From af3a96b69ac02dba4c9afdce27a97992eb00362d Mon Sep 17 00:00:00 2001 From: dsweber2 Date: Thu, 16 May 2024 23:33:19 -0500 Subject: [PATCH 01/13] nssp documentation draft --- docs/Gemfile | 3 + docs/Gemfile.lock | 246 +++++++++++++++-------------- docs/api/covidcast-signals/nssp.md | 84 ++++++++++ 3 files changed, 212 insertions(+), 121 deletions(-) create mode 100644 docs/api/covidcast-signals/nssp.md diff --git a/docs/Gemfile b/docs/Gemfile index 3af1f7382..d61359ba5 100644 --- a/docs/Gemfile +++ b/docs/Gemfile @@ -10,6 +10,7 @@ source "https://rubygems.org" # Happy Jekylling! #gem "jekyll", "~> 3.8.7" +gem "jekyll-include-cache" # This is the default theme for new Jekyll sites. You may change this to anything you like. gem "minima", "~> 2.0" @@ -32,3 +33,5 @@ end # Performance-booster for watching directories on Windows gem "wdm", "~> 0.1.0", :install_if => Gem.win_platform? + +gem "webrick", "~> 1.8" diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock index 6ba650506..b88901522 100644 --- a/docs/Gemfile.lock +++ b/docs/Gemfile.lock @@ -7,43 +7,42 @@ GEM minitest (~> 5.1) tzinfo (~> 1.1) zeitwerk (~> 2.2, >= 2.2.2) - addressable (2.8.0) - public_suffix (>= 2.0.2, < 5.0) + addressable (2.8.6) + public_suffix (>= 2.0.2, < 6.0) coffee-script (2.4.1) coffee-script-source execjs - coffee-script-source (1.11.1) + coffee-script-source (1.12.2) colorator (1.1.0) - commonmarker (0.17.13) - ruby-enum (~> 0.5) - concurrent-ruby (1.2.0) - dnsruby (1.61.5) - simpleidn (~> 0.1) - em-websocket (0.5.2) + commonmarker (0.23.10) + concurrent-ruby (1.2.3) + dnsruby (1.72.0) + simpleidn (~> 0.2.1) + em-websocket (0.5.3) eventmachine (>= 0.12.9) - http_parser.rb (~> 0.6.0) - ethon (0.12.0) - ffi (>= 1.3.0) + http_parser.rb (~> 0) + ethon (0.16.0) + ffi (>= 1.15.0) eventmachine (1.2.7) - execjs (2.7.0) - faraday (1.3.0) - faraday-net_http (~> 1.0) - multipart-post (>= 1.2, < 3) - ruby2_keywords - faraday-net_http (1.0.1) - ffi (1.15.0) + execjs (2.9.1) + faraday (2.9.0) + faraday-net_http (>= 2.0, < 3.2) + faraday-net_http (3.1.0) + net-http + ffi (1.16.3) forwardable-extended (2.6.0) - gemoji (3.0.1) - github-pages (214) - github-pages-health-check (= 1.17.0) - jekyll (= 3.9.0) - jekyll-avatar (= 0.7.0) - jekyll-coffeescript (= 1.1.1) - jekyll-commonmark-ghpages (= 0.1.6) - jekyll-default-layout (= 0.1.4) - jekyll-feed (= 0.15.1) + gemoji (4.1.0) + github-pages (231) + github-pages-health-check (= 1.18.2) + jekyll (= 3.9.5) + jekyll-avatar (= 0.8.0) + jekyll-coffeescript (= 1.2.2) + jekyll-commonmark-ghpages (= 0.4.0) + jekyll-default-layout (= 0.1.5) + jekyll-feed (= 0.17.0) jekyll-gist (= 1.5.0) - jekyll-github-metadata (= 2.13.0) + jekyll-github-metadata (= 2.16.1) + jekyll-include-cache (= 0.2.1) jekyll-mentions (= 1.6.0) jekyll-optional-front-matter (= 0.3.2) jekyll-paginate (= 1.1.0) @@ -52,49 +51,49 @@ GEM jekyll-relative-links (= 0.6.1) jekyll-remote-theme (= 0.4.3) jekyll-sass-converter (= 1.5.2) - jekyll-seo-tag (= 2.7.1) + jekyll-seo-tag (= 2.8.0) jekyll-sitemap (= 1.4.0) jekyll-swiss (= 1.0.0) - jekyll-theme-architect (= 0.1.1) - jekyll-theme-cayman (= 0.1.1) - jekyll-theme-dinky (= 0.1.1) - jekyll-theme-hacker (= 0.1.2) - jekyll-theme-leap-day (= 0.1.1) - jekyll-theme-merlot (= 0.1.1) - jekyll-theme-midnight (= 0.1.1) - jekyll-theme-minimal (= 0.1.1) - jekyll-theme-modernist (= 0.1.1) - jekyll-theme-primer (= 0.5.4) - jekyll-theme-slate (= 0.1.1) - jekyll-theme-tactile (= 0.1.1) - jekyll-theme-time-machine (= 0.1.1) + jekyll-theme-architect (= 0.2.0) + jekyll-theme-cayman (= 0.2.0) + jekyll-theme-dinky (= 0.2.0) + jekyll-theme-hacker (= 0.2.0) + jekyll-theme-leap-day (= 0.2.0) + jekyll-theme-merlot (= 0.2.0) + jekyll-theme-midnight (= 0.2.0) + jekyll-theme-minimal (= 0.2.0) + jekyll-theme-modernist (= 0.2.0) + jekyll-theme-primer (= 0.6.0) + jekyll-theme-slate (= 0.2.0) + jekyll-theme-tactile (= 0.2.0) + jekyll-theme-time-machine (= 0.2.0) jekyll-titles-from-headings (= 0.5.3) - jemoji (= 0.12.0) - kramdown (= 2.3.1) + jemoji (= 0.13.0) + kramdown (= 2.4.0) kramdown-parser-gfm (= 1.1.0) - liquid (= 4.0.3) + liquid (= 4.0.4) mercenary (~> 0.3) minima (= 2.5.1) - nokogiri (>= 1.10.4, < 2.0) - rouge (= 3.26.0) + nokogiri (>= 1.13.6, < 2.0) + rouge (= 3.30.0) terminal-table (~> 1.4) - github-pages-health-check (1.17.0) + github-pages-health-check (1.18.2) addressable (~> 2.3) dnsruby (~> 1.60) - octokit (~> 4.0) - public_suffix (>= 2.0.2, < 5.0) + octokit (>= 4, < 8) + public_suffix (>= 3.0, < 6.0) typhoeus (~> 1.3) - html-pipeline (2.14.0) + html-pipeline (2.14.3) activesupport (>= 2) nokogiri (>= 1.4) - http_parser.rb (0.6.0) - i18n (0.9.5) + http_parser.rb (0.8.0) + i18n (1.14.4) concurrent-ruby (~> 1.0) - jekyll (3.9.0) + jekyll (3.9.5) addressable (~> 2.4) colorator (~> 1.0) em-websocket (~> 0.5) - i18n (~> 0.7) + i18n (>= 0.7, < 2) jekyll-sass-converter (~> 1.0) jekyll-watch (~> 2.0) kramdown (>= 1.17, < 3) @@ -103,27 +102,29 @@ GEM pathutil (~> 0.9) rouge (>= 1.7, < 4) safe_yaml (~> 1.0) - jekyll-avatar (0.7.0) + jekyll-avatar (0.8.0) jekyll (>= 3.0, < 5.0) - jekyll-coffeescript (1.1.1) + jekyll-coffeescript (1.2.2) coffee-script (~> 2.2) - coffee-script-source (~> 1.11.1) - jekyll-commonmark (1.3.1) - commonmarker (~> 0.14) - jekyll (>= 3.7, < 5.0) - jekyll-commonmark-ghpages (0.1.6) - commonmarker (~> 0.17.6) - jekyll-commonmark (~> 1.2) - rouge (>= 2.0, < 4.0) - jekyll-default-layout (0.1.4) - jekyll (~> 3.0) - jekyll-feed (0.15.1) + coffee-script-source (~> 1.12) + jekyll-commonmark (1.4.0) + commonmarker (~> 0.22) + jekyll-commonmark-ghpages (0.4.0) + commonmarker (~> 0.23.7) + jekyll (~> 3.9.0) + jekyll-commonmark (~> 1.4.0) + rouge (>= 2.0, < 5.0) + jekyll-default-layout (0.1.5) + jekyll (>= 3.0, < 5.0) + jekyll-feed (0.17.0) jekyll (>= 3.7, < 5.0) jekyll-gist (1.5.0) octokit (~> 4.2) - jekyll-github-metadata (2.13.0) + jekyll-github-metadata (2.16.1) jekyll (>= 3.4, < 5.0) - octokit (~> 4.0, != 4.4.0) + octokit (>= 4, < 7, != 4.4.0) + jekyll-include-cache (0.2.1) + jekyll (>= 3.7, < 5.0) jekyll-mentions (1.6.0) html-pipeline (~> 2.3) jekyll (>= 3.7, < 5.0) @@ -143,65 +144,65 @@ GEM rubyzip (>= 1.3.0, < 3.0) jekyll-sass-converter (1.5.2) sass (~> 3.4) - jekyll-seo-tag (2.7.1) + jekyll-seo-tag (2.8.0) jekyll (>= 3.8, < 5.0) jekyll-sitemap (1.4.0) jekyll (>= 3.7, < 5.0) jekyll-swiss (1.0.0) - jekyll-theme-architect (0.1.1) - jekyll (~> 3.5) + jekyll-theme-architect (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-cayman (0.1.1) - jekyll (~> 3.5) + jekyll-theme-cayman (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-dinky (0.1.1) - jekyll (~> 3.5) + jekyll-theme-dinky (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-hacker (0.1.2) + jekyll-theme-hacker (0.2.0) jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-leap-day (0.1.1) - jekyll (~> 3.5) + jekyll-theme-leap-day (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-merlot (0.1.1) - jekyll (~> 3.5) + jekyll-theme-merlot (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-midnight (0.1.1) - jekyll (~> 3.5) + jekyll-theme-midnight (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-minimal (0.1.1) - jekyll (~> 3.5) + jekyll-theme-minimal (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-modernist (0.1.1) - jekyll (~> 3.5) + jekyll-theme-modernist (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-primer (0.5.4) + jekyll-theme-primer (0.6.0) jekyll (> 3.5, < 5.0) jekyll-github-metadata (~> 2.9) jekyll-seo-tag (~> 2.0) - jekyll-theme-slate (0.1.1) - jekyll (~> 3.5) + jekyll-theme-slate (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-tactile (0.1.1) - jekyll (~> 3.5) + jekyll-theme-tactile (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) - jekyll-theme-time-machine (0.1.1) - jekyll (~> 3.5) + jekyll-theme-time-machine (0.2.0) + jekyll (> 3.5, < 5.0) jekyll-seo-tag (~> 2.0) jekyll-titles-from-headings (0.5.3) jekyll (>= 3.3, < 5.0) jekyll-watch (2.2.1) listen (~> 3.0) - jemoji (0.12.0) - gemoji (~> 3.0) + jemoji (0.13.0) + gemoji (>= 3, < 5) html-pipeline (~> 2.2) jekyll (>= 3.0, < 5.0) - kramdown (2.3.1) + kramdown (2.4.0) rexml kramdown-parser-gfm (1.1.0) kramdown (~> 2.0) - liquid (4.0.3) - listen (3.5.1) + liquid (4.0.4) + listen (3.9.0) rb-fsevent (~> 0.10, >= 0.10.3) rb-inotify (~> 0.9, >= 0.9.10) mercenary (0.3.6) @@ -210,53 +211,54 @@ GEM jekyll (>= 3.5, < 5.0) jekyll-feed (~> 0.9) jekyll-seo-tag (~> 2.1) - minitest (5.17.0) multipart-post (2.1.1) nokogiri (1.16.5) - mini_portile2 (~> 