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/.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 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/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 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. 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) 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