This dataset of U.S. mortality trends since 1900 highlights trends in age-adjusted death rates for five selected major causes of death. Age-adjusted death rates (deaths per 100,000) after 1998 are calculated based on the 2000 U.S. standard population. Populations used for computing death rates for 2011–2017 are postcensal estimates based on the 2010 census, estimated as of July 1, 2010. Rates for census years are based on populations enumerated in the corresponding censuses. Rates for noncensus years between 2000 and 2010 are revised using updated intercensal population estimates and may differ from rates previously published. Data on age-adjusted death rates prior to 1999 are taken from historical data (see References below). Revisions to the International Classification of Diseases (ICD) over time may result in discontinuities in cause-of-death trends. SOURCES CDC/NCHS, National Vital Statistics System, historical data, 1900-1998 (see https://www.cdc.gov/nchs/nvss/mortality_historical_data.htm); CDC/NCHS, National Vital Statistics System, mortality data (see http://www.cdc.gov/nchs/deaths.htm); and CDC WONDER (see http://wonder.cdc.gov). REFERENCES National Center for Health Statistics, Data Warehouse. Comparability of cause-of-death between ICD revisions. 2008. Available from: http://www.cdc.gov/nchs/nvss/mortality/comparability_icd.htm. National Center for Health Statistics. Vital statistics data available. Mortality multiple cause files. Hyattsville, MD: National Center for Health Statistics. Available from: https://www.cdc.gov/nchs/data_access/vitalstatsonline.htm. Kochanek KD, Murphy SL, Xu JQ, Arias E. Deaths: Final data for 2017. National Vital Statistics Reports; vol 68 no 9. Hyattsville, MD: National Center for Health Statistics. 2019. Available from: https://www.cdc.gov/nchs/data/nvsr/nvsr68/nvsr68_09-508.pdf. Arias E, Xu JQ. United States life tables, 2017. National Vital Statistics Reports; vol 68 no 7. Hyattsville, MD: National Center for Health Statistics. 2019. Available from: https://www.cdc.gov/nchs/data/nvsr/nvsr68/nvsr68_07-508.pdf. National Center for Health Statistics. Historical Data, 1900-1998. 2009. Available from: https://www.cdc.gov/nchs/nvss/mortality_historical_data.htm.

This dataset of U.S. mortality trends since 1900 highlights childhood mortality rates by age group for age at death. Age-adjusted death rates (deaths per 100,000) after 1998 are calculated based on the 2000 U.S. standard population. Populations used for computing death rates for 2011–2017 are postcensal estimates based on the 2010 census, estimated as of July 1, 2010. Rates for census years are based on populations enumerated in the corresponding censuses. Rates for noncensus years between 2000 and 2010 are revised using updated intercensal population estimates and may differ from rates previously published. Data on age-adjusted death rates prior to 1999 are taken from historical data (see References below). Age groups for childhood death rates are based on age at death. SOURCES CDC/NCHS, National Vital Statistics System, historical data, 1900-1998 (see https://www.cdc.gov/nchs/nvss/mortality_historical_data.htm); CDC/NCHS, National Vital Statistics System, mortality data (see http://www.cdc.gov/nchs/deaths.htm); and CDC WONDER (see http://wonder.cdc.gov). REFERENCES National Center for Health Statistics, Data Warehouse. Comparability of cause-of-death between ICD revisions. 2008. Available from: http://www.cdc.gov/nchs/nvss/mortality/comparability_icd.htm. National Center for Health Statistics. Vital statistics data available. Mortality multiple cause files. Hyattsville, MD: National Center for Health Statistics. Available from: https://www.cdc.gov/nchs/data_access/vitalstatsonline.htm. Kochanek KD, Murphy SL, Xu JQ, Arias E. Deaths: Final data for 2017. National Vital Statistics Reports; vol 68 no 9. Hyattsville, MD: National Center for Health Statistics. 2019. Available from: https://www.cdc.gov/nchs/data/nvsr/nvsr68/nvsr68_09-508.pdf. Arias E, Xu JQ. United States life tables, 2017. National Vital Statistics Reports; vol 68 no 7. Hyattsville, MD: National Center for Health Statistics. 2019. Available from: https://www.cdc.gov/nchs/data/nvsr/nvsr68/nvsr68_07-508.pdf. National Center for Health Statistics. Historical Data, 1900-1998. 2009. Available from: https://www.cdc.gov/nchs/nvss/mortality_historical_data.htm.

Note: DPH is updating and streamlining the COVID-19 cases, deaths, and testing data. As of 6/27/2022, the data will be published in four tables instead of twelve.

The COVID-19 Cases, Deaths, and Tests by Day dataset contains cases and test data by date of sample submission. The death data are by date of death. This dataset is updated daily and contains information back to the beginning of the pandemic. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-Cases-Deaths-and-Tests-by-Day/g9vi-2ahj.

The COVID-19 State Metrics dataset contains over 93 columns of data. This dataset is updated daily and currently contains information starting June 21, 2022 to the present. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-State-Level-Data/qmgw-5kp6 .

The COVID-19 County Metrics dataset contains 25 columns of data. This dataset is updated daily and currently contains information starting June 16, 2022 to the present. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-County-Level-Data/ujiq-dy22 .

The COVID-19 Town Metrics dataset contains 16 columns of data. This dataset is updated daily and currently contains information starting June 16, 2022 to the present. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-Town-Level-Data/icxw-cada . To protect confidentiality, if a town has fewer than 5 cases or positive NAAT tests over the past 7 days, those data will be suppressed.

This dataset includes a count and rate per 100,000 population for COVID-19 cases, a count of COVID-19 molecular diagnostic tests, and a percent positivity rate for tests among people living in community settings for the previous two-week period. Dates are based on date of specimen collection (cases and positivity).

A person is considered a new case only upon their first COVID-19 testing result because a case is defined as an instance or bout of illness. If they are tested again subsequently and are still positive, it still counts toward the test positivity metric but they are not considered another case.

Percent positivity is calculated as the number of positive tests among community residents conducted during the 14 days divided by the total number of positive and negative tests among community residents during the same period. If someone was tested more than once during that 14 day period, then those multiple test results (regardless of whether they were positive or negative) are included in the calculation.

These case and test counts do not include cases or tests among people residing in congregate settings, such as nursing homes, assisted living facilities, or correctional facilities.

These data are updated weekly and reflect the previous two full Sunday-Saturday (MMWR) weeks (https://wwwn.cdc.gov/nndss/document/MMWR_week_overview.pdf).

DPH note about change from 7-day to 14-day metrics: Prior to 10/15/2020, these metrics were calculated using a 7-day average rather than a 14-day average. The 7-day metrics are no longer being updated as of 10/15/2020 but the archived dataset can be accessed here: https://data.ct.gov/Health-and-Human-Services/COVID-19-case-rate-per-100-000-population-and-perc/s22x-83rd

As you know, we are learning more about COVID-19 all the time, including the best ways to measure COVID-19 activity in our communities. CT DPH has decided to shift to 14-day rates because these are more stable, particularly at the town level, as compared to 7-day rates. In addition, since the school indicators were initially published by DPH last summer, CDC has recommended 14-day rates and other states (e.g., Massachusetts) have started to implement 14-day metrics for monitoring COVID transmission as well.

With respect to geography, we also have learned that many people are looking at the town-level data to inform decision making, despite emphasis on the county-level metrics in the published addenda. This is understandable as there has been variation within counties in COVID-19 activity (for example, rates that are higher in one town than in most other towns in the county).

Additional notes: As of 11/5/2020, CT DPH has added antigen testing for SARS-CoV-2 to reported test counts in this dataset. The tests included in this dataset include both molecular and antigen datasets. Molecular tests reported include polymerase chain reaction (PCR) and nucleic acid amplicfication (NAAT) tests.

