diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 000000000..d992b0ffa --- /dev/null +++ b/.dockerignore @@ -0,0 +1,2 @@ +node_modules +.git \ No newline at end of file diff --git a/.github/workflows/ci_fast.yaml b/.github/workflows/ci_fast.yaml index e1d1948ea..8a635fa9f 100644 --- a/.github/workflows/ci_fast.yaml +++ b/.github/workflows/ci_fast.yaml @@ -35,3 +35,39 @@ jobs: with: name: website path: ./public + + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@v1 + with: + aws-access-key-id: ${{ secrets.DELPHI_ECR_ACCESS_ID }} + aws-secret-access-key: ${{ secrets.DELPHI_ECR_ACCESS_KEY }} + aws-region: us-east-1 + + - name: Login to Amazon ECR + id: login-ecr + uses: aws-actions/amazon-ecr-login@v1 + + - name: Build, tag, and push image to Amazon ECR + env: + ECR_REGISTRY: ${{ steps.login-ecr.outputs.registry }} + ECR_REPOSITORY: ${{ github.event.repository.name }} + run: | + baseRef="${GITHUB_REF#*/}" + baseRef="${baseRef#*/}" + case "${baseRef}" in + main) + awsTag="latest" + ;; + *) + awsTag="${baseRef//\//_}" # replace `/` with `_` in branch name + ;; + esac + echo "using tag: --${awsTag}--" + docker build -t $ECR_REGISTRY/$ECR_REPOSITORY:$awsTag --file ./devops/precompiled/Dockerfile . + docker push $ECR_REGISTRY/$ECR_REPOSITORY:$awsTag + + # trigger a webhook update + curl -H "Authorization: Bearer ${{ secrets.DELPHI_DEPLOY_WEBHOOK_TOKEN }}" \ + -X POST ${{ secrets.DELPHI_DEPLOY_WEBHOOK_URL }} \ + -H "Content-Type: application/x-www-form-urlencoded" \ + -d "repository=$ECR_REGISTRY/$ECR_REPOSITORY&tag=$awsTag" diff --git a/.prettierignore b/.prettierignore index 80f9e07c5..74222a5af 100644 --- a/.prettierignore +++ b/.prettierignore @@ -24,7 +24,9 @@ *.woff2 *.R *.xml +.dockerignore *.Rmd *.md *.jpeg -*.ico \ No newline at end of file +*.ico +/themes/delphi/layouts/partials/webp-image.html \ No newline at end of file diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 9c9d16d61..000000000 --- a/Dockerfile +++ /dev/null @@ -1,8 +0,0 @@ -FROM continuumio/miniconda - -ADD ./environment.yml . -RUN conda env create -f environment.yml - -ADD ./dependencies.R . - -RUN conda run -n www-main Rscript ./dependencies.R \ No newline at end of file diff --git a/config.toml b/config.toml index ddacf6f18..91cf26117 100644 --- a/config.toml +++ b/config.toml @@ -46,16 +46,21 @@ relativeURLs = false name = "Surveys" url = "/covidcast/surveys" weight = 2 +[[menu.main]] + parent = "covidcast" + name = "Survey Results" + url = "/covidcast/survey-results" + weight = 3 [[menu.main]] parent = "covidcast" name = "Release Log" url = "/covidcast/release-log" - weight = 3 + weight = 4 [[menu.main]] parent = "covidcast" name = "Terms Of Use" url = "/covidcast/terms-of-use" - weight = 4 + weight = 5 [[menu.main]] identifier = "flu" name = "Flu and Other Diseases" @@ -83,6 +88,6 @@ relativeURLs = false [params] description = "Developing the Theory and Practice of Epidemiological Forecasting" - mission = "Develop the theory and practice of epidemiological forecasting, with a long-term vision of seeing this technology become as universally accepted and useful as weather forecasting is today." + 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" diff --git a/content/_index.md b/content/_index.md index 5f36b8ff8..3e741f837 100644 --- a/content/_index.md +++ b/content/_index.md @@ -4,19 +4,24 @@ description: Developing the Theory and Practice of Epidemiological Forecasting layout: landing carousel: + - pre: Our Tools + title: National COVID Survey Dashboard + ref: covidcast/survey-results + alt: Explore the Survey Results + image: covidcast_survey.jpg - pre: Our Tools title: Real-time Indicators of COVID-19 Activity ref: covidcast alt: Explore COVIDCast - image: covidcast_withfill.png + image: covidcast_withfill.jpg - pre: Our Blog Post title: New and improved COVID Symptom Survey Tracks Testing and Mask-Wearing ref: 2020-10-06-survey-wave-4 alt: Learn more - image: landing-pg_hero-img-2_New and Improved COVID Symptom Survey Tracks Testing and Mask-Wearing.png + image: landing-pg_hero-img-2_New and Improved COVID Symptom Survey Tracks Testing and Mask-Wearing.jpg - pre: Our Research and White Papers title: "Pancasting: forecasting epidemics from provisional data" link: https://delphi.cmu.edu/~lcbrooks/brooks2020pancasting.pdf alt: View Paper - image: landing-pg_hero-img-2_Pancasting_ forecasting epidemics from provisional data.png + image: landing-pg_hero-img-2_Pancasting_ forecasting epidemics from provisional data.jpg --- diff --git a/content/about/publications/images/evaluation.jpg b/content/about/publications/images/evaluation.jpg new file mode 100644 index 000000000..36ee42d10 Binary files /dev/null and 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b/content/about/publications/images/pancasting.jpg new file mode 100644 index 000000000..5b4a4b968 Binary files /dev/null and b/content/about/publications/images/pancasting.jpg differ diff --git a/content/about/publications/images/pancasting.png b/content/about/publications/images/pancasting.png deleted file mode 100644 index 2a4af5481..000000000 