Crude birth rates, age-specific fertility rates and total fertility rates (live births), 2000 to most recent year.

This dataset provides a global gridded (5 arc-min resolution) detailed annual net-migration dataset for 2000-2019. We also provide global annual birth and death rate datasets – that were used to estimate the net-migration – for same years. The dataset is presented in details, with some further analyses, in the following publication. Please cite this paper when using data.

Niva et al. 2023. World's human migration patterns in 2000-2019 unveiled by high-resolution data. Nature Human Behaviour 7: 2023–2037. Doi: https://doi.org/10.1038/s41562-023-01689-4

You can explore the data in our online net-migration explorer: https://wdrg.aalto.fi/global-net-migration-explorer/

Short introduction to the data

For the dataset, we collected, gap-filled, and harmonised:

a comprehensive national level birth and death rate datasets for altogether 216 countries or sovereign states; and

sub-national data for births (data covering 163 countries, divided altogether into 2555 admin units) and deaths (123 countries, 2067 admin units).

These birth and death rates were downscaled with selected socio-economic indicators to 5 arc-min grid for each year 2000-2019. These allowed us to calculate the 'natural' population change and when this was compared with the reported changes in population, we were able to estimate the annual net-migration. See more about the methods and calculations at Niva et al (2023).

We recommend using the data either over multiple years (we provide 3, 5 and 20 year net-migration sums at gridded level) or then aggregated over larger area (we provide adm0, adm1 and adm2 level geospatial polygon files). This is due to some noise in the gridded annual data.

Due to copy-right issues we are not able to release all the original data collected, but those can be requested from the authors.

List of datasets

Birth and death rates:

raster_birth_rate_2000_2019.tif: Gridded birth rate for 2000-2019 (5 arc-min; multiband tif)

raster_death_rate_2000_2019.tif: Gridded death rate for 2000-2019 (5 arc-min; multiband tif)

tabulated_adm1adm0_birth_rate.csv: Tabulated sub-national birth rate for 2000-2019 at the division to which data was collected (subnational data when available, otherwise national)

tabulated_ adm1adm0_death_rate.csv: Tabulated sub-national death rate for 2000-2019 at the division to which data was collected (subnational data when available, otherwise national)

Net-migration:

raster_netMgr_2000_2019_annual.tif: Gridded annual net-migration 2000-2019 (5 arc-min; multiband tif)

raster_netMgr_2000_2019_3yrSum.tif: Gridded 3-yr sum net-migration 2000-2019 (5 arc-min; multiband tif)

raster_netMgr_2000_2019_5yrSum.tif: Gridded 5-yr sum net-migration 2000-2019 (5 arc-min; multiband tif)

raster_netMgr_2000_2019_20yrSum.tif: Gridded 20-yr sum net-migration 2000-2019 (5 arc-min)

polyg_adm0_dataNetMgr.gpkg: National (adm 0 level) net-migration geospatial file (gpkg)

polyg_adm1_dataNetMgr.gpkg: Provincial (adm 1 level) net-migration geospatial file (gpkg) (if not adm 1 level division, adm 0 used)

polyg_adm2_dataNetMgr.gpkg: Communal (adm 2 level) net-migration geospatial file (gpkg) (if not adm 2 level division, adm 1 used; and if not adm 1 level division either, adm 0 used)

Files to run online net migration explorer

masterData.rds and admGeoms.rds are related to our online ‘Net-migration explorer’ tool (https://wdrg.aalto.fi/global-net-migration-explorer/). The source code of this application is available in https://github.com/vvirkki/net-migration-explorer. Running the application locally requires these two .rds files from this repository.