The population data used to calculate rates is based on the CT DPH population statistics for 2019, which is available online here: https://portal.ct.gov/DPH/Health-Information-Systems--Reporting/Population/Population-Statistics. Prior to 5/10/2021, the population estimates from 2018 were used.

Data suppression is applied when the rate is <5 cases per 100,000 or if there are <5 cases within the town. Information on why data suppression rules are applied can be found online here: https://www.cdc.gov/cancer/uscs/technical_notes/stat_methods/suppression.htm

Updates

• Notice of data discontinuation: Since the start of the pandemic, AP has reported case and death counts from data provided by Johns Hopkins University. Johns Hopkins University has announced that they will stop their daily data collection efforts after March 10. As Johns Hopkins stops providing data, the AP will also stop collecting daily numbers for COVID cases and deaths. The HHS and CDC now collect and visualize key metrics for the pandemic. AP advises using those resources when reporting on the pandemic going forward.

  • CDC Weekly case and death counts (national and state level)
  • CDC County level cases and deaths
  • HHS New hospital admissions
  • CDC NowCast COVID variant proportions (national and regional level)

• April 9, 2020

  • The population estimate data for New York County, NY has been updated to include all five New York City counties (Kings County, Queens County, Bronx County, Richmond County and New York County). This has been done to match the Johns Hopkins COVID-19 data, which aggregates counts for the five New York City counties to New York County.

• April 20, 2020

  • Johns Hopkins death totals in the US now include confirmed and probable deaths in accordance with CDC guidelines as of April 14. One significant result of this change was an increase of more than 3,700 deaths in the New York City count. This change will likely result in increases for death counts elsewhere as well. The AP does not alter the Johns Hopkins source data, so probable deaths are included in this dataset as well.

• April 29, 2020

  • The AP is now providing timeseries data for counts of COVID-19 cases and deaths. The raw counts are provided here unaltered, along with a population column with Census ACS-5 estimates and calculated daily case and death rates per 100,000 people. Please read the updated caveats section for more information.

• September 1st, 2020

  • Johns Hopkins is now providing counts for the five New York City counties individually.

• February 12, 2021

  • The Ohio Department of Health recently announced that as many as 4,000 COVID-19 deaths may have been underreported through the state’s reporting system, and that the "daily reported death counts will be high for a two to three-day period."
  • Because deaths data will be anomalous for consecutive days, we have chosen to freeze Ohio's rolling average for daily deaths at the last valid measure until Johns Hopkins is able to back-distribute the data. The raw daily death counts, as reported by Johns Hopkins and including the backlogged death data, will still be present in the new_deaths column.

• February 16, 2021

  - Johns Hopkins has reconciled Ohio's historical deaths data with the state.

  Overview

The AP is using data collected by the Johns Hopkins University Center for Systems Science and Engineering as our source for outbreak caseloads and death counts for the United States and globally.

The Hopkins data is available at the county level in the United States. The AP has paired this data with population figures and county rural/urban designations, and has calculated caseload and death rates per 100,000 people. Be aware that caseloads may reflect the availability of tests -- and the ability to turn around test results quickly -- rather than actual disease spread or true infection rates.

This data is from the Hopkins dashboard that is updated regularly throughout the day. Like all organizations dealing with data, Hopkins is constantly refining and cleaning up their feed, so there may be brief moments where data does not appear correctly. At this link, you’ll find the Hopkins daily data reports, and a clean version of their feed.

The AP is updating this dataset hourly at 45 minutes past the hour.

To learn more about AP's data journalism capabilities for publishers, corporations and financial institutions, go here or email kromano@ap.org.

Queries

Use AP's queries to filter the data or to join to other datasets we've made available to help cover the coronavirus pandemic

• Filter cases by state here

• Rank states by their status as current hotspots. Calculates the 7-day rolling average of new cases per capita in each state: https://data.world/associatedpress/johns-hopkins-coronavirus-case-tracker/workspace/query?queryid=481e82a4-1b2f-41c2-9ea1-d91aa4b3b1ac

• Find recent hotspots within your state by running a query to calculate the 7-day rolling average of new cases by capita in each county: https://data.world/associatedpress/johns-hopkins-coronavirus-case-tracker/workspace/query?queryid=b566f1db-3231-40fe-8099-311909b7b687&showTemplatePreview=true

• Join county-level case data to an earlier dataset released by AP on local hospital capacity here. To find out more about the hospital capacity dataset, see the full details.

• Pull the 100 counties with the highest per-capita confirmed cases here

• Rank all the counties by the highest per-capita rate of new cases in the past 7 days here. Be aware that because this ranks per-capita caseloads, very small counties may rise to the very top, so take into account raw caseload figures as well.

Interactive

The AP has designed an interactive map to track COVID-19 cases reported by Johns Hopkins.

@(https://datawrapper.dwcdn.net/nRyaf/15/)

Interactive Embed Code

<iframe title="USA counties (2018) choropleth map Mapping COVID-19 cases by county" aria-describedby="" id="datawrapper-chart-nRyaf" src="https://datawrapper.dwcdn.net/nRyaf/10/" scrolling="no" frameborder="0" style="width: 0; min-width: 100% !important;" height="400"></iframe><script type="text/javascript">(function() {'use strict';window.addEventListener('message', function(event) {if (typeof event.data['datawrapper-height'] !== 'undefined') {for (var chartId in event.data['datawrapper-height']) {var iframe = document.getElementById('datawrapper-chart-' + chartId) || document.querySelector("iframe[src*='" + chartId + "']");if (!iframe) {continue;}iframe.style.height = event.data['datawrapper-height'][chartId] + 'px';}}});})();</script>

Caveats

• This data represents the number of cases and deaths reported by each state and has been collected by Johns Hopkins from a number of sources cited on their website.
• In some cases, deaths or cases of people who've crossed state lines -- either to receive treatment or because they became sick and couldn't return home while traveling -- are reported in a state they aren't currently in, because of state reporting rules.
• In some states, there are a number of cases not assigned to a specific county -- for those cases, the county name is "unassigned to a single county"
• This data should be credited to Johns Hopkins University's COVID-19 tracking project. The AP is simply making it available here for ease of use for reporters and members.
• Caseloads may reflect the availability of tests -- and the ability to turn around test results quickly -- rather than actual disease spread or true infection rates.
• Population estimates at the county level are drawn from 2014-18 5-year estimates from the American Community Survey.
• The Urban/Rural classification scheme is from the Center for Disease Control and Preventions's National Center for Health Statistics. It puts each county into one of six categories -- from Large Central Metro to Non-Core -- according to population and other characteristics. More details about the classifications can be found here.

