From cc56f000d488d85c53aa23e0fece48771a8e8186 Mon Sep 17 00:00:00 2001 From: Tina Townes Date: Tue, 10 Dec 2024 17:38:44 -0500 Subject: [PATCH 1/7] updates to COVIDcast inactive signals. (#1562) --- docs/api/covidcast-signals/google-survey.md | 2 +- docs/api/covidcast-signals/indicator-combination.md | 10 +++++----- docs/api/covidcast-signals/safegraph.md | 8 ++++---- docs/api/covidcast-signals/usa-facts.md | 8 ++++---- 4 files changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/api/covidcast-signals/google-survey.md b/docs/api/covidcast-signals/google-survey.md index 208bf23d4..d758d6a8b 100644 --- a/docs/api/covidcast-signals/google-survey.md +++ b/docs/api/covidcast-signals/google-survey.md @@ -9,7 +9,7 @@ nav_order: 2 {: .no_toc} * **Source name:** `google-survey` -* **Earliest issue available:** April 29, 2020 +* **Earliest issue available:** May 01, 2020 * **Number of data revisions since May 19, 2020:** 0 * **Date of last change:** Never * **Available for:** county, hrr, msa, state (see [geography coding docs](../covidcast_geography.md)) diff --git a/docs/api/covidcast-signals/indicator-combination.md b/docs/api/covidcast-signals/indicator-combination.md index e818011e9..fe2edd3cf 100644 --- a/docs/api/covidcast-signals/indicator-combination.md +++ b/docs/api/covidcast-signals/indicator-combination.md @@ -41,7 +41,7 @@ These signals were updated daily until March 17, 2021. | Signal | Description | | --- | --- | | `nmf_day_doc_fbc_fbs_ght` | This signal uses a rank-1 approximation, from a nonnegative matrix factorization approach, to identify an underlying signal that best reconstructs the Doctor Visits (`smoothed_adj_cli`), Facebook Symptoms surveys (`smoothed_cli`), Facebook Symptoms in Community surveys (`smoothed_hh_cmnty_cli`), and Search Trends (`smoothed_search`) indicators. It does not include official reports (cases and deaths from the `jhu-csse` source). Higher values of the combined signal correspond to higher values of the other indicators, but the scale (units) of the combination is arbitrary. Note that the Search Trends source is not available at the county level, so county values of this signal do not use it. This signal is deprecated and is no longer updated as of March 17, 2021.
**Earliest date available:** 2020-04-15 | -| `nmf_day_doc_fbs_ght` | This signal is calculated in the same way as `nmf_day_doc_fbc_fbs_ght`, but does *not* include the Symptoms in Community survey signal, which was not available at the time this signal was introduced. It also uses `smoothed_cli` from the `doctor-visits` source instead of `smoothed_adj_cli`. This signal is deprecated and is no longer updated as of May 28, 2020.
**Earliest date available:** 2020-04-06 | +| `nmf_day_doc_fbs_ght` | This signal is calculated in the same way as `nmf_day_doc_fbc_fbs_ght`, but does *not* include the Symptoms in Community survey signal, which was not available at the time this signal was introduced. It also uses `smoothed_cli` from the `doctor-visits` source instead of `smoothed_adj_cli`. This signal is deprecated and is no longer updated as of May 27, 2020.
