diff --git a/.github/workflows/blog.yaml b/.github/workflows/blog.yaml index 61b271309..05c7b05e8 100644 --- a/.github/workflows/blog.yaml +++ b/.github/workflows/blog.yaml @@ -37,7 +37,7 @@ jobs: run: | Rscript ./dependencies.R - name: Restore Blogdown Cache - uses: actions/cache@v3.3.2 + uses: actions/cache@v4.0.0 with: path: | ./blogdown diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index c2c76f933..235dcd69a 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -14,7 +14,7 @@ jobs: - uses: actions/setup-node@v4 with: node-version: 16 - - uses: actions/cache@v3.3.2 + - uses: actions/cache@v4.0.0 with: path: ~/.npm key: ${{ runner.os }}-node3-${{ hashFiles('**/package-lock.json') }} diff --git a/.github/workflows/release_main.yml b/.github/workflows/release_main.yml index 1e4e061b6..6845a5ffb 100644 --- a/.github/workflows/release_main.yml +++ b/.github/workflows/release_main.yml @@ -47,7 +47,7 @@ jobs: with: node-version: 16 - name: Cache Node.js modules - uses: actions/cache@v3.3.2 + uses: actions/cache@v4.0.0 with: path: ~/.npm # npm cache files are stored in `~/.npm` on Linux/macOS key: ${{ runner.OS }}-node2-${{ hashFiles('**/package-lock.json') }} diff --git a/assets/images/landing-page/hero-images/landing-pg-hero-exploratory_analysis.jpg b/assets/images/landing-page/hero-images/landing-pg-hero-exploratory_analysis.jpg new file mode 100644 index 000000000..6177e0a51 Binary files /dev/null and b/assets/images/landing-page/hero-images/landing-pg-hero-exploratory_analysis.jpg differ diff --git a/assets/images/landing-page/hero-images/landing-pg-hero-introducing_epidata.jpg b/assets/images/landing-page/hero-images/landing-pg-hero-introducing_epidata.jpg new file mode 100644 index 000000000..bb8eaeb95 Binary files /dev/null and b/assets/images/landing-page/hero-images/landing-pg-hero-introducing_epidata.jpg differ diff --git a/content/_index.md b/content/_index.md index bbbaf1004..b959feecb 100644 --- a/content/_index.md +++ b/content/_index.md @@ -5,7 +5,7 @@ layout: landing carousel: - pre: Tools - title: Real-time Indicators of COVID-19 Activity + title: Real-time Indicators of Infectious Disease Activity ref: covidcast alt: Explore the COVIDcast Dashboard image: covidcast_v2.jpg @@ -14,16 +14,16 @@ carousel: link: https://www.cs.cmu.edu/news/2023/delphi-cdc-center alt: Learn More image: landing-pg-hero-_cfa_oadm.jpg + - pre: Blog + title: Exploratory Analysis - Identifying Changing Variant Behavior during a Pandemic + ref: 2023-12-20-changepoint_explore + alt: View Post + image: landing-pg-hero-exploratory_analysis.jpg - pre: Tools - title: Evaluation of COVID-19 Forecasts - link: /forecast-eval - alt: Explore the Forecast Evaluation Dashboard - image: forecast_evaluation_dashboard.jpg - - pre: Tools - title: COVID Trends and Impact Survey (CTIS) - ref: covidcast/survey-results - alt: Explore the CTIS Dashboard - image: covidcast_survey.jpg + title: Introducing Epidata + link: https://delphi.cmu.edu/blog/2022/12/14/introducing-epidata-v4/ + alt: View Post + image: landing-pg-hero-introducing_epidata.jpg - pre: Blog title: On the Predictability of COVID-19 ref: 2021-09-30-ensemble-analysis @@ -40,7 +40,7 @@ carousel: alt: View Paper image: research-hero-collaborative-hubs.jpg - pre: Research - title: An Open Repository of Real-Time COVID-19 Indicators + title: Introduction to the Delphi Real-Time Signal Repository link: https://www.medrxiv.org/content/10.1101/2021.07.12.21259660v1 alt: View Paper image: landing-pg_hero-img_An Open Repository of Real-Time COVID-19 Indicators.jpg diff --git a/content/about/publications/images/rtestim.jpg b/content/about/publications/images/rtestim.jpg new file mode 100644 index 000000000..5558d4dab Binary files /dev/null and b/content/about/publications/images/rtestim.jpg differ diff --git a/content/about/publications/index.md b/content/about/publications/index.md