first draft tooling update

config.toml

@@ -75,11 +75,6 @@ relativeURLs = false
     name = "About COVIDcast"
     url = "/covid19/"
     weight = 1
-[[menu.main]]
-    parent = "covid19"
-    name = "About CTIS"
-    url = "/covid19/ctis"
-    weight = 10
 [[menu.main]]
     identifier = "covid19-covidcast"
     parent = "covid19"
@@ -124,36 +119,63 @@ relativeURLs = false
     weight = 1
 [[menu.main]]
     parent = "tools"
-    name = "Delphi Epidata Dashboard"
-    url = "/covidcast/"
-    weight = 10
+    name = "Delphi Tooling Book"
+    url = "https://cmu-delphi.github.io/delphi-tooling-book/"
+    weight = 5
+# packages
 [[menu.main]]
     parent = "tools"
-    name = "COVIDcast R Package"
-    url = "https://cmu-delphi.github.io/covidcast/covidcastR/"
-    weight = 11
+    identifier = "Packages"
+    name = "Packages"
+    weight = 6
 [[menu.main]]
-    parent = "tools"
-    name = "COVIDcast Python Package"
-    url = "https://cmu-delphi.github.io/covidcast/covidcast-py/html/"
-    weight = 12
+    parent = "Packages"
+    name = "Epidatr"
+    url = "https://cmu-delphi.github.io/epidatr/"
+    weight = 7
+[[menu.main]]
+    parent = "Packages"
+    name = "Epidatpy"
+    url = "https://github.com/cmu-delphi/epidatpy"
+    weight = 20
+[[menu.main]]
+    parent = "Packages"
+    name = "EpiProcess"
+    url = "https://cmu-delphi.github.io/epiprocess/"
+    weight = 7
+[[menu.main]]
+    parent = "Packages"
+    name = "EpiPredict"
+    url = "https://cmu-delphi.github.io/epipredict/"
+    weight = 7
+# utils
 [[menu.main]]
     parent = "tools"
+    identifier = "utils"
+    name = "Dashboards and online utils"
+    weight = 9
+[[menu.main]]
+    parent = "utils"
+    name = "Delphi Epidata Dashboard"
+    url = "/covidcast/"
+    weight = 10
+[[menu.main]]
+    parent = "utils"
     name = "Indicator Status"
     url = "/covidcast/indicator-status"
     weight = 20
 [[menu.main]]
-    parent = "tools"
+    parent = "utils"
     name = "Dashboard Builder"
     url = "/covidcast/dashboard"
     weight = 30
 [[menu.main]]
-    parent = "tools"
+    parent = "utils"
     name = "Forecast Evaluation"
     url = "/forecast-eval/"
     weight = 40
 [[menu.main]]
-    parent = "tools"
+    parent = "utils"
     name = "EpiVis"
     url = "/epivis/"
     weight = 50
@@ -163,6 +185,23 @@ relativeURLs = false
     url = "/tools/archive/"
     weight = 80
 
+[[menu.main]]
+    parent = "tools"
+    identifier = "forecasting"
+    name = "Forecasting"
+    url = "https://www.cdc.gov/flu/weekly/flusight/index.html"
+    weight = 50
+
+[[menu.main]]
+    parent = "forecasting"
+    name = "COVID Forecasting"
+    url = "https://covid19forecasthub.org/"
+    weight = 1
+[[menu.main]]
+    parent = "forecasting"
+    name = "Flu Forecasting"
+    url = "https://www.cdc.gov/flu/weekly/flusight/index.html"
+    weight = 2
 
 [[menu.main]]
     identier = "github"

content/tools/_index.md

@@ -3,14 +3,16 @@ title: Tools Overview
 linkTitle: Tools
 layout: single
 ---
+## Forecasting
 
-## Operational Systems
-
-{{<systems>}}
+{{<forecasting>}}
 
+## Packages
 
-## Publicly Available Tools
+All source code is freely available on [GitHub](https://github.com/cmu-delphi/).
 
 {{<tools>}}
 
-All source code is freely available on [GitHub](https://github.com/cmu-delphi/).
+## Operational Systems
+
+{{<systems>}}

content/tools/archive.md

@@ -4,10 +4,37 @@ layout: single
 ---
 
 
-### [COVIDcast 1.0 ("Classic")]({{<relref "/covidcast/classic" >}})
+### [COVIDcast 1.0 ("Classic")](/covidcast/classic)
 
 A map-first single-page webapp for visualizing COVID-19 pandemic indicators.
 
