From 09834c21a18976169ad569748892f14bf9283a53 Mon Sep 17 00:00:00 2001 From: Dmitry Shemetov Date: Tue, 30 Apr 2024 17:13:43 -0700 Subject: [PATCH] refactor+fix: tools update * packages and dashboards now link to tools overview * consistent capitalization of epiprocess/epipredict * aggregate all the tooling subpages into a single .md file for simplicity and to fix the header links * remove unused shortcode --- config.toml | 6 +- content/tools/_index.md | 77 ++++++++++++++++++- content/tools/archive.md | 1 - .../tools/forecasting/covid_forecasting.md | 10 --- content/tools/forecasting/flu_forecasting.md | 8 -- content/tools/forecasting/index.md | 5 -- .../tools/systems/covid_forecast_dashboard.md | 7 -- content/tools/systems/dashboard_builder.md | 7 -- content/tools/systems/epidata.md | 7 -- content/tools/systems/epivis.md | 7 -- content/tools/systems/index.md | 4 - content/tools/systems/indicator_status.md | 7 -- content/tools/tools/delphi_tooling_book.md | 7 -- content/tools/tools/epidatpy.md | 7 -- content/tools/tools/epidatr.md | 7 -- content/tools/tools/epipredict.md | 20 ----- content/tools/tools/epiprocess.md | 20 ----- content/tools/tools/index.md | 4 - .../layouts/shortcodes/forecasting.html | 5 -- 19 files changed, 78 insertions(+), 138 deletions(-) delete mode 100644 content/tools/forecasting/covid_forecasting.md delete mode 100644 content/tools/forecasting/flu_forecasting.md delete mode 100644 content/tools/forecasting/index.md delete mode 100644 content/tools/systems/covid_forecast_dashboard.md delete mode 100644 content/tools/systems/dashboard_builder.md delete mode 100644 content/tools/systems/epidata.md delete mode 100644 content/tools/systems/epivis.md delete mode 100644 content/tools/systems/index.md delete mode 100644 content/tools/systems/indicator_status.md delete mode 100644 content/tools/tools/delphi_tooling_book.md delete mode 100644 content/tools/tools/epidatpy.md delete mode 100644 content/tools/tools/epidatr.md delete mode 100644 content/tools/tools/epipredict.md delete mode 100644 content/tools/tools/epiprocess.md delete mode 100644 content/tools/tools/index.md delete mode 100644 themes/delphi/layouts/shortcodes/forecasting.html diff --git a/config.toml b/config.toml index 8d881a97..89d0cf22 100644 --- a/config.toml +++ b/config.toml @@ -127,6 +127,7 @@ relativeURLs = false parent = "tools" identifier = "Packages" name = "Packages" + url = "https://delphi.cmu.edu/tools/" weight = 6 [[menu.main]] parent = "Packages" @@ -140,12 +141,12 @@ relativeURLs = false weight = 20 [[menu.main]] parent = "Packages" - name = "EpiProcess" + name = "Epiprocess" url = "https://cmu-delphi.github.io/epiprocess/" weight = 7 [[menu.main]] parent = "Packages" - name = "EpiPredict" + name = "Epipredict" url = "https://cmu-delphi.github.io/epipredict/" weight = 7 # utils @@ -153,6 +154,7 @@ relativeURLs = false parent = "tools" identifier = "utils" name = "Dashboards" + url = "https://delphi.cmu.edu/tools/" weight = 9 [[menu.main]] parent = "utils" diff --git a/content/tools/_index.md b/content/tools/_index.md index e1fff09e..be936aaa 100644 --- a/content/tools/_index.md +++ b/content/tools/_index.md @@ -3,16 +3,87 @@ title: Tools Overview linkTitle: Tools layout: single --- + ## Forecasting -{{}} +### [COVID Forecasting](https://covid19forecasthub.org/) + +We participate in weekly COVID hospital admissions forecasting at the state and national level. +Our current system for generating forecasts can be found [here](https://github.com/cmu-delphi/covid-hosp-forecast). +In addition to publishing the individual forecasts from the participating groups, the Reich lab makes an ensemble prediction, and hosts a [visualization of both](https://viz.covid19forecasthub.org). +We host a comparison tool for [retrospective analysis of the forecasters](https://delphi.cmu.edu/forecast-eval/). + +### [Flu Forecasting (FluSight)](https://www.cdc.gov/flu/weekly/flusight/index.html) + +We participate in the weekly Flu forecasting hub run by the CDC during the flu season. Our current system for generating forecasts can be found [here](https://github.com/cmu-delphi/flu-hosp-forecast/). +From these dozens of individual forecasts by various groups, the CDC publishes a weekly [ensemble prediction](https://www.cdc.gov/flu/weekly/flusight/flu-forecasts.htm). ## Packages All source code is freely available on [GitHub](https://github.com/cmu-delphi/). -{{}} +### [Epidatr](https://cmu-delphi.github.io/epidatr/) + +R client for our [Epidata API](https://cmu-delphi.github.io/delphi-epidata/). It allows you to cache queries locally to speed up data access and seamlessly integrate pulling from our API into your pipelines. + +### [Delphi