Merge pull request #985 from cmu-delphi/release/v3.2.15

Release v3.2.17

config.toml

@@ -63,52 +63,49 @@ relativeURLs = false
     url = "https://docs.google.com/forms/d/e/1FAIpQLScqgT1fKZr5VWBfsaSp-DNaN03aV6EoZU4YljIzHJ1Wl_zmtg/viewform"
     weight = 9
 
-# covid19
+# epidemic-signals
 [[menu.main]]
-    identifier = "covid19"
-    name = "COVID-19"
+    identifier = "epidemic-signals"
+    name = "Epidemic Signals"
     pre = "solid/virus"
-    url = "/covid19/"
+    url = "/epidemic-signals/"
     weight = 2
 [[menu.main]]
-    parent = "covid19"
+    parent = "epidemic-signals"
     name = "About COVIDcast"
-    url = "/covid19/"
+    url = "/epidemic-signals/"
     weight = 1
 [[menu.main]]
-    parent = "covid19"
+    parent = "epidemic-signals"
     name = "About CTIS"
-    url = "/covid19/ctis"
+    url = "/epidemic-signals/ctis"
     weight = 10
 [[menu.main]]
-    identifier = "covid19-covidcast"
-    parent = "covid19"
+    identifier = "epidemic-signals-covidcast"
+    parent = "epidemic-signals"
     name = "COVIDcast Dashboard"
     url = "/covidcast/"
     weight = 20
 [[menu.main]]
-    parent = "covid19"
+    parent = "epidemic-signals"
     name = "CTIS Dashboard"
     url = "/covidcast/survey-results"
     weight = 30
 [[menu.main]]
-    parent = "covid19"
+    parent = "epidemic-signals"
     name = "Export Data"
     url = "/covidcast/export"
     weight = 40
 [[menu.main]]
-    parent = "covid19"
-    name = "Terms Of Use"
-    url = "/covid19/terms-of-use"
-    weight = 50
-
-# flu
-[[menu.main]]
-    identifier = "flu"
+    parent = "epidemic-signals"
     name = "Flu & Other Pathogens"
-    pre = "solid/disease"
     url = "/flu/"
-    weight = 3
+    weight = 50
+[[menu.main]]
+    parent = "epidemic-signals"
+    name = "Terms Of Use"
+    url = "/epidemic-signals/terms-of-use"
+    weight = 60
 
 # tools
 [[menu.main]]
@@ -122,59 +119,125 @@ relativeURLs = false
     name = "Tools Overview"
     url = "/tools/"
     weight = 1
+# utils
 [[menu.main]]
     parent = "tools"
-    name = "COVIDcast Dashboard"
+    identifier = "utils"
+    name = "Dashboards"
+    url = "/tools/#dashboards"
+    weight = 9
+[[menu.main]]
+    parent = "utils"
+    name = "Delphi Epidata Dashboard"
     url = "/covidcast/"
     weight = 10
 [[menu.main]]
-    parent = "tools"
-    name = "COVIDcast R Package"
-    url = "https://cmu-delphi.github.io/covidcast/covidcastR/"
-    weight = 11
-[[menu.main]]
-    parent = "tools"
-    name = "COVIDcast Python Package"
-    url = "https://cmu-delphi.github.io/covidcast/covidcast-py/html/"
-    weight = 12
-[[menu.main]]
-    parent = "tools"
+    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"
-    name = "EpiVis"
+    parent = "utils"
+    name = "Epi Signal Visualization"
     url = "/epivis/"
     weight = 50
 [[menu.main]]
     parent = "tools"
-    name = "Archived Tools"
-    url = "/tools/archive/"
+    name = "Archived"
+    url = "/tools/#archived"
     weight = 80
 
+[[menu.main]]
+    parent = "tools"
+    identifier = "forecasting"
+    name = "Forecasting"
+    url = "/tools/#forecasting"
+    weight = 50
 