Johns Hopkins timeseries data - Johns Hopkins pulls data regularly to update their dashboard. Once a day, around 8pm EDT, Johns Hopkins adds the counts for all areas they cover to the timeseries file. These counts are snapshots of the latest cumulative counts provided by the source on that day. This can lead to inconsistencies if a source updates their historical data for accuracy, either increasing or decreasing the latest cumulative count. - Johns Hopkins periodically edits their historical timeseries data for accuracy. They provide a file documenting all errors in their timeseries files that they have identified and fixed here

Attribution

This data should be credited to Johns Hopkins University COVID-19 tracking project

Note: DPH is updating and streamlining the COVID-19 cases, deaths, and testing data. As of 6/27/2022, the data will be published in four tables instead of twelve. The COVID-19 Cases, Deaths, and Tests by Day dataset contains cases and test data by date of sample submission. The death data are by date of death. This dataset is updated daily and contains information back to the beginning of the pandemic. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-Cases-Deaths-and-Tests-by-Day/g9vi-2ahj. The COVID-19 State Metrics dataset contains over 93 columns of data. This dataset is updated daily and currently contains information starting June 21, 2022 to the present. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-State-Level-Data/qmgw-5kp6 . The COVID-19 County Metrics dataset contains 25 columns of data. This dataset is updated daily and currently contains information starting June 16, 2022 to the present. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-County-Level-Data/ujiq-dy22 . The COVID-19 Town Metrics dataset contains 16 columns of data. This dataset is updated daily and currently contains information starting June 16, 2022 to the present. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-Town-Level-Data/icxw-cada . To protect confidentiality, if a town has fewer than 5 cases or positive NAAT tests over the past 7 days, those data will be suppressed. COVID-19 cases and associated deaths that have been reported among Connecticut residents, broken down by race and ethnicity. All data in this report are preliminary; data for previous dates will be updated as new reports are received and data errors are corrected. Deaths reported to the either the Office of the Chief Medical Examiner (OCME) or Department of Public Health (DPH) are included in the COVID-19 update. The following data show the number of COVID-19 cases and associated deaths per 100,000 population by race and ethnicity. Crude rates represent the total cases or deaths per 100,000 people. Age-adjusted rates consider the age of the person at diagnosis or death when estimating the rate and use a standardized population to provide a fair comparison between population groups with different age distributions. Age-adjustment is important in Connecticut as the median age of among the non-Hispanic white population is 47 years, whereas it is 34 years among non-Hispanic blacks, and 29 years among Hispanics. Because most non-Hispanic white residents who died were over 75 years of age, the age-adjusted rates are lower than the unadjusted rates. In contrast, Hispanic residents who died tend to be younger than 75 years of age which results in higher age-adjusted rates. The population data used to calculate rates is based on the CT DPH population statistics for 2019, which is available online here: https://portal.ct.gov/DPH/Health-Information-Systems--Reporting/Population/Population-Statistics. Prior to 5/10/2021, the population estimates from 2018 were used. Rates are standardized to the 2000 US Millions Standard population (data available here: https://seer.cancer.gov/stdpopulations/). Standardization was done using 19 age groups (0, 1-4, 5-9, 10-14, ..., 80-84, 85 years and older). More information about direct standardization for age adjustment is available here: https://www.cdc.gov/nchs/data/statnt/statnt06rv.pdf Categories are mutually exclusive. The category “multiracial” includes people who answered ‘yes’ to more than one race category. Counts may not add up to total case counts as data on race and ethnicity may be missing. Age adjusted rates calculated only for groups with more than 20 deaths. Abbreviation: NH=Non-Hispanic. Data on Connecticut deaths were obtained from the Connecticut Deaths Registry maintained by the DPH Office of Vital Records. Cause of death was determined by a death certifier (e.g., physician, APRN, medical

Synthetic indicator of premature mortality that provides an explicit means of estimating deaths that occur early. To calculate potential years of life lost (PYLL), the number of deaths at different ages is added and multiplied by the number of years remaining to live to a given age limit (70 years here). The results are standardised, the reference population is the 2013 European population. Infant deaths (first year of life) are excluded from the calculation of PYLL because they are due to specific causes and often have a different etiology than deaths at a later age This indicator is presented as an overall figure. It is expressed in lost years per 100,000 population aged 1 to 69.

Correction 20 January 2023 - An error was found in the population data used to calculate 2021 rates in this publication. This has been corrected, with the overall Scotland avoidable mortality rate for 2021 changing from 350 deaths per 100,000 population to 347 deaths per 100,000. There were minor changes also to council and health board rates, but not for rates by SIMD which used a different population file.

This data set depicts unintentional overdose deaths by county for Tennessee from 1999-2017.Data was compiled from the CDC Wonder database for each year and combined into a single spreadsheet. Each year has both a death field and a rate of fatalities per 100,000 people. The CDC does not publish the number of fatalities by county if the total is less than 10 in a given year. The CDC does not post a rate of fatalities if the total number of deaths per county is less than 20. The population field contains estimates from 2018 and is NOT the data used to generate the rates over time.The following details are copied directly from the CDC Wonder database text file. Note that the year is different for each data download from the original database."Dataset: Underlying Cause of Death, 1999-2017""Query Parameters:""Drug/Alcohol Induced Causes: Drug poisonings (overdose) Unintentional (X40-X44)""States: Tennessee (47)""Year/Month: 1999""Group By: County""Show Totals: True""Show Zero Values: False""Show Suppressed: False""Calculate Rates Per: 100,000""Rate Options: Default intercensal populations for years 2001-2009 (except Infant Age Groups)""---""Help: See http://wonder.cdc.gov/wonder/help/ucd.html for more information.""---""Query Date: Aug 19, 2019 10:22:15 PM""1. Rows with suppressed Deaths are hidden, but the Deaths and Population values in those rows are included in the totals. Use""Quick Options above to show suppressed rows.""---"Caveats:"1. Data are Suppressed when the data meet the criteria for confidentiality constraints. More information:""http://wonder.cdc.gov/wonder/help/ucd.html#Assurance of Confidentiality.""2. Death rates are flagged as Unreliable when the rate is calculated with a numerator of 20 or less. More information:""http://wonder.cdc.gov/wonder/help/ucd.html#Unreliable.""3. The population figures for year 2017 are bridged-race estimates of the July 1 resident population, from the Vintage 2017""postcensal series released by NCHS on June 27, 2018. The population figures for year 2016 are bridged-race estimates of the July""1 resident population, from the Vintage 2016 postcensal series released by NCHS on June 26, 2017. The population figures for""year 2015 are bridged-race estimates of the July 1 resident population, from the Vintage 2015 postcensal series released by NCHS""on June 28, 2016. The population figures for year 2014 are bridged-race estimates of the July 1 resident population, from the""Vintage 2014 postcensal series released by NCHS on June 30, 2015. The population figures for year 2013 are bridged-race""estimates of the July 1 resident population, from the Vintage 2013 postcensal series released by NCHS on June 26, 2014. The""population figures for year 2012 are bridged-race estimates of the July 1 resident population, from the Vintage 2012 postcensal""series released by NCHS on June 13, 2013. The population figures for year 2011 are bridged-race estimates of the July 1 resident""population, from the Vintage 2011 postcensal series released by NCHS on July 18, 2012. Population figures for 2010 are April 1""Census counts. The population figures for years 2001 - 2009 are bridged-race estimates of the July 1 resident population, from""the revised intercensal county-level 2000 - 2009 series released by NCHS on October 26, 2012. Population figures for 2000 are""April 1 Census counts. Population figures for 1999 are from the 1990-1999 intercensal series of July 1 estimates. Population""figures for the infant age groups are the number of live births.
Note: Rates and population figures for years 2001 -""2009 differ slightly from previously published reports, due to use of the population estimates which were available at the time""of release.""4. The population figures used in the calculation of death rates for the age group 'under 1 year' are the estimates of the""resident population that is under one year of age. More information: http://wonder.cdc.gov/wonder/help/ucd.html#Age Group."

