment.yml` or `dependencies.R`.
-A Github action should runs when Rmd files changes so it will verify that the blog post can be built.
+A Github action should run when Rmd files changes so it will verify that the blog post can be built.
 However, the converted HTML file along with all generated images are committed to the repository.
 This simplifies the deployment and ensures that we have a blog post even when the API or data changes.
 
+### Edit Blog Header
+
+The header of a blog file contains numerous attributes to be defined, including: name, publication date (`date`), tags, a short summary (at most 150 characters), and a list of authors. The author list `authors` is a list of people keys, see below for how to add people.
+
+The `heroImage` is an optional hero image banner. The image is optional but its thumbnail version is not. However, the template post has good default value for this one. The hero image should be a JPG file with 1120x440 pixels. The thumbnail hero image should be a JPG file with 300x300 pixels. The files should be stored in `/content/blog/images`.
+
+The `related` list is a list of related blog links identified by their file name without the Rmd suffix.
+
+### Linking within the blog post
+
+In order to generate links that are relative to the whole website there are two short codes for R Markdown available.
 
-### Release Process
+#### Linking to another page
+
+using the `reflink` shortcode. For example, `r blogdown::shortcode_html("reflink", "2020-09-18-google-survey", "Google")` will generate a relative link to the blog post with the filename `2020-09-18-google-survey` and anchor text `Google`.
+
+#### Linking to the API docs
+
+using the `apireflink` shortcode. For example, `r blogdown::shortcode_html("apireflink", "api/covidcast.html", "COVIDcast API")` will generate a link to the API docs and its sub page `api/covidcast.html` and will look like: [`COVIDcast API`](https://cmu-delphi.github.io/delphi-epidata/).
+
+### Creating wide figures
+
+In case of a wide figure, one can break out of the layout by adding the `out.extra = 'class="wide-figure"'` extra argument to the corresponding R chunk.
+
+e.g.,
+```
+{r, message = FALSE, warning = FALSE, fig.width = 9, fig.height = 5, out.extra = 'class="wide-figure"'}
+ggplot(...)
+```
+
+### Adding static images
+
+Static images (e.g. pre-generated plots) should be stored in a `/static/blog/<BLOGFILE_NAME>_files` directory and referenced using something like
+
+```
+![](/blog/2021-04-29-vaccine-trends-hispanic_files/hesitancy_over_time_hispanic_and_white_adults.png)
+```
+
+### Building the blog file
+
+see before using `Rscript -e 'blogdown::build_site(local=TRUE, run_hugo=FALSE, build_rmd="content/blog/<NAME>.Rmd")'` where `<NAME>` should be replaced by the name of the Rmd file. **The generated files should be committed to this repository to ensure reproducibility.**
+
+
+## Adding new people (team, blog authors)
+
+People on this website are centrally managed in the `/content/people/index.md` file. Each entry should have the following attributes:
+
+ * `key` ... short key to identify this person when referencing them in the blog section
+ * `firstName`, `lastName`, `affiliation`
+ * `image` ... name of the head shot image (preferred 500x500px in JPG format) stored in `/content/people/headshots`
+ * `description` ... used within the blog footer as an about the author text
+ * `note` ...optional note about past contributors
+ * `link` ... optional used for linking to a personal website
+ * `team` ... list of teams this person is part of. used to assign places on the teams page. possible values are:
+    * `core` ... core member
+    * `blog` ... blog author
+    * `highlight` ... highlight person on front page
+    * `external` ... external person not to be listed in the teams page
+    * `past` ... past member team section
+    * `leadership` ... ryan and roni
+    * `contributors` ... contributor team section
+    * `google` ... google team section
+
+
+## Adding new news item
+
+News items are short announcements that should be persistent. The are centrally managed in the `/content/news/headless` directory. Each news item is its own file with content, title, and publication date.
+
+## Release Process
 
 The release consists of multiple steps which can be all done via the GitHub website:
 