Binary files a/content/about/publications/images/pancasting.png and /dev/null differ diff --git a/content/about/publications/images/predicting.jpg b/content/about/publications/images/predicting.jpg new file mode 100644 index 000000000..ac3a09f4c Binary files /dev/null and b/content/about/publications/images/predicting.jpg differ diff --git a/content/about/publications/images/predicting.png b/content/about/publications/images/predicting.png deleted file mode 100644 index c25b5edd0..000000000 Binary files a/content/about/publications/images/predicting.png and /dev/null differ diff --git a/content/about/publications/index.md b/content/about/publications/index.md index 2ba78888b..d3a133b5a 100644 --- a/content/about/publications/index.md +++ b/content/about/publications/index.md @@ -2,49 +2,49 @@ title: Research and White Papers papers: - title: "Pancasting: forecasting epidemics from provisional data" - image: pancasting.png + image: pancasting.jpg authors: Brooks link: https://delphi.cmu.edu/~lcbrooks/brooks2020pancasting.pdf journal: PhD thesis year: 2020 - title: "Kalman filter, sensor fusion, and constrained regression: equivalences and insights" - image: kalman_filter.png + image: kalman_filter.jpg authors: Jahja, Farrow, Rosenfeld, Tibshirani link: https://papers.nips.cc/paper/9475-kalman-filter-sensor-fusion-and-constrained-regression-equivalences-and-insights journal: Neural Information Processing Systems year: 2019 - title: "Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions" - image: nonmechanistic_forecasts.png + image: nonmechanistic_forecasts.jpg authors: Brooks, Farrow, Hyun, Tibshirani, Rosenfeld link: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006134 journal: PLOS Computational Biology year: 2018 - title: "A human judgment approach to epidemiological forecasting" - image: human.png + image: human.jpg authors: Farrow, Brooks, Hyun, Tibshirani, Burke, Rosenfeld link: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005248 journal: PLOS Computational Biology year: 2017 - title: "Modeling the past, present, and future of influenza" - image: modeling.png + image: modeling.jpg authors: Farrow link: https://delphi.cmu.edu/~dfarrow/thesis.pdf journal: PhD thesis year: 2016 - title: "Flexible modeling of epidemics with an empirical Bayes framework" - image: flexible_modeling.png + image: flexible_modeling.jpg authors: Brooks, Farrow, Hyun, Tibshirani, Rosenfeld link: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004382 journal: PLOS Computational Biology year: 2015 - title: "Predicting the predictable" - image: predicting.png + image: predicting.jpg authors: Rosenfeld link: https://delphi.cmu.edu/files/PredictingThePredictable_13-04-03.pdf journal: presentation year: 2013 - title: "A proposal for standardized evaluation of epidemiological models" - image: evaluation.png + image: evaluation.jpg authors: Rosenfeld, Grefenstette, Burke link: http://www.cs.cmu.edu/~roni/standardized-evaluation-of-epi-models-rev-09nov2012.pdf journal: White paper diff --git a/content/about/team/images/lee-kenneth.png b/content/about/team/images/lee-kenneth.png new file mode 100644 index 000000000..7af93c171 Binary files /dev/null and b/content/about/team/images/lee-kenneth.png differ diff --git a/content/about/team/index.md b/content/about/team/index.md index ca73255f1..c6cbc99e2 100644 --- a/content/about/team/index.md +++ b/content/about/team/index.md @@ -235,8 +235,8 @@ team: note: Intern, Summer 2020 - firstName: Kenneth lastName: Lee - image: profile-placeholder.png - affiliation: + image: lee-kenneth.png + affiliation: UC Davis team: - contributors - firstName: Natalia diff --git a/content/blog/2015-07-23-template-post.Rmd b/content/blog/2015-07-23-template-post.Rmd index ba4887db3..c44aa5852 100644 --- a/content/blog/2015-07-23-template-post.Rmd +++ b/content/blog/2015-07-23-template-post.Rmd @@ -9,8 +9,8 @@ tags: draft: true # remove this line in new blog posts authors: # list of author keys, see /data/authors.yaml - frida -heroImage: /blog/images/blog-lg-img_hello-world.png -heroImageThumb: /blog/images/blog-thumb-img_hello-world.png +heroImage: /blog/images/blog-lg-img_hello-world.jpg +heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg summary: | Blog summary, the first 150 characters are used for the blog list acknowledgements: | diff --git a/content/blog/2015-07-23-template-post.html b/content/blog/2015-07-23-template-post.html index 03936f4cc..19cc04435 100644 --- a/content/blog/2015-07-23-template-post.html +++ b/content/blog/2015-07-23-template-post.html @@ -9,8 +9,8 @@ draft: true # remove this line in new blog posts authors: # list of author keys, see /data/authors.yaml - frida -heroImage: /blog/images/blog-lg-img_hello-world.png -heroImageThumb: /blog/images/blog-thumb-img_hello-world.png +heroImage: /blog/images/blog-lg-img_hello-world.jpg +heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg summary: | Blog summary, the first 150 characters are used for the blog list acknowledgements: | @@ -49,21 +49,21 @@ see http://rmarkdown.rstudio.com.