2.8.2) + minitest (5.22.3) + net-http (0.4.1) + uri + nokogiri (1.16.3) racc (~> 1.4) - octokit (4.20.0) - faraday (>= 0.9) - sawyer (~> 0.8.0, >= 0.5.3) + octokit (4.25.1) + faraday (>= 1, < 3) + sawyer (~> 0.9) pathutil (0.16.2) forwardable-extended (~> 2.6) - public_suffix (4.0.6) + public_suffix (5.0.4) racc (1.7.3) - rb-fsevent (0.10.4) + rb-fsevent (0.11.2) rb-inotify (0.10.1) ffi (~> 1.0) - rexml (3.2.5) - rouge (3.26.0) - ruby-enum (0.9.0) - i18n - ruby2_keywords (0.0.4) - rubyzip (2.3.0) + rexml (3.2.6) + rouge (3.30.0) + rubyzip (2.3.2) safe_yaml (1.0.5) sass (3.7.4) sass-listen (~> 4.0.0) sass-listen (4.0.0) rb-fsevent (~> 0.9, >= 0.9.4) rb-inotify (~> 0.9, >= 0.9.7) - sawyer (0.8.2) + sawyer (0.9.2) addressable (>= 2.3.5) - faraday (> 0.8, < 2.0) + faraday (>= 0.17.3, < 3) simpleidn (0.2.1) unf (~> 0.1.4) terminal-table (1.8.0) unicode-display_width (~> 1.1, >= 1.1.1) thread_safe (0.3.6) - typhoeus (1.4.0) + typhoeus (1.4.1) ethon (>= 0.9.0) - tzinfo (1.2.10) + tzinfo (1.2.11) thread_safe (~> 0.1) tzinfo-data (1.2021.1) tzinfo (>= 1.0.0) unf (0.1.4) unf_ext - unf_ext (0.0.7.7) - unicode-display_width (1.7.0) + unf_ext (0.0.9.1) + unicode-display_width (1.8.0) + uri (0.13.0) wdm (0.1.1) - zeitwerk (2.6.6) + webrick (1.8.1) + zeitwerk (2.6.13) PLATFORMS ruby @@ -264,10 +266,12 @@ PLATFORMS DEPENDENCIES github-pages jekyll-feed (~> 0.6) + jekyll-include-cache minima (~> 2.0) tzinfo (~> 1.2) tzinfo-data wdm (~> 0.1.0) + webrick (~> 1.8) BUNDLED WITH 2.2.15 diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md new file mode 100644 index 000000000..a8719193e --- /dev/null +++ b/docs/api/covidcast-signals/nssp.md @@ -0,0 +1,84 @@ +--- +title: NSSP +parent: Data Sources and Signals +grand_parent: COVIDcast Main Endpoint +--- +# National Syndromic Surveillance Program (NSSP) Emerency Department (ED) visits +{: .no_toc} + +* **Source name:** `nssp` +* **Earliest issue available:** (TODO ask Minh) +* **Number of data revisions since 19 May 2020:** (TODO) +* **Date of last change:** TODO +* **Available for:** county, hrr, msa, state (see [geography coding docs](../covidcast_geography.md)) +* **Time type:** week (see [date format docs](../covidcast_times.md)) +* **License:** [Public Domain US Government](https://www.usa.gov/government-works) + +[The National Syndromic Surveillance Program (NSSP)](https://www.cdc.gov/nssp/php/about/index.html) is an effort to track epidemiologically relevant conditions. +This dataset in particular tracks emergency department (ED) visits arising from a subset of influenza-like illnesses, specifically flu, COVID-19, and RSV. +It is derived from [this cdc dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data). +Originating in late 2022, as of May 2024, NSSP received data from 78% of US EDs. + +| Signal | Description | +|---------------------------------|-------------------------------------------------------------------------| +| `pct_visits_covid` | Percent of visits with a discharge diagnosis code of covid | +| `pct_visits_influenza` | Percent of visits with a discharge diagnosis code of influenza | +| `pct_visits_rsv` | Percent of visits with a discharge diagnosis code of rsv | +| `pct_visits_combined` | Percent of visits with a discharge diagnosis code of covid, flu, or rsv | +| `smoothed_pct_visits_covid` | 3 week moving average of `pct_visits_covid` | +| `smoothed_pct_visits_influenza` | 3 week moving average of `pct_visits_influenza` | +| `smoothed_pct_visits_rsv` | 3 week moving average of `pct_visits_rsv` | +| `smoothed_pct_visits_combined` | 3 week moving average of `pct_visits_combined` | + +## Table of contents +{: .no_toc .text-delta} + +1. TOC +{:toc} + +## Estimation + +The percent visits is as a fraction of visits at facilities reporting to NSSP, rather than all facilities in the area. +The county and state level are direct data sources, while `hrr` and `msa` are estimated. + +### Geographic weighting +As the original data is a percentage, to compute `hrr` and `msa` from county-level, we do a weighted mean, weighting by the county's population in the last census (2020). +This assumes that the number of ED visits is proportional to the overall population of the county, which may not strictly be the case (e.g. denser counties having easier access and thus may have a higher rate of ED visits per capita). + +State-level data is reported separately, and is **not** simply an average of the county-level data, but may contain facilities omitted at the regional level (for example, if small facilities are excluded for privacy reasons).[^1] + +### Smoothing + +The smoothed values are a simple 3 week average of the corresponding signals (note that since this is weekly data, this is 3 values rather than 21). + +## Limitations + +As of May 2024, NSSP received data from 78% of US EDs. +The geographic distribution of those sites can be seen [here](https://www.cdc.gov/nssp/media/images/2024/04/Participation-with-date.png); the most noticeable gaps in coverage are in California, Oklahoma, and Colorado, though most states have some counties that are absent. + +NSSP notes that not every patient entering an ED is tested for these conditions, so this may represent an undercount of total cases. + +## Missingness + +Counties which do not have data are listed, but with an `NA` value. + +## Lag and Backfill + +There is significant backfill in this signal, primarily arising when a new facility joins the network and its data is included in a region. +This has the strongest effects at the highest levels of aggregation. + + +The weekly signal is reported on Friday mornings. + +## Source and Licensing + +This source is processed from this [data.cdc.gov site](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data). +There is another version of the state-only data available [here](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/7mra-9cq9/about_data). + +This data was originally published by the National Center for Health Statistics, and is made available here as a convenience to the forecasting community under the terms of the original license, which is [U.S. Government Public Domain](https://www.usa.gov/government-copyright). + +If the signal has specific licensing or sourcing that should be acknowledged, +describe it here. Also, include links to source websites for data that is +scraped or received from another source. + +[^1]: (TODO should probably confirm this in some way) From dc918b6701cfc4c3648b9407a59ed9593fc49008 Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Wed, 5 Jun 2024 18:14:27 -0400 Subject: [PATCH 02/13] limitations detail and wording improvements --- docs/api/covidcast-signals/nssp.md | 41 +++++++++++++++++------------- 1 file changed, 24 insertions(+), 17 deletions(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index a8719193e..11f238bc1 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -1,5 +1,5 @@ --- -title: NSSP +title: NSSP emergency department visits parent: Data Sources and Signals grand_parent: COVIDcast Main Endpoint --- @@ -8,23 +8,25 @@ grand_parent: COVIDcast Main Endpoint * **Source name:** `nssp` * **Earliest issue available:** (TODO ask Minh) -* **Number of data revisions since 19 May 2020:** (TODO) -* **Date of last change:** TODO +* **Number of data revisions since 19 May 2020:** 0 +* **Date of last change:** Never * **Available for:** county, hrr, msa, state (see [geography coding docs](../covidcast_geography.md)) * **Time type:** week (see [date format docs](../covidcast_times.md)) * **License:** [Public Domain US Government](https://www.usa.gov/government-works) +## Overview + [The National Syndromic Surveillance Program (NSSP)](https://www.cdc.gov/nssp/php/about/index.html) is an effort to track epidemiologically relevant conditions. -This dataset in particular tracks emergency department (ED) visits arising from a subset of influenza-like illnesses, specifically flu, COVID-19, and RSV. -It is derived from [this cdc dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data). -Originating in late 2022, as of May 2024, NSSP received data from 78% of US EDs. +This dataset in particular tracks emergency department (ED) visits arising from a subset of influenza-like illnesses, specifically influenza, COVID-19, and RSV. +It is derived from the CDC's [Respiratory Virus Response NSSP Emergency Department Visit Trajectories dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data), which started reporting data in late 