DPH is updating and streamlining the COVID-19 cases, deaths, and testing data. As of 6/27/2022, the data will be published in four tables instead of twelve. The COVID-19 Cases, Deaths, and Tests by Day dataset contains cases and test data by date of sample submission. The death data are by date of death. This dataset is updated daily and contains information back to the beginning of the pandemic. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-Cases-Deaths-and-Tests-by-Day/g9vi-2ahj. The COVID-19 State Metrics dataset contains over 93 columns of data. This dataset is updated daily and currently contains information starting June 21, 2022 to the present. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-State-Level-Data/qmgw-5kp6 . The COVID-19 County Metrics dataset contains 25 columns of data. This dataset is updated daily and currently contains information starting June 16, 2022 to the present. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-County-Level-Data/ujiq-dy22 . The COVID-19 Town Metrics dataset contains 16 columns of data. This dataset is updated daily and currently contains information starting June 16, 2022 to the present. The data can be found at https://data.ct.gov/Health-and-Human-Services/COVID-19-Town-Level-Data/icxw-cada . To protect confidentiality, if a town has fewer than 5 cases or positive NAAT tests over the past 7 days, those data will be suppressed. COVID-19 cases, tests, and associated deaths from COVID-19 that have been reported among Connecticut residents. All data in this report are preliminary; data for previous dates will be updated as new reports are received and data errors are corrected. Deaths reported to the either the Office of the Chief Medical Examiner (OCME) or Department of Public Health (DPH) are included in the daily COVID-19 update. The case rate per 100,000 includes probable and confirmed cases. Probable and confirmed are defined using the CSTE case definition, which is available online: https://cdn.ymaws.com/www.cste.org/resource/resmgr/2020ps/Interim-20-ID-01_COVID-19.pdf The population data used to calculate rates is based on the CT DPH population statistics for 2019, which is available online here: https://portal.ct.gov/DPH/Health-Information-Systems--Reporting/Population/Population-Statistics. Prior to 5/10/2021, the population estimates from 2018 were used. Data on Connecticut deaths were obtained from the Connecticut Deaths Registry maintained by the DPH Office of Vital Records. Cause of death was determined by a death certifier (e.g., physician, APRN, medical examiner) using their best clinical judgment. Additionally, all COVID-19 deaths, including suspected or related, are required to be reported to OCME. On April 4, 2020, CT DPH and OCME released a joint memo to providers and facilities within Connecticut providing guidelines for certifying deaths due to COVID-19 that were consistent with the CDC’s guidelines and a reminder of the required reporting to OCME.25,26 As of July 1, 2021, OCME had reviewed every case reported and performed additional investigation on about one-third of reported deaths to better ascertain if COVID-19 did or did not cause or contribute to the death. Some of these investigations resulted in the OCME performing postmortem swabs for PCR testing on individuals whose deaths were suspected to be due to COVID-19, but antemortem diagnosis was unable to be made.31 The OCME issued or re-issued about 10% of COVID-19 death certificates and, when appropriate, removed COVID-19 from the death certificate. For standardization and tabulation of mortality statistics, written cause of death statements made by the certifiers on death certificates are sent to the National Center for Health Statistics (NCHS) at the CDC which assigns cause of death codes according to the International Causes of Disease 10th Revision (ICD-10) classification system.25,26 CO

Data was compiled from the CDC Wonder database for each year and combined into a single spreadsheet. Each year has both a death field and a rate of fatalities per 100,000 people. The CDC does not publish the number of fatalities by county if the total is less than 10 in a given year. The CDC does not post a rate of fatalities if the total number of deaths per county is less than 20. The population field contains estimates from 2018 and is NOT the data used to generate the rates over time.The following details are copied directly from the CDC Wonder database text file. Note that the year is different for each data download from the original database."Dataset: Underlying Cause of Death, 1999-2017""Query Parameters:""Drug/Alcohol Induced Causes: Drug poisonings (overdose) Unintentional (X40-X44)""States: Tennessee (47)""Year/Month: 1999""Group By: County""Show Totals: True""Show Zero Values: False""Show Suppressed: False""Calculate Rates Per: 100,000""Rate Options: Default intercensal populations for years 2001-2009 (except Infant Age Groups)""---""Help: See http://wonder.cdc.gov/wonder/help/ucd.html for more information.""---""Query Date: Aug 19, 2019 10:22:15 PM""1. Rows with suppressed Deaths are hidden, but the Deaths and Population values in those rows are included in the totals. Use""Quick Options above to show suppressed rows.""---"Caveats:"1. Data are Suppressed when the data meet the criteria for confidentiality constraints. More information:""http://wonder.cdc.gov/wonder/help/ucd.html#Assurance of Confidentiality.""2. Death rates are flagged as Unreliable when the rate is calculated with a numerator of 20 or less. More information:""http://wonder.cdc.gov/wonder/help/ucd.html#Unreliable.""3. The population figures for year 2017 are bridged-race estimates of the July 1 resident population, from the Vintage 2017""postcensal series released by NCHS on June 27, 2018. The population figures for year 2016 are bridged-race estimates of the July""1 resident population, from the Vintage 2016 postcensal series released by NCHS on June 26, 2017. The population figures for""year 2015 are bridged-race estimates of the July 1 resident population, from the Vintage 2015 postcensal series released by NCHS""on June 28, 2016. The population figures for year 2014 are bridged-race estimates of the July 1 resident population, from the""Vintage 2014 postcensal series released by NCHS on June 30, 2015. The population figures for year 2013 are bridged-race""estimates of the July 1 resident population, from the Vintage 2013 postcensal series released by NCHS on June 26, 2014. The""population figures for year 2012 are bridged-race estimates of the July 1 resident population, from the Vintage 2012 postcensal""series released by NCHS on June 13, 2013. The population figures for year 2011 are bridged-race estimates of the July 1 resident""population, from the Vintage 2011 postcensal series released by NCHS on July 18, 2012. Population figures for 2010 are April 1""Census counts. The population figures for years 2001 - 2009 are bridged-race estimates of the July 1 resident population, from""the revised intercensal county-level 2000 - 2009 series released by NCHS on October 26, 2012. Population figures for 2000 are""April 1 Census counts. Population figures for 1999 are from the 1990-1999 intercensal series of July 1 estimates. Population""figures for the infant age groups are the number of live births.
Note: Rates and population figures for years 2001 -""2009 differ slightly from previously published reports, due to use of the population estimates which were available at the time""of release.""4. The population figures used in the calculation of death rates for the age group 'under 1 year' are the estimates of the""resident population that is under one year of age. More information: http://wonder.cdc.gov/wonder/help/ucd.html#Age Group."

Context

This is the US Coronavirus data repository from The New York Times . This data includes COVID-19 cases and deaths reported by state and county. The New York Times compiled this data based on reports from state and local health agencies. More information on the data repository is available here . For additional reporting and data visualizations, see The New York Times’ U.S. coronavirus interactive site

Sample Queries

Query 1

Which US counties have the most confirmed cases per capita? This query determines which counties have the most cases per 100,000 residents. Note that this may differ from similar queries of other datasets because of differences in reporting lag, methodologies, or other dataset differences.

SELECT covid19.county, covid19.state_name, total_pop AS county_population, confirmed_cases, ROUND(confirmed_cases/total_pop *100000,2) AS confirmed_cases_per_100000, deaths, ROUND(deaths/total_pop *100000,2) AS deaths_per_100000 FROM bigquery-public-data.covid19_nyt.us_counties covid19 JOIN bigquery-public-data.census_bureau_acs.county_2017_5yr acs ON covid19.county_fips_code = acs.geo_id WHERE date = DATE_SUB(CURRENT_DATE(),INTERVAL 1 day) AND covid19.county_fips_code != "00000" ORDER BY confirmed_cases_per_100000 desc

Query 2

How do I calculate the number of new COVID-19 cases per day? This query determines the total number of new cases in each state for each day available in the dataset SELECT b.state_name, b.date, MAX(b.confirmed_cases - a.confirmed_cases) AS daily_confirmed_cases FROM (SELECT state_name AS state, state_fips_code , confirmed_cases, DATE_ADD(date, INTERVAL 1 day) AS date_shift FROM bigquery-public-data.covid19_nyt.us_states WHERE confirmed_cases + deaths > 0) a JOIN bigquery-public-data.covid19_nyt.us_states b ON a.state_fips_code = b.state_fips_code AND a.date_shift = b.date GROUP BY b.state_name, date ORDER BY date desc