You can embed an R code chunk like this:

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 <- lm(dist ~ speed, data = cars)
 fit
-## 
+##
 ## Call:
 ## lm(formula = dist ~ speed, data = cars)
-## 
+##
 ## Coefficients:
-## (Intercept)        speed  
+## (Intercept)        speed
 ##     -17.579        3.932

Including Plots

diff --git a/content/blog/2020-08-10-hello-world.Rmd b/content/blog/2020-08-10-hello-world.Rmd index 31d12e6b7..572115a12 100644 --- a/content/blog/2020-08-10-hello-world.Rmd +++ b/content/blog/2020-08-10-hello-world.Rmd @@ -7,8 +7,8 @@ tags: authors: - roni - ryan -heroImage: /blog/images/blog-lg-img_hello-world.png -heroImageThumb: /blog/images/blog-thumb-img_hello-world.png +heroImage: /blog/images/blog-lg-img_hello-world.jpg +heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg summary: | Hello from the Delphi research group at Carnegie Mellon University! We're a group of faculty, students, and staff, based primarily out of CMU diff --git a/content/blog/2020-08-10-hello-world.html b/content/blog/2020-08-10-hello-world.html index bca6020a8..f683c0b12 100644 --- a/content/blog/2020-08-10-hello-world.html +++ b/content/blog/2020-08-10-hello-world.html @@ -7,18 +7,18 @@ authors: - roni - ryan -heroImage: /blog/images/blog-lg-img_hello-world.png -heroImageThumb: /blog/images/blog-thumb-img_hello-world.png +heroImage: /blog/images/blog-lg-img_hello-world.jpg +heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg summary: | 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: diff --git a/content/blog/2020-08-26-fb-survey.Rmd b/content/blog/2020-08-26-fb-survey.Rmd index 01082460b..cf7ca4e82 100644 --- a/content/blog/2020-08-26-fb-survey.Rmd +++ b/content/blog/2020-08-26-fb-survey.Rmd @@ -9,8 +9,8 @@ tags: authors: - alex - ryan -heroImage: /blog/images/blog-lg-img_facebook-survey-post.png -heroImageThumb: /blog/images/blog-thumb-img_facebook-survey-post.png +heroImage: /blog/images/blog-lg-img_facebook-survey-post.jpg +heroImageThumb: /blog/images/blog-thumb-img_facebook-survey-post.jpg summary: | Since April 2020, in collaboration with Facebook, partner universities, and public health officials, diff --git a/content/blog/2020-08-26-fb-survey.html b/content/blog/2020-08-26-fb-survey.html index 3138a7e7a..cd2bdc214 100644 --- a/content/blog/2020-08-26-fb-survey.html +++ b/content/blog/2020-08-26-fb-survey.html @@ -9,8 +9,8 @@ authors: - alex - ryan -heroImage: /blog/images/blog-lg-img_facebook-survey-post.png -heroImageThumb: /blog/images/blog-thumb-img_facebook-survey-post.png +heroImage: /blog/images/blog-lg-img_facebook-survey-post.jpg +heroImageThumb: /blog/images/blog-thumb-img_facebook-survey-post.jpg summary: | Since April 2020, in collaboration with Facebook, partner universities, and public health officials, @@ -36,7 +36,7 @@ survey data. The COVIDcast API, which serves these estimates and is updated daily, is a much larger effort run by the Delphi group, and our entire engineering team is owed a lot of credit here. Ryan came up with the - idea of running the surveys, and worked with Facebook to make this a reality. + idea of running the surveys, and worked with Facebook to make this a reality. On the Facebook side, Curtiss Cobb and Jonathan McKay played big roles. The University of Maryland team, including Adrianne Bradford and Samantha Chiu and led by Frauke Kreuter, made many contributions to the survey design. diff --git a/content/blog/2020-08-28-api.Rmd b/content/blog/2020-08-28-api.Rmd index 4d8bc32f0..926f08767 100644 --- a/content/blog/2020-08-28-api.Rmd +++ b/content/blog/2020-08-28-api.Rmd @@ -10,8 +10,8 @@ tags: authors: - kathryn - alex -heroImage: /blog/images/blog-lg-img_Accessing Open COVID-19.png -heroImageThumb: /blog/images/blog-thumb-img_Accessing Open COVID-19.png +heroImage: /blog/images/blog-lg-img_Accessing Open COVID-19.jpg +heroImageThumb: /blog/images/blog-thumb-img_Accessing Open COVID-19.jpg summary: | One of our primary initiatives at the Delphi COVIDcast project has been to curate a diverse set of COVID-related data streams, diff --git a/content/blog/2020-08-28-api.html b/content/blog/2020-08-28-api.html index 8f3c6d8a4..8fa1a3ee2 100644 --- a/content/blog/2020-08-28-api.html +++ b/content/blog/2020-08-28-api.html @@ -10,8 +10,8 @@ authors: - kathryn - alex -heroImage: /blog/images/blog-lg-img_Accessing Open COVID-19.png -heroImageThumb: /blog/images/blog-thumb-img_Accessing Open COVID-19.png +heroImage: /blog/images/blog-lg-img_Accessing Open COVID-19.jpg +heroImageThumb: /blog/images/blog-thumb-img_Accessing Open COVID-19.jpg summary: | One of our primary initiatives at the Delphi COVIDcast project has been to curate a diverse set of COVID-related data streams, diff --git a/content/blog/2020-09-18-google-survey.Rmd b/content/blog/2020-09-18-google-survey.Rmd index 86b22e618..ea565b0ca 100644 --- a/content/blog/2020-09-18-google-survey.Rmd +++ b/content/blog/2020-09-18-google-survey.Rmd @@ -8,8 +8,8 @@ tags: - R authors: - ryan -heroImage: /blog/images/blog-lg-img_google-survey-post.png -heroImageThumb: /blog/images/blog-thumb-img_google-survey-post.png +heroImage: /blog/images/blog-lg-img_google-survey-post.jpg +heroImageThumb: /blog/images/blog-thumb-img_google-survey-post.jpg summary: | Since April 2020, in addition to our massive daily survey advertised on Facebook, we've been running (even-more-massive) surveys through Google to diff --git a/content/blog/2020-09-18-google-survey.html b/content/blog/2020-09-18-google-survey.html index 83520de30..a58fca1bc 100644 --- a/content/blog/2020-09-18-google-survey.html +++ b/content/blog/2020-09-18-google-survey.html @@ -8,30 +8,30 @@ - R authors: - ryan -heroImage: /blog/images/blog-lg-img_google-survey-post.png -heroImageThumb: /blog/images/blog-thumb-img_google-survey-post.png +heroImage: /blog/images/blog-lg-img_google-survey-post.jpg +heroImageThumb: /blog/images/blog-thumb-img_google-survey-post.jpg summary: | - Since April 2020, in addition to our massive daily survey advertised on - Facebook, we've been running (even-more-massive) surveys through Google to - track the spread of COVID-19 in the United States. - At its peak, our Google survey was taken by over 1.2 million people in a single - day, and over its first month in operation, averaged over 600,000 daily - respondents. In mid-May, we paused daily dissemination of this survey in order + Since April 2020, in addition to our massive daily survey advertised on + Facebook, we've been running (even-more-massive) surveys through Google to + track the spread of COVID-19 in the United States. + At its peak, our Google survey was taken by over 1.2 million people in a single + day, and over its first month in operation, averaged over 600,000 daily + respondents. In mid-May, we paused daily dissemination of this survey in order to focus on our (longer, more complex) survey through Facebook, - but we plan to bring back the Google survey this fall. - This short post covers some key differences between our Google and Facebook + but we plan to bring back the Google survey this fall. + This short post covers some key differences between our Google and Facebook surveys, explains the backstory behind the "CLI-in-community" question - as it arose through our collaboration with Google, + as it arose through our collaboration with Google, and shares some of our thinking about next steps for the Google survey. acknowledgements: | - Ryan Tibshirani wrote the initial code for producing - estimates from the aggregated survey data. Sangwon Hyun, Natalia Lombardi de + Ryan Tibshirani wrote the initial code for producing + estimates from the aggregated survey data. Sangwon Hyun, Natalia Lombardi de Oliveira, and Lester Mackey greatly extended and improved this codebase, and - they developed, along with Ryan, the underlying statistical methodology. Ryan - came up with the idea of running the surveys, and worked with Google to make - this a reality. On the Google side, Brett Slatkin and Hal Varian have been key - collaborators; Brett wrote the code to get daily survey data over to Delphi's - estimation pipeline; and both contributed numerous important ideas at various + they developed, along with Ryan, the underlying statistical methodology. Ryan + came up with the idea of running the surveys, and worked with Google to make + this a reality. On the Google side, Brett Slatkin and Hal Varian have been key + collaborators; Brett wrote the code to get daily survey data over to Delphi's + estimation pipeline; and both contributed numerous important ideas at various stages of the project. output: html_document: diff --git a/content/blog/2020-09-21-forecast-demo.Rmd b/content/blog/2020-09-21-forecast-demo.Rmd index e360aa9e3..d10b13a81 100644 --- a/content/blog/2020-09-21-forecast-demo.Rmd +++ b/content/blog/2020-09-21-forecast-demo.Rmd @@ -9,8 +9,8 @@ tags: - R authors: - ryan -heroImage: /blog/images/blog-Lg-img_can symptoms surveys improve covid-19.png -heroImageThumb: /blog/images/blog-thumbnail_can symptoms surveys improve covid-19.png +heroImage: /blog/images/blog-Lg-img_can symptoms surveys improve covid-19.jpg +heroImageThumb: /blog/images/blog-thumbnail_can symptoms surveys improve covid-19.jpg summary: | Building on our previous two posts (on our COVID-19 symptom surveys through Facebook and Google) diff --git a/content/blog/2020-09-21-forecast-demo.html b/content/blog/2020-09-21-forecast-demo.html index defcebb63..632638cf3 100644 --- a/content/blog/2020-09-21-forecast-demo.html +++ b/content/blog/2020-09-21-forecast-demo.html @@ -9,19 +9,19 @@ - R authors: - ryan -heroImage: /blog/images/blog-Lg-img_can symptoms surveys improve covid-19.png -heroImageThumb: /blog/images/blog-thumbnail_can symptoms surveys improve covid-19.png +heroImage: /blog/images/blog-Lg-img_can symptoms surveys improve covid-19.jpg +heroImageThumb: /blog/images/blog-thumbnail_can symptoms surveys improve covid-19.jpg 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 @@ -217,17 +217,17 @@