2022. +As of May 2024, NSSP received data from 78% of US EDs. | Signal | Description | |---------------------------------|-------------------------------------------------------------------------| -| `pct_visits_covid` | Percent of visits with a discharge diagnosis code of covid | -| `pct_visits_influenza` | Percent of visits with a discharge diagnosis code of influenza | -| `pct_visits_rsv` | Percent of visits with a discharge diagnosis code of rsv | -| `pct_visits_combined` | Percent of visits with a discharge diagnosis code of covid, flu, or rsv | +| `pct_visits_covid` | Percent of ED visits that had a discharge diagnosis code of covid | +| `pct_visits_influenza` | Percent of ED visits that had a discharge diagnosis code of influenza | +| `pct_visits_rsv` | Percent of ED visits that had a discharge diagnosis code of rsv | +| `pct_visits_combined` | Percent of ED visits that had a discharge diagnosis code of covid, influenza, or rsv | | `smoothed_pct_visits_covid` | 3 week moving average of `pct_visits_covid` | | `smoothed_pct_visits_influenza` | 3 week moving average of `pct_visits_influenza` | | `smoothed_pct_visits_rsv` | 3 week moving average of `pct_visits_rsv` | @@ -38,25 +40,30 @@ Originating in late 2022, as of May 2024, NSSP received data from 78% of US EDs. ## Estimation -The percent visits is as a fraction of visits at facilities reporting to NSSP, rather than all facilities in the area. -The county and state level are direct data sources, while `hrr` and `msa` are estimated. +The percent visits signals are calculated as a fraction of visits at facilities reporting to NSSP, rather than all facilities in the area. +County and state level data is reported as-is from NSSP, without modification, while `hrr` and `msa` are estimated by Delphi. ### Geographic weighting -As the original data is a percentage, to compute `hrr` and `msa` from county-level, we do a weighted mean, weighting by the county's population in the last census (2020). -This assumes that the number of ED visits is proportional to the overall population of the county, which may not strictly be the case (e.g. denser counties having easier access and thus may have a higher rate of ED visits per capita). +As the original data is a percentage and raw case counts are not available, `hrr` and `msa` values are computed from county-level data using a weighted mean. Each county is assigned a weight equal to its population in the last census (2020). +This assumes that the number of ED visits is proportional to the overall population of a county, i.e. the per-capita ED visit rate is the same for all counties, which may not be the case (for example, denser counties may have easier access to EDs and thus higher rates of ED visits per capita). State-level data is reported separately, and is **not** simply an average of the county-level data, but may contain facilities omitted at the regional level (for example, if small facilities are excluded for privacy reasons).[^1] ### Smoothing -The smoothed values are a simple 3 week average of the corresponding signals (note that since this is weekly data, this is 3 values rather than 21). +Smoothed signals are calculated using a simple 3 week moving average of the relevant weekly signals. Note that since the unsmoothed `pct_visits_*` signals report weekly data, each smoothed signal value is computed from 3 points rather than 21, as would be used if the unsmoothed data were reported daily. ## Limitations As of May 2024, NSSP received data from 78% of US EDs. -The geographic distribution of those sites can be seen [here](https://www.cdc.gov/nssp/media/images/2024/04/Participation-with-date.png); the most noticeable gaps in coverage are in California, Oklahoma, and Colorado, though most states have some counties that are absent. +The most noticeable gaps in [geographic coverage](https://www.cdc.gov/nssp/media/images/2024/04/Participation-with-date.png) are in California, Colorado, Missouri, Oklahoma, and Virginia, though most states have some counties that are absent. + +NSSP notes that not every patient entering an ED is tested for the conditions of interest, so the data may undercount total cases and as a result underreport percent visits. + +Our [geographic weighting approach](#geographic-weighting) assumes that the number of ED visits is proportional to the overall population of a county. However, in reality we expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that someone living in an urban county will make, that is, the average urban resident may make more ED visits than the average rural resident. + +As a result, total ED visits per capita in rural counties may be lower than total ED visits per capita in urban counties. Since our weighting approach uses population as the weighting factor, rural counties would tend to be overrepresented in estimated values. -NSSP notes that not every patient entering an ED is tested for these conditions, so this may represent an undercount of total cases. ## Missingness From a65a8083f90ed74dd88e0999bfc106d35bad9509 Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Thu, 6 Jun 2024 11:22:23 -0400 Subject: [PATCH 03/13] limitations detail --- docs/api/covidcast-signals/nssp.md | 30 +++++++++++++++++++----------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index 11f238bc1..debff9c84 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -53,39 +53,47 @@ State-level data is reported separately, and is **not** simply an average of the Smoothed signals are calculated using a simple 3 week moving average of the relevant weekly signals. Note that since the unsmoothed `pct_visits_*` signals report weekly data, each smoothed signal value is computed from 3 points rather than 21, as would be used if the unsmoothed data were reported daily. + ## Limitations -As of May 2024, NSSP received data from 78% of US EDs. -The most noticeable gaps in [geographic coverage](https://www.cdc.gov/nssp/media/images/2024/04/Participation-with-date.png) are in California, Colorado, Missouri, Oklahoma, and Virginia, though most states have some counties that are absent. +There is substantial missingness at the county level. This tends to impact more rural and lower population locations. See the [missingness section below](#missingness) for more information. NSSP notes that not every patient entering an ED is tested for the conditions of interest, so the data may undercount total cases and as a result underreport percent visits. -Our [geographic weighting approach](#geographic-weighting) assumes that the number of ED visits is proportional to the overall population of a county. However, in reality we expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that someone living in an urban county will make, that is, the average urban resident may make more ED visits than the average rural resident. +Our [geographic weighting approach](#geographic-weighting) assumes that the number of ED visits is proportional to the overall population of a county. However, in reality, there are various factors that could affect the accuracy of this assumption. + +For example, we might expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that someone living in an urban county will make, that is, the average urban resident may make more ED visits than the average rural resident. As a result, total ED visits per capita in rural counties may be lower than total ED visits per capita in urban counties. Since our weighting approach uses population as the weighting factor, rural counties would tend to be overrepresented in estimated values. +Some low population counties occasionally report outliers, e.g. 33.33%, 50%, 100% of ER visits being covid-related. As of May 2024, an analysis shows around 10 unusually high values across the full history of all signals, so they are rare. We expect that these high rates are by chance, due to a small total number of ED visits in a given week. + ## Missingness +As of May 2024, NSSP received data from 78% of US EDs. +The most noticeable gaps in [county coverage](https://www.cdc.gov/nssp/media/images/2024/04/Participation-with-date.png) are in California, Colorado, Missouri, Oklahoma, and Virginia, though most states have some counties that are absent. + +The following states have no country-level data at all: CA, WA, AK, AZ, AL, CO, SD, ND, MO, AR, FL, OH, NH, CT, NJ. Counties which do not have data are listed, but with an `NA` value. +At the state level, South Dakota, Missouri, and