Merge pull request #359 from cmu-delphi/sgratzl/newmenu

Change to New Menu Structure

README.md

@@ -24,7 +24,7 @@ A relative reference to another page can be created using the `relref` shortcode
 **Examples**
 
 ```
-national daily survey]({{< relref "surveys">}})
+national daily survey]({{< relref "ctis">}})
 [syndromic COVID-19 indicator based on doctor visits]({{< relref "2020-10-14-dv-signal" >}})
 [self-reported symptoms]({{< relref "2020-08-26-fb-survey#whats-in-the-survey" >}})
 ```

config.toml

@@ -15,14 +15,16 @@ relativeURLs = false
     pre = "solid/info-circle"
     url = "/about"
     weight = 1
+
+# About
 [[menu.main]]
     parent = "about"
-    name = "Delphi Research Group"
+    name = "About Delphi"
     url = "/about"
     weight = 1
 [[menu.main]]
     parent = "about"
-    name = "Team"
+    name = "Our Team"
     url = "/about/team"
     weight = 2
 [[menu.main]]
@@ -32,109 +34,140 @@ relativeURLs = false
     weight = 3
 [[menu.main]]
     parent = "about"
-    name = "Publications"
+    name = "Research"
     url = "/about/publications"
     weight = 4
+[[menu.main]]
+    parent = "about"
+    name = "Blog"
+    url = "/blog"
+    weight = 5
 [[menu.main]]
     parent = "about"
     name = "News"
     url = "/about/news"
-    weight = 4
-[[menu.main]]
-    identifier = "covidcast"
-    name = "COVIDcast"
-    pre = "solid/map"
-    url = "/covidcast/"
-    weight = 2
+    weight = 6
 [[menu.main]]
-    parent = "covidcast"
-    name = "COVIDcast Overview"
-    url = "/covidcast/"
-    weight = 1
+    parent = "about"
+    name = "Careers"
+    url = "/about/careers"
+    weight = 7
+
+# covid19
 [[menu.main]]
-    parent = "covidcast"
-    name = "Explore a Location"
-    url = "/covidcast/summary"
+    identifier = "covid19"
+    name = "COVID-19"
+    pre = "solid/virus"
+    url = "/covid19/"
     weight = 2
 [[menu.main]]
-    parent = "covidcast"
-    name = "Explore an Indicator"
-    url = "/covidcast/indicator"
-    weight = 3
+    parent = "covid19"
+    name = "About COVIDcast"
+    url = "/covid19/"
+    weight = 1
 [[menu.main]]
-    parent = "covidcast"
-    name = "Explore Correlations"
-    url = "/covidcast/correlation"
-    weight = 4
+    parent = "covid19"
+    name = "About CTIS"
+    url = "/covid19/ctis"
+    weight = 10
 [[menu.main]]
-    parent = "covidcast"
-    name = "Dashboard Builder"
-    url = "/covidcast/dashboard"
+    identifier = "covid19-covidcast"
+    parent = "covid19"
+    name = "COVIDcast Dashboard"
+    url = "/covidcast/"
     weight = 20
 [[menu.main]]
-    parent = "covidcast"
-    name = "Classic Map"
-    url = "/covidcast/classic"
+    parent = "covid19"
+    name = "CTIS Dashboard"
+    url = "/covidcast/survey-results"
     weight = 30
 [[menu.main]]
-    parent = "covidcast"
-    name = "Forecast Evaluation"
-    url = "/forecast-eval/"
+    parent = "covid19"
+    name = "Export Data"
+    url = "/covidcast/export"
     weight = 40
 [[menu.main]]
-    parent = "covidcast"
-    name = "Surveys"
-    url = "/covidcast/surveys"
+    parent = "covid19"
+    name = "Terms Of Use"
+    url = "/covid19/terms-of-use"
     weight = 50
+
+# flu
 [[menu.main]]
-    parent = "covidcast"
-    name = "CTIS Results Dashboard"
-    url = "/covidcast/survey-results"
-    weight = 51
+    identifier = "flu"
+    name = "Flu & Other Pathogens"
+    pre = "solid/disease"
+    url = "/flu/"
+    weight = 3
+
+# tools
 [[menu.main]]
-    parent = "covidcast"
-    name = "Indicator Status Overview"
-    url = "/covidcast/indicator-status"
-    weight = 60
+    identifier = "tools"
+    name = "Tools"
+    pre = "solid/tools"
+    url = "/tools/"
+    weight = 5
 [[menu.main]]
-    parent = "covidcast"
-    name = "Export Data"
-    url = "/covidcast/export"
-    weight = 70
+    parent = "tools"
+    name = "Tools Overview"
+    url = "/tools/"
+    weight = 1
 [[menu.main]]
-    parent = "covidcast"
-    name = "Release Log"
-    url = "/covidcast/release-log"
-    weight = 80
+    parent = "tools"
+    name = "COVIDcast Dashboard"
+    url = "/covidcast/"
+    weight = 10
 [[menu.main]]
-    parent = "covidcast"
-    name = "Terms Of Use"
-    url = "/covidcast/terms-of-use"
-    weight = 90
+    parent = "tools"
+    name = "COVIDcast R Package"
+    url = "https://cmu-delphi.github.io/covidcast/covidcastR/"
+    weight = 11
 [[menu.main]]
-    identifier = "flu"
-    name = "Flu and Other Diseases"
-    pre = "solid/virus"
-    url = "/flu"
-    weight = 3
+    parent = "tools"
+    name = "COVIDcast Python Package"
+    url = "https://cmu-delphi.github.io/covidcast/covidcast-py/html/"
+    weight = 12
 [[menu.main]]
-    identifier = "blog"
-    name = "Blog"
-    pre = "solid/book"
-    url = "/blog"
-    weight = 4
+    parent = "tools"
+    name = "Indicator Status"
+    url = "/covidcast/indicator-status"
+    weight = 20
 [[menu.main]]
-    identifier = "github"
-    name = "GitHub"
+    parent = "tools"
+    name = "Dashboard Builder"
+    url = "/covidcast/dashboard"
+    weight = 30
+[[menu.main]]
+    parent = "tools"
+    name = "Forecast Evaluation"
+    url = "/forecast-eval/"
+    weight = 40
+[[menu.main]]
+    parent = "tools"
+    name = "EpiVis"
+    url = "/epivis/"
+    weight = 50
+[[menu.main]]
+    parent = "tools"
+    name = "Archived Tools"
+    url = "/tools/archive/"
+    weight = 80
+
+
+[[menu.main]]
+    identier = "github"
     pre = "brands/github"
+    name = "GitHub"
     url = "https://github.com/cmu-delphi/"
-    weight = 5
+    weight = 90
+
+
 [[menu.main]]
     identifier = "api"
     name = "API"
     pre = "solid/database"
     url = "https://cmu-delphi.github.io/delphi-epidata/"
-    weight = 6
+    weight = 100
 