Forecasting Code

as.Date(max(time_value)), by = "day")) %>% ungroup() df = full_join(df, df_all, by = c("geo_value", "time_value")) - + # Group by geo value, sort rows by increasing time - df = df %>% group_by(geo_value) %>% arrange(time_value) - + df = df %>% group_by(geo_value) %>% arrange(time_value) + # Load over shifts, and add lag value or lead value for (shift in shifts) { fun = ifelse(shift < 0, lag, lead) varname = sprintf("value%+d", shift) df = mutate(df, !!varname := fun(value, n = abs(shift))) } - + # Ungroup and return return(ungroup(df)) } @@ -261,40 +261,40 @@

Forecasting Code

case_num = 200 geo_values = covidcast_signal("jhu-csse", "confirmed_cumulative_num", "2020-05-14", "2020-05-14") %>% - filter(value >= case_num) %>% pull(geo_value) + filter(value >= case_num) %>% pull(geo_value) # Fetch county-level Google and Facebook % CLI-in-community signals, and JHU # confirmed case incidence proportion start_day = "2020-04-11" end_day = "2020-09-01" g = covidcast_signal("google-survey", "smoothed_cli") %>% - filter(geo_value %in% geo_values) %>% - select(geo_value, time_value, value) -f = covidcast_signal("fb-survey", "smoothed_hh_cmnty_cli", + filter(geo_value %in% geo_values) %>% + select(geo_value, time_value, value) +f = covidcast_signal("fb-survey", "smoothed_hh_cmnty_cli", start_day, end_day) %>% - filter(geo_value %in% geo_values) %>% - select(geo_value, time_value, value) + filter(geo_value %in% geo_values) %>% + select(geo_value, time_value, value) c = covidcast_signal("jhu-csse", "confirmed_7dav_incidence_prop", start_day, end_day) %>% - filter(geo_value %in% geo_values) %>% + filter(geo_value %in% geo_values) %>% select(geo_value, time_value, value) -# Find "complete" counties, present in all three data signals at all times +# Find "complete" 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 %>% filter(geo_value %in% geo_values_complete) %>% - mutate(value = trans(value * rescale_g)) %>% - append_shifts(shifts = lags) -f = f %>% filter(geo_value %in% geo_values_complete) %>% - mutate(value = trans(value * rescale_f)) %>% - append_shifts(shifts = lags) +g = g %>% filter(geo_value %in% geo_values_complete) %>% + mutate(value = trans(value * rescale_g)) %>% + append_shifts(shifts = lags) +f = f %>% filter(geo_value %in% geo_values_complete) %>% + mutate(value = trans(value * rescale_f)) %>% + append_shifts(shifts = lags) c = c %>% filter(geo_value %in% geo_values_complete) %>% - mutate(value = trans(value * rescale_c)) %>% + mutate(value = trans(value * rescale_c)) %>% append_shifts(shifts = c(lags, leads)) # Rename columns @@ -310,47 +310,47 @@

Forecasting Code

# 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("list", 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("***", lead, "***\n") - + # 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 %>% - 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 %>% + filter(between(time_value, as.Date(start_day) - min(lags) + lead, as.Date(end_day) - lead)) %>% select(geo_value, time_value) %>% - 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]]$time_value) - + for (k in 1:length(valid_dates)) { date = valid_dates[k]; if (verbose) cat(format(date), "... ") - + # Filter down to training set and test set z_tr = z %>% filter(between(time_value, date - lead - n, date - lead)) z_te = z %>% filter(time_value == date) inds = which(res_list[[i]]$time_value == date) - + # Create training and test responses y_tr = z_tr %>% pull(paste0("case+", lead)) y_te = z_te %>% pull(paste0("case+", lead)) - + # Strawman model if (verbose) cat("0") y_hat = z_te %>% pull(case) res_list[[i]][inds,]$err0 = abs(inv_trans(y_hat) - inv_trans(y_te)) - + # Cases only model if (verbose) cat("1") x_tr_case = z_tr %>% select(starts_with("case") & !contains("+")) x_te_case = z_te %>% select(starts_with("case") & !contains("+")) - 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) > 0) { obj = quantile_lasso(as.matrix(x_tr[ok,]), y_tr[ok], tau = 0.5, @@ -358,7 +358,7 @@

Forecasting Code

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("2") x_tr_fb = z_tr %>% select(starts_with("fb")) @@ -386,7 +386,7 @@

Forecasting Code

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("4\n") x_tr = cbind(x_tr_case, x_tr_fb, x_tr_goog) @@ -401,7 +401,7 @@