index 81742e7a2..367223e6b 100644 --- a/content/about/publications/index.md +++ b/content/about/publications/index.md @@ -1,11 +1,24 @@ --- title: Research papers: + - title: "Smooth Multi-Period Forecasting with Application to Prediction of COVID-19 Cases" + image: smoothing-paper-teaser.jpg + authors: Tuzhilina, Hastie, McDonald, Tay, Tibshirani + link: https://doi.org/10.1080/10618600.2023.2285337 + journal: Journal of Computational and Graphical Statistics + year: 2024 + - title: "RtEstim: Effective reproduction number estimation with trend filtering" + image: rtestim.jpg + authors: Liu, Cai, Gustafson, McDonald + link: https://doi.org/10.1101/2023.12.18.23299302 + journal: medRxiv + year: 2023 - title: "Computationally Assisted Quality Control for Public Health Data Streams" image: forecast.png authors: Joshi, Mazaitis, Rosenfeld, Wilder link: https://arxiv.org/abs/2306.16914 - journal: International Joint Conference on Artificial Intelligence + year: 2023 + journal: International Joint Conference on Artificial Intelligence - title: "Nowcasting Reported COVID-19 Hospitalizations Using De-Identified, Aggregated Medical Insurance Claims Data" image: paper-2023-nowcasting-reported.jpg authors: Shen, Rumack, Wilder, Tibshirani @@ -36,12 +49,6 @@ papers: link: https://doi.org/10.2105/AJPH.2022.306831 journal: American Journal of Public Health year: 2022 - - title: "Smooth Multi-Period Forecasting with Application to Prediction of COVID-19 Cases" - image: smoothing-paper-teaser.jpg - authors: Tuzhilina, Hastie, McDonald, Tay, Tibshirani - link: https://arxiv.org/abs/2202.09723 - journal: arXiv - year: 2022 - title: "Recalibrating Probabilistic Forecasts of Epidemics" image: recalibrating-thumb.jpg authors: Rumack, Tibshirani, Rosenfeld diff --git a/content/blog/2023-09-27-epidatr.Rmd b/content/blog/2023-09-27-epidatr.Rmd new file mode 100644 index 000000000..dd4dde9ca --- /dev/null +++ b/content/blog/2023-09-27-epidatr.Rmd @@ -0,0 +1,124 @@ +--- +title: New package released! Epidatr, an R client for Delphi Epidata API +author: Dmitry Shemetov, David Weber +date: 2023-09-27 +tags: + - r + - epidata + - covidcast +authors: + - dmitry + - davidweb +heroImage: blog-lg-epidatr.jpg +heroImageThumb: blog-thumb-epidatr.jpg +summary: | + `epidatr` is designed to streamline the downloading and usage of data from the [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/). It provides a simple R interface to the API, including functions for downloading data, parsing the results, and converting the data into a tidy format. + +output: + blogdown::html_page: + toc: true +--- + +The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides +real-time access to epidemiological surveillance data for influenza, COVID-19, +and other diseases from both official government sources such as the [Centers +for Disease Control and Prevention +(CDC)](https://www.cdc.gov/datastatistics/index.html), private partners such as +[Facebook (now +Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) +and [Change Healthcare](https://www.changehealthcare.com/), and other public +datasets like [Google +Trends](https://console.cloud.google.com/marketplace/product/bigquery-public-datasets/covid19-search-trends). +It is built and maintained by the Carnegie Mellon University [Delphi Research +Group](https://delphi.cmu.edu/). + +Today we introduce the R package `epidatr`, available [on +CRAN](https://cloud.r-project.org/web/packages/epidatr/index.html), with the +source and development [on github](https://github.com/cmu-delphi/epidatr). + +This package is designed to streamline the downloading and usage of data from +the Delphi Epidata API. It provides a simple R interface to the API, including +functions for downloading data, parsing the results, and converting the data +into a tidy format. The API stores a historical record of all data, including +corrections and updates, which is particularly useful for accurately backtesting +forecasting models. We also provide packages for downstream data processing +([epiprocess](https://github.com/cmu-delphi/epiprocess)) and modeling +([epipredict](https://github.com/cmu-delphi/epipredict)). + +## Usage + +``` +library(epidatr) +# Obtain the smoothed covid-like illness (CLI) signal from Delphi's US COVID-19 +# Trends and Impact Survey (CTIS), in partnership with Facebook, as it was on +# April 10, 2021 for the US at the national level +epidata <- pub_covidcast( + source = "fb-survey", + signals = "smoothed_cli", + geo_type = "nation", + time_type = "day", + geo_values = "us", + time_values = epirange(20210101, 20210601), + as_of = 20210601 +) +epidata +``` + +``` +# A tibble: 151 × 15 + geo_value signal source geo_type time_type time_value + + 1 us smoothed_cli fb-su… nation day 2021-01-01 + 2 us smoothed_cli fb-su… nation day 2021-01-02 + 3 us smoothed_cli fb-su… nation day 2021-01-03 + 4 us smoothed_cli fb-su… nation day 2021-01-04 + 5 us smoothed_cli fb-su… nation day 2021-01-05 + 6 us smoothed_cli fb-su… nation day 2021-01-06 + 7 us smoothed_cli fb-su… nation day 2021-01-07 + 8 us smoothed_cli fb-su… nation day 2021-01-08 + 9 us smoothed_cli fb-su… nation day 2021-01-09 +10 us smoothed_cli fb-su… nation day 2021-01-10 +# ℹ 141 more rows +# ℹ 9 more variables: direction , issue , +# lag , missing_value , missing_stderr , +# missing_sample_size , value , stderr , +# sample_size +# ℹ Use `print(n = ...)` to see more rows +``` + +## Installation + +Installing the package is straightforward. + +``` +# Install the CRAN version +pak::pkg_install("epidatr") + +# Install the development version from the GitHub dev branch +pak::pkg_install("cmu-delphi/epidatr@dev") +``` + +### API Keys + +The Delphi API requires a (free) API key for full functionality. To generate +your key, register for a pseudo-anonymous account +[here](https://api.delphi.cmu.edu/epidata/admin/registration_form) and see more +discussion on the [general API +website](https://cmu-delphi.github.io/delphi-epidata/api/api_keys.html). The +`epidatr` client will automatically look for this key in the environment +variable `DELPHI_EPIDATA_KEY`. We recommend storing your key in your `.Renviron` +file, which R will read by default. + +Note that for the time being, the private endpoints (i.e. those prefixed with +`pvt`) will require a separate key that needs to be passed as an argument. + +## For users of the covidcast R package + +The `covidcast` package is deprecated and will no longer be updated. The +`epidatr` package is a complete rewrite of the [`covidcast` +package](https://cmu-delphi.github.io/covidcast/covidcastR/), with a focus on +speed, reliability, and ease of use. It also supports more endpoints and data +sources than `covidcast`. When migrating from that package, you will need to use +the +[`pub_covidcast`](https://cmu-delphi.github.io/epidatr/reference/pub_covidcast.html) +function in `epidatr`. diff --git a/content/blog/2023-09-27-epidatr.html b/content/blog/2023-09-27-epidatr.html new file mode 100644 index 000000000..840d21b04 --- /dev/null +++ b/content/blog/2023-09-27-epidatr.html @@ -0,0 +1,123 @@ +--- +title: New package released! Epidatr, an R client for Delphi Epidata API +author: Dmitry Shemetov, David Weber +date: 2023-09-27 +tags: + - r + - epidata + - covidcast +authors: + - dmitry + - davidweb +heroImage: blog-lg-epidatr.jpg +heroImageThumb: blog-thumb-epidatr.jpg +summary: | + `epidatr` is designed to streamline the downloading and usage of data from the [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/). It provides a simple R interface to the API, including functions for downloading data, parsing the results, and converting the data into a tidy format. + +output: + blogdown::html_page: + toc: true +--- + + + +