 [params]
     description = "Developing the Theory and Practice of Epidemiological Forecasting"
@@ -148,4 +181,4 @@ relativeURLs = false
     feedbackDelayMin = 45  # in sec
     feedbackDelayMax = 180 # in sec
     feedbackDuration = 60  # show it for 60sec
-    highlightLinks = "/covidcast/dashboard"
+    highlightLinks = ""

content/about/_index.md

@@ -1,5 +1,6 @@
 ---
 title: Delphi Research Group
+linkTitle: About Delphi
 layout: about
 
 collaborators:
@@ -49,7 +50,7 @@ In reverse chronological order.
 
     * Several of the underlying data sources (on which these indicators are built) would not exist or be publicly available without our efforts. This includes:
 
-        *  A massive [national daily survey]({{< relref "surveys">}}) we're running in [partnership with Facebook](https://covid-survey.dataforgood.fb.com/survey_and_map_data.html). Over 20 million Americans have answered the survey since April 2020, providing real-time insights into, e.g., self-reported symptoms, mask wearing, testing, contacts, and vaccination.
+        *  A massive [national daily survey]({{< relref "ctis">}}) we're running in [partnership with Facebook](https://covid-survey.dataforgood.fb.com/survey_and_map_data.html). Over 20 million Americans have answered the survey since April 2020, providing real-time insights into, e.g., self-reported symptoms, mask wearing, testing, contacts, and vaccination.
 
         *  An enormous database of medical insurance claims that have been de-identified in accordance with HIPAA privacy regulations, covering more than half the U.S. population. This data is made available by health system partners including Change Healthcare, and provides insights into disease activity through outpatient visits and hospitalizations.
 