Forecasting Code

} } -# 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 = "demo.rda")
diff --git a/content/blog/2020-10-06-survey-wave-4.Rmd b/content/blog/2020-10-06-survey-wave-4.Rmd index 4878617ec..ad8ea7d5f 100644 --- a/content/blog/2020-10-06-survey-wave-4.Rmd +++ b/content/blog/2020-10-06-survey-wave-4.Rmd @@ -12,8 +12,8 @@ summary: | Today we release new public datasets and share maps revealing access to COVID testing, test results, and public use of masks. authors: - alex -heroImage: /blog/images/blog-lg-img_New and Improved COVID.png -heroImageThumb: /blog/images/blog-thumb-img_New and Improved COVID.png +heroImage: /blog/images/blog-lg-img_New and Improved COVID.jpg +heroImageThumb: /blog/images/blog-thumb-img_New and Improved COVID.jpg acknowledgements: | Many items in Wave 4 of our survey are based on work by the team at the Joint Program in Survey Methodology at the University of diff --git a/content/blog/2020-10-06-survey-wave-4.html b/content/blog/2020-10-06-survey-wave-4.html index 9dd48f166..bea390eb1 100644 --- a/content/blog/2020-10-06-survey-wave-4.html +++ b/content/blog/2020-10-06-survey-wave-4.html @@ -7,13 +7,13 @@ - COVIDcast - R summary: | - Beginning on September 8, 2020, we deployed a new version of our symptom survey. - Facebook helps us recruit tens of thousands of respondents daily, and the new survey gives us unprecedented insights into the effects of COVID-19 across the United States. + Beginning on September 8, 2020, we deployed a new version of our symptom survey. + Facebook helps us recruit tens of thousands of respondents daily, and the new survey gives us unprecedented insights into the effects of COVID-19 across the United States. Today we release new public datasets and share maps revealing access to COVID testing, test results, and public use of masks. authors: - alex -heroImage: /blog/images/blog-lg-img_New and Improved COVID.png -heroImageThumb: /blog/images/blog-thumb-img_New and Improved COVID.png +heroImage: /blog/images/blog-lg-img_New and Improved COVID.jpg +heroImageThumb: /blog/images/blog-thumb-img_New and Improved COVID.jpg acknowledgements: | Many items in Wave 4 of our survey are based on work by the team at the Joint Program in Survey Methodology at the University of diff --git a/content/blog/2020-10-14-dv-signal.Rmd b/content/blog/2020-10-14-dv-signal.Rmd index 0abe6dd81..f5b4119ba 100644 --- a/content/blog/2020-10-14-dv-signal.Rmd +++ b/content/blog/2020-10-14-dv-signal.Rmd @@ -9,8 +9,8 @@ tags: authors: - aaron - roni -heroImage: /blog/images/blog-img_A Syndromic COVID-19.png -heroImageThumb: /blog/images/blog-thumb-img_A Syndromic COVID-19.png +heroImage: /blog/images/blog-img_A Syndromic COVID-19.jpg +heroImageThumb: /blog/images/blog-thumb-img_A Syndromic COVID-19.jpg related: - 2020-09-18-google-survey - 2020-08-26-fb-survey diff --git a/content/blog/2020-10-14-dv-signal.html b/content/blog/2020-10-14-dv-signal.html index 0eec260d0..deaebcd25 100644 --- a/content/blog/2020-10-14-dv-signal.html +++ b/content/blog/2020-10-14-dv-signal.html @@ -9,16 +9,16 @@ authors: - aaron - roni -heroImage: /blog/images/blog-img_A Syndromic COVID-19.png -heroImageThumb: /blog/images/blog-thumb-img_A Syndromic COVID-19.png +heroImage: /blog/images/blog-img_A Syndromic COVID-19.jpg +heroImageThumb: /blog/images/blog-thumb-img_A Syndromic COVID-19.jpg related: - 2020-09-18-google-survey - 2020-08-26-fb-survey summary: | In previous posts, we discussed our massive ongoing symptom surveys that have reached over 12 million people in the U.S. since April 2020, in partnership with Facebook and Google. Another one of our major data initiatives is based on partnerships with healthcare systems, granting us access to various aggregate statistics from hospital records and insurance claims covering 10-15% of the United States population. From these data, we can extract informative indicators that can be early indicators of COVID activity. This post focuses on one indicator in particular, based on outpatient visits, and demonstrates both the challenges and promises associated with medical records data. acknowledgements: | - Maria Jahja contributed immensely to every stage of this project, from determining which ICD codes to use to the final implementation of the indicator. - Aaron Rumack devised the weekday adjustment and analyzed the performance of the DV indicator. + Maria Jahja contributed immensely to every stage of this project, from determining which ICD codes to use to the final implementation of the indicator. + Aaron Rumack devised the weekday adjustment and analyzed the performance of the DV indicator. Roni Rosenfeld worked closely with our health systems partners to get access to the data and provided domain knowledge to ensure that the data was useful. Both Roni and Ryan Tibshirani provided helpful suggestions and insights towards the methodology and analysis. output: diff --git a/content/covidcast/_index.md b/content/covidcast/_index.md index d0e3e71b2..c3c2d7e58 100644 --- a/content/covidcast/_index.md +++ b/content/covidcast/_index.md @@ -1,4 +1,6 @@ --- -title: COVIDCast +title: COVIDcast layout: covidcast_app +description: COVIDcast tracks and forecasts the spread of COVID-19. By Carnegie Mellon's Delphi Research Group. +heroImage: /images/landing-page/hero-images/covidcast_withfill.jpg --- diff --git a/content/covidcast/export.md b/content/covidcast/export.md new file mode 100644 index 000000000..db607385d --- /dev/null +++ b/content/covidcast/export.md @@ -0,0 +1,7 @@ +--- +title: COVIDCast Export Data +linkTitle: Export Data +description: Use COVIDcast data in your own analysis +layout: covidcast_app +heroImage: /images/landing-page/hero-images/covidcast_withfill.jpg +--- diff --git a/content/covidcast/release-log/headless/v1.12.0.md b/content/covidcast/release-log/headless/v1.12.0.md new file mode 100644 index 000000000..40ac350de --- /dev/null +++ b/content/covidcast/release-log/headless/v1.12.0.md @@ -0,0 +1,27 @@ +--- +title: v1.12.0 +date: 2020-12-23 +--- + +This release introduces the new National COVID Survey Dashboard showing aggregated survey results. In addition, the overall style of COVIDCast has been adapted to the new website. + +#### New Features + +- [#600](https://github.com/cmu-delphi/www-covidcast/pull/600) National COVID Survey Dashboard +- [#688](https://github.com/cmu-delphi/www-covidcast/pull/688) (re: [#536](https://github.com/cmu-delphi/www-covidcast/issues/536)) Default ratio cases/deaths +- [#616](https://github.com/cmu-delphi/www-covidcast/pull/616), [#678](https://github.com/cmu-delphi/www-covidcast/pull/678) UIKit Adaptations +- [#692](https://github.com/cmu-delphi/www-covidcast/pull/692), [#671](https://github.com/cmu-delphi/www-covidcast/pull/671) (re: [#651](https://github.com/cmu-delphi/www-covidcast/issues/651)) Simplify URL parameters +- [#677](https://github.com/cmu-delphi/www-covidcast/pull/677) (re: [#632](https://github.com/cmu-delphi/www-covidcast/issues/632)) Compute mega counties (`Rest of ...