**Earliest date available:** 2020-04-06 | ### Estimation @@ -207,11 +207,11 @@ These signals were updated daily until November 18, 2021. | Signal | 7-day average signal | Description | | --- | --- | --- | -| `confirmed_cumulative_num` | | Cumulative number of confirmed COVID-19 cases
**Earliest date available:** 2020-02-20 | -| `confirmed_cumulative_prop` | | Cumulative number of confirmed COVID-19 cases per 100,000 population
**Earliest date available:** 2020-02-20 | +| `confirmed_cumulative_num` | `confirmed_7dav_cumulative_num` | Cumulative number of confirmed COVID-19 cases
**Earliest date available:** 2020-02-20 | +| `confirmed_cumulative_prop` | `confirmed_7dav_cumulative_prop`| Cumulative number of confirmed COVID-19 cases per 100,000 population
**Earliest date available:** 2020-02-20 | | `confirmed_incidence_num` | `confirmed_7dav_incidence_num` | Number of new confirmed COVID-19 cases, daily
**Earliest date available:** 2020-02-20 | | `confirmed_incidence_prop` | `confirmed_7dav_incidence_prop` | Number of new confirmed COVID-19 cases per 100,000 population, daily
**Earliest date available:** 2020-02-20 | -| `deaths_cumulative_num` | | Cumulative number of confirmed deaths due to COVID-19
**Earliest date available:** 2020-02-20 | -| `deaths_cumulative_prop` | | Cumulative number of confirmed due to COVID-19, per 100,000 population
**Earliest date available:** 2020-02-20 | +| `deaths_cumulative_num` | `deaths_7dav_cumulative_num` | Cumulative number of confirmed deaths due to COVID-19
**Earliest date available:** 2020-02-20 | +| `deaths_cumulative_prop` | `deaths_7dav_cumulative_prop` | Cumulative number of confirmed due to COVID-19, per 100,000 population
**Earliest date available:** 2020-02-20 | | `deaths_incidence_num` | `deaths_7dav_incidence_num` | Number of new confirmed deaths due to COVID-19, daily
**Earliest date available:** 2020-02-20 | | `deaths_incidence_prop` | `deaths_7dav_incidence_prop` | Number of new confirmed deaths due to COVID-19 per 100,000 population, daily
**Earliest date available:** 2020-02-20 | diff --git a/docs/api/covidcast-signals/safegraph.md b/docs/api/covidcast-signals/safegraph.md index 6bf377437..96775de0f 100644 --- a/docs/api/covidcast-signals/safegraph.md +++ b/docs/api/covidcast-signals/safegraph.md @@ -106,16 +106,16 @@ Patterns documentation](https://docs.safegraph.com/docs/weekly-patterns). SafeGraph delivered the number of daily visits to U.S. POIs, the details of which are described in the [Places -Manual](https://readme.safegraph.com/docs/places-manual#section-placekey) +Manual](https://docs.safegraph.com/docs/places-base-attributes#placekey) dataset. Delphi aggregates the number of visits to certain types of places, such as bars (places with [NAICS code = -722410](https://www.census.gov/cgi-bin/sssd/naics/naicsrch?input=722410&search=2017+NAICS+Search&search=2017)) +722410](https://www.census.gov/naics/?008967)) and restaurants (places with [NAICS code = -722511](https://www.census.gov/cgi-bin/sssd/naics/naicsrch)). For example, +722511](https://www.census.gov/naics/?008967)). For example, Adagio Teas is coded as a bar because it serves alcohol, while Napkin Burger is considered to be a full-service restaurant. More information on NAICS codes is available from the [US Census Bureau: North American Industry Classification -System](https://www.census.gov/eos/www/naics/index.html). +System](https://www.census.gov/naics/reference_files_tools/2022_NAICS_Manual.pdf). The number of POIs coded as bars is much smaller than the number of POIs coded as restaurants. SafeGraph's [Weekly Patterns](https://docs.safegraph.com/docs/weekly-patterns) data consistently lacks data on bar visits for Alaska, Delaware, Maine, North Dakota, New Hampshire, South Dakota, Vermont, West Virginia, and Wyoming. diff --git a/docs/api/covidcast-signals/usa-facts.md b/docs/api/covidcast-signals/usa-facts.md index fe08dc911..3c972cfcd 100644 --- a/docs/api/covidcast-signals/usa-facts.md +++ b/docs/api/covidcast-signals/usa-facts.md @@ -21,12 +21,12 @@ available by [USAFacts](https://usafacts.org/). | Signal and 7-day average signal | Description | |---|---| -| `confirmed_cumulative_num` | Cumulative number of confirmed COVID-19 cases
**Earliest date available:** 2020-01-25 & 2020-02-01 | -| `confirmed_cumulative_prop` | Cumulative number of confirmed COVID-19 cases per 100,000 population
**Earliest date available:** 2020-01-25 & 2020-02-01 | +| `confirmed_cumulative_num` and `confirmed_7dav_cumulative_num`| Cumulative number of confirmed COVID-19 cases
**Earliest date available:** 2020-01-25 & 2020-02-01 | +| `confirmed_cumulative_prop` and `confirmed_7dav_cumulative_prop`| Cumulative number of confirmed COVID-19 cases per 100,000 population
**Earliest date available:** 2020-01-25 & 2020-02-01 | | `confirmed_incidence_num` and `confirmed_7dav_incidence_num` | Number of new confirmed COVID-19 cases, daily
**Earliest date available:** 2020-01-25 & 2020-02-01 | | `confirmed_incidence_prop` and `confirmed_7dav_incidence_prop` | Number of new confirmed COVID-19 cases per 100,000 population, daily
**Earliest date available:** 2020-01-25 & 2020-02-01 | -| `deaths_cumulative_num` | Cumulative number of confirmed deaths due to COVID-19
**Earliest date available:** 2020-01-25 & 2020-02-01 | -| `deaths_cumulative_prop` | Cumulative number of confirmed due to COVID-19, per 100,000 population
**Earliest date available:** 2020-01-25 & 2020-02-01 | +| `deaths_cumulative_num` and `deaths_7dav_cumulative_num`| Cumulative number of confirmed deaths due to COVID-19
**Earliest date available:** 2020-01-25 & 2020-02-01 | +| `deaths_cumulative_prop` and `deaths_7dav_cumulative_prop`| Cumulative number of confirmed due to COVID-19, per 100,000 population
**Earliest date available:** 2020-01-25 & 2020-02-01 | | `deaths_incidence_num` and `deaths_7dav_incidence_num` | Number of new confirmed deaths due to COVID-19, daily
**Earliest date available:** 2020-01-25 & 2020-02-01 | | `deaths_incidence_prop` and `deaths_7dav_incidence_prop` | Number of new confirmed deaths due to COVID-19 per 100,000 population, daily
**Earliest date available:** 2020-01-25 & 2020-02-01 | From 0924b85e28754ad6051cf55686ea83250f6fa967 Mon Sep 17 00:00:00 2001 From: aysim319 Date: Mon, 13 Jan 2025 11:52:01 -0500 Subject: [PATCH 2/7] adding nhsn docs (#1570) * first commit * remove weighting for now * cleaned up some sections * reorg details * newline * added clarifying words * added more information on missingness * added more on limitations * missingness and hhs analysis cleanup * clarify prelim vs finalized data * mandate links and section * added input and output field * backfill analysis * initial issue date fix --------- Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com> --- docs/api/covidcast-signals/nhsn.md | 127 +++++++++++++++++++++++++++++ 1 file changed, 127 insertions(+) create mode 100644 docs/api/covidcast-signals/nhsn.md diff --git a/docs/api/covidcast-signals/nhsn.md b/docs/api/covidcast-signals/nhsn.md new file mode 100644 index 000000000..30ea5e9da --- /dev/null +++ b/docs/api/covidcast-signals/nhsn.md @@ -0,0 +1,127 @@ +--- +title: NHSN ED Visits +parent: Data Sources and Signals +grand_parent: Main Endpoint (COVIDcast) +nav_order: 1 +--- +# National Syndromic Surveillance Program Emergency Department Visits +{: .no_toc} + +* **Source name:** `nhsn` +* **Earliest issue available:** November 19, 2024 +* **Number of data revisions since 18 Nov 2024:** 0 +* **Date of last change:** Never +* **Available for:** state, hhs, 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) + +## Overview + +[The National Healthcare Safety Network (NHSN)](https://www.cdc.gov/nhsn/index.html) is the nation’s most widely used healthcare-associated infection tracking system. +This dataset reports preliminary and finalized weekly hospital respiratory data and metrics aggregated to national and state/territory levels reported to the CDC’s National Health Safety Network (NHSN). Values are available for reference