content/about/center-of-excellence/index.md

@@ -1,5 +1,6 @@
 ---
 title: Delphi National Center of Excellence for Epidemic Forecasting
+linkTitle: Center of Excellence
 layout: coe
 members:
 - name: Carnegie Mellon University

content/about/publications/index.md

@@ -1,5 +1,5 @@
 ---
-title: Research and White Papers
+title: Research
 papers:
   - title: "Big Data, Big Problems: Responding to \"Are We There Yet?\""
     image: response.jpg

content/about/team/index.md

@@ -1,5 +1,6 @@
 ---
 title: Delphi Team Members
+linkTitle: Our Team
 layout: team
 ---
 

content/blog/2020-08-28-api.Rmd

@@ -173,7 +173,7 @@ cover most levels of the severity pyramid and include:
   Our `r blogdown::shortcode_html("reflink", "2020-08-26-fb-survey", "previous blog post")`
   showed how the survey can indicate COVID-19 activity,
   and preliminary analysis also suggests `r blogdown::shortcode_html("reflink", "2020-09-21-forecast-demo", "it can help forecast COVID-19 cases")`.
-  See our `r blogdown::shortcode_html("reflink", "surveys", "surveys site")`
+  See our `r blogdown::shortcode_html("reflink", "ctis", "surveys site")`
   for more on the survey, its questions, and getting access to data.
 - Massive surveys we run through Google:
   From April 11 to May 14, 2020, Delphi conducted a single-question symptoms survey

content/blog/2020-08-28-api.html

@@ -173,7 +173,7 @@ <h2>Unique Data Sources</h2>
 Our {{< reflink "2020-08-26-fb-survey" "previous blog post" >}}
 showed how the survey can indicate COVID-19 activity,
 and preliminary analysis also suggests {{< reflink "2020-09-21-forecast-demo" "it can help forecast COVID-19 cases" >}}.
-See our {{< reflink "surveys" "surveys site" >}}
+See our {{< reflink "ctis" "surveys site" >}}
 for more on the survey, its questions, and getting access to data.</li>
 <li>Massive surveys we run through Google:
 From April 11 to May 14, 2020, Delphi conducted a single-question symptoms survey

content/blog/2020-10-06-survey-wave-4.Rmd

@@ -363,7 +363,7 @@ available through our COVIDcast API, and the exact technical details are
 described in our `r blogdown::shortcode_html("apireflink", "api/covidcast-signals/fb-survey.html", "signal documentation")`.
 The symptom and mask data is already featured on our `r blogdown::shortcode_html("reflink", "covidcast?sensor=fb-survey-smoothed_wearing_mask&level=county&signalType=value&encoding=color&mode=overview&region=42003", "COVIDcast interactive map")`,
 and other survey signals will soon be added as well. More information about the
-surveys, including preliminary results, is given on our `r blogdown::shortcode_html("reflink", "surveys", "survey site")`.
+surveys, including preliminary results, is given on our `r blogdown::shortcode_html("reflink", "ctis", "survey site")`.
 
 But we also know that many researchers will have questions that can't be
 answered from these simple county- and state-level averages. What occupations
@@ -392,7 +392,7 @@ data, we can make decisions needed to protect public health and permit safe
 reopening.
 
 _For more information about Delphi's symptom surveys, and for media contact
-details, see `r blogdown::shortcode_html("reflink", "surveys", "our surveys page")`. For
+details, see `r blogdown::shortcode_html("reflink", "ctis", "our surveys page")`. For
 updates, you can follow [CmuDelphi on Twitter](https://twitter.com/cmudelphi)._
 
 **Note.** _This post was updated on October 17, 2020 to correct an error in the

content/blog/2020-10-06-survey-wave-4.html

@@ -342,7 +342,7 @@ <h2>You Can Help Analyze This Data</h2>
 described in our {{< apireflink "api/covidcast-signals/fb-survey.html" "signal documentation" >}}.
 The symptom and mask data is already featured on our {{< reflink "covidcast?sensor=fb-survey-smoothed_wearing_mask&level=county&signalType=value&encoding=color&mode=overview&region=42003" "COVIDcast interactive map" >}},
 and other survey signals will soon be added as well. More information about the
-surveys, including preliminary results, is given on our {{< reflink "surveys" "survey site" >}}.</p>
+surveys, including preliminary results, is given on our {{< reflink "ctis" "survey site" >}}.</p>
 <p>But we also know that many researchers will have questions that can’t be
 answered from these simple county- and state-level averages. What occupations
 have the highest rate of COVID-19? What age groups engage in the most behavior
@@ -367,7 +367,7 @@ <h2>You Can Help Analyze This Data</h2>
 data, we can make decisions needed to protect public health and permit safe
 reopening.</p>
 <p><em>For more information about Delphi’s symptom surveys, and for media contact
-details, see {{< reflink "surveys" "our surveys page" >}}. For
+details, see {{< reflink "ctis" "our surveys page" >}}. For
 updates, you can follow <a href="https://twitter.com/cmudelphi">CmuDelphi on Twitter</a>.</em></p>
 <p><strong>Note.</strong> <em>This post was updated on October 17, 2020 to correct an error in the
 scatterplot of mask usage and reported case rates. An error in our data