La statistique de mortalité maternelle est établie à partir de la base de données des causes de décès. Dans celle-ci, une sélection des « décès maternels » est faite, en suivant une longue procédure (décrite en détail dans les Métadonnées) qui respecte la définition de l’OMS. D’après la dixième révision de la Classification internationale des maladies (CIM-10), le décès maternel se définit comme « le décès d’une femme survenu au cours de la grossesse ou dans un délai de 42 jours après sa terminaison, quelles qu’en soient la durée ou la localisation, pour une cause quelconque déterminée ou aggravée par la grossesse ou les soins qu’elle a motivés, mais ni accidentelle, ni fortuite ». « Les décès maternels se subdivisent en deux groupes. Les décès par cause obstétricale directe sont ceux qui résultent de complications obstétricales (grossesse, travail et suites de couches), d’interventions, d’omissions, d’un traitement incorrect ou d’un enchaînement d’événements résultant de l’un quelconque des facteurs ci-dessus. Les décès par cause obstétricale indirecte sont ceux qui résultent d’une maladie préexistante ou d’une affection apparue au cours de la grossesse sans qu’elle soit due à des causes obstétricales directes, mais qui a été aggravée par les effets physiologiques de la grossesse ». La CIM-10 définit également le décès maternel tardif comme étant « le décès d’une femme résultant de causes obstétricales directes ou indirectes survenu plus de 42 jours, mais moins d’un an, après la terminaison de la grossesse ». Le ratio de mortalité maternelle est le rapport entre le nombre de décès maternels, directs et indirects, observés en une année, et le nombre de naissances vivantes de la même année, exprimé pour 100.000 naissances vivantes. Les décès maternels tardifs ne sont pas pris en compte pour le calcul de ce ratio. Etant donné le petit nombre de cas identifiés en Belgique chaque année et la grande variabilité de cet effectif, le choix a été fait de calculer le ratio en cumulant les décès maternels et les naissances vivantes de 5 années successives, en centrant le ratio sur l’année médiane. Lors de l’identification de ces décès maternels, le Groupe de travail ad hoc, qui rassemble autour de l’office belge de statistique toutes les entités fédérées productrices de données, n’a pas écarté le risque d’une sous-évaluation de ces décès, sur la base du seul bulletin statistique qui sert de source principale. Il demande donc de poursuivre les efforts afin d’améliorer davantage le suivi des décès liés à la maternité et soutient l’initiative prise récemment par le Collège de médecins pour la mère et le nouveau-né d’examiner la possibilité de création d’un Registre de la mortalité maternelle. Métadonnées La statistique de mortalité maternelle

NOTE: This dataset has been retired and marked as historical-only. Weekly rates of COVID-19 cases, hospitalizations, and deaths among people living in Chicago by vaccination status and age. Rates for fully vaccinated and unvaccinated begin the week ending April 3, 2021 when COVID-19 vaccines became widely available in Chicago. Rates for boosted begin the week ending October 23, 2021 after booster shots were recommended by the Centers for Disease Control and Prevention (CDC) for adults 65+ years old and adults in certain populations and high risk occupational and institutional settings who received Pfizer or Moderna for their primary series or anyone who received the Johnson & Johnson vaccine. Chicago residency is based on home address, as reported in the Illinois Comprehensive Automated Immunization Registry Exchange (I-CARE) and Illinois National Electronic Disease Surveillance System (I-NEDSS). Outcomes: • Cases: People with a positive molecular (PCR) or antigen COVID-19 test result from an FDA-authorized COVID-19 test that was reported into I-NEDSS. A person can become re-infected with SARS-CoV-2 over time and so may be counted more than once in this dataset. Cases are counted by week the test specimen was collected. • Hospitalizations: COVID-19 cases who are hospitalized due to a documented COVID-19 related illness or who are admitted for any reason within 14 days of a positive SARS-CoV-2 test. Hospitalizations are counted by week of hospital admission. • Deaths: COVID-19 cases who died from COVID-19-related health complications as determined by vital records or a public health investigation. Deaths are counted by week of death. Vaccination status: • Fully vaccinated: Completion of primary series of a U.S. Food and Drug Administration (FDA)-authorized or approved COVID-19 vaccine at least 14 days prior to a positive test (with no other positive tests in the previous 45 days). • Boosted: Fully vaccinated with an additional or booster dose of any FDA-authorized or approved COVID-19 vaccine received at least 14 days prior to a positive test (with no other positive tests in the previous 45 days). • Unvaccinated: No evidence of having received a dose of an FDA-authorized or approved vaccine prior to a positive test. CLARIFYING NOTE: Those who started but did not complete all recommended doses of an FDA-authorized or approved vaccine prior to a positive test (i.e., partially vaccinated) are excluded from this dataset. Incidence rates for fully vaccinated but not boosted people (Vaccinated columns) are calculated as total fully vaccinated but not boosted with outcome divided by cumulative fully vaccinated but not boosted at the end of each week. Incidence rates for boosted (Boosted columns) are calculated as total boosted with outcome divided by cumulative boosted at the end of each week. Incidence rates for unvaccinated (Unvaccinated columns) are calculated as total unvaccinated with outcome divided by total population minus cumulative boosted, fully, and partially vaccinated at the end of each week. All rates are multiplied by 100,000. Incidence rate ratios (IRRs) are calculated by dividing the weekly incidence rates among unvaccinated people by those among fully vaccinated but not boosted and boosted people. Overall age-adjusted incidence rates and IRRs are standardized using the 2000 U.S. Census standard population. Population totals are from U.S. Census Bureau American Community Survey 1-year estimates for 2019. All data are provisional and subject to change. Information is updated as additional details are received and it is, in fact, very common for recent dates to be incomplete and to be updated as time goes on. This dataset reflects data known to CDPH at the time when the dataset is updated each week. Numbers in this dataset may differ from other public sources due to when data are reported and how City of Chicago boundaries are defined. For all datasets related to COVID-19, see https://data.cityofchic