Tooling Book](https://cmu-delphi.github.io/delphi-tooling-book/) + +An introduction to epidemiological forecasting using our tools: epiprocess and epipredict. + +### [Epiprocess](https://cmu-delphi.github.io/epiprocess/) + +A collection of data structures and methods for handling epidemiological data measured over space, time, and other potential keys like age or ethnicity. +The major methods are: +- Sliding functions, both for generic user-supplied function and optimized commonly used functions (e.g. rolling mean and sum). These build on tools like [slider](https://slider.r-lib.org/) by + - handling gaps in time + - automatically handling grouping of keys + - being version aware; this enables version-aware forecast evaluation, so that you can compare forecasters using only data that would have available at the time of forecast. +- Growth rate estimation, as estimated using relative rates of change, linear regression, smooth splines, or polynomial trend filtering. +- Outlier detection and correction, using rolling median or LOESS trend decomposition. +- Signal correlation over space, time and other keys. It also supports lagged correlations, automatically handles grouping by the specified keys, and handles time gaps. + +Epiprocess also has methods for growth rate estimation, + +R client for our [Epidata API](https://cmu-delphi.github.io/delphi-epidata/). It allows you to cache queries locally to speed up data access and seamlessly integrate pulling from our API into your pipelines. + +### [Epipredict](https://cmu-delphi.github.io/epipredict/) + +A collection of data structures and methods for handling epidemiological data measured over space, time, and other potential keys like age or ethnicity. +The major methods are: +- Sliding functions, both for generic user-supplied function and optimized commonly used functions (e.g. rolling mean and sum). These build on tools like [slider](https://slider.r-lib.org/) by + - handling gaps in time + - automatically handling grouping of keys + - being version aware; this enables version-aware forecast evaluation, so that you can compare forecasters using only data that would have available at the time of forecast. +- Growth rate estimation, as estimated using relative rates of change, linear regression, smooth splines, or polynomial trend filtering. +- Outlier detection and correction, using rolling median or LOESS trend decomposition. +- Signal correlation over space, time and other keys. It also supports lagged correlations, automatically handles grouping by the specified keys, and handles time gaps. + +Epiprocess also has methods for growth rate estimation, + +R client for our [Epidata API](https://cmu-delphi.github.io/delphi-epidata/). It allows you to cache queries locally to speed up data access and seamlessly integrate pulling from our API into your pipelines. + +### [Epidatpy](https://github.com/cmu-delphi/epidatpy) (WIP) + +A work in progress Python client for our [Epidata API](https://cmu-delphi.github.io/delphi-epidata/). Not yet ready for production, but let us know if you are interested, so we can prioritize it! ## Operational Systems -{{}} +### [EpiData](https://github.com/cmu-delphi/delphi-epidata) + +API for getting up-to-date epidemiological data (also available via a web interface through [EpiVis](https://delphi.cmu.edu/epivis/epivis.html)) + +### [Indicator Status](https://delphi.cmu.edu/covidcast/indicator-status/) + +A dashboard for displaying the lags for various signals in the delphi epidata API. + +### [Dashboard Builder](https://delphi.cmu.edu/covidcast/dashboard) + +A builder that allows you to customize the [Delphi Epidata Dashboard](/covidcast/). + +### [COVID Forecasting Evaluation](https://delphi.cmu.edu/forecast-eval/) + +A forecast evaluation dashboard to compare the historical performance of the forecasts submitted to the [COVID-19 Forecast Hub](https://covid19forecasthub.org/), a collaboration between various modeling teams to produce forecasts of daily hospital admissions. + +### [EpiVis](https://delphi.cmu.edu/epivis/) + +Epidemiological time series visualizer. diff --git a/content/tools/archive.md b/content/tools/archive.md index 8b5dc41a..0f2a17b5 100644 --- a/content/tools/archive.md +++ b/content/tools/archive.md @@ -3,7 +3,6 @@ title: Archived Tools layout: single --- - ### [COVIDcast 1.0 ("Classic")](/covidcast/classic) A map-first single-page webapp for visualizing COVID-19 pandemic indicators. diff --git a/content/tools/forecasting/covid_forecasting.md b/content/tools/forecasting/covid_forecasting.md deleted file mode 100644 index b5bf5b3e..00000000 --- a/content/tools/forecasting/covid_forecasting.