territories are not reported. + + ## Lag and Backfill +The weekly signal is reported on Friday mornings, adding data from the prior week. +For example, on Friday, 2024-04-19, the source added new data from the week ending 2024-04-13. + There is significant backfill in this signal, primarily arising when a new facility joins the network and its data is included in a region. This has the strongest effects at the highest levels of aggregation. -The weekly signal is reported on Friday mornings. - ## Source and Licensing -This source is processed from this [data.cdc.gov site](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data). -There is another version of the state-only data available [here](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/7mra-9cq9/about_data). +This source is derived from the CDC's [Respiratory Virus Response NSSP Emergency Department Visit Trajectories dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data). +There is another version of the dataset that includes [state data only](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/7mra-9cq9/about_data). This data was originally published by the National Center for Health Statistics, and is made available here as a convenience to the forecasting community under the terms of the original license, which is [U.S. Government Public Domain](https://www.usa.gov/government-copyright). -If the signal has specific licensing or sourcing that should be acknowledged, -describe it here. Also, include links to source websites for data that is -scraped or received from another source. - [^1]: (TODO should probably confirm this in some way) From 0d1d2a2fafeeb6c13516ff2a409fca47865a1dcb Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Thu, 6 Jun 2024 11:51:06 -0400 Subject: [PATCH 04/13] lag and backfill details --- docs/api/covidcast-signals/nssp.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index debff9c84..28f09a63f 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -85,8 +85,9 @@ At the state level, South Dakota, Missouri, and territories are not reported. The weekly signal is reported on Friday mornings, adding data from the prior week. For example, on Friday, 2024-04-19, the source added new data from the week ending 2024-04-13. -There is significant backfill in this signal, primarily arising when a new facility joins the network and its data is included in a region. -This has the strongest effects at the highest levels of aggregation. +This data source has frequent backfill, primarily arising from newly included EDs. When a new facility joins the reporting network, its historical data is added to the dataset, resulting in changes to historical values for every geographic level that ED is part of (county through nation). Because of this, the broadest geographic levels are more likely to be revised. + +In previous revisions, we have noted changes to values dating back about 2 years. ## Source and Licensing From 6a3eadd8c8dcd8c45383f8f92bbfa9c9a195c112 Mon Sep 17 00:00:00 2001 From: dsweber2 Date: Thu, 6 Jun 2024 11:33:06 -0500 Subject: [PATCH 05/13] don't update Gem by hand --- docs/Gemfile | 3 - docs/Gemfile.lock | 246 +++++++++++++++++++++++----------------------- 2 files changed, 121 insertions(+), 128 deletions(-) diff --git a/docs/Gemfile b/docs/Gemfile index d61359ba5..3af1f7382 100644 --- a/docs/Gemfile +++ b/docs/Gemfile @@ -10,7 +10,6 @@ source "https://rubygems.org" # Happy Jekylling! #gem "jekyll", "~> 3.8.7" -gem "jekyll-include-cache" # This is the default theme for new Jekyll sites. You may change this to anything you like. gem "minima", "~> 2.0" @@ -33,5 +32,3 @@ end # Performance-booster for watching directories on Windows gem "wdm", "~> 0.1.0", :install_if => Gem.win_platform? - -gem "webrick", "~> 1.8" diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock index b88901522..6ba650506 100644 --- a/docs/Gemfile.lock +++ b/docs/Gemfile.lock @@ -7,42 +7,43 @@ GEM minitest (~> 5.1) tzinfo (~> 1.1) zeitwerk (~> 2.2, >= 2.2.2) - addressable (2.8.6) - public_suffix (>= 2.0.2, < 6.0) + addressable (2.8.0) + public_suffix (>= 2.0.2, < 5.0) coffee-script (2.4.1) coffee-script-source execjs - coffee-script-source (1.12.2) + coffee-script-source (1.11.1) colorator (1.1.0) - commonmarker (0.23.10) - concurrent-ruby (1.2.3) - dnsruby (1.72.0) - simpleidn (~> 0.2.1) - em-websocket (0.5.3) + commonmarker (0.17.13) + ruby-enum (~> 0.5) + concurrent-ruby (1.2.0) + dnsruby (1.61.5) + simpleidn (~> 0.1) + em-websocket (0.5.2) eventmachine (>= 0.12.9) - http_parser.rb (~> 0) - ethon (0.16.0) - ffi (>= 1.15.0) + http_parser.rb (~> 0.6.0) + ethon (0.12.0) + ffi (>= 1.3.0) eventmachine (1.2.7) - execjs (2.9.1) - faraday (2.9.0) - faraday-net_http (>= 2.0, < 3.2) - faraday-net_http (3.1.0) - net-http - ffi (1.16.3) + execjs (2.7.0) + faraday (1.3.0) + faraday-net_http (~> 1.0) + multipart-post (>= 1.2, < 3) + ruby2_keywords + faraday-net_http (1.0.1) + ffi (1.15.0) forwardable-extended (2.6.0) - gemoji (4.1.0) - github-pages (231) - github-pages-health-check (= 1.18.2) - jekyll (= 3.9.5) - jekyll-avatar (= 0.8.0) - jekyll-coffeescript (= 1.2.2) - jekyll-commonmark-ghpages (= 0.4.0) - jekyll-default-layout (= 0.1.5) - jekyll-feed (= 0.17.0) + gemoji (3.0.1) + github-pages (214) + github-pages-health-check (= 1.17.0) + jekyll (= 3.9.0) + jekyll-avatar (= 0.7.0) + jekyll-coffeescript (= 1.1.1) + jekyll-commonmark-ghpages (= 0.1.6) + jekyll-default-layout (= 0.1.4) + jekyll-feed (= 0.15.1) jekyll-gist (= 1.5.0) - jekyll-github-metadata (= 2.16.1) - jekyll-include-cache (= 0.2.1) + jekyll-github-metadata (= 2.13.0) jekyll-mentions (= 1.6.0) jekyll-optional-front-matter (= 0.3.2) jekyll-paginate (= 1.1.0) @@ -51,49 +52,49 @@ GEM jekyll-relative-links (= 0.6.1) jekyll-remote-theme (= 0.4.3) jekyll-sass-converter (= 1.5.2) - jekyll-seo-tag (= 2.8.0) + jekyll-seo-tag (= 2.7.1) jekyll-sitemap (= 1.4.0) jekyll-swiss (= 1.0.0) - jekyll-theme-architect (= 0.2.0) - jekyll-theme-cayman (= 0.2.0) - jekyll-theme-dinky (= 0.2.0) - jekyll-theme-hacker (= 0.2.0) - jekyll-theme-leap-day (= 0.2.0) - jekyll-theme-merlot (= 0.2.0) - jekyll-theme-midnight (= 0.2.0) - jekyll-theme-minimal (= 0.2.0) - jekyll-theme-modernist (= 0.2.0) - jekyll-theme-primer (= 0.6.0) - jekyll-theme-slate (= 0.2.0) - jekyll-theme-tactile (= 0.2.0) - jekyll-theme-time-machine (= 0.2.0) + jekyll-theme-architect (= 0.1.1) + jekyll-theme-cayman (= 0.1.1) + jekyll-theme-dinky (= 0.1.1) + jekyll-theme-hacker (= 0.1.2) + jekyll-theme-leap-day (= 0.1.1) + jekyll-theme-merlot (= 0.1.1) + jekyll-theme-midnight (= 0.1.1) + jekyll-theme-minimal (= 0.1.1) + jekyll-theme-modernist (= 0.1.1) + jekyll-theme-primer (= 0.5.4) + jekyll-theme-slate (= 0.1.1) + jekyll-theme-tactile (= 0.1.1) + jekyll-theme-time-machine (= 0.1.1) jekyll-titles-from-headings (= 0.5.3) - jemoji (= 0.13.0) - kramdown (= 2.4.0) + jemoji (= 0.12.0) + kramdown (= 2.3.1) kramdown-parser-gfm (= 1.1.0) - liquid (= 4.0.4) + liquid (= 4.0.3) mercenary (~> 0.3) minima (= 2.5.1) - nokogiri (>= 1.13.6, < 2.0) - rouge (= 3.30.0) + nokogiri (>= 1.10.4, < 2.0) + rouge (= 3.26.0) terminal-table (~> 1.4) - github-pages-health-check (1.18.2) + github-pages-health-check (1.17.0) addressable (~> 2.3) dnsruby (~> 1.60) - octokit (>= 4, < 8) - public_suffix (>= 3.0, < 6.0) + octokit (~> 4.0) + public_suffix (>= 2.0.2, < 5.0) typhoeus (~> 1.3) - html-pipeline (2.14.3) + html-pipeline (2.14.0) activesupport (>= 2) nokogiri (>= 1.4) - http_parser.rb (0.8.0) - i18n (1.14.4) + http_parser.rb (0.6.0) + i18n (0.9.5) concurrent-ruby (~> 1.0) - jekyll (3.9.5) + jekyll (3.9.0) addressable (~> 2.4) colorator (~> 1.0) em-websocket (~> 0.5) - i18n (>= 0.7, < 2) + i18n (~> 0.7) jekyll-sass-converter (~> 1.0) jekyll-watch (~> 2.0) kramdown (>= 1.17, < 3) @@ -102,29 +103,27 @@ GEM pathutil (~> 0.9) rouge (>= 1.7, < 4) safe_yaml (~> 1.0) - jekyll-avatar (0.8.0) + jekyll-avatar (0.7.0) jekyll (>= 3.0, < 5.0) - jekyll-coffeescript (1.2.2) + jekyll-coffeescript (1.1.1) coffee-script (~> 2.2) - coffee-script-source (~> 1.12) - jekyll-commonmark (1.4.0) - commonmarker (~> 0.22) - jekyll-commonmark-ghpages (0.4.0) - commonmarker (~> 0.23.7) - jekyll (~> 3.9.0) - jekyll-commonmark (~> 1.4.0) - rouge (>= 2.0, < 5.0) - jekyll-default-layout (0.1.5) - jekyll (>= 3.0, < 5.0) - jekyll-feed (0.17.0) + coffee-script-source (~> 1.11.1) + jekyll-commonmark (1.3.1) + commonmarker (~> 0.14) + jekyll (>= 3.7, < 5.0) + jekyll-commonmark-ghpages (0.1.6) + commonmarker (~> 0.17.6) + jekyll-commonmark (~> 1.2) + rouge (>= 2.0, < 4.0) + jekyll-default-layout (0.1.4) + jekyll (~> 3.0) + jekyll-feed (0.15.1) jekyll (>= 3.7, < 5.0) jekyll-gist (1.5.0) octokit (~> 4.2) - jekyll-github-metadata (2.16.1) + jekyll-github-metadata (2.13.0) jekyll (>= 3.4, < 5.0) - octokit (>= 4, < 7, != 4.4.0) - jekyll-include-cache (0.2.1) - jekyll (>= 3.7, < 5.0) + octokit (~> 4.0, != 4.4.0) jekyll-mentions (1.6.0) html-pipeline (~> 2.3) jekyll (>= 3.7, < 5.0) @@ -144,65 +143,65 @@ GEM rubyzip (>= 1.3.0, < 3.0) jekyll-sass-converter (1.5.2) sass (~> 3.4) - 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jekyll-theme-minimal (0.2.0) - jekyll (> 3.5, < 5.0) + jekyll-theme-minimal (0.1.1) + jekyll (~> 3.5) jekyll-seo-tag (~> 2.0) - jekyll-theme-modernist (0.2.0) - jekyll (> 3.5, < 5.0) + jekyll-theme-modernist (0.1.1) + jekyll (~> 3.5) jekyll-seo-tag (~> 2.0) - jekyll-theme-primer (0.6.0) + jekyll-theme-primer (0.5.4) jekyll (> 3.5, < 5.0) jekyll-github-metadata (~> 2.9) jekyll-seo-tag (~> 2.0) - jekyll-theme-slate (0.2.0) - jekyll (> 3.5, < 5.0) + jekyll-theme-slate (0.1.1) + jekyll (~> 3.5) jekyll-seo-tag (~> 2.0) - jekyll-theme-tactile (0.2.0) - jekyll (> 3.5, < 5.0) + jekyll-theme-tactile (0.1.1) + jekyll (~> 3.5) jekyll-seo-tag (~> 2.0) - jekyll-theme-time-machine (0.2.0) - jekyll (> 3.5, < 5.0) + jekyll-theme-time-machine (0.1.1) + jekyll (~> 3.5) jekyll-seo-tag (~> 2.0) jekyll-titles-from-headings (0.5.3) jekyll (>= 3.3, < 5.0) jekyll-watch (2.2.1) listen (~> 3.0) - jemoji (0.13.0) - gemoji (>= 3, < 5) + jemoji (0.12.0) + gemoji (~> 3.0) html-pipeline (~> 2.2) jekyll (>= 3.0, < 5.0) - kramdown (2.4.0) + kramdown (2.3.1) rexml kramdown-parser-gfm (1.1.0) kramdown (~> 2.0) - liquid (4.0.4) - listen (3.9.0) + liquid (4.0.3) + listen (3.5.1) rb-fsevent (~> 0.10, >= 0.10.3) rb-inotify (~> 0.9, >= 0.9.10) mercenary (0.3.6) @@ -211,54 +210,53 @@ GEM jekyll (>= 3.5, < 5.0) jekyll-feed (~> 0.9) jekyll-seo-tag (~> 2.1) + minitest (5.17.0) multipart-post (2.1.1) nokogiri (1.16.5) - minitest (5.22.3) - net-http (0.4.1) - uri - nokogiri (1.16.3) + mini_portile2 (~> 2.8.2) racc (~> 1.4) - octokit (4.25.1) - faraday (>= 1, < 3) - sawyer (~> 0.9) + octokit (4.20.0) + faraday (>= 0.9) + sawyer (~> 0.8.0, >= 0.5.3) pathutil (0.16.2) forwardable-extended (~> 2.6) - public_suffix (5.0.4) + public_suffix (4.0.6) racc (1.7.3) - rb-fsevent (0.11.2) + rb-fsevent (0.10.4) rb-inotify (0.10.1) ffi (~> 1.0) - rexml (3.2.6) - rouge (3.30.0) - rubyzip (2.3.2) + rexml (3.2.5) + rouge (3.26.0) + ruby-enum (0.9.0) + i18n + ruby2_keywords (0.0.4) + rubyzip (2.3.0) safe_yaml (1.0.5) sass (3.7.4) sass-listen (~> 4.0.0) sass-listen (4.0.0) rb-fsevent (~> 0.9, >= 0.9.4) rb-inotify (~> 0.9, >= 0.9.7) - sawyer (0.9.2) + sawyer (0.8.2) addressable (>= 2.3.5) - faraday (>= 0.17.3, < 3) + faraday (> 0.8, < 2.0) simpleidn (0.2.1) unf (~> 0.1.4) terminal-table (1.8.0) unicode-display_width (~> 1.1, >= 1.1.1) thread_safe (0.3.6) - typhoeus (1.4.1) + typhoeus (1.4.0) ethon (>= 0.9.0) - tzinfo (1.2.11) + tzinfo (1.2.10) thread_safe (~> 0.1) tzinfo-data (1.2021.1) tzinfo (>= 1.0.0) unf (0.1.4) unf_ext - unf_ext (0.0.9.1) - unicode-display_width (1.8.0) - uri (0.13.0) + unf_ext (0.0.7.7) + unicode-display_width (1.7.0) wdm (0.1.1) - webrick (1.8.1) - zeitwerk (2.6.13) + zeitwerk (2.6.6) PLATFORMS ruby @@ -266,12 +264,10 @@ PLATFORMS DEPENDENCIES github-pages jekyll-feed (~> 0.6) - jekyll-include-cache minima (~> 2.0) tzinfo (~> 1.2) tzinfo-data wdm (~> 0.1.0) - webrick (~> 1.8) BUNDLED WITH 2.2.15 From fff0654897ed539153bdbc8763aa074211905547 Mon Sep 17 00:00:00 2001 From: David Weber Date: Thu, 6 Jun 2024 11:12:51 -0700 Subject: [PATCH 06/13] include national data Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com> --- docs/api/covidcast-signals/nssp.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index 28f09a63f..8cf67d936 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -10,7 +10,7 @@ grand_parent: COVIDcast Main Endpoint * **Earliest issue available:** (TODO ask Minh) * **Number of data revisions since 19 May 2020:** 0 * **Date of last change:** Never -* **Available for:** county, hrr, msa, state (see [geography coding docs](../covidcast_geography.md)) +* **Available for:** county, hrr, msa, state, nation (see [geography coding docs](../covidcast_geography.md)) * **Time type:** week (see [date format docs](../covidcast_times.md)) * **License:** [Public Domain US Government](https://www.usa.gov/government-works) From 761a808b8b8e4909550b1719b6c464666a7b8026 Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Thu, 6 Jun 2024 18:15:14 -0400 Subject: [PATCH 07/13] missingness detail --- docs/api/covidcast-signals/nssp.md | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index 8cf67d936..eeea67e6f 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -44,10 +44,11 @@ The percent visits signals are calculated as a fraction of visits at facilities County and state level data is reported as-is from NSSP, without modification, while `hrr` and `msa` are estimated by Delphi. ### Geographic weighting -As the original data is a percentage and raw case counts are not available, `hrr` and `msa` values are computed from county-level data using a weighted mean. Each county is assigned a weight equal to its population in the last census (2020). -This assumes that the number of ED visits is proportional to the overall population of a county, i.e. the per-capita ED visit rate is the same for all counties, which may not be the case (for example, denser counties may have easier access to EDs and thus higher rates of ED visits per capita). +As the original data is a percentage and raw case counts are not available, `hrr` and `msa` values are computed from county-level data using a weighted mean. Each county is assigned a weight equal to its population in the last census (2020). Unreported counties are implicitly treated as having a weight of 0 or a value equal to the group mean. -State-level data is reported separately, and is **not** simply an average of the county-level data, but may contain facilities omitted at the regional level (for example, if small facilities are excluded for privacy reasons).[^1] +This weighting approach assumes that the number of ED visits is proportional to the overall population of a county, i.e. the per-capita ED visit rate is the same for all counties, which may not be the case (for example, denser counties may have easier access to EDs and thus higher rates of ED visits per capita). + +State reporting process is separate from the county reporting process. As such, state-level data is **not** simply an average of the county-level data, but may contain facilities omitted at the regional level. For example, state-level values are available for California, even though no California county data is reported. ### Smoothing @@ -58,26 +59,31 @@ Smoothed signals are calculated using a simple 3 week moving average of the rele There is substantial missingness at the county level. This tends to impact more rural and lower population locations. See the [missingness section below](#missingness) for more information. -NSSP notes that not every patient entering an ED is tested for the conditions of interest, so the data may undercount total cases and as a result underreport percent visits. +NSSP notes that not every patient entering an ED is tested for the conditions of interest, so the data may undercount total cases and as a result percent visits may be biased downward. Our [geographic weighting approach](#geographic-weighting) assumes that the number of ED visits is proportional to the overall population of a county. However, in reality, there are various factors that could affect the accuracy of this assumption. -For example, we might expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that someone living in an urban county will make, that is, the average urban resident may make more ED visits than the average rural resident. +For example, we might expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that someone living in an urban county will make, that is, the average urban resident may make more ED visits than the average rural resident over a given period of time. -As a result, total ED visits per capita in rural counties may be lower than total ED visits per capita in urban counties. Since our weighting approach uses population as the weighting factor, rural counties would tend to be overrepresented