On March 10, 2023, the Johns Hopkins Coronavirus Resource Center ceased its collecting and reporting of global COVID-19 data. For updated cases, deaths, and vaccine data please visit: World Health Organization (WHO)For more information, visit the Johns Hopkins Coronavirus Resource Center.COVID-19 Trends MethodologyOur goal is to analyze and present daily updates in the form of recent trends within countries, states, or counties during the COVID-19 global pandemic. The data we are analyzing is taken directly from the Johns Hopkins University Coronavirus COVID-19 Global Cases Dashboard, though we expect to be one day behind the dashboard’s live feeds to allow for quality assurance of the data.DOI: https://doi.org/10.6084/m9.figshare.125529863/7/2022 - Adjusted the rate of active cases calculation in the U.S. to reflect the rates of serious and severe cases due nearly completely dominant Omicron variant.6/24/2020 - Expanded Case Rates discussion to include fix on 6/23 for calculating active cases.6/22/2020 - Added Executive Summary and Subsequent Outbreaks sectionsRevisions on 6/10/2020 based on updated CDC reporting. This affects the estimate of active cases by revising the average duration of cases with hospital stays downward from 30 days to 25 days. The result shifted 76 U.S. counties out of Epidemic to Spreading trend and no change for national level trends.Methodology update on 6/2/2020: This sets the length of the tail of new cases to 6 to a maximum of 14 days, rather than 21 days as determined by the last 1/3 of cases. This was done to align trends and criteria for them with U.S. CDC guidance. The impact is areas transition into Controlled trend sooner for not bearing the burden of new case 15-21 days earlier.Correction on 6/1/2020Discussion of our assertion of an abundance of caution in assigning trends in rural counties added 5/7/2020. Revisions added on 4/30/2020 are highlighted.Revisions added on 4/23/2020 are highlighted.Executive SummaryCOVID-19 Trends is a methodology for characterizing the current trend for places during the COVID-19 global pandemic. Each day we assign one of five trends: Emergent, Spreading, Epidemic, Controlled, or End Stage to geographic areas to geographic areas based on the number of new cases, the number of active cases, the total population, and an algorithm (described below) that contextualize the most recent fourteen days with the overall COVID-19 case history. Currently we analyze the countries of the world and the U.S. Counties. The purpose is to give policymakers, citizens, and analysts a fact-based data driven sense for the direction each place is currently going. When a place has the initial cases, they are assigned Emergent, and if that place controls the rate of new cases, they can move directly to Controlled, and even to End Stage in a short time. However, if the reporting or measures to curtail spread are not adequate and significant numbers of new cases continue, they are assigned to Spreading, and in cases where the spread is clearly uncontrolled, Epidemic trend.We analyze the data reported by Johns Hopkins University to produce the trends, and we report the rates of cases, spikes of new cases, the number of days since the last reported case, and number of deaths. We also make adjustments to the assignments based on population so rural areas are not assigned trends based solely on case rates, which can be quite high relative to local populations.Two key factors are not consistently known or available and should be taken into consideration with the assigned trend. First is the amount of resources, e.g., hospital beds, physicians, etc.that are currently available in each area. Second is the number of recoveries, which are often not tested or reported. On the latter, we provide a probable number of active cases based on CDC guidance for the typical duration of mild to severe cases.Reasons for undertaking this work in March of 2020:The popular online maps and dashboards show counts of confirmed cases, deaths, and recoveries by country or administrative sub-region. Comparing the counts of one country to another can only provide a basis for comparison during the initial stages of the outbreak when counts were low and the number of local outbreaks in each country was low. By late March 2020, countries with small populations were being left out of the mainstream news because it was not easy to recognize they had high per capita rates of cases (Switzerland, Luxembourg, Iceland, etc.). Additionally, comparing countries that have had confirmed COVID-19 cases for high numbers of days to countries where the outbreak occurred recently is also a poor basis for comparison.The graphs of confirmed cases and daily increases in cases were fit into a standard size rectangle, though the Y-axis for one country had a maximum value of 50, and for another country 100,000, which potentially misled people interpreting the slope of the curve. Such misleading circumstances affected comparing large population countries to small population counties or countries with low numbers of cases to China which had a large count of cases in the early part of the outbreak. These challenges for interpreting and comparing these graphs represent work each reader must do based on their experience and ability. Thus, we felt it would be a service to attempt to automate the thought process experts would use when visually analyzing these graphs, particularly the most recent tail of the graph, and provide readers with an a resulting synthesis to characterize the state of the pandemic in that country, state, or county.The lack of reliable data for confirmed recoveries and therefore active cases. Merely subtracting deaths from total cases to arrive at this figure progressively loses accuracy after two weeks. The reason is 81% of cases recover after experiencing mild symptoms in 10 to 14 days. Severe cases are 14% and last 15-30 days (based on average days with symptoms of 11 when admitted to hospital plus 12 days median stay, and plus of one week to include a full range of severely affected people who recover). Critical cases are 5% and last 31-56 days. Sources:U.S. CDC. April 3, 2020 Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19). Accessed online. Initial older guidance was also obtained online. Additionally, many people who recover may not be tested, and many who are, may not be tracked due to privacy laws. Thus, the formula used to compute an estimate of active cases is: Active Cases = 100% of new cases in past 14 days + 19% from past 15-25 days + 5% from past 26-49 days - total deaths. On 3/17/2022, the U.S. calculation was adjusted to: Active Cases = 100% of new cases in past 14 days + 6% from past 15-25 days + 3% from past 26-49 days - total deaths. Sources: https://www.cdc.gov/mmwr/volumes/71/wr/mm7104e4.htm https://covid.cdc.gov/covid-data-tracker/#variant-proportions If a new variant arrives and appears to cause higher rates of serious cases, we will roll back this adjustment. We’ve never been inside a pandemic with the ability to learn of new cases as they are confirmed anywhere in the world. After reviewing epidemiological and pandemic scientific literature, three needs arose. We need to specify which portions of the pandemic lifecycle this map cover. The World Health Organization (WHO) specifies six phases. The source data for this map begins just after the beginning of Phase 5: human to human spread and encompasses Phase 6: pandemic phase. Phase six is only characterized in terms of pre- and post-peak. However, these two phases are after-the-fact analyses and cannot ascertained during the event. Instead, we describe (below) a series of five trends for Phase 6 of the COVID-19 pandemic.Choosing terms to describe the five trends was informed by the scientific literature, particularly the use of epidemic, which signifies uncontrolled spread. The five trends are: Emergent, Spreading, Epidemic, Controlled, and End Stage. Not every locale will experience all five, but all will experience at least three: emergent, controlled, and end stage.This layer presents the current trends for the COVID-19 pandemic by country (or appropriate level). There are five trends:Emergent: Early stages of outbreak. Spreading: Early stages and depending on an administrative area’s capacity, this may represent a manageable rate of spread. Epidemic: Uncontrolled spread. Controlled: Very low levels of new casesEnd Stage: No New cases These trends can be applied at several levels of administration: Local: Ex., City, District or County – a.k.a. Admin level 2State: Ex., State or Province – a.k.a. Admin level 1National: Country – a.k.a. Admin level 0Recommend that at least 100,000 persons be represented by a unit; granted this may not be possible, and then the case rate per 100,000 will become more important.Key Concepts and Basis for Methodology: 10 Total Cases minimum threshold: Empirically, there must be enough cases to constitute an outbreak. Ideally, this would be 5.0 per 100,000, but not every area has a population of 100,000 or more. Ten, or fewer, cases are also relatively less difficult to track and trace to sources. 21 Days of Cases minimum threshold: Empirically based on COVID-19 and would need to be adjusted for any other event. 21 days is also the minimum threshold for analyzing the “tail” of the new cases curve, providing seven cases as the basis for a likely trend (note that 21 days in the tail is preferred). This is the minimum needed to encompass the onset and duration of a normal case (5-7 days plus 10-14 days). Specifically, a median of 5.1 days incubation time, and 11.2 days for 97.5% of cases to incubate. This is also driven by pressure to understand trends and could easily be adjusted to 28 days. Source

Accuracy:Data are from the "Suspect drug-related and confirmed opioid toxicity deaths in Ottawa Public Health" custom report provided by the OCCO.Confirmed opioid toxicity deaths are deaths for which a coroner or forensic pathologist determined the cause of death to be drug toxicity with opioid involvement. These may include drug toxicity deaths involving multiple substances. Conclusions on cause of death may take several months to become available.Deaths have been assigned to public health unit based on six-digit postal code of the residence of the decedent. If residence postal code was unavailable, the postal code of the incident location was used. If postal code of the incident location was unavailable, the postal code of the death location was used. This methodology aligns with how deaths are assigned in PHO's Interactive Opioid Tool.The attribution of deaths to an ONS neighbourhood reflects the location of incident or death, based on postal code, and not necessarily the neighbourhood where the decedent resided. Postal codes that straddle more than one ONS neighbourhood are allocated to neighbourhoods based on the area of overlap between the straddled neighbourhoods. If there is no postal code information for the location of incident, the location of incident/death is not attributed to an ONS neighbourhood. Update Frequency: Yearly