`) population on the fly +- [#658](https://github.com/cmu-delphi/www-covidcast/pull/658) (re: [#485](https://github.com/cmu-delphi/www-covidcast/issues/485), [#639](https://github.com/cmu-delphi/www-covidcast/issues/639)) Additional export options + +#### Improvements + +- [#689](https://github.com/cmu-delphi/www-covidcast/pull/689) (re: [#687](https://github.com/cmu-delphi/www-covidcast/issues/687)) Change date shortcuts +- [#676](https://github.com/cmu-delphi/www-covidcast/pull/676) Improve Map Selection UX +- [#659](https://github.com/cmu-delphi/www-covidcast/pull/659) (re: [#656](https://github.com/cmu-delphi/www-covidcast/issues/656)) Shrink card header font size, adjust spacing. + +#### Bug-fixes + +- [#690](https://github.com/cmu-delphi/www-covidcast/pull/690) (re: [#686](https://github.com/cmu-delphi/www-covidcast/issues/686)) Add special case for old safari +- [#674](https://github.com/cmu-delphi/www-covidcast/pull/674) Refactor: use vega resize method +- [#666](https://github.com/cmu-delphi/www-covidcast/pull/666) (re: [#664](https://github.com/cmu-delphi/www-covidcast/issues/664), [#665](https://github.com/cmu-delphi/www-covidcast/issues/665)) Add HRR Population data and fix Orlando bug \ No newline at end of file diff --git a/content/covidcast/single.md b/content/covidcast/single.md new file mode 100644 index 000000000..23ad81bb1 --- /dev/null +++ b/content/covidcast/single.md @@ -0,0 +1,7 @@ +--- +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 +heroImage: /images/landing-page/hero-images/covidcast_withfill.jpg +--- diff --git a/content/covidcast/survey-results.md b/content/covidcast/survey-results.md new file mode 100644 index 000000000..b0f78bc9c --- /dev/null +++ b/content/covidcast/survey-results.md @@ -0,0 +1,8 @@ +--- +title: COVIDCast Survey Results +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 +heroImage: /images/landing-page/hero-images/covidcast_survey.jpg +--- diff --git a/content/covidcast/surveys.md b/content/covidcast/surveys.md index 832ab7616..63cd975d1 100644 --- a/content/covidcast/surveys.md +++ b/content/covidcast/surveys.md @@ -2,7 +2,11 @@ title: Delphi's COVID-19 Surveys --- -In collaboration with Facebook, along with a consortium of universities and public health officials, the [Delphi group]({{< relref "/" >}}) at [Carnegie Mellon University](https://www.cmu.edu/) 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, and about 50,000 people in the United States participate **every day**. Survey results are publicly available on our [COVIDcast map]({{< relref "covidcast" >}}) and in our [COVIDcast API]({{< apiref "api/covidcast.html" >}}). +{{< alert category="primary">}} + Summary results for the survey are now available. [Click here to explore]({{< relref "covidcast/survey-results" >}}) +{{< /alert >}} + +In collaboration with Facebook, along with a consortium of universities and public health officials, the [Delphi group]({{< relref "/" >}}) at [Carnegie Mellon University](https://www.cmu.edu/) 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, and about 50,000 people in the United States participate **every day**. Survey results are publicly available on our [National COVID Survey Dashboard]({{< relref "covidcast/survey-results" >}}), [COVIDcast Map]({{< relref "covidcast" >}}), [COVIDcast Exporter]({{< relref "covidcast/export" >}}), and in our [COVIDcast API]({{< apiref "api/covidcast.html" >}}). Such detailed data has never before been available during a public health emergency, and it will help public health officials understand how to save lives and how to safely reopen public life. The data will also help researchers understand the social, economic, and health effects of the COVID-19 pandemic. @@ -14,7 +18,7 @@ The [Symptom Data Challenge](https://www.symptomchallenge.org/) challenged parti The survey asks respondents whether they are experiencing any symptoms, then asks a series of questions designed to help researchers understand the spread of COVID-19 and its effect on people in the United States. These include questions about COVID-19 testing, prior medical conditions, social distancing measures, mental health, demographics, and the economic effects of the pandemic. -Delphi uses information from the survey as part of its public [COVIDcast map]({{< relref "covidcast" >}}), to inform its forecasts (currently in development) of the pandemic’s spread, and to assist public health agency partners. By providing daily data from all parts of the United States, the survey allows comparisons between regions and allows careful tracking of changes over time. Other researchers use the survey to study factors related to the pandemic's spread, its effects on mental health, how different demographic groups are affected by the pandemic, and numerous other important questions. +Delphi uses information from the survey as part of its public [COVIDcast Map]({{< relref "covidcast" >}}), to inform its forecasts (currently in development) of the pandemic’s spread, and to assist public health agency partners. By providing daily data from all parts of the United States, the survey allows comparisons between regions and allows careful tracking of changes over time. Other researchers use the survey to study factors related to the pandemic's spread, its effects on mental health, how different demographic groups are affected by the pandemic, and numerous other important questions. Because the survey can reach thousands of respondents every day, its questions focus on what the respondents are experiencing right now. This allows us to track how conditions change across the country every day. @@ -34,7 +38,7 @@ To account for the differences between Facebook users and the United States popu ## Where can I see the results? -Our [COVIDcast map]({{< relref "covidcast" >}}) shows basic aggregate survey results, revealing the rates of mask usage and COVID-like symptoms across the United States, and this data is also freely available for download through the [COVIDcast API]({{< apiref "api/covidcast.html">}}). Facebook also publishes [a map](https://covid-survey.dataforgood.fb.com/) based on the United States and international aggregate data. +Our [National COVID Survey Dashboard]({{< relref "covidcast/survey-results" >}}) shows aggregate survey results, ranging from rates of COVID-like symptoms over mask usage to mental health. In addition, our [COVIDcast map]({{< relref "covidcast" >}}) shows basic aggregate survey results, revealing the rates of mask usage and COVID-like symptoms across the United States. The data used by both tools is also freely available for download through the [COVIDcast API]({{< apiref "api/covidcast.html">}}) and our [COVIDcast Exporter]({{< relref "covidcast/export" >}}). Facebook also publishes [a map](https://covid-survey.dataforgood.fb.com/) based on the United States and international aggregate data. ### Blog posts and presentations diff --git a/content/covidcast/timelapse.md b/content/covidcast/timelapse.md new file mode 100644 index 000000000..8710382d4 --- /dev/null +++ b/content/covidcast/timelapse.md @@ -0,0 +1,7 @@ +--- +title: COVIDCast Timelapse +linkTitle: Timelapse +description: COVIDcast tracks and forecasts the spread of COVID-19. By Carnegie Mellon's Delphi Research Group. +layout: covidcast_app +heroImage: /images/landing-page/hero-images/covidcast_withfill.jpg +--- diff --git a/content/covidcast/top10.md b/content/covidcast/top10.md new file mode 100644 index 000000000..881909044 --- /dev/null +++ b/content/covidcast/top10.md @@ -0,0 +1,7 @@ +--- +title: COVIDCast Top 10 +linkTitle: Top 10 +description: COVIDcast tracks and forecasts the spread of COVID-19. By Carnegie Mellon's Delphi Research Group. +layout: covidcast_app +heroImage: /images/landing-page/hero-images/covidcast_withfill.jpg +--- diff --git a/data/authors.yaml b/data/authors.yaml index efbbdac39..da08074f5 100644 --- a/data/authors.yaml +++ b/data/authors.yaml @@ -17,6 +17,7 @@ name: Alex Reinhart link: https://www.refsmmat.com description: manages