 [[menu.main]]
-    identier = "github"
-    pre = "brands/github"
-    name = "GitHub"
-    url = "https://github.com/cmu-delphi/"
+    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 = "Code"
+    pre = "solid/code"
+    name = "Code"
+    url = "code"
     weight = 90
+[[menu.main]]
+    parent = "Code"
+    name = "Code Overview"
+    url = "code"
+    weight = 1
+[[menu.main]]
+    parent = "Code"
+    identifier = "APIClients"
+    name = "API and Clients"
+    url = "/code/#api-and-clients"
+    weight = 2
+[[menu.main]]
+    parent = "APIClients"
+    name = "Epidata"
+    url = "https://github.com/cmu-delphi/delphi-epidata"
+    weight = 7
+[[menu.main]]
+    parent = "APIClients"
+    name = "Epidatr"
+    url = "https://cmu-delphi.github.io/epidatr/"
+    weight = 8
+[[menu.main]]
+    parent = "APIClients"
+    name = "Epidatpy"
+    url = "https://github.com/cmu-delphi/epidatpy"
+    weight = 9
 
+[[menu.main]]
+    parent = "Code"
+    identifier = "forecastingCode"
+    name = "Forecasting"
+    url = "code#forecasting"
+    weight = 10
+[[menu.main]]
+    parent = "forecastingCode"
+    name = "Forecasting Manual"
+    weight = 1
+[[menu.main]]
+    parent = "forecastingCode"
+    name = "Epiprocess"
+    url = "https://cmu-delphi.github.io/epiprocess/"
+    weight = 7
+[[menu.main]]
+    parent = "forecastingCode"
+    name = "Epipredict"
+    url = "https://cmu-delphi.github.io/epipredict/"
+    weight = 7
+[[menu.main]]
+    parent = "Code"
+    name = "Github"
+    pre = "brands/github"
+    url = "https://github.com/cmu-delphi/"
+    weight = 70
 
 [[menu.main]]
     identifier = "api"
-    name = "API"
+    name = "Epidata API"
     pre = "solid/database"
     url = "https://cmu-delphi.github.io/delphi-epidata/"
     weight = 100
@@ -183,6 +246,7 @@ relativeURLs = false
     description = "Developing the Theory and Practice of Epidemiological Forecasting"
     mission = "To develop the theory and practice of epidemic detection, tracking and forecasting, and their use in decision making, both public and private.  Our vision is to make this technology as useful as weather forecasting is today."
     apiUrl = "https://cmu-delphi.github.io/delphi-epidata"
+    toolUrl = "/tools/"
     twitter = "CmuDelphi"
     contactForm = "https://docs.google.com/forms/d/e/1FAIpQLScqgT1fKZr5VWBfsaSp-DNaN03aV6EoZU4YljIzHJ1Wl_zmtg/viewform"
     feedbackForm = "https://docs.google.com/forms/d/e/1FAIpQLSeIeOJtrAhdOriEyiRY7LkpQX8DZBY19dl6De8l56Q9CZhmxw/viewform?usp=pp_url&entry.1245962748="

content/_index.md

@@ -12,7 +12,7 @@ carousel:
   - pre: Tools
     title: Real-time Indicators of Infectious Disease Activity
     ref: covidcast
-    alt: Explore the COVIDcast Dashboard
+    alt: Explore the Delphi Epidata Dashboard
     image: covidcast_v2.jpg
   - pre: News
     title: CDC Selects Delphi Research Group at CMU as Center of Innovation in Outbreak Analytics and Disease Modeling

content/about/milestones/index.md

@@ -12,11 +12,11 @@ layout: milestones
 
 * **September 2022.** We launched [Epidata v4](https://delphi.cmu.edu/blog/2022/12/14/introducing-epidata-v4/), prioritizing fast access to the most up-to-date data while retaining the deep data revision history needed by researchers.
 