Attributes:ONS neighbourhood ID – the identification number for the Ottawa Neighbourhood Study (ONS) neighbourhood.ONS neighbourhood name – the name of the ONS neighbourhood.Cumulative number of confirmed opioid toxicity deaths – the cumulative number of confirmed opioid toxicity deaths of Ottawa residents based on the location of the incident.Yearly average of confirmed opioid toxicity deaths – the cumulative number of confirmed opioid toxicity deaths of Ottawa residents divided by the number of years of data.Average yearly rate (per 100,000 population) of confirmed opioid toxicity deaths – the average of the yearly rate (per 100,000 population) of confirmed opioid toxicity deaths of Ottawa residents. To calculate each neighbourhood’s annual rate, the total number of drug overdose deaths by ONS neighbourhood is divided by the neighbourhood population estimate for that year and then multiplied by 100,000. This gives us an annual neighbourhood rate per 100,000 population for each year of data and neighbourhood. For each neighbourhood, the annual rates are summed to create a cumulative neighbourhood rate, which is then divided by the number of years to create the average yearly rate for each neighbourhood.Years – the range of years during which the deaths occurred. Contact: Ottawa Public Health Epidemiology Team

The birth-death exposed-infectious (BDEI) phylodynamic model describes the transmission of pathogens featuring an incubation period (when there is a delay between the moment of infection and becoming infectious, as for Ebola and SARS-CoV-2), and permits its estimation along with other parameters, from time-scaled phylogenetic trees. We implemented a highly parallelizable estimator for the BDEI model in a maximum likelihood framework (PyBDEI) using a combination of numerical analysis methods for efficient equation resolution. This dataset contains the assessment of PyBDEI in comparison with a Bayesian implementation in BEAST2 (mtbd package) and a deep learning estimator PhyloDeep: the parameter values estimated by the 3 tools.The PyBDEI and the theoretical findings behind it are described in A Zhukova, F Hecht, Y Maday, and O Gascuel. Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth-Death Epidemiological Models from Phylogenetic Trees Syst Biol 2023. This dataset contains the online Appendix (Fig S1-S3 and Table S1). Methods Simulated data We assessed the performance of our estimator on two data sets from Voznica et al. 2021 (accessible at (doi.org/10.5281/zenodo.7358555)):

medium, a data set of 100 medium-sized trees (200 − 500 tips),

large, a data set of 100 large trees (5 000 − 10 000 tips)

The data were downloaded from github.com/evolbioinfo/phylodeep (also accessible at (doi.org/10.5281/zenodo.7358555), under GNU GPL v3 licence). To produce medium trees, Voznica et al. generated 10 000 trees with 200 − 500 tips under the BDEI model, with the parameter values sampled uniformly at random within the following boundaries:

incubation period 1/µ ∈ [0.2, 50] basic reproductive number R_0 = λ/ψ ∈ [1, 5] infectious period 1/ψ ∈ [1, 10].

Then randomly selected 100 out of those 10 000 trees to evaluate them with the gold standard method, BEAST2. For 100 large tree generation, the same parameter values as for the 100 medium ones were used, but the tree size varied between 5000 and 10 000 tips. Large forest data set To evaluate PyBDEI performance on forests, we additionally generated two types of forests for the large data set. Type 1 forests (e.g. health policy change) The first type of forests was produced by cutting the oldest (i.e., closest to the root) 25% of each full tree, and keeping the forest of bottom-75% subtrees (in terms of time). We hence obtained 100 forests representing sup-epidemics that all started at the same time. They can be found in large/forests folder. Type 2 forests (e.g. multiple introductions to a country) The second type of forests represented epidemics that started with multiple introductions happening at different times. To generate them we

took the parameter values Θi corresponding to each tree Treei in the large dataset (i ∈ {1, . . . , 100}) calculated the time Ti between the start of the tree Treei and the time of its last sampled tip kept

uniformly drawing a time Ti,j ∈ [0, Ti], and generating a (potentially hidden) tree Treei,j under parameters Θi till reaching the time Ti,j.

Steps (3.i) and (3.ii) were repeated till the total number of sampled tips in the generated trees reached at least 5 000: tips(Treei,j) ⩾ 5 000. The resulting forest Fi included those of the trees Treei,j that contained at least one sampled tip (i.e., observed trees). These forests can be found in large/subepidemics folder. As the BDEI model requires one of the parameters to be fixed in order to become asymptomatically identifiable, ρ was fixed to the real value. Data preparation and parameter estimation pipelines are available at github.com/evolbioinfo/bdei This dataset contains:

a forest of Type 1 for each large tree: large/forests/forest.[0-99].nwk a forest of Type 2 for each large tree: large/subepidemics/subepidemic.[0-99].nwk the estimated and real parameter values for fixed ρ: medium/estimates.tab and large/estimates.tab tab-separated tables

Deaths from alcohol-related conditions, all ages, directly age-standardised rate per 100,000 population (standardised to the European standard population).

Rationale Alcohol consumption is a contributing factor to hospital admissions and deaths from a diverse range of conditions. Alcohol misuse is estimated to cost the NHS about £3.5 billion per year and society as a whole £21 billion annually.

The Government has said that everyone has a role to play in reducing the harmful use of alcohol - this indicator is one of the key contributions by the Government (and the Department of Health and Social Care) to promote measurable, evidence-based prevention activities at a local level, and supports the national ambitions to reduce harm set out in the Government's Alcohol Strategy. This ambition is part of the monitoring arrangements for the Responsibility Deal Alcohol Network. Alcohol-related deaths can be reduced through local interventions to reduce alcohol misuse and harm.

The proportion of disease attributable to alcohol (alcohol attributable fraction) is calculated using a relative risk (a fraction between 0 and 1) specific to each disease, age group, and sex combined with the prevalence of alcohol consumption in the population. All mortality records are extracted that contain an attributable disease and the age and sex-specific fraction applied. The results are summed into quinary age bands for the numerator and a directly standardised rate calculated using the European Standard Population. This revised indicator uses updated alcohol attributable fractions, based on new relative risks from ‘Alcohol-attributable fractions for England: an update’ (1) published by PHE in 2020. A detailed comparison between the 2013 and 2020 alcohol attributable fractions is available in Appendix 3 of the PHE report (2). A consultation was also undertaken with stakeholders where the impact of the new methodology on the LAPE indicators was quantified and explored (3).

The calculation that underlies all alcohol-related indicators has been updated to take account of the latest academic evidence and more recent alcohol-consumption figures. The result has been that the newly published mortality and admission rates are lower than those previously published. This is due to a change in methodology, mainly because alcohol consumption across the population has reduced since 2010. Therefore, the number of deaths and hospital admissions that we attribute to alcohol has reduced because in general people are drinking less today than they were when the original calculation was made.

Figures published previously did not misrepresent the burden of alcohol based on the previous evidence – the methodology used in this update is as close as sources and data allow to the original method. Though the number of deaths and admissions attributed to alcohol each year has reduced, the direction of trend and the key inequalities due to alcohol harm remain the same. Alcohol remains a significant burden on the health of the population and the harm alcohol causes to individuals remains unchanged.

References:

PHE (2020) Alcohol-attributable fractions for England: an update PHE (2020) Alcohol-attributable fractions for England: an update: Appendix 3 PHE (2021) Proposed changes for calculating alcohol-related mortality

Definition of numerator Deaths from alcohol-related conditions based on underlying cause of death, registered in the calendar year for all ages. Each alcohol-related death is assigned an alcohol attributable fraction based on underlying cause of death (and all cause of deaths fields for the conditions: ethanol poisoning, methanol poisoning, toxic effect of alcohol). Alcohol-attributable fractions were not available for children.

Mortality data includes all deaths registered in the calendar year where the local authority of usual residence of the deceased is one of the English geographies and an alcohol attributable diagnosis is given as the underlying cause of death. Counts of deaths for years up to and including 2019 have been adjusted where needed to take account of the MUSE ICD-10 coding change introduced in 2020. Detailed guidance on the MUSE implementation is available at: MUSE implementation guidance.