dates beginning August 2020. + +Each signal below is derived from one of the two following datasets: + +- Main: [Weekly Hospital Respiratory Data (HRD) Metrics by Jurisdiction, National Healthcare Safety Network (NHSN)](https://data.cdc.gov/Public-Health-Surveillance/Weekly-Hospital-Respiratory-Data-HRD-Metrics-by-Ju/ua7e-t2fy/about_data) +- Preliminary: [Weekly Hospital Respiratory Data (HRD) Metrics by Jurisdiction, National Healthcare Safety Network (NHSN) (Preliminary)](https://data.cdc.gov/Public-Health-Surveillance/Weekly-Hospital-Respiratory-Data-HRD-Metrics-by-Ju/mpgq-jmmr/about_data). Signals derived from the preliminary dataset have suffix `_prelim` in their signal names. + +Both datasets started reporting data in late 2024. +For reference dates in May 2024, NHSN received data from 78% of US EDs. + +State and nation-level values are pulled directly from the source; HHS-level values are aggregated up from the state level. + + +| Signal | Description | +|---------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| `confirmed_admissions_covid_ew` | Total number of patients hospitalized with confirmed COVID-19 over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week. **Earliest date available:** 2020-08-08 | +| `confirmed_admissions_covid_ew_prelim` | Total number of patients hospitalized with confirmed COVID-19 over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week.
**Earliest date available:** 2020-08-08 | +| `confirmed_admissions_flu_ew` | Total number of patients hospitalized with confirmed influenza over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Friday or Saturday of the following week.
**Earliest date available:** 2020-08-08 | +| `confirmed_admissions_flu_ew_prelim` | Total number of patients hospitalized with confirmed influenza over the entire week (Sunday-Saturday). Only includes hospitalizations whose report was received before the Wednesday of the following week.
**Earliest date available:** 2020-08-08 | + +## Table of Contents +{: .no_toc .text-delta} + +1. TOC +{:toc} + +## Estimation + +All data is weekly such that each reported value represents a total from Sunday to Saturday of the reference week. +The `confirmed_admissions_covid_ew` signal mirrors the `totalconfc19newadm` field for all geographic resolutions except HHS. +For `confirmed_admissions_flu_ew` signal mirrors the `totalconfflunewadm` field for all geographic resolutions except HHS. + +We report both preliminary (`*_prelim`) and finalized signals. +Preliminary data is made available on the Wednesday following the end of the week being reported on. For example, the data for the week Dec 1-7, 2024 would first be available on 2024-12-11, the Wednesday of the following week. +Finalized data is made available on the Friday or Saturday following the end of the week being reported on. + +Preliminary data is available 2 days earlier than finalized data. However, preliminary data will tend to underreport the true value since it is made available closer to the end of the week being reported on, allowing less time for hospitalization reports to be received. + + +### Geographic weighting + +State and nation-level values are pulled directly from the source; HHS-level values are aggregated up from the state level by summing the values of member states. + + +## Missingness + +Data is available for reference dates August 1, 2020 and later. + +Data reported for reference dates December 1, 2020 or later are subject to thorough, routine data quality review procedures, including identifying and excluding invalid values and application of error correction methodology; +data for reference dates prior to this may be anomalous or invalid. + +Data for reference dates through April 30, 2024 were reported during a federally-mandated reporting period +as specified by the Secretary of the Department of Health and Human Services. + +Data for reference dates May 1, 2024-October 31, 2024 were voluntarily reported in the absence of a mandate. +As a result, during this period