@@ -115,4 +190,3 @@ The release consists of multiple steps which can be all done via the GitHub webs
    1. create docker image and the production system will be notified to pull this update
 1. Once the jobs are completed the new release should be available at https://delphi.cmu.edu within minutes.
 1. Done
-

config.toml

@@ -141,6 +141,7 @@ relativeURLs = false
     mission = "Develop the theory and practice of epidemiological forecasting, with a long-term vision of making this technology as universally accepted and useful as weather forecasting is today."
     apiUrl = "https://cmu-delphi.github.io/delphi-epidata"
     twitter = "CmuDelphi"
+    contactForm = "https://docs.google.com/forms/d/e/1FAIpQLScqgT1fKZr5VWBfsaSp-DNaN03aV6EoZU4YljIzHJ1Wl_zmtg/viewform"
     feedbackForm = "https://docs.google.com/forms/d/e/1FAIpQLSeIeOJtrAhdOriEyiRY7LkpQX8DZBY19dl6De8l56Q9CZhmxw/viewform?usp=pp_url&entry.1245962748="
     feedbackLikelihoodMobile = 0.2
     feedbackLikelihoodDesktop = 1

content/about/news/headless/2020_12_chng_partnership.md

@@ -0,0 +1,7 @@
+---
+date: 2020-12-01
+title: COVIDcast enhanced with Change Healthcare COVID-19 de-identified claims data
+category: update
+---
+
+[Change Healthcare and Carnegie Mellon University’s Delphi Research Group announce the launch of Delphi's enhanced COVIDcast real-time COVID-19 indicators](https://newsroom.changehealthcare.com/press-releases/carnegie-mellon-university-s-delphi-research-group-enhances-covi)

content/about/news/headless/2021_05_12_spaig_award.md

@@ -0,0 +1,7 @@
+---
+date: 2021-05-12
+title: Delphi Research Group and collaborators honored for COVIDcast
+category: update
+---
+
+[The American Statistical Association (ASA) presented the 2021 Statistical Partnerships Among Academe, Industry, and Government (SPAIG) Award to Carnegie Mellon University’s Delphi Research Group and their COVIDcast partners](https://www.cmu.edu/dietrich/news/news-stories/2021/may/spaig-covid.html)

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

@@ -11,7 +11,7 @@ authors: # list of team member keys, see /content/about/team/index.md -> team
   - frida
 # uncomment to enable a big hero image
 # heroImage: blog-lg-img_hello-world.jpg # size: 1120x440 jpg format
-heroImageThumb: blog-thumb.jpg # size: 300x200 jpg format
+heroImageThumb: blog-thumb.jpg # size: 300x300 jpg format
 summary: |
   Blog summary, the first 150 characters are used for the blog list
 acknowledgements: |

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

@@ -11,7 +11,7 @@
   - frida
 # uncomment to enable a big hero image
 # heroImage: blog-lg-img_hello-world.jpg # size: 1120x440 jpg format
-heroImageThumb: blog-thumb.jpg # size: 300x200 jpg format
+heroImageThumb: blog-thumb.jpg # size: 300x300 jpg format
 summary: |
   Blog summary, the first 150 characters are used for the blog list
 acknowledgements: |

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

@@ -328,9 +328,9 @@ plot_one = function(geo_value, title = NULL, xlab = NULL,
   trans21 = function(x) trans(x, range2, range1)
 
   # Find state name, find abbreviation, then set title
-  state_name = fips_to_name(paste0(substr(geo_value, 1, 2), "000"))
+  state_name = state_fips_to_name(paste0(substr(geo_value, 1, 2), "000"))
   state_abbr = name_to_abbr(state_name)
-  title = paste0(fips_to_name(geo_value), ", ", state_abbr)
+  title = paste0(county_fips_to_name(geo_value), ", ", state_abbr)
 
   # Transform the combined signal to the incidence range, then stack
   # these rowwise into one data frame

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

@@ -322,9 +322,9 @@ <h2>Some Interesting Examples</h2>
   trans21 = function(x) trans(x, range2, range1)
 