Counts of deaths for years up to and including 2013 have been double adjusted by applying comparability ratios from both the IRIS coding change and the MUSE coding change where needed to take account of both the MUSE ICD-10 coding change and the IRIS ICD-10 coding change introduced in 2014. The detailed guidance on the IRIS implementation is available at: IRIS implementation guidance.

Counts of deaths for years up to and including 2010 have been triple adjusted by applying comparability ratios from the 2011 coding change, the IRIS coding change, and the MUSE coding change where needed to take account of the MUSE ICD-10 coding change, the IRIS ICD-10 coding change, and the ICD-10 coding change introduced in 2011. The detailed guidance on the 2011 implementation is available at: 2011 implementation guidance.

Definition of denominator ONS mid-year population estimates aggregated into quinary age bands.

Caveats There is the potential for the underlying cause of death to be incorrectly attributed on the death certificate and the cause of death misclassified. Alcohol-attributable fractions were not available for children. Conditions where low levels of alcohol consumption are protective (have a negative alcohol-attributable fraction) are not included in the calculation of the indicator.

The confidence intervals do not take into account the uncertainty involved in the calculation of the AAFs – that is, the proportion of deaths that are caused by alcohol and the alcohol consumption prevalence that are included in the AAF formula are only an estimate and so include uncertainty. The confidence intervals published here are based only on the observed number of deaths and do not account for this uncertainty in the calculation of attributable fraction - as such the intervals may be too narrow.

Introduction and objectivesStudies assessing the health benefits of air pollution reduction in Vietnam are scarce. This study quantified the annual mortality burden due to PM2.5 pollution in Vietnam above the World Health Organization recommendation for community health (AQG: 5 μg/m3) and the proposed National Technical Regulation on Ambient Air Quality (proposed QCVN: 15 μg/m3).MethodologyThis study applied a health impact assessment methodology with the hazard risk function for non-communicable diseases (NCDs) and lower respiratory infections (LRIs) in the Global Exposure Mortality Model (GEMM) to calculate attributable deaths, Years of Life lost, and Loss of Life expectancy at birth due to air pollution in the Vietnamese population above 25 years of age in 11 provinces. We obtained annual average PM2.5 concentrations for Vietnam in 2019 at a 3x3 km grid modeled using Mixed Linear regression and multi-data sources. Population and baseline mortality data were obtained from administrative data system in Vietnam. We reported the findings at both the provincial and smaller district levels.ResultsAnnual PM2.5 concentrations in all studied provinces exceeded both the AQG and the proposed QCVN. The maximum annual number of attributable deaths in the studied provinces if they had complied with WHO air quality guidelines was in Ha Noi City, with 5,090 (95%CI: 4,253–5,888) attributable deaths. At the district level, the highest annual rate of attributable deaths if the WHO recommendation for community health had been met was 104.6 (95%CI: 87.0–121.5) attributable deaths per 100,000 population in Ly Nhan (Ha Nam province).ConclusionA much larger number of premature deaths in Vietnam could potentially be avoided by lowering the recommended air quality standard. These results highlight the need for effective clean air action plans by local authorities to reduce air pollution and improve community health.

This group of datasets describe the suicides in Scotland for the period 1982-2009. There are 4 separate datasets: All Suicides/Male Suicides/Female Suicides/All Suicide Rate (expressed per 100,000 people). The data is broken down into Local Authority Areas making it easier to investigate any spatial disparity in the suicide figures. A couple of points are worth noting are that it is unclear if the suicide data shows all suicides or just those of Adults. A recent Scottish Government report(http://www.scotland.gov.uk/Publications/2007/03/01145422/20) used deaths of people over 15 years old. Differences in the rates between this data and the results presented in the Scottish Government report may also be due to different population datasets being used. Suicide data sources form the Scottish Public Health Observatory (http://www.scotpho.org.uk/home/Healthwell-beinganddisease/suicide/suicide_data/suicide_la.asp) and the population data used to calculate the rates was sourced from ShareGeo Open (http://hdl.handle.net/10672/95) which uses mid-year estimates downloaded from Nomis (www.nomisweb.co.uk/. Datasets were joined to Local Authority (district, unitary authority and borough) boundaries downloaded from Ordnance Survey OpenData Boundary Line dataset. All spatial analysis was carried out in ArcGIS. GIS vector data. This dataset was first accessioned in the EDINA ShareGeo Open repository on 2011-01-13 and migrated to Edinburgh DataShare on 2017-02-21.

Admissions to hospital where the primary diagnosis or any of the secondary diagnoses are an alcohol-specific (wholly attributable) condition. Directly age standardised rate per 100,000 population (standardised to the European standard population).

Rationale Alcohol consumption is a contributing factor to hospital admissions and deaths from a diverse range of conditions. Alcohol misuse is estimated to cost the NHS about £3.5 billion per year and society as a whole £21 billion annually.

The Government has said that everyone has a role to play in reducing the harmful use of alcohol - this indicator is one of the key contributions by the Government (and the Department of Health) to promote measurable, evidence-based prevention activities at a local level, and supports the national ambitions to reduce harm set out in the Government's Alcohol Strategy. This ambition is part of the monitoring arrangements for the Responsibility Deal Alcohol Network. Alcohol-related admissions can be reduced through local interventions to reduce alcohol misuse and harm.

Reducing alcohol-related harm is one of Public Health England’s seven priorities for the next five years (from the “Evidence into action” report 2014).

Definition of numerator Admissions to hospital where the primary diagnosis or any of the secondary diagnoses are an alcohol-specific (wholly attributable) condition code only. More specifically, hospital admissions records are identified where:

The admission is a finished episode [epistat = 3] The admission is an ordinary admission, day case or maternity [classpat = 1, 2 or 5] It is an admission episode [epiorder = 1] The sex of the patient is valid [sex = 1 or 2] There is a valid age at start of episode [startage between 0 and 150 or between 7001 and 7007] The region of residence is one of the English regions, no fixed abode or unknown [resgor<= K or U or Y] The episode end date [epiend] falls within the financial year A wholly alcohol-attributable ICD10 code appears in any diagnosis field [diag_nn]

Definition of denominator ONS mid-year population estimates.

Caveats In 2023, NHS England announced a requirement for Trusts to report Same Day Emergency Care (SDEC) to the Emergency Care Data Set (ECDS) by July 2024. Early adopter sites began to report SDEC to ECDS from 2021/22, with other Trusts changing their reporting in 2022/23 or 2023/24. Some Trusts had previously reported this activity as part of the Admitted Patient Care data set, and moving to report to ECDS may reduce the number of admissions reported for this/these indicator/s. NHSE have advised it is not possible accurately to identify SDEC in current data flows, but the impact of the change is expected to vary by diagnosis, with indicators related to injuries and external causes potentially most affected.

When considering if SDEC recording practice has reduced the number of admissions reported for this indicator at local level, please refer to the list of sites who have reported when they began to report SDEC to ECDS.

Hospital admission data can be coded differently in different parts of the country. In some cases, details of the patient's residence are insufficient to allocate the patient to a particular area and in other cases, the patient has no fixed abode. These cases are included in the England total but not in the local authority figures. Conditions where low levels of alcohol consumption are protective (have a negative alcohol-attributable fraction) are not included in the calculation of the indicator. Does not include attendance at Accident and Emergency departments.

In order to allow comparison of groups with different age structures it is common to present “age standardised” rates. These are calculated by summing the product of age specific rates for each age band in the group by the number in that age band in the standard population. The sum is then divided by the total number in all age bands in the standard population to obtain the age standardised rate. This improves the comparability of rates for different areas, or between different time periods, by taking into account differences in the age structure of the populations being compared. Any difference between groups in age standardised rates is then not due to difference in age structure since the same standard population was used to calculate all age standardised rates. The method does however assume that minor differences in age structure within age bands are unimportant and in general this is true.