 ### [Crowdcast](/crowdcast)
 
-Delphi’s "Wisdom of crowds" forecasting system: Used for Chikungunya, flu and most recently Covid. In it's archived configuration, this system is set up to forecast ILI during the COVID-19 pandemic
+Delphi’s "Wisdom of crowds" forecasting system: Used for Chikungunya, flu and most recently Covid. In it's archived configuration, this system was set up to forecast ILI during the COVID-19 pandemic
+
+### [ILI Nearby](/nowcast)
+
+Flu nowcasting system.
+
+**Note:** This system is designed to nowcast ILI driven by seasonal
+influenza and is NOT designed to nowcast ILI during the COVID-19 pandemic.
+
+### [Epiforecast](https://github.com/cmu-delphi/epiforecast-R)
+
+R package that implements several methods for epidemiological forecasting empirical bayes (EB), basis regression (BR), and time-weighted kernel density estimation (twkde).
+
+### [Nowcast](https://github.com/cmu-delphi/nowcast)
+
+A sensor fusion based nowcasting system developed to predict ILI before the COVID-19 pandemic
+
+### [utils](https://github.com/cmu-delphi/utils)
+
+Old python utility package, mainly for handling dates and locations.
+
+### [Fluscores](https://delphi.cmu.edu/misc/fluscores/)
+
+Visual comparison of scored submissions to CDC Flu Forecasting Challenge for 2014-16 (provide your own score files).
+
+## COVIDcast packages
+### [COVIDcast R package](https://cmu-delphi.github.io/covidcast/covidcastR/)
+### [COVIDcast Python package](https://cmu-delphi.github.io/covidcast/covidcast-py/html/)

content/tools/forecasting/covid_forecasting.md

@@ -0,0 +1,10 @@
+---
+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/).

content/tools/forecasting/flu_forecasting.md

@@ -0,0 +1,8 @@
+---
+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).

content/tools/forecasting/index.md

@@ -0,0 +1,5 @@
+---
+# flag to disable rendering individual pages
+headless: true
+---
+

content/tools/systems/covid_forecast_dashboard.md

@@ -0,0 +1,7 @@
+---
+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.

content/tools/systems/dashboard_builder.md

@@ -0,0 +1,7 @@
+---
+title: Dashboard Builder
+internallink: covidcast/dashboard
+order: 21
+---
+
+A builder that allows you to customize the [Delphi Epidata Dashboard](/covidcast/).

content/tools/systems/indicator_status.md

@@ -0,0 +1,7 @@
+---
+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.

content/tools/tools/delphi_tooling_book.md

@@ -0,0 +1,7 @@
+---
+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.

content/tools/tools/epidatpy.md

@@ -0,0 +1,7 @@
+---
+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/).

content/tools/tools/epidatr.md

@@ -0,0 +1,7 @@
+---
+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.

content/tools/tools/epipredict.md

@@ -0,0 +1,20 @@
+---
+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.
+

content/tools/tools/epiprocess.md

@@ -0,0 +1,20 @@
+---
+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.
+

themes/delphi/assets/css/layout/_header_footer.scss

@@ -194,3 +194,35 @@ li.nav-entry {
   margin-top: 3px;
   margin-bottom: 5px;
 }
+
+ul.nestedmenu {
+  margin-left: 0;
+}
+ul.nestedmenu li {
+  list-style: none;
+}
+ul.nestedmenu li > ul {
+  display: none;
+}
+ul.nestedmenu li > a::before {
+  content: "•";
+  display: inline-block;
+  margin-right: 0.25rem;
+  width: 0.5rem;
+  text-align: center;
+}
+ul.nestedmenu li.haschildren > a::before {
+  content: "›";
+}
+ul.nestedmenu li.haschildren.active > a::before {
+  transform: rotate(90deg);
+}
+ul.nestedmenu li.active > ul {
+  display: block;
+}
+ul.nestedmenu li > a {
+  color: #444444 !important;
+}
+ul.nestedmenu li.active > a {
+  color: rgb(247, 44, 114) !important;
+}