The Delphi Epidata API provides +real-time access to epidemiological surveillance data for influenza, COVID-19, +and other diseases from both official government sources such as the Centers +for Disease Control and Prevention +(CDC), private partners such as +Facebook (now +Meta) +and Change Healthcare, and other public +datasets like Google +Trends. +It is built and maintained by the Carnegie Mellon University Delphi Research +Group.

+

Today we introduce the R package epidatr, available on +CRAN, with the +source and development on github.

+

This package is designed to streamline the downloading and usage of data from +the Delphi Epidata API. It provides a simple R interface to the API, including +functions for downloading data, parsing the results, and converting the data +into a tidy format. The API stores a historical record of all data, including +corrections and updates, which is particularly useful for accurately backtesting +forecasting models. We also provide packages for downstream data processing +(epiprocess) and modeling +(epipredict).

+
+

Usage

+
library(epidatr)
+# Obtain the smoothed covid-like illness (CLI) signal from Delphi's US COVID-19
+# Trends and Impact Survey (CTIS), in partnership with Facebook, as it was on
+# April 10, 2021 for the US at the national level
+epidata <- pub_covidcast(
+    source = "fb-survey",
+    signals = "smoothed_cli",
+    geo_type = "nation",
+    time_type = "day",
+    geo_values = "us",
+    time_values = epirange(20210101, 20210601),
+    as_of = 20210601
+)
+epidata
+
# A tibble: 151 × 15
+   geo_value signal       source geo_type time_type time_value
+   <chr>     <chr>        <chr>  <fct>    <fct>     <date>
+ 1 us        smoothed_cli fb-su… nation   day       2021-01-01
+ 2 us        smoothed_cli fb-su… nation   day       2021-01-02
+ 3 us        smoothed_cli fb-su… nation   day       2021-01-03
+ 4 us        smoothed_cli fb-su… nation   day       2021-01-04
+ 5 us        smoothed_cli fb-su… nation   day       2021-01-05
+ 6 us        smoothed_cli fb-su… nation   day       2021-01-06
+ 7 us        smoothed_cli fb-su… nation   day       2021-01-07
+ 8 us        smoothed_cli fb-su… nation   day       2021-01-08
+ 9 us        smoothed_cli fb-su… nation   day       2021-01-09
+10 us        smoothed_cli fb-su… nation   day       2021-01-10
+# ℹ 141 more rows
+# ℹ 9 more variables: direction <dbl>, issue <date>,
+#   lag <dbl>, missing_value <dbl>, missing_stderr <dbl>,
+#   missing_sample_size <dbl>, value <dbl>, stderr <dbl>,
+#   sample_size <dbl>
+# ℹ Use `print(n = ...)` to see more rows
+
+
+

Installation

+

Installing the package is straightforward.

+
# Install the CRAN version
+pak::pkg_install("epidatr")
+
+# Install the development version from the GitHub dev branch
+pak::pkg_install("cmu-delphi/epidatr@dev")
+
+

API Keys

+

The Delphi API requires a (free) API key for full functionality. To generate +your key, register for a pseudo-anonymous account +here and see more +discussion on the general API +website. The +epidatr client will automatically look for this key in the environment +variable DELPHI_EPIDATA_KEY. We recommend storing your key in your .Renviron +file, which R will read by default.

+

Note that for the time being, the private endpoints (i.e. those prefixed with +pvt) will require a separate key that needs to be passed as an argument.

+
+
+
+

For users of the covidcast R package

+

The covidcast package is deprecated and will no longer be updated. The +epidatr package is a complete rewrite of the covidcast +package, with a focus on +speed, reliability, and ease of use. It also supports more endpoints and data +sources than covidcast. When migrating from that package, you will need to use +the +pub_covidcast +function in epidatr.