-* **June 2022.** We ended data collection for the [COVID-19 Trends and Impact Survey (CTIS)](https://delphi.cmu.edu/covid19/ctis/) after more than two years, during which we received 29.5 million survey responses in the US (and [well over 100m globally](https://covidmap.umd.edu/)).
+* **June 2022.** We ended data collection for the [COVID-19 Trends and Impact Survey (CTIS)](https://delphi.cmu.edu/epidemic-signals/ctis/) after more than two years, during which we received 29.5 million survey responses in the US (and [well over 100m globally](https://covidmap.umd.edu/)).
 
 * **April 2022.** We received the [Allen Newell Award for Research Excellence in SCS at CMU](https://www.cs.cmu.edu/events/newell-award), which is awarded annually and recognizes an outstanding body of work that epitomizes Allen Newell's research style.
 
-* **April 2022.** We received [the Policy Impact Award and the Warren J. Mitofsky Innovators Award from the the American Association of Public Opinion Research (AAPOR)](https://www.cs.cmu.edu/news/2022/delphi-aapor-awards), along with our partners from the University of Maryland Social Data Science Center and Meta, for our work on the [COVID-19 Trends and Impact Survey](https://delphi.cmu.edu/covid19/ctis/) (CTIS).
+* **April 2022.** We received [the Policy Impact Award and the Warren J. Mitofsky Innovators Award from the the American Association of Public Opinion Research (AAPOR)](https://www.cs.cmu.edu/news/2022/delphi-aapor-awards), along with our partners from the University of Maryland Social Data Science Center and Meta, for our work on the [COVID-19 Trends and Impact Survey](https://delphi.cmu.edu/epidemic-signals/ctis/) (CTIS).
 
 * **January 2022.** We added selected signals from the White House COVID-19 Data Strategy and Execution Workgroup’s [Community Profile Report (CPR)](https://healthdata.gov/Health/COVID-19-Community-Profile-Report/gqxm-d9w9), including hospital admission and vaccination rates. This data source was discontinued in February 2023.
 
@@ -54,7 +54,7 @@ layout: milestones
 
 * **May 2020.** We added signals for COVID-19 Cases and Deaths, mirrored from the [Center for Systems Science and Engineering](https://systems.jhu.edu/research/public-health/ncov/) at Johns Hopkins University.
 
-* **April 2020.** We partnered with Meta to launch the [COVID-19 Trends and Impact Survey (CTIS)](https://delphi.cmu.edu/covid19/ctis/) to monitor in real-time the spread and impact of the COVID-19 pandemic in the United States.
+* **April 2020.** We partnered with Meta to launch the [COVID-19 Trends and Impact Survey (CTIS)](https://delphi.cmu.edu/epidemic-signals/ctis/) to monitor in real-time the spread and impact of the COVID-19 pandemic in the United States.
 
 * **April 2020.** We added signals from two new data sources:
 

content/code/_index.md

@@ -0,0 +1,65 @@
+---
+title: Code Overview
+linkTitle: Code
+layout: single
+---
+
+In addition to the Delphi Epidata API server code, we have a number of user-oriented code packages, such as API clients and time-series modeling for epidemiology.
+All source code is freely available on [GitHub](https://github.com/cmu-delphi/).
+
+## API and clients
+
+### [Epidata](https://github.com/cmu-delphi/delphi-epidata)
+
+The core server code for the [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/).
+
+### [Epidatr](https://cmu-delphi.github.io/epidatr/)
+
+R client for the [Delphi 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 the [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/).
+Not yet recommended for production, but we are happy to receive feedback!
+
+## Forecasting
+
+### [Introduction to Epidemiological Forecasting: Delphi Tools, Data, and Lessons](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.
+The major features are:
+- The epi_df structure, which allows you track epidemiological data measured over location and time (and other potential keys).
+- The epi_archive structure, which allows you to store epi_df objects in a versioned archive and to query the archive for the state of the data at any point in time.
+- Support for applying generic functions across a sliding time window, building on tools like [slider](https://slider.r-lib.org/). Comes with support for
+  - handling gaps in time
+  - automatically handling grouping of keys
+- Support for version aware data transformation and forecasting, which allows for simple and accurate backtesting of forecasting models (using only the actual data that was available at the time of the forecast and not the revised versions).
+- 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.
+
+### [Epipredict](https://cmu-delphi.github.io/epipredict/)
+
+A framework for building epidata pipelines involving transformation and forecasting. It is designed to work smoothly with epiprocess and provides a simple interface for defining and running forecasting workflows. It supports:
+- A simple interface for defining a sequence of data pre-processing, forecasting, and post-processing steps.
+- A collection of data processing steps common to epidata.
+- A collection of pre-packaged forecasting models commonly used by Delphi's forecasting team.
+
+## Deprecated Packages
+
+### [Covidcast](https://github.com/cmu-delphi/covidcast)
+
+A collection of R and Python packages for accessing and analyzing data from the Delphi COVIDcast API.
+
+### [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).
+
+### [utils](https://github.com/cmu-delphi/utils)
+
+Python utility package for handling dates and locations.