reported hospitalizations may not be fully representative. + +Data for reference dates beginning November 1, 2024 were reported during the [current mandated reporting period](https://www.cms.gov/medicare/health-safety-standards/quality-safety-oversight-general-information/policy-memos-states-and-cms-locations/updates-condition-participation-cop-requirements-hospitals-and-critical-access-hospitals-cahs-report). +More information regarding the mandate beginning November 1, 2024, is available [from the CDC](https://www.cdc.gov/nhsn/psc/hospital-respiratory-reporting.html) + +## Limitations + +HHS collects data from state and territorial health departments about many, but not all, hospitals in the U.S. +Notably excluded from this dataset are psychiatric and rehabilitation facilities,and religious non-medical facilities. +Number of reporting hospitals is determined based on the NHSN unique hospital identifier and not aggregated to the CMS certification number (CCN). +Only hospitals indicated as active reporters in NHSN are included. + +Between reference dates 2024-05-01 and 2024-10-31, reported hospitalizations may not be fully representative, since reporting was voluntary. +See the [missingness section](#missingness) for more information about voluntary and mandatory reporting periods. + +Standard errors and sample sizes are not applicable to these metrics. + + +### Differences with HHS reports +An analysis comparing flu and COVID-19 data from the [HHS](https://healthdata.gov/Hospital/COVID-19-Reported-Patient-Impact-and-Hospital-Capa/g62h-syeh/about_data) and NHSN datasets, for reference dates appearing in both sources, suggests that the data are largely equivalent. However, there are notable differences in a handful of states; GA (untill 2023), LA, NV, PR (late 2020-early 2021), and TN all have substantially lower values in HHS data than in NHSN. + +Occasionally, data for a single geographic region will have a spike in NHSN or HHS that does not appear in the other source or in other geographic regions. + +There may be other mismatches between the datasets, so exercise caution when comparing work based on NHSN data with work based on HHS data. + + +## Lag and Backfill + +Finalized signals are currently updated weekly, generally on Friday or Saturday. +Preliminary signals are currently updated weekly, on Wednesday. +Each report adds data for the week prior. +For example, on Friday, 2024-04-19, the source added new data representing hospitalizations from the week ending 2024-04-13. +For finalized signals, this results in a reporting lag of 6-7 days from the end of the reference week. +For preliminary signals, this results in a reporting lag of 4 days from the end of the reference week. + +As a result of continuous data quality checks and revisions to data for prior reference dates (also known as "backfill"), data may fluctuate or change week-over-week after initial posting. + +In practice, revisions tend to happen within 2 months of the initial release; older data is unlikely to be revised. +Of values reported recently (reference date 2 months or less before the issue date), 20% were revisions. +Values that are revised tend to be revised a small number of times (once or twice). Revisions tend to increase values. Revisions tend to be small, with a median 2% (mean 5.4%) difference between highest and lowest values seen for a given reference date. + +A handful of values have large revisions, for example, being revised from 10 to 100, but these are rare. + +Texas has many more revisions than other states (7 times more than California during the analysis period). However Texas has the lowest median percent difference (0.08%) between high and low values seen for a given reference date. Idaho, New Hampshire, Hawaii, and North Dakota have some of the highest median percent differences. + + +## Source and Licensing + +This source is derived from the CDC's [Weekly Hospital Respiratory Data (HRD) Metrics by Jurisdiction, National Healthcare Safety Network (NHSN)](https://data.cdc.gov/Public-Health-Surveillance/Weekly-Hospital-Respiratory-Data-HRD-Metrics-by-Ju/ua7e-t2fy/about_data) and +[Weekly Hospital Respiratory Data (HRD) Metrics by Jurisdiction, National Healthcare Safety Network (NHSN) (Preliminary)](https://data.cdc.gov/Public-Health-Surveillance/Weekly-Hospital-Respiratory-Data-HRD-Metrics-by-Ju/mpgq-jmmr/about_data). + +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 d20b357a89b0372281ea9a1bc60246574547e0da Mon Sep 17 00:00:00 2001 From: Brian Clark Date: Thu, 16 Jan 2025 09:37:05 -0500 Subject: [PATCH 3/7] Remove WireGuard step (#1557) --- .github/workflows/performance-tests-one-time.yml | 8 -------- .github/workflows/performance-tests.yml | 8 -------- 2 files changed, 16 deletions(-) diff --git a/.github/workflows/performance-tests-one-time.yml b/.github/workflows/performance-tests-one-time.yml index c924e206e..d62a4cf21 100644 --- a/.github/workflows/performance-tests-one-time.yml +++ b/.github/workflows/performance-tests-one-time.yml @@ -23,14 +23,6 @@ jobs: max_time: ${{ steps.output.outputs.max_time }} requests_per_sec: ${{ steps.output.outputs.requests_per_sec }} steps: - - name: Set up WireGuard - uses: egor-tensin/setup-wireguard@v1.2.0 - with: - endpoint: '${{ secrets.WG_PERF_ENDPOINT }}' - endpoint_public_key: '${{ secrets.WG_PERF_ENDPOINT_PUBLIC_KEY }}' - ips: '${{ secrets.WG_PERF_IPS }}' - allowed_ips: '${{ secrets.WG_PERF_ALLOWED_IPS }}' - private_key: '${{ secrets.WG_PERF_PRIVATE_KEY }}' - name: Clean files from previous runs uses: AutoModality/action-clean@v1 - name: Check out repository diff --git a/.github/workflows/performance-tests.yml b/.github/workflows/performance-tests.yml index 910bde1ca..826ac153d 100644 --- a/.github/workflows/performance-tests.yml +++ b/.github/workflows/performance-tests.yml @@ -25,14 +25,6 @@ jobs: max_time: ${{ steps.output.outputs.max_time }} requests_per_sec: ${{ steps.output.outputs.requests_per_sec }} steps: - - name: Set up WireGuard - uses: egor-tensin/setup-wireguard@v1.2.0 - with: - endpoint: '${{ secrets.WG_PERF_ENDPOINT }}' - endpoint_public_key: '${{ secrets.WG_PERF_ENDPOINT_PUBLIC_KEY }}' - ips: '${{ secrets.WG_PERF_IPS }}' - allowed_ips: '${{ secrets.WG_PERF_ALLOWED_IPS }}' - private_key: '${{ secrets.WG_PERF_PRIVATE_KEY }}' - name: Clean files from previous runs uses: AutoModality/action-clean@v1 - name: Check out repository From 70a2d8677567af20e1cbc1db152f9e5001abc66b Mon Sep 17 00:00:00 2001 From: george Date: Tue, 21 Jan 2025 16:13:34 -0500 Subject: [PATCH 4/7] fix unittest.mock import error (#1574) --- tests/server/test_pandas.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/server/test_pandas.py b/tests/server/test_pandas.py index e1c3ee8fe..b2abda13e 100644 --- a/tests/server/test_pandas.py +++ b/tests/server/test_pandas.py @@ -2,7 +2,7 @@ # standard library import unittest -from mock import patch, sentinel, ANY +from unittest.mock import patch, sentinel, ANY # first party from delphi.epidata.server.main import app From f4d32a5700ad23ff422814ad4421512e143d8ab4 Mon Sep 17 00:00:00 2001 From: Alex Reinhart Date: Thu, 23 Jan 2025 13:24:55 -0500 Subject: [PATCH 5/7] Add new publication and update older ones (#1571) --- docs/symptom-survey/publications.md | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/docs/symptom-survey/publications.md b/docs/symptom-survey/publications.md index d6ccf23be..46fd8f37a 100644 --- a/docs/symptom-survey/publications.md +++ b/docs/symptom-survey/publications.md @@ -26,17 +26,24 @@ Pandemic"](https://www.pnas.org/topic/548) in *PNAS*: Research publications using the survey data include: +- S. Santos, M. Humbard, A. Lambrou et al. (2025). [The SARS-CoV-2 test + scale-up in the USA: an analysis of the number of tests produced and used + over time and their modelled impact on the COVID-19 pandemic](https://doi.org/10.1016/S2468-2667(24)00279-2). + *The Lancet Public Health* 10 (1), e47-e57. +- H. Bui, S. Ekşioğlu, R. Proano, and S. N. Pinkley (2025). [An Analysis of + COVID-19 Vaccine