+
diff --git a/content/blog/2023-12-20-changepoint_explore.Rmd b/content/blog/2023-12-20-changepoint_explore.Rmd index 091dbca21..4dfc3cd25 100644 --- a/content/blog/2023-12-20-changepoint_explore.Rmd +++ b/content/blog/2023-12-20-changepoint_explore.Rmd @@ -1,5 +1,5 @@ --- -title: Exploratory Analysis - Identifying Changing Variant Behavior during a Pandemic +title: 'Identifying Changing Variant Behavior during a Pandemic: An Exploratory Analysis' author: Tara Lakdawala, Ananya Joshi date: 2023-12-20 tags: @@ -9,8 +9,8 @@ tags: authors: - tara - ajoshi -heroImage: changepoint-hero.png -heroImageThumb: changepoint-blog.png +heroImage: blog-lg-changepoint.jpeg +heroImageThumb: blog-thumb-changepoint.jpeg summary: | We use changepoint detection algorithms to analyze Delphi's indicators and classify them as early, on-time, late, undefined, or undetermined. diff --git a/content/blog/2023-12-20-changepoint_explore.html b/content/blog/2023-12-20-changepoint_explore.html index e31a258ef..4f6c71a4e 100644 --- a/content/blog/2023-12-20-changepoint_explore.html +++ b/content/blog/2023-12-20-changepoint_explore.html @@ -1,5 +1,5 @@ --- -title: Exploratory Analysis - Identifying Changing Variant Behavior during a Pandemic +title: 'Identifying Changing Variant Behavior during a Pandemic: An Exploratory Analysis' author: Tara Lakdawala, Ananya Joshi date: 2023-12-20 tags: @@ -9,8 +9,8 @@ authors: - tara - ajoshi -heroImage: changepoint-hero.png -heroImageThumb: changepoint-blog.png +heroImage: blog-lg-changepoint.jpeg +heroImageThumb: blog-thumb-changepoint.jpeg summary: | We use changepoint detection algorithms to analyze Delphi's indicators and classify them as early, on-time, late, undefined, or undetermined. diff --git a/content/blog/2024-01-01-flash-intro.Rmd b/content/blog/2024-01-01-flash-intro.Rmd index b3c34e4f9..6f34dc739 100644 --- a/content/blog/2024-01-01-flash-intro.Rmd +++ b/content/blog/2024-01-01-flash-intro.Rmd @@ -1,5 +1,5 @@ --- -title: Introducing the FlaSH Group +title: 'Introducing FlaSH, Part 1: Meet the Team' author: Ananya Joshi, Nolan Gormley, Richa Gadgil, Tina Townes date: 2024-01-01 tags: @@ -9,8 +9,8 @@ authors: - nolan - richa - tina -heroImage: flash_long.png -heroImageThumb: flash_logo.png +heroImage: blog-lg-flash.jpeg +heroImageThumb: blog-thumb-flash.jpeg summary: | Delphi's FlaSH group works to alert experts about data that suggests quality issues or changes in disease dynamics from the millions of data points they publish daily to improve the efficacy of Delphi's data. output: diff --git a/content/blog/2024-01-01-flash-intro.html b/content/blog/2024-01-01-flash-intro.html index 790fe6a76..c0da0036a 100644 --- a/content/blog/2024-01-01-flash-intro.html +++ b/content/blog/2024-01-01-flash-intro.html @@ -1,5 +1,5 @@ --- -title: Introducing the FlaSH Group +title: 'Introducing FlaSH, Part 1: Meet the Team' author: Ananya Joshi, Nolan Gormley, Richa Gadgil, Tina Townes date: 2024-01-01 tags: @@ -9,8 +9,8 @@ - nolan - richa - tina -heroImage: flash_long.png -heroImageThumb: flash_logo.png +heroImage: blog-lg-flash.jpeg +heroImageThumb: blog-thumb-flash.jpeg summary: | Delphi's FlaSH group works to alert experts about data that suggests quality issues or changes in disease dynamics from the millions of data points they publish daily to improve the efficacy of Delphi's data. output: diff --git a/content/blog/images/blog-lg-changepoint.jpeg b/content/blog/images/blog-lg-changepoint.jpeg new file mode 100644 index 000000000..87fcbaa22 Binary files /dev/null and b/content/blog/images/blog-lg-changepoint.jpeg differ diff --git a/content/blog/images/blog-lg-epidatr.jpg b/content/blog/images/blog-lg-epidatr.jpg