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -title: COVID forecasting -externallink: https://covid19forecasthub.org/ -order: 20 ---- - -We participate in weekly COVID hospital admissions forecasting at the state and national level. -Our current system for generating forecasts can be found [here](https://github.com/cmu-delphi/covid-hosp-forecast). -In addition to publishing the individual forecasts from the participating groups, the Reich lab makes an ensemble prediction, and hosts a [visualization of both](https://viz.covid19forecasthub.org). -We host a comparison tool for [retrospective analysis of the forecasters](https://delphi.cmu.edu/forecast-eval/). diff --git a/content/tools/forecasting/flu_forecasting.md b/content/tools/forecasting/flu_forecasting.md deleted file mode 100644 index ce36da24..00000000 --- a/content/tools/forecasting/flu_forecasting.md +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: Flu forecasting FluSight -externallink: https://www.cdc.gov/flu/weekly/flusight/index.html -order: 22 ---- - -We participate in the weekly Flu forecasting hub run by the CDC during the flu season. Our current system for generating forecasts can be found [here](https://github.com/cmu-delphi/flu-hosp-forecast/). -From these dozens of individual forecasts by various groups, the CDC publishes a weekly [ensemble prediction](https://www.cdc.gov/flu/weekly/flusight/flu-forecasts.htm). diff --git a/content/tools/forecasting/index.md b/content/tools/forecasting/index.md deleted file mode 100644 index 1a3deaa1..00000000 --- a/content/tools/forecasting/index.md +++ /dev/null @@ -1,5 +0,0 @@ ---- -# flag to disable rendering individual pages -headless: true ---- - diff --git a/content/tools/systems/covid_forecast_dashboard.md b/content/tools/systems/covid_forecast_dashboard.md deleted file mode 100644 index 2eb785ac..00000000 --- a/content/tools/systems/covid_forecast_dashboard.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: COVID Forecasting Evaluation -externallink: https://delphi.cmu.edu/forecast-eval/ -order: 20 ---- - -A forecast evaluation dashboard to compare the historical performance of the forecasts submitted to the [COVID-19 Forecast Hub](https://covid19forecasthub.org/), a collaboration between various modeling teams to produce forecasts of daily hospital admissions. diff --git a/content/tools/systems/dashboard_builder.md b/content/tools/systems/dashboard_builder.md deleted file mode 100644 index 7ac0295f..00000000 --- a/content/tools/systems/dashboard_builder.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: Dashboard Builder -internallink: covidcast/dashboard -order: 21 ---- - -A builder that allows you to customize the [Delphi Epidata Dashboard](/covidcast/). diff --git a/content/tools/systems/epidata.md b/content/tools/systems/epidata.md deleted file mode 100644 index 990016e9..00000000 --- a/content/tools/systems/epidata.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: EpiData -link: https://github.com/cmu-delphi/delphi-epidata -order: 2 ---- - -API for getting up-to-date epidemiological data (also available via a web interface through [EpiVis](https://delphi.cmu.edu/epivis/epivis.html)) diff --git a/content/tools/systems/epivis.md b/content/tools/systems/epivis.md deleted file mode 100644 index e6990332..00000000 --- a/content/tools/systems/epivis.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: EpiVis -link: /epivis/ -order: 1 ---- - -Epidemiological time series visualizer diff --git a/content/tools/systems/index.md b/content/tools/systems/index.md deleted file mode 100644 index 441ef3a5..00000000 --- a/content/tools/systems/index.md +++ /dev/null @@ -1,4 +0,0 @@ ---- -# flag to disable rendering individual pages -headless: true ---- diff --git a/content/tools/systems/indicator_status.md b/content/tools/systems/indicator_status.md deleted file mode 100644 index 2b5c5a17..00000000 --- a/content/tools/systems/indicator_status.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: Indicator Status -externallink: https://delphi.cmu.edu/covidcast/indicator-status/ -order: 21 ---- - -A dashboard for displaying the lags for various signals in the delphi epidata API. diff --git a/content/tools/tools/delphi_tooling_book.md b/content/tools/tools/delphi_tooling_book.md deleted file mode 100644 index e9040f01..00000000 --- a/content/tools/tools/delphi_tooling_book.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: Delphi Tooling Book -link: https://cmu-delphi.github.io/delphi-tooling-book/ -order: 1 ---- - -An introduction to epidemiological forecasting using our tools: epiprocess and epipredict. diff --git a/content/tools/tools/epidatpy.md b/content/tools/tools/epidatpy.md deleted file mode 100644 index 4b8e9803..00000000 --- a/content/tools/tools/epidatpy.