Hesitancy in the U.S.](https://doi.org/10.1080/24725854.2024.2301966). + *IISE Transactions* 57 (3), 246-260. - K.M. Geffel, H.P. Dyer, A.D. Casas, S.N. Christian-Afflu, D.D. Méndez, and T.L. Gary-Webb (2024). [COVID-19 vaccine uptake and intention of Black adults: A county-wide analysis of an online survey](https://doi.org/10.1016/j.jnma.2024.07.007). - *Journal of the National Medical Association*. + *Journal of the National Medical Association* 116 (5), 526-538. - C.K. Ettman, E. Badillo-Goicoechea, E.A. Stuart, and L.T. Dean (2024). [Area-level credit scores and symptoms of depression and anxiety in adults](https://doi.org/10.1093/aje/kwae275). *American Journal of Epidemiology* kwae275. - C.K. Ettman, E. Badillo-Goicoechea, E.A. Stuart (2024). [Financial strain, schooling modality and mental health of US adults living with children during the COVID-19 pandemic](https://doi.org/10.1136/jech-2023-221672). - *Journal of Epidemiology & Community Health*. + *Journal of Epidemiology & Community Health* 78 (10), 662-668. - K. Sasse, R. Mahabir, O. Gkountouna, A. Crooks, A. Croitoru (2024). [Understanding the determinants of vaccine hesitancy in the United States: A comparison of social surveys and social media](https://doi.org/10.1371/journal.pone.0301488). @@ -68,10 +75,8 @@ Research publications using the survey data include: *Social Science & Medicine* 348, 116775. - R.R. Andridge (2024). [Using proxy pattern-mixture models to explain bias in estimates of COVID-19 vaccine uptake from two large surveys](https://doi.org/10.1093/jrsssa/qnae005). - *Journal of the Royal Statistical Society Series A: Statistics in Society*. -- H. Bui, S. Ekşioğlu, R. Proano, and S. N. Pinkley (2024). [An Analysis of - COVID-19 Vaccine Hesitancy in the U.S.](https://doi.org/10.1080/24725854.2024.2301966). - *IISE Transactions*. + *Journal of the Royal Statistical Society Series A: Statistics in Society* + 187 (3), 831-843. - de Vries, M., Kim, J.Y. & Han, H. (2023). [The unequal landscape of civic opportunity in America](https://doi.org/10.1038/s41562-023-01743-1). *Nature Human Behavior* 8, 256-263. From 7b33f6a90f7dda663367b29d07b90f174361a504 Mon Sep 17 00:00:00 2001 From: minhkhul <118945681+minhkhul@users.noreply.github.com> Date: Thu, 23 Jan 2025 13:31:01 -0500 Subject: [PATCH 6/7] Remove mention of secondary signals from NSSP docs (#1573) * remove mention of secondary signals --- docs/api/covidcast-signals/nssp.md | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/docs/api/covidcast-signals/nssp.md b/docs/api/covidcast-signals/nssp.md index 77b320186..3f69a7cd0 100644 --- a/docs/api/covidcast-signals/nssp.md +++ b/docs/api/covidcast-signals/nssp.md @@ -19,11 +19,8 @@ nav_order: 1 [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 respiratory syncytial virus (RSV). -Each signal below is derived from one of two following datasets: -- Primary: [NSSP Emergency Department Visit Trajectories by State and Sub State Regions- COVID-19, Flu, RSV, Combined dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data) -- Secondary: [2023 Respiratory Virus Response - NSSP Emergency Department Visit Trajectories by State- COVID-19, Flu, RSV, Combined](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/7mra-9cq9/data_preview). Signals derived from the secondary dataset have suffix `_2023RVR` in their signal names. - -Both datasets started reporting data in late 2022. As of May 2024, NSSP received data from 78% of US EDs. +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 | |---------------------------------|--------------------------------------------------------------------------------------------------------------------------------------| @@ -35,10 +32,6 @@ Both datasets started reporting data in late 2022. As of May 2024, NSSP received | `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 | -| `pct_ed_visits_covid_2023RVR` | Percent of ED visits that had a discharge diagnosis code of COVID-19
**Earliest date available:** 2022-10-01 | -| `pct_ed_visits_influenza_2023RVR` | Percent of ED visits that had a discharge diagnosis code of influenza
**Earliest date available:** 2022-10-01 | -| `pct_ed_visits_rsv_2023RVR` | Percent of ED visits that had a discharge diagnosis code of rsv
**Earliest date available:** 2022-10-01 | -| `pct_ed_visits_combined_2023RVR` | Percent of ED visits that had a discharge diagnosis code of COVID-19, influenza, or rsv
**Earliest date available:** 2022-10-01 | ## Table of Contents {: .no_toc .text-delta} @@ -49,8 +42,7 @@ Both datasets started reporting data in late 2022. As of May 2024, NSSP received ## Estimation The percent visits signals are calculated as a fraction of visits at facilities reporting to NSSP, rather than all facilities in the area. -For primary signals, `county`, `state` and `nation` level data is reported as-is from NSSP, without modification, while `hhs`, `hrr` and `msa` are estimated by Delphi. -For secondary signals, `state`, `hhs` and `nation` level data is reported as-is from NSSP, without modification. +`county`, `state` and `nation` level data is reported as-is from NSSP, without modification, while `hhs`, `hrr` and `msa` are estimated by Delphi. ### Geographic weighting As the original data is a percentage and raw case counts are not available, `hrr`,`msa`, and `hhs` 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. @@ -112,4 +104,4 @@ 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 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). +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). \ No newline at end of file From ff9400d78242caf5873827b5554d0ee3983e4af3 Mon Sep 17 00:00:00 2001 From: melange396 Date: Thu, 23 Jan 2025 18:32:06 +0000 Subject: [PATCH 7/7] chore: release delphi-epidata 4.1.28 --- .bumpversion.cfg | 2 +- dev/local/setup.cfg | 2 +- src/client/delphi_epidata.R | 2 +- src/client/delphi_epidata.js | 2 +- src/client/packaging/npm/package.json | 2 +- src/server/_config.py | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index e5baffd7f..406cc8fe9 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 4.1.27 +current_version = 4.1.28 commit = False tag = False diff --git a/dev/local/setup.cfg b/dev/local/setup.cfg index 52ecda6d3..d8dc0147d 100644 --- a/dev/local/setup.cfg +++ b/dev/local/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = Delphi Development -version = 4.1.27 +version = 4.1.28 [options] packages = diff --git a/src/client/delphi_epidata.R b/src/client/delphi_epidata.R index 684ea90ed..3fd8a8b09 100644 --- a/src/client/delphi_epidata.R +++ b/src/client/delphi_epidata.R @@ -15,7 +15,7 @@ Epidata <- (function() { # API base url BASE_URL <- getOption('epidata.url', default = 'https://api.delphi.cmu.edu/epidata/') - client_version <- '4.1.27' + client_version <- '4.1.28' auth <- getOption("epidata.auth", default = NA) diff --git a/src/client/delphi_epidata.js b/src/client/delphi_epidata.js index 59e5a9aaa..87752339c 100644 --- a/src/client/delphi_epidata.js +++ b/src/client/delphi_epidata.js @@ -22,7 +22,7 @@ } })(this, function (exports, fetchImpl, jQuery) { const BASE_URL = "https://api.delphi.cmu.edu/epidata/"; - const client_version = "4.1.27"; + const client_version = "4.1.28"; // Helper function to cast values and/or ranges to strings function _listitem(value) { diff --git a/src/client/packaging/npm/package.json b/src/client/packaging/npm/package.json index 68e746eff..4271cbbbb 100644 --- a/src/client/packaging/npm/package.json +++ b/src/client/packaging/npm/package.json @@ -2,7 +2,7 @@ "name": "delphi_epidata", "description": "Delphi Epidata API Client", "authors": "Delphi Group", - "version": "4.1.27", + "version": "4.1.28", "license": "MIT", "homepage": "https://github.com/cmu-delphi/delphi-epidata", "bugs": { diff --git a/src/server/_config.py b/src/server/_config.py index 252ccf35c..b5b71d5e4 100644 --- a/src/server/_config.py +++ b/src/server/_config.py @@ -7,7 +7,7 @@ load_dotenv() -VERSION = "4.1.27" +VERSION = "4.1.28" MAX_RESULTS = int(10e6) MAX_COMPATIBILITY_RESULTS = int(3650)