Delphi's surveys, and is an Assistant Teaching Professor in the Department of Statistics & Data Science at CMU. + twitter: capnrefsmmat - key: kathryn name: Kathryn Mazaitis link: https://cs.cmu.edu/~krivard diff --git a/devops/Dockerfile b/devops/Dockerfile new file mode 100644 index 000000000..55d62c461 --- /dev/null +++ b/devops/Dockerfile @@ -0,0 +1,11 @@ +# docker image building and packaging the website +FROM node:lts-buster AS builder +WORKDIR /src +COPY . ./ +RUN npm ci --unsafe-perm +RUN npm run build + +FROM nginx:stable-alpine +COPY --from=builder /src/public /usr/share/nginx/html +# ensure files are readable at runtime +RUN chmod o+r -R /usr/share/nginx/html/ \ No newline at end of file diff --git a/devops/precompiled/Dockerfile b/devops/precompiled/Dockerfile new file mode 100644 index 000000000..bb229551a --- /dev/null +++ b/devops/precompiled/Dockerfile @@ -0,0 +1,6 @@ +# docker image using the current built website +FROM nginx:stable-alpine + +COPY ./public /usr/share/nginx/html +# ensure files are readable at runtime +RUN chmod o+r -R /usr/share/nginx/html/ \ No newline at end of file diff --git a/devops/r/Dockerfile b/devops/r/Dockerfile new file mode 100644 index 000000000..04e2d7e8a --- /dev/null +++ b/devops/r/Dockerfile @@ -0,0 +1,11 @@ +# docker image for setting up an R environment +FROM continuumio/miniconda + +ADD ./environment.yml . +RUN conda env create -f environment.yml + +ADD ./dependencies.R . + +RUN conda run -n www-main Rscript ./dependencies.R + +ENV PATH /opt/conda/envs/www-main/bin:$PATH \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index ad2448947..fe0ce77bb 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -3,13 +3,14 @@ version: "3.1" # docker services for R environment and Hugo runner services: r: - build: "." + build: + context: . + dockerfile: devops/r/Dockerfile working_dir: "/app" command: tail -F anything volumes: - "./:/app" # run: docker-compose exec r bash - # conda activate www-main # Rscript -e 'blogdown::build_site(run_hugo=FALSE, build_rmd=TRUE)' # see https://github.com/peaceiris/hugo-extended-docker diff --git a/package-lock.json b/package-lock.json index 6cc9ddb3c..952dc3d5e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "www-main", - "version": "0.1.0", + "version": "1.12.0", "lockfileVersion": 1, "requires": true, "dependencies": { @@ -95,6 +95,59 @@ "color-convert": "^1.9.0" } }, + "anymatch": { + "version": "1.3.2", + "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-1.3.2.tgz", + "integrity": "sha512-0XNayC8lTHQ2OI8aljNCN3sSx6hsr/1+rlcDAotXJR7C1oZZHCNsfpbKwMjRA3Uqb5tF1Rae2oloTr4xpq+WjA==", + "dev": true, + "requires": { + "micromatch": "^2.1.5", + "normalize-path": "^2.0.0" + }, + "dependencies": { + "braces": { + "version": "1.8.5", + "resolved": "https://registry.npmjs.org/braces/-/braces-1.8.5.tgz", + "integrity": "sha1-uneWLhLf+WnWt2cR6RS3N4V79qc=", + "dev": true, + "requires": { + "expand-range": "^1.8.1", + "preserve": "^0.2.0", + "repeat-element": "^1.1.2" + } + }, + "micromatch": { + "version": "2.3.11", + "resolved": "https://registry.npmjs.org/micromatch/-/micromatch-2.3.11.tgz", + "integrity": "sha1-hmd8l9FyCzY0MdBNDRUpO9OMFWU=", + "dev": true, + "requires": { + "arr-diff": "^2.0.0", + "array-unique": "^0.2.1", + "braces": "^1.8.2", + "expand-brackets": "^0.1.4", + "extglob": "^0.3.1", + "filename-regex": "^2.0.0", + "is-extglob": "^1.0.0", + "is-glob": "^2.0.1", + "kind-of": "^3.0.2", + "normalize-path": "^2.0.1", + "object.omit": "^2.0.0", + "parse-glob": 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b36fbab81..000000000 Binary files a/static/images/supporters/about/tai-s-captures-0I52FCHNjoU-unsplash.jpg and /dev/null differ diff --git a/static/images/supporters/about/zane-lee-IHj0xtWtLKE-unsplash.jpg b/static/images/supporters/about/zane-lee-IHj0xtWtLKE-unsplash.jpg deleted file mode 100644 index 628c3697f..000000000 Binary files a/static/images/supporters/about/zane-lee-IHj0xtWtLKE-unsplash.jpg and /dev/null differ diff --git a/themes/delphi/assets/css/components/_card_grid.scss b/themes/delphi/assets/css/components/_card_grid.scss index 170fce8bb..5ec421bec 100644 --- a/themes/delphi/assets/css/components/_card_grid.scss +++ b/themes/delphi/assets/css/components/_card_grid.scss @@ -30,9 +30,14 @@ margin: 1em 1em 0 8em; } + .card-grid-item > picture { + width: 12em; + flex-shrink: 0; + } + .card-grid-item-img { - width: 14em; - height: unset; + width: 12em; + height: 100%; border-radius: 8px 0 0 8px; } diff --git a/themes/delphi/assets/css/pages/_about.scss b/themes/delphi/assets/css/pages/_about.scss index 44371bbc6..e1860578c 100644 --- a/themes/delphi/assets/css/pages/_about.scss +++ b/themes/delphi/assets/css/pages/_about.scss @@ -1,7 +1,14 @@ .about-mission { - background-image: url("../images/red-bubble-map_mission-pg-short.jpg"); - background-size: auto; height: 200px; + display: flex; + + > picture { + display: flex; + flex: 1 1 0; + } +} +.about-mission-img { + flex: 1 1 0; } .mission-text { diff --git a/themes/delphi/assets/css/pages/_blog.scss b/themes/delphi/assets/css/pages/_blog.scss index 5e307be7d..b8f886b82 100644 --- a/themes/delphi/assets/css/pages/_blog.scss +++ b/themes/delphi/assets/css/pages/_blog.scss @@ -72,7 +72,7 @@ $blog-list-date-width: 5em; @media (min-width: $breakpoint-medium) { .blog-blog > *, .blog-blog div.section > * { - margin-right: 25%; + margin-right: 13%; } .blog-blog div.section, .blog-blog .blog-image-wrapper.wide-figure { diff --git a/themes/delphi/assets/css/pages/_landing.scss b/themes/delphi/assets/css/pages/_landing.scss index a0c060695..22a5de2de 100644 --- a/themes/delphi/assets/css/pages/_landing.scss +++ b/themes/delphi/assets/css/pages/_landing.scss @@ -21,6 +21,10 @@ $carousel-height: 500px; img { z-index: -1; + width: 100%; + height: 100%; + object-fit: cover; + position: absolute; } } @@ -54,11 +58,11 @@ $carousel-height: 500px; } } -.white-area { +.landing-white-area { padding-top: 2rem; padding-bottom: 2rem; } -.gray-area { +.landing-gray-area { padding-top: 3rem; padding-bottom: 3rem; background-color: #eee; @@ -99,6 +103,9 @@ $carousel-height: 500px; max-width: 100%; max-height: 100%; } + > img { + border-radius: 5px; + } } .latest-news { @@ -112,4 +119,16 @@ $carousel-height: 500px; > img { filter: grayscale(100%); } + > img:first-of-type { + border-top-left-radius: 5px; + } + > img:nth-child(4) { + border-top-right-radius: 5px; + } + > img:nth-child(5) { + border-bottom-left-radius: 5px; + } + > img:last-of-type { + border-bottom-right-radius: 5px; + } } diff --git a/themes/delphi/assets/js/main.js b/themes/delphi/assets/js/main.js index a1a98c6b0..22055015b 100644 --- a/themes/delphi/assets/js/main.js +++ b/themes/delphi/assets/js/main.js @@ -1,6 +1,8 @@ import UIkit from "uikit/dist/js/uikit.js"; -// import plugin from 'uikit/dist/js/uikit-icons.js'; -// UIkit.use(plugin); +import plugin from "uikit/dist/js/uikit-icons.js"; +UIkit.use(plugin); // re export for COVIDCast window.UIkit = UIkit; +// define for covidcast at which base url it is embedded +window.DELPHI_COVIDCAST_PAGE = "/covidcast/"; diff --git a/themes/delphi/layouts/_default/about.html b/themes/delphi/layouts/_default/about.html index a828d9841..9998980cc 100644 --- a/themes/delphi/layouts/_default/about.html +++ b/themes/delphi/layouts/_default/about.html @@ -1,5 +1,7 @@ {{ define "main" }} -
+
+ {{ partial "webp-image.html" (dict "src" "/images/red-bubble-map_mission-pg-short.jpg" "class" "about-mission-img" "width" 1920 "height" 250 "alt" "Banner") }} +