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: Epidatpy -externallink: https://github.com/cmu-delphi/epidatpy -order: 25 ---- - -A work in progress Python client for our [Epidata API](https://cmu-delphi.github.io/delphi-epidata/). diff --git a/content/tools/tools/epidatr.md b/content/tools/tools/epidatr.md deleted file mode 100644 index 192dbedf..00000000 --- a/content/tools/tools/epidatr.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: EpiDatr -link: https://cmu-delphi.github.io/epidatr/ -order: 2 ---- - -R client for our [Epidata API](https://cmu-delphi.github.io/delphi-epidata/). It allows you to cache queries locally to speed up data access and seamlessly integrate pulling from our API into your pipelines. diff --git a/content/tools/tools/epipredict.md b/content/tools/tools/epipredict.md deleted file mode 100644 index 04fb8f5c..00000000 --- a/content/tools/tools/epipredict.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: EpiPredict -link: https://cmu-delphi.github.io/epipredict/ -order: 3 ---- - -A collection of data structures and methods for handling epidemiological data measured over space, time, and other potential keys like age or ethnicity. -The major methods are: -- Sliding functions, both for generic user-supplied function and optimized commonly used functions (e.g. rolling mean and sum). These build on tools like [slider](https://slider.r-lib.org/) by - - handling gaps in time - - automatically handling grouping of keys - - being version aware; this enables version-aware forecast evaluation, so that you can compare forecasters using only data that would have available at the time of forecast. -- Growth rate estimation, as estimated using relative rates of change, linear regression, smooth splines, or polynomial trend filtering. -- Outlier detection and correction, using rolling median or LOESS trend decomposition. -- Signal correlation over space, time and other keys. It also supports lagged correlations, automatically handles grouping by the specified keys, and handles time gaps. - -Epiprocess also has methods for growth rate estimation, - -R client for our [Epidata API](https://cmu-delphi.github.io/delphi-epidata/). It allows you to cache queries locally to speed up data access and seamlessly integrate pulling from our API into your pipelines. - diff --git a/content/tools/tools/epiprocess.md b/content/tools/tools/epiprocess.md deleted file mode 100644 index 5bc6ffe9..00000000 --- a/content/tools/tools/epiprocess.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: EpiProcess -link: https://cmu-delphi.github.io/epiprocess/ -order: 2 ---- - -A collection of data structures and methods for handling epidemiological data measured over space, time, and other potential keys like age or ethnicity. -The major methods are: -- Sliding functions, both for generic user-supplied function and optimized commonly used functions (e.g. rolling mean and sum). These build on tools like [slider](https://slider.r-lib.org/) by - - handling gaps in time - - automatically handling grouping of keys - - being version aware; this enables version-aware forecast evaluation, so that you can compare forecasters using only data that would have available at the time of forecast. -- Growth rate estimation, as estimated using relative rates of change, linear regression, smooth splines, or polynomial trend filtering. -- Outlier detection and correction, using rolling median or LOESS trend decomposition. -- Signal correlation over space, time and other keys. It also supports lagged correlations, automatically handles grouping by the specified keys, and handles time gaps. - -Epiprocess also has methods for growth rate estimation, - -R client for our [Epidata API](https://cmu-delphi.github.io/delphi-epidata/). It allows you to cache queries locally to speed up data access and seamlessly integrate pulling from our API into your pipelines. - diff --git a/content/tools/tools/index.md b/content/tools/tools/index.md deleted file mode 100644 index 441ef3a5..00000000 --- a/content/tools/tools/index.md +++ /dev/null @@ -1,4 +0,0 @@ ---- -# flag to disable rendering individual pages -headless: true ---- diff --git a/themes/delphi/layouts/shortcodes/forecasting.html b/themes/delphi/layouts/shortcodes/forecasting.html deleted file mode 100644 index 38b5bdb2..00000000 --- a/themes/delphi/layouts/shortcodes/forecasting.html +++ /dev/null @@ -1,5 +0,0 @@ -{{ $tools := .Site.GetPage "/tools/forecasting" }} -{{ range sort ($tools.Resources.ByType "page") "Params.order" }} -

{{ .Title }}

- {{ .Content }} -{{ end }}