in estimated values. +As a result, total ED visits per capita in rural counties may be lower than total ED visits per capita in urban counties. Since our weighting approach uses population as the weights, rural counties would tend to be overrepresented in estimated values. Some low population counties occasionally report outliers, e.g. 33.33%, 50%, 100% of ER visits being covid-related. As of May 2024, an analysis shows around 10 unusually high values across the full history of all signals, so they are rare. We expect that these high rates are by chance, due to a small total number of ED visits in a given week. +Not all counties contain reporting EDs, including in states where NSSP reports state-level data. + ## Missingness As of May 2024, NSSP received data from 78% of US EDs. -The most noticeable gaps in [county coverage](https://www.cdc.gov/nssp/media/images/2024/04/Participation-with-date.png) are in California, Colorado, Missouri, Oklahoma, and Virginia, though most states have some counties that are absent. -The following states have no country-level data at all: CA, WA, AK, AZ, AL, CO, SD, ND, MO, AR, FL, OH, NH, CT, NJ. -Counties which do not have data are listed, but with an `NA` value. +[The NSSP site participation map](https://www.cdc.gov/nssp/media/images/2024/04/Participation-with-date.png) shows counties containing at least one reporting ED between January 2023 and April 2024. +California, Colorado, Missouri, Oklahoma, and Virginia have the most noticeable gaps in coverage, with many component counties having either no eligible EDs or having no recently reported data in NSSP. However, most states have some counties that are absent. + +NSSP does not report county-level data for all counties with reporting EDs; some reporting EDs are only included in state-level values. -At the state level, South Dakota, Missouri, and territories are not reported. +The following states report no data through NSSP at the county level: CA, WA, AK, AZ, AL, CO, SD, ND, MO, AR, FL, OH, NH, CT, NJ. + +South Dakota, Missouri, and territories report no data through NSSP at the state level. ## Lag and Backfill @@ -96,5 +102,3 @@ This source is derived from the CDC's [Respiratory Virus Response NSSP Emergency There is another version of the dataset that includes [state data only](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/7mra-9cq9/about_data). This data was originally published by the National Center for Health Statistics, and is made available here as a convenience to the forecasting community under the terms of the original license, which is [U.S. Government Public Domain](https://www.usa.gov/government-copyright). - -[^1]: (TODO should probably confirm this in some way) From 889abe1ec044377457c61caa705492fb012d2b93 Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Thu, 6 Jun 2024 18:18:31 -0400 Subject: [PATCH 08/13] move limitations down --- docs/api/covidcast-signals/nssp.md | 34 +++++++++++++++--------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index eeea67e6f..868a71223 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -55,23 +55,6 @@ State reporting process is separate from the county reporting process. As such, Smoothed signals are calculated using a simple 3 week moving average of the relevant weekly signals. Note that since the unsmoothed `pct_visits_*` signals report weekly data, each smoothed signal value is computed from 3 points rather than 21, as would be used if the unsmoothed data were reported daily. -## Limitations - -There is substantial missingness at the county level. This tends to impact more rural and lower population locations. See the [missingness section below](#missingness) for more information. - -NSSP notes that not every patient entering an ED is tested for the conditions of interest, so the data may undercount total cases and as a result percent visits may be biased downward. - -Our [geographic weighting approach](#geographic-weighting) assumes that the number of ED visits is proportional to the overall population of a county. However, in reality, there are various factors that could affect the accuracy of this assumption. - -For example, we might expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that someone living in an urban county will make, that is, the average urban resident may make more ED visits than the average rural resident over a given period of time. - -As a result, total ED visits per capita in rural counties may be lower than total ED visits per capita in urban counties. Since our weighting approach uses population as the weights, rural counties would tend to be overrepresented in estimated values. - -Some low population counties occasionally report outliers, e.g. 33.33%, 50%, 100% of ER visits being covid-related. As of May 2024, an analysis shows around 10 unusually high values across the full history of all signals, so they are rare. We expect that these high rates are by chance, due to a small total number of ED visits in a given week. - -Not all counties contain reporting EDs, including in states where NSSP reports state-level data. - - ## Missingness As of May 2024, NSSP received data from 78% of US EDs. @@ -96,6 +79,23 @@ This data source has frequent backfill, primarily arising from newly included ED In previous revisions, we have noted changes to values dating back about 2 years. +## Limitations + +There is substantial missingness at the county level. This tends to impact more rural and lower population locations. See the [missingness section](#missingness) for more information. + +Not all counties contain reporting EDs, including in states where NSSP reports state-level data. + +NSSP notes that not every patient entering an ED is tested for the conditions of interest, so the data may undercount total cases and as a result percent visits may be biased downward. + +Our [geographic weighting approach](#geographic-weighting) assumes that the number of ED visits is proportional to the overall population of a county. However, in reality, there are various factors that could affect the accuracy of this assumption. + +For example, we might expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that someone living in an urban county will make, that is, the average urban resident may make more ED visits than the average rural resident over a given period of time. + +As a result, total ED visits per capita in rural counties may be lower than total ED visits per capita in urban counties. Since our weighting approach uses population as the weights, rural counties would tend to be overrepresented in estimated values. + +Some low population counties occasionally report outliers, e.g. 33.33%, 50%, 100% of ER visits being covid-related. As of May 2024, an analysis shows around 10 unusually high values across the full history of all signals, so they are rare. We expect that these high rates are by chance, due to a small total number of ED visits in a given week. + + ## Source and Licensing This source is derived from the CDC's [Respiratory Virus Response NSSP Emergency Department Visit Trajectories dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data). From 2a455280172f95960c27f38bad13c6a9700eb106 Mon Sep 17 00:00:00 2001 From: dsweber2 Date: Thu, 6 Jun 2024 18:21:41 -0500 Subject: [PATCH 09/13] earliest dates, checked states missing Counties --- docs/api/covidcast-signals/nssp.md | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index 868a71223..704165b9d 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -21,16 +21,16 @@ This dataset in particular tracks emergency department (ED) visits arising from It is derived from the CDC's [Respiratory Virus Response NSSP Emergency Department Visit Trajectories dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data), which started reporting data in late 2022. As of May 2024, NSSP received data from 78% of US EDs. -| Signal | Description | -|---------------------------------|-------------------------------------------------------------------------| -| `pct_visits_covid` | Percent of ED visits that had a discharge diagnosis code of covid | -| `pct_visits_influenza` | Percent of ED visits that had a discharge diagnosis code of influenza | -| `pct_visits_rsv` | Percent of ED visits that had a discharge diagnosis code of rsv | -| `pct_visits_combined` | Percent of ED visits that had a discharge diagnosis code of covid, influenza, or rsv | -| `smoothed_pct_visits_covid` | 3 week moving average of `pct_visits_covid` | -| `smoothed_pct_visits_influenza` | 3 week moving average of `pct_visits_influenza` | -| `smoothed_pct_visits_rsv` | 3 week moving average of `pct_visits_rsv` | -| `smoothed_pct_visits_combined` | 3 week moving average of `pct_visits_combined` | +| Signal | Description | +|---------------------------------|--------------------------------------------------------------------------------------------------------------------------------------| +| `pct_visits_covid` | Percent of ED visits that had a discharge diagnosis code of covid