   # Find state name, find abbreviation, then set title
-  state_name = fips_to_name(paste0(substr(geo_value, 1, 2), &quot;000&quot;))
+  state_name = state_fips_to_name(paste0(substr(geo_value, 1, 2), &quot;000&quot;))
   state_abbr = name_to_abbr(state_name)
-  title = paste0(fips_to_name(geo_value), &quot;, &quot;, state_abbr)
+  title = paste0(county_fips_to_name(geo_value), &quot;, &quot;, state_abbr)
 
   # Transform the combined signal to the incidence range, then stack
   # these rowwise into one data frame

content/blog/2021-03-10_c2b.Rmd

@@ -12,13 +12,13 @@ authors:
   - roni
   - cscott
 heroImage: blog-lg-c2b.jpg # size: 1120x440 jpg format
-heroImageThumb: blog-thumb-c2b-1.jpg # size: 300x200 jpg format
+heroImageThumb: blog-thumb-c2b-1.jpg # size: 300x300 jpg format
 # related:
 summary: |
   In partnership with the Allegheny County Health Department,
   we explored solutions to pressing challenges
-  during the pandemic. 
-  
+  during the pandemic.
+
 acknowledgements: |
  Thank you to the Allegheny County Health Department (especially Antony Gnalian,
  Dr. LuAnn Brink, and Dr. Debra Bogen) for their invaluable feedback, efforts, and

content/blog/2021-03-10_c2b.html

@@ -12,13 +12,13 @@
   - roni
   - cscott
 heroImage: blog-lg-c2b.jpg # size: 1120x440 jpg format
-heroImageThumb: blog-thumb-c2b-1.jpg # size: 300x200 jpg format
+heroImageThumb: blog-thumb-c2b-1.jpg # size: 300x300 jpg format
 # related:
 summary: |
   In partnership with the Allegheny County Health Department,
   we explored solutions to pressing challenges
-  during the pandemic. 
-  
+  during the pandemic.
+
 acknowledgements: |
  Thank you to the Allegheny County Health Department (especially Antony Gnalian,
  Dr. LuAnn Brink, and Dr. Debra Bogen) for their invaluable feedback, efforts, and

content/covidcast/surveys.md

@@ -52,12 +52,15 @@ Our [National COVID Survey Dashboard]({{< relref "covidcast/survey-results" >}})
 