new file mode 100644 index 000000000..37ab60175 Binary files /dev/null and b/content/blog/images/blog-lg-epidatr.jpg differ diff --git a/content/blog/images/blog-lg-flash.jpeg b/content/blog/images/blog-lg-flash.jpeg new file mode 100644 index 000000000..7f2250191 Binary files /dev/null and b/content/blog/images/blog-lg-flash.jpeg differ diff --git a/content/blog/images/blog-thumb-changepoint.jpeg b/content/blog/images/blog-thumb-changepoint.jpeg new file mode 100644 index 000000000..b952996be Binary files /dev/null and b/content/blog/images/blog-thumb-changepoint.jpeg differ diff --git a/content/blog/images/blog-thumb-epidatr.jpg b/content/blog/images/blog-thumb-epidatr.jpg new file mode 100644 index 000000000..507b0f730 Binary files /dev/null and b/content/blog/images/blog-thumb-epidatr.jpg differ diff --git a/content/blog/images/blog-thumb-flash.jpeg b/content/blog/images/blog-thumb-flash.jpeg new file mode 100644 index 000000000..e3883a042 Binary files /dev/null and b/content/blog/images/blog-thumb-flash.jpeg differ diff --git a/content/blog/images/changepoint-blog.png b/content/blog/images/changepoint-blog.png deleted file mode 100644 index 1961d102a..000000000 Binary files a/content/blog/images/changepoint-blog.png and /dev/null differ diff --git a/content/blog/images/changepoint-hero.png b/content/blog/images/changepoint-hero.png deleted file mode 100644 index deb60770c..000000000 Binary files a/content/blog/images/changepoint-hero.png and /dev/null differ diff --git a/content/blog/images/flash_logo.png b/content/blog/images/flash_logo.png deleted file mode 100644 index c7b029a13..000000000 Binary files a/content/blog/images/flash_logo.png and /dev/null differ diff --git a/content/blog/images/flash_long.png b/content/blog/images/flash_long.png deleted file mode 100644 index 85a6bc2cc..000000000 Binary files a/content/blog/images/flash_long.png and /dev/null differ diff --git a/content/people/index.md b/content/people/index.md index 2dd6f648c..52efdc250 100644 --- a/content/people/index.md +++ b/content/people/index.md @@ -343,6 +343,7 @@ people: affiliation: CMU/MLD and OVPR team: - leadership + - highlight leaderOrder: 3 - firstName: Jaemin lastName: Jo @@ -522,6 +523,7 @@ people: affiliation: CMU/MLD team: - core + - highlight - firstName: Ruiqi lastName: Lyu image: ruiqi-lyu.jpg @@ -720,7 +722,6 @@ people: affiliation: CMU/MLD team: - core - - highlight - blog description: is a Ph.D. student in the Machine Learning Department at CMU, advised by Roni Rosenfeld. He has been a member of the Delphi group since 2017. - firstName: Wael Al @@ -772,8 +773,10 @@ people: lastName: Shemetov image: dmitry-shemetov-500x500-min.jpg affiliation: CMU/MLD + description: is a statistical developer on the Delphi team. team: - core + - blog - firstName: Xueda lastName: Shen image: xueda-shen.jpg @@ -834,7 +837,6 @@ people: affiliation: CMU/CompBio team: - core - - highlight - firstName: Kenneth lastName: Tay image: kenneth-tay.jpg @@ -957,12 +959,15 @@ people: team: - past note: Google Fellow, October 2020-March 2021 -- firstName: David +- key: davidweb + firstName: David lastName: Weber image: david-weber.jpg affiliation: CMU/MLD + description: is a statistical developer on the Delphi team. team: - - core + - core + - blog - key: jweiss firstName: Jeremy Chen lastName: Weiss diff --git a/package-lock.json b/package-lock.json index e38a63852..3070a2404 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "www-main", - "version": "3.2.10", + "version": "3.2.11", "lockfileVersion": 1, "requires": true, "dependencies": { @@ -194,9 +194,9 @@ "dev": true }, "b4a": { - 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