**Earliest date available:** 2022-10-01 | +| `pct_visits_influenza` | Percent of ED visits that had a discharge diagnosis code of influenza
**Earliest date available:** 2022-10-01 | +| `pct_visits_rsv` | Percent of ED visits that had a discharge diagnosis code of rsv
**Earliest date available:** 2022-10-01 | +| `pct_visits_combined` | Percent of ED visits that had a discharge diagnosis code of covid, influenza, or rsv
**Earliest date available:** 2022-10-01 | +| `smoothed_pct_visits_covid` | 3 week moving average of `pct_visits_covid`
**Earliest date available:** 2022-10-01 | +| `smoothed_pct_visits_influenza` | 3 week moving average of `pct_visits_influenza`
**Earliest date available:** 2022-10-01 | +| `smoothed_pct_visits_rsv` | 3 week moving average of `pct_visits_rsv`
**Earliest date available:** 2022-10-01 | +| `smoothed_pct_visits_combined` | 3 week moving average of `pct_visits_combined`
**Earliest date available:** 2022-10-01 | ## Table of contents {: .no_toc .text-delta} @@ -48,7 +48,7 @@ As the original data is a percentage and raw case counts are not available, `hrr This weighting approach assumes that the number of ED visits is proportional to the overall population of a county, i.e. the per-capita ED visit rate is the same for all counties, which may not be the case (for example, denser counties may have easier access to EDs and thus higher rates of ED visits per capita). -State reporting process is separate from the county reporting process. As such, state-level data is **not** simply an average of the county-level data, but may contain facilities omitted at the regional level. For example, state-level values are available for California, even though no California county data is reported. +State reporting process is separate from the county reporting process. As such, state-level data is **not** simply an average of the county-level data, but may contain facilities omitted at the regional level. For example, state-level values are available for California, even though no California county data is reported; see the [missingness section below](#missingness) for a list of such states. ### Smoothing @@ -77,6 +77,8 @@ For example, on Friday, 2024-04-19, the source added new data from the week endi This data source has frequent backfill, primarily arising from newly included EDs. When a new facility joins the reporting network, its historical data is added to the dataset, resulting in changes to historical values for every geographic level that ED is part of (county through nation). Because of this, the broadest geographic levels are more likely to be revised. In previous revisions, we have noted changes to values dating back about 2 years. +The following states have no county-level data at all: AK, AL, AR, AZ, CA, FL, MO, ND, NH, NJ, OH, SD, WA. +Counties with `NA` values are as originally reported in the dataset from which this source is derived; this is not a complete list of counties, and reflects missing data as collected by the NSSP. ## Limitations @@ -84,14 +86,14 @@ In previous revisions, we have noted changes to values dating back about 2 years There is substantial missingness at the county level. This tends to impact more rural and lower population locations. See the [missingness section](#missingness) for more information. Not all counties contain reporting EDs, including in states where NSSP reports state-level data. +A minority of these (as of June 2024) are counties without EDs, while others are only covered by the ~22% of EDs that don't yet report to the NSSP. NSSP notes that not every patient entering an ED is tested for the conditions of interest, so the data may undercount total cases and as a result percent visits may be biased downward. Our [geographic weighting approach](#geographic-weighting) assumes that the number of ED visits is proportional to the overall population of a county. However, in reality, there are various factors that could affect the accuracy of this assumption. -For example, we might expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that someone living in an urban county will make, that is, the average urban resident may make more ED visits than the average rural resident over a given period of time. - -As a result, total ED visits per capita in rural counties may be lower than total ED visits per capita in urban counties. Since our weighting approach uses population as the weights, rural counties would tend to be overrepresented in estimated values. +For example, we might expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that the typical urban resident will make relative to the typical rural resident. +As a result, total ED visits per capita in rural counties may be lower than total ED visits per capita in urban counties. If this is a strong dynamic, since our weighting approach uses population as the weights, rural counties would tend to be overrepresented in estimated values. Some low population counties occasionally report outliers, e.g. 33.33%, 50%, 100% of ER visits being covid-related. As of May 2024, an analysis shows around 10 unusually high values across the full history of all signals, so they are rare. We expect that these high rates are by chance, due to a small total number of ED visits in a given week. From 28482cf5547ee3e7c4c5be4c96ae5cd96fa0fe7b Mon Sep 17 00:00:00 2001 From: dsweber2 Date: Fri, 7 Jun 2024 13:04:29 -0500 Subject: [PATCH 10/13] earliest issue from Minh --- docs/api/covidcast-signals/nssp.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index 704165b9d..bfe526494 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -7,7 +7,7 @@ grand_parent: COVIDcast Main Endpoint {: .no_toc} * **Source name:** `nssp` -* **Earliest issue available:** (TODO ask Minh) +* **Earliest issue available:** April 17, 2024 * **Number of data revisions since 19 May 2020:** 0 * **Date of last change:** Never * **Available for:** county, hrr, msa, state, nation (see [geography coding docs](../covidcast_geography.md)) From a028cbe4b0af00699a5d1ef2d07e5e0584f9a9f3 Mon Sep 17 00:00:00 2001 From: dsweber2 Date: Tue, 25 Jun 2024 11:09:00 -0500 Subject: [PATCH 11/13] adding ed, right source --- docs/api/covidcast-signals/nssp.md | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index bfe526494..5071c8304 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -23,16 +23,16 @@ As of May 2024, NSSP received data from 78% of US EDs. | Signal | Description | |---------------------------------|--------------------------------------------------------------------------------------------------------------------------------------| -| `pct_visits_covid` | Percent of ED visits that had a discharge diagnosis code of covid
**Earliest date available:** 2022-10-01 | -| `pct_visits_influenza` | Percent of ED visits that had a discharge diagnosis code of influenza
**Earliest date available:** 2022-10-01 | -| `pct_visits_rsv` | Percent of ED visits that had a discharge diagnosis code of rsv
**Earliest date available:** 2022-10-01 | -| `pct_visits_combined` | Percent of ED visits that had a discharge diagnosis code of covid, influenza, or rsv
**Earliest date available:** 2022-10-01 | -| `smoothed_pct_visits_covid` | 3 week moving average of `pct_visits_covid`
**Earliest date available:** 2022-10-01 | -| `smoothed_pct_visits_influenza` | 3 week moving average of `pct_visits_influenza`
**Earliest date available:** 2022-10-01 | -| `smoothed_pct_visits_rsv` | 3 week moving average of `pct_visits_rsv`
**Earliest date available:** 2022-10-01 | -| `smoothed_pct_visits_combined` | 3 week moving average of `pct_visits_combined`
**Earliest date available:** 2022-10-01 | - -## Table of contents +| `pct_ed_visits_covid` | Percent of ED visits that had a discharge diagnosis code of covid
**Earliest date available:** 2022-10-01 | +| `pct_ed_visits_influenza` | Percent of ED visits that had a discharge diagnosis code