Delphi Research Group

diff --git a/themes/delphi/layouts/_default/baseof.html b/themes/delphi/layouts/_default/baseof.html index f70a407fa..f2389b0a8 100644 --- a/themes/delphi/layouts/_default/baseof.html +++ b/themes/delphi/layouts/_default/baseof.html @@ -8,7 +8,7 @@ {{ partial "nav.html" . }} - {{ partial "menu/breadcrumb.html" . }} + {{ block "breadcrumb" . }}{{ partial "menu/breadcrumb.html" . }}{{ end }} {{ 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 7f9876b78..1e4cbfd4b 100644 --- a/themes/delphi/layouts/_default/covidcast_app.html +++ b/themes/delphi/layouts/_default/covidcast_app.html @@ -7,6 +7,7 @@ {{ end }} +{{ define "breadcrumb" }}{{ end }} {{ define "body_class" }}covidcast_wrapper{{ end }} {{ define "main" }}
diff --git a/themes/delphi/layouts/_default/team.html b/themes/delphi/layouts/_default/team.html index 589afab80..e1611a24f 100644 --- a/themes/delphi/layouts/_default/team.html +++ b/themes/delphi/layouts/_default/team.html @@ -8,6 +8,8 @@

World map of team members @@ -26,7 +28,7 @@

Thank you for your contributions

- {{ .Params.others }} + {{ .Params.others | .RenderString }}

diff --git a/themes/delphi/layouts/blog/list.html b/themes/delphi/layouts/blog/list.html index d76ea371d..ee3aeb736 100644 --- a/themes/delphi/layouts/blog/list.html +++ b/themes/delphi/layouts/blog/list.html @@ -7,13 +7,7 @@

{{ .Description }}

{{ range .Paginator.Pages }}
{{ .Date.Format "Jan _2" }}
- {{ .Title }} - Hero Image + {{ partial "webp-image.html" (dict "src" .Params.heroImageThumb "alt" .Title "class" "card-grid-item-img" "width" 300 "height" 200) }}

{{ .Title }}

diff --git a/themes/delphi/layouts/blog/single.html b/themes/delphi/layouts/blog/single.html index 6bb8435d3..61d532b06 100644 --- a/themes/delphi/layouts/blog/single.html +++ b/themes/delphi/layouts/blog/single.html @@ -13,7 +13,7 @@

{{ .Title }}

{{ partial "blog/tags.html" . }} {{ if isset .Params "heroimage" }}
- {{ .Title }} - Hero Image + {{ partial "webp-image.html" (dict "src" .Params.heroImage "width" 1120 "height" 440 "alt" .Title) }}
{{ end }}
@@ -47,7 +47,7 @@
Outline
{{ if isset .Params "acknowledgements" }}

Acknowledgements: - {{ .Params.acknowledgements | markdownify }} + {{ .Params.acknowledgements | .RenderString }}

{{ end }} {{ if isset .Params "related" }} diff --git a/themes/delphi/layouts/landing.html b/themes/delphi/layouts/landing.html index 25f8de2d4..05d5e6f08 100644 --- a/themes/delphi/layouts/landing.html +++ b/themes/delphi/layouts/landing.html @@ -1,38 +1,36 @@ {{ define "main" }} -
- {{ partial "landing/carousel.html" . }} -
-
-
-

Our Mission

-

- {{ .Site.Params.mission }} -

-
+ {{ partial "landing/carousel.html" . }} +
+
+
+

Our Mission

+

+ {{ .Site.Params.mission }} +

+
-
-
-
-
- {{ partial "landing/teampic.html" (dict "Site" .Site "team" "highlight") }} -
-

Our Team

-

Meet the Delphi team

- {{ partial "arrow-link.html" (dict "link" (relref . "team") "alt" "View all") }} +
+
+
+
+ {{ partial "landing/teampic.html" (dict "Site" .Site "team" "highlight") }}
-
-
- -
-

Our API

-

Access our data and tools

- {{ partial "arrow-link.html" (dict "link" .Site.Params.apiUrl "alt" "Learn more") }} +

Our Team

+

Meet the Delphi team

+ {{ partial "arrow-link.html" (dict "link" (relref . "team") "alt" "View all") }} +
+
+
+ API Image
+

Our API

+

Access our data and tools

+ {{ partial "arrow-link.html" (dict "link" .Site.Params.apiUrl "alt" "Learn more") }}
- - {{ partial "landing/latest-news.html" . }}
+ + {{ partial "landing/latest-news.html" . }} {{ end }} diff --git a/themes/delphi/layouts/partials/blog/card.html b/themes/delphi/layouts/partials/blog/card.html index 9e650dceb..d17020c6e 100644 --- a/themes/delphi/layouts/partials/blog/card.html +++ b/themes/delphi/layouts/partials/blog/card.html @@ -1,13 +1,8 @@
- {{ .Title }} - Hero Image + + {{ partial "webp-image.html" (dict "src" .Params.heroImageThumb "width" 300 "height" 200 "alt" .Title) }} +
{{ partial "blog/tags.html" . }} diff --git a/themes/delphi/layouts/partials/footer.html b/themes/delphi/layouts/partials/footer.html index c448317e7..fe94b349a 100644 --- a/themes/delphi/layouts/partials/footer.html +++ b/themes/delphi/layouts/partials/footer.html @@ -1,12 +1,17 @@