content/blog/2021-01-22-holiday-surveys.Rmd

@@ -39,7 +39,7 @@ gatherings during the holidays and a number of states expanded COVID-19
 restrictions to prevent further escalation in cases.
 [Reports](https://www.washingtonpost.com/travel/2020/12/21/christmas-flights-cdc-restrictions-covid/)
 from airlines suggest air travel was up significantly during the holiday season,
-but `r blogdown::shortcode_html("reflink", "surveys", "Delphi’s COVID-19 Surveys")` can
+but `r blogdown::shortcode_html("reflink", "ctis", "Delphi’s COVID-19 Surveys")` can
 provide a broader picture of the travel Americans took during the holiday
 season. In taking greater risks with travel, did Americans change their
 behaviors in other preventative measures like mask wearing during this time?
@@ -410,7 +410,7 @@ Since April 2020, Carnegie Mellon University’s Delphi Group and Facebook’s D
 for Good have partnered to conduct large-scale daily surveys to monitor the
 spread and impact of the COVID-19 pandemic in the United States. To date, the
 survey has collected more than 50 million responses. In this post, we show how
-the data from the `r blogdown::shortcode_html("reflink", "surveys", "COVID-19 survey")`
+the data from the `r blogdown::shortcode_html("reflink", "ctis", "COVID-19 survey")`
 can be used to provide a broader picture of how American’s risk behaviors and
 sentiments amidst a global pandemic.
 

content/blog/2021-01-22-holiday-surveys.html

@@ -49,7 +49,7 @@
 restrictions to prevent further escalation in cases.
 <a href="https://www.washingtonpost.com/travel/2020/12/21/christmas-flights-cdc-restrictions-covid/">Reports</a>
 from airlines suggest air travel was up significantly during the holiday season,
-but {{< reflink "surveys" "Delphi’s COVID-19 Surveys" >}} can
+but {{< reflink "ctis" "Delphi’s COVID-19 Surveys" >}} can
 provide a broader picture of the travel Americans took during the holiday
 season. In taking greater risks with travel, did Americans change their
 behaviors in other preventative measures like mask wearing during this time?</p>
@@ -396,7 +396,7 @@ <h2>See the Data Yourself!</h2>
 for Good have partnered to conduct large-scale daily surveys to monitor the
 spread and impact of the COVID-19 pandemic in the United States. To date, the
 survey has collected more than 50 million responses. In this post, we show how
-the data from the {{< reflink "surveys" "COVID-19 survey" >}}
+the data from the {{< reflink "ctis" "COVID-19 survey" >}}
 can be used to provide a broader picture of how American’s risk behaviors and
 sentiments amidst a global pandemic.</p>
 <p>All of the above plots were built using aggregate data for the United States

content/blog/_index.md

@@ -1,4 +1,6 @@
 ---
 title: Blog
 description: News, findings, and musings from the team
+aliases:
+ - /about/blog/
 ---

content/covid19/_index.md

@@ -0,0 +1,14 @@
+---
+title: About COVIDcast
+linkTitle: COVID-19
+layout: single
+---
+
+In March 2020, Delphi pivoted from seasonal epidemic forecasting to COVID-19 tracking. Since then, we’ve created and maintained the nation’s largest public repository of diverse, geographically-detailed, real-time indicators of COVID-19 activity in the U.S. Our indicators cover every rung of the severity pyramid, and are freely available through our public API or our data export tool.
+
+Several of the underlying data sources (on which these indicators are built) would not exist or be publicly available without our efforts. This includes:
+
+* A massive national daily survey we’re running in partnership with Facebook. Over 20 million Americans have answered the survey since April 2020, providing real-time insights into, e.g., self-reported symptoms, mask wearing, testing, and contacts, all broken down by various demographics.
+* An enormous database of medical insurance claims that have been de-identified in accordance with HIPAA privacy regulations, covering more than half the US population, made possible through health system partners including Change Healthcare. We use this to produce a new syndromic COVID-19 indicator based on doctor visits, and other indicators based on hospitalizations and ICU admissions.
+
+We have selected a small number of indicators to showcase in COVIDcast, a visualization system that helps place pandemic activity in geographic and temporal context. It includes a notion of correlation across time, for example, a spike in cases is often followed by a spike in hospital admissions some number of days later.