of influenza
**Earliest date available:** 2022-10-01 | +| `pct_ed_visits_rsv` | Percent of ED visits that had a discharge diagnosis code of rsv
**Earliest date available:** 2022-10-01 | +| `pct_ed_visits_combined` | Percent of ED visits that had a discharge diagnosis code of covid, influenza, or rsv
**Earliest date available:** 2022-10-01 | +| `smoothed_pct_ed_visits_covid` | 3 week moving average of `pct_ed_visits_covid`
**Earliest date available:** 2022-10-01 | +| `smoothed_pct_ed_visits_influenza` | 3 week moving average of `pct_ed_visits_influenza`
**Earliest date available:** 2022-10-01 | +| `smoothed_pct_ed_visits_rsv` | 3 week moving average of `pct_ed_visits_rsv`
**Earliest date available:** 2022-10-01 | +| `smoothed_pct_ed_visits_combined` | 3 week moving average of `pct_ed_visits_combined`
**Earliest date available:** 2022-10-01 | + +## Table of Contents {: .no_toc .text-delta} 1. TOC @@ -52,7 +52,7 @@ State reporting process is separate from the county reporting process. As such, ### Smoothing -Smoothed signals are calculated using a simple 3 week moving average of the relevant weekly signals. Note that since the unsmoothed `pct_visits_*` signals report weekly data, each smoothed signal value is computed from 3 points rather than 21, as would be used if the unsmoothed data were reported daily. +Smoothed signals are calculated using a simple 3 week moving average of the relevant weekly signals. Note that since the unsmoothed `pct_ed_visits_*` signals report weekly data, each smoothed signal value is computed from 3 points rather than 21, as would be used if the unsmoothed data were reported daily. ## Missingness @@ -103,4 +103,4 @@ Some low population counties occasionally report outliers, e.g. 33.33%, 50%, 100 This source is derived from the CDC's [Respiratory Virus Response NSSP Emergency Department Visit Trajectories dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data). There is another version of the dataset that includes [state data only](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/7mra-9cq9/about_data). -This data was originally published by the National Center for Health Statistics, and is made available here as a convenience to the forecasting community under the terms of the original license, which is [U.S. Government Public Domain](https://www.usa.gov/government-copyright). +This data was originally published by the CDC, and is made available here as a convenience to the forecasting community under the terms of the original license, which is [U.S. Government Public Domain](https://www.usa.gov/government-copyright). From cafa9d6756c61ccc726cf4b9f8a2bf3137fd6d84 Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Tue, 25 Jun 2024 13:37:30 -0400 Subject: [PATCH 12/13] title --- docs/api/covidcast-signals/nssp.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index 5071c8304..41ce78c93 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -1,9 +1,9 @@ --- -title: NSSP emergency department visits +title: NSSP ED Visits parent: Data Sources and Signals grand_parent: COVIDcast Main Endpoint --- -# National Syndromic Surveillance Program (NSSP) Emerency Department (ED) visits +# National Syndromic Surveillance Program Emergency Department Visits {: .no_toc} * **Source name:** `nssp` @@ -23,10 +23,10 @@ As of May 2024, NSSP received data from 78% of US EDs. | Signal | Description | |---------------------------------|--------------------------------------------------------------------------------------------------------------------------------------| -| `pct_ed_visits_covid` | Percent of ED visits that had a discharge diagnosis code of covid
**Earliest date available:** 2022-10-01 | +| `pct_ed_visits_covid` | Percent of ED visits that had a discharge diagnosis code of COVID-19
**Earliest date available:** 2022-10-01 | | `pct_ed_visits_influenza` | Percent of ED visits that had a discharge diagnosis code of influenza
**Earliest date available:** 2022-10-01 | | `pct_ed_visits_rsv` | Percent of ED visits that had a discharge diagnosis code of rsv
**Earliest date available:** 2022-10-01 | -| `pct_ed_visits_combined` | Percent of ED visits that had a discharge diagnosis code of covid, influenza, or rsv
**Earliest date available:** 2022-10-01 | +| `pct_ed_visits_combined` | Percent of ED visits that had a discharge diagnosis code of COVID-19, influenza, or rsv
**Earliest date available:** 2022-10-01 | | `smoothed_pct_ed_visits_covid` | 3 week moving average of `pct_ed_visits_covid`
**Earliest date available:** 2022-10-01 | | `smoothed_pct_ed_visits_influenza` | 3 week moving average of `pct_ed_visits_influenza`
**Earliest date available:** 2022-10-01 | | `smoothed_pct_ed_visits_rsv` | 3 week moving average of `pct_ed_visits_rsv`
**Earliest date available:** 2022-10-01 | @@ -60,7 +60,7 @@ Smoothed signals are calculated using a simple 3 week moving average of the rele As of May 2024, NSSP received data from 78% of US EDs. [The NSSP site participation map](https://www.cdc.gov/nssp/media/images/2024/04/Participation-with-date.png) shows counties containing at least one reporting ED between January 2023 and April 2024. -California, Colorado, Missouri, Oklahoma, and Virginia have the most noticeable gaps in coverage, with many component counties having either no eligible EDs or having no recently reported data in NSSP. However, most states have some counties that are absent. +California, Colorado, Missouri, Oklahoma, and Virginia have the most noticeable gaps in coverage, with many counties in those states having either no eligible EDs or having no recently reported data in NSSP. However, most states have some counties that do not contain any reporting EDs. NSSP does not report county-level data for all counties with reporting EDs; some reporting EDs are only included in state-level values. @@ -95,7 +95,7 @@ Our [geographic weighting approach](#geographic-weighting) assumes that the numb For example, we might expect denser, more urban counties to have 1) more and larger EDs and 2) easier access to EDs. The first factor may mean that residents of rural counties are more likely to go to EDs in urban counties. The second factor may increase the total number of ED visits that the typical urban resident will make relative to the typical rural resident. As a result, total ED visits per capita in rural counties may be lower than total ED visits per capita in urban counties. If this is a strong dynamic, since our weighting approach uses population as the weights, rural counties would tend to be overrepresented in estimated values. -Some low population counties occasionally report outliers, e.g. 33.33%, 50%, 100% of ER visits being covid-related. As of May 2024, an analysis shows around 10 unusually high values across the full history of all signals, so they are rare. We expect that these high rates are by chance, due to a small total number of ED visits in a given week. +Some low population counties occasionally report outliers, e.g. 33.33%, 50%, 100% of ER visits being COVID-19-related. We expect that these high rates are by chance, due to a small total number of ED visits in a given week. As of May 2024, an analysis shows around 10 unusually high values across the full history of all signals, so they are rare. ## Source and Licensing From fb7c54d0de8a1908cd5d00eee3c27e880e576d1b Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Tue, 25 Jun 2024 13:39:28 -0400 Subject: [PATCH 13/13] rsv full name --- docs/api/covidcast-signals/nssp.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index 41ce78c93..b2eb618c0 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -17,7 +17,7 @@ grand_parent: COVIDcast Main Endpoint ## Overview [The National Syndromic Surveillance Program (NSSP)](https://www.cdc.gov/nssp/php/about/index.html) is an effort to track epidemiologically relevant conditions. -This dataset in particular tracks emergency department (ED) visits arising from a subset of influenza-like illnesses, specifically influenza, COVID-19, and RSV. +This dataset in particular tracks emergency department (ED) visits arising from a subset of influenza-like illnesses, specifically influenza, COVID-19, and respiratory syncytial virus (RSV). It is derived from the CDC's [Respiratory Virus Response NSSP Emergency Department Visit Trajectories dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data), which started reporting data in late 2022. As of May 2024, NSSP received data from 78% of US EDs.