content/covidcast/_index.md

@@ -1,6 +1,6 @@
 ---
-title: COVIDcast Dashboard
-description: COVIDcast tracks and forecasts the spread of COVID-19. By Carnegie Mellon's Delphi Research Group.
+title: Delphi Epidata Dashboard
+description: Delphi Epidata tracks and forecasts the spread of COVID-19. By Carnegie Mellon's Delphi Research Group.
 layout: covidcast_app
 app_mode: landing
 order: 1

content/covid19/_index.md → content/epidemic-signals/_index.md

@@ -2,6 +2,9 @@
 title: About COVIDcast
 linkTitle: COVID-19
 layout: single
+aliases:
+ - /covid19
+
 ---
 
 COVIDcast is the name for Delphi's project in support of the COVID-19 response
@@ -13,24 +16,24 @@ in the United States. It has several parts.
   constitute what we believe may be the nation's largest public repository of
   real-time, geographically-detailed indicators of COVID activity in the U.S.
 
-2. We make all COVID-19 indicators freely available through a
+1. We make all COVID-19 indicators freely available through a
   [public API](https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html),
   which is updated with new data daily. We also provide associated
   [R](https://cmu-delphi.github.io/covidcast/covidcastR/) and
   [Python](https://cmu-delphi.github.io/covidcast/covidcast-py/html/) packages, 
   and a [dashboard]({{< relref "covidcast" >}}) to visualize a core set of
   indicators. 
 
-3. Some of the underlying data sources (on which these indicators are built) 
+1. Some of the underlying data sources (on which these indicators are built) 
   would not exist or be publicly available without Delphi's efforts. These
   include a massive national daily survey called the [COVID-19 Trends and
-  Impact Survey (CTIS)]({{< relref "covid19/ctis" >}}) that we're running in
+  Impact Survey (CTIS)]({{< relref "epidemic-signals/ctis" >}}) that we're running in
   partnership with Facebook, which has been taken by over 25 million Americans
   since April 2020; and an enormous database of de-identified medical insurance
   claims, covering more than 35% of the U.S. population, made possible through
   health system partners including Change Healthcare. 
 
-4. We support and advise the U.S. CDC (in collaboration with the
+1. We support and advise the U.S. CDC (in collaboration with the
   [Reich Lab](https://reichlab.io/)) on short-term COVID forecasting, which 
   includes creating and evaluating an ensemble forecast out of the models
   submitted to the [COVID-19 Forecast Hub](https://covid19forecasthub.org/),
@@ -39,7 +42,7 @@ in the United States. It has several parts.
 
 ## See Also
 
-- [COVIDcast dashboard]({{< relref "covidcast" >}})
+- [Delphi Epidata dashboard]({{< relref "covidcast" >}})
 - [CTIS dashboard]({{< relref "covidcast/survey-results" >}})
 - [Export data tool]({{< relref "covidcast/export" >}})
 - [API documentation](https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html)