Metadata

Grids:

Resolution: 5 arc-min (0.083333333 degrees)

Spatial extent: Lon: -180, 180; -90, 90 (xmin, xmax, ymin, ymax)

Coordinate ref system: EPSG:4326 - WGS 84

Format: Multiband geotiff; each band for each year over 2000-2019

Units:

Birth and death rates: births/deaths per 1000 people per year

Net-migration: persons per 1000 people per time period (year, 3yr, 5yr, 20yr, depending on the dataset)

Geospatial polygon (gpkg) files:

Spatial extent: -180, 180; -90, 83.67 (xmin, xmax, ymin, ymax)

Temporal extent: annual over 2000-2019

Coordinate ref system: EPSG:4326 - WGS 84

Format: gkpk

Units:

Net-migration: persons per 1000 people per year

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

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 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 COVID-19 deaths in this report are defined as those for which the death certificate has an ICD-10 code of U07.1 as either a primary (underlying) or a contributing cause of death. More information on COVID-19 mortality can be found at the following link: https://portal.ct.gov/DPH/Health-Information-Systems--Reporting/Mortality/Mortality-Statistics

Data are subject to future revision as reporting changes.

Starting in July 2020, this dataset will be updated every weekday.

Additional notes: A delay in the data pull schedule occurred on 06/23/2020. Data from 06/22/2020 was processed on 06/23/2020 at 3:30 PM. The normal data cycle resumed with the data for 06/23/2020.

A network outage on 05/19/2020 resulted in a change in the data pull schedule. Data from 5/19/2020 was processed on 05/20/2020 at 12:00 PM. Data from 5/20/2020 was processed on 5/20/2020 8:30 PM. The normal data cycle resumed on 05/20/2020 with the 8:30 PM data pull. As a result of the network outage, the timestamp on the datasets on the Open Data Portal differ from the timestamp in DPH's daily PDF reports.

Starting 5/10/2021, the date field will represent the date this data was updated on data.ct.gov. Previously the date the data was pulled by DPH was listed, which typically coincided with the date before the data was published on data.ct.gov. This change was made to standardize the COVID-19 data sets on data.ct.gov.

Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under constant-rate birth-death (crBD) tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between crBD and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which crBD differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used crBD priors with those that used other non-BD Bayesian and non-Bayesian methods, we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using crBD in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios but also highlight that empirically observed phylogenetic imbalance is highly improbable under crBD, leading to systematic bias in data sets with limited information content. Methods Empirical trees used in the study are trees from the literature, collected by TimeTree (timetree.org). Run Tree_Selection.R to select the empirical phylogenetic trees to be included from TimeTree. The output file final_timetrees.RData contains the final subset of empirical phylogenetic TimeTree trees used for analysis with anonymized tip labels. 2. Run Simulation_And_Analysis.R to fit birth and death parameters (assuming rho = 1) for each of the 1189 empirical trees, simulate 1000 trees per empirical tree, calculate tree index values for both empirical and simulated trees, and calculate z-scores comparing the simulated and empirical trees. Note that calculating the tree index values for the simulated trees is VERY time-consuming due to the number of trees. Run Supplementary_Fig_S1_Analysis.R to generate data for Supplementary Figure S1. 3. Run Meta_analysis.R to run the linear regression models to investigate the role of the prior/analysis type for the subset (n=300) of the included empirical trees. The metadata for the 300 trees can be found in the supplementary files (Table S3). 4. Run Imbalance_Simulation.R to run the simulations for the imbalanced data subset (100 trees). Simulated sequences for each tree were run through RevBayes and IQ-TREE 2, as mentioned previously. Note: To avoid later confusion, the three various substitution rates used (0.5, 0.05, 0.005) are referred to as Rates 2-4 in the code. There is therefore no Rate 1; apologies in advance for any confusion. The shell scripts to run the inferences in each software are as follows: 4a. RevBayes: fasta_to_revbayes_code_rate2.sh, fasta_to_revbayes_code_rate3.sh, fasta_to_revbayes_code_rate4.sh These shell scripts use the following .Rev files: MCMC_Revbayes_code_rate2.Rev, MCMC_Revbayes_code_rate3.Rev, MCMC_Revbayes_code_rate4.Rev And rely on the following supplementary .Rev files: tree_