 ### Publications
 
-- J. Lessler, M. K. Grabowski, K. H. Grantz, E. Badillo-Goicoechea, C. J. E. Metcalf, C. Lupton-Smith, A. S. Azman, and E. A. Stuart (2021). [Household COVID-19 risk and in-person schooling](https://doi.org/10.1126/science.abh2939). *Science*.
+- C. M. Zipfel, V. Colizza, and S. Bansal (2021). [The missing season: The impacts of the COVID-19 pandemic on influenza](https://doi.org/10.1016/j.vaccine.2021.05.049). *Vaccine*.
+- J. Lessler, M. K. Grabowski, K. H. Grantz, E. Badillo-Goicoechea, C. J. E. Metcalf, C. Lupton-Smith, A. S. Azman, and E. A. Stuart (2021). [Household COVID-19 risk and in-person schooling](https://doi.org/10.1126/science.abh2939). *Science* 372 (6545), 1092-1097.
+- Doerr, A.J. (2021). [Locked (Down) and Loaded (Language): Effect of Policy and Speech on COVID-19 Outcomes](https://doi.org/10.1177/15480518211012404). *Journal of Leadership & Organizational Studies*.
 - Bilinski, A., Emanuel, E., Salomon, J.A. and Venkataramani, A. (2021). [Better Late Than Never: Trends in COVID-19 Infection Rates, Risk Perceptions, and Behavioral Responses in the USA](https://doi.org/10.1007/s11606-021-06633-8). *Journal of General Internal Medicine*.
+- Molteni, E., Astley, C.M., Ma, W. et al. (2021). [Symptoms and syndromes associated with SARS-CoV-2 infection and severity in pregnant women from two community cohorts](https://doi.org/10.1038/s41598-021-86452-3). *Scientific Reports* 11, 6928.
 - Rebeiro, P., Aronoff, D, and Smith, M.K. (2021). [The Impact of State Mask-Wearing Requirements on the Growth of COVID-19 Cases, Hospitalizations, and Deaths in the United States](https://doi.org/10.1093/cid/ciab101). *Clinical Infectious Diseases*, ciab101.
-- Rader, White, Burns, Chen, Brilliant, Cohen, Shaman, Brilliant, Kraemer, Moritz, Hawkins, Scarpino, Astley, and Brownstein (2021). [Mask-wearing and control of SARS-CoV-2 transmission in the USA: a cross-sectional study](https://doi.org/10.1016/S2589-7500(20)30293-4). *Lancet Digital Health* volume 3, issue 3, e148-e157.
+- Rader, White, Burns, Chen, Brilliant, Cohen, Shaman, Brilliant, Kraemer, Moritz, Hawkins, Scarpino, Astley, and Brownstein (2021). [Mask-wearing and control of SARS-CoV-2 transmission in the USA: a cross-sectional study](https://doi.org/10.1016/S2589-7500(20)30293-4). *Lancet Digital Health* 3 (3), e148-e157.
 -  Flaxman AD, Henning DJ and Duber HC (2020). [The relative incidence of COVID-19 in healthcare workers versus non-healthcare workers: evidence from a web-based survey of Facebook users in the United States](https://doi.org/10.12688/gatesopenres.13202.1). *Gates Open Research*, 4:174.
-- Kreuter, F., Barkay, N., Bilinski, A., Bradford, A., Chiu, S., Eliat, R., Fan, J., Galili, T., Haimovich, D., Kim, B., LaRocca, S., Li, Y., Morris, K., Presser, S., Sarig, T., Salomon, J. A., Stewart, K., Stuart, E. A., & Tibshirani, R. J. (2020). [Partnering with a global platform to inform research and public policy making](https://doi.org/10.18148/srm/2020.v14i2.7761). *Survey Research Methods*, 14(2), 159-163.
+- Kreuter, F., Barkay, N., Bilinski, A., Bradford, A., Chiu, S., Eliat, R., Fan, J., Galili, T., Haimovich, D., Kim, B., LaRocca, S., Li, Y., Morris, K., Presser, S., Sarig, T., Salomon, J. A., Stewart, K., Stuart, E. A., & Tibshirani, R. J. (2020). [Partnering with a global platform to inform research and public policy making](https://doi.org/10.18148/srm/2020.v14i2.7761). *Survey Research Methods*, 14 (2), 159-163.
 
 If you have used the survey data, or the aggregate data available in the COVIDcast API, to publish research results, please [contact us](#who-can-i-contact) so we can include your work here.
 

content/epivis/_index.md

@@ -0,0 +1,8 @@
+---
+title: EPIVis
+description: EpiVis is an interactive tool for visualizing epidemiological time-series data.
+layout: epivis_app
+order: 1
+feedback: true
+footer: false
+---

content/tools/epivis.md

@@ -1,6 +1,6 @@
 ---
 title: EpiVis
-link: https://delphi.cmu.edu/epivis/epivis.html
+link: /epivis/
 order: 1
 ---
 

dependencies.R

@@ -3,6 +3,7 @@
 
 # blogdown::install_hugo()
 
-devtools::install_github("cmu-delphi/covidcast", ref = "main",
-                         upgrade = 'never', 
-                         subdir = "R-packages/covidcast")
+install.packages("covidcast", repo="http://cran.rstudio.com/")
+# devtools::install_github("cmu-delphi/covidcast", ref = "main",
+#                          upgrade = 'never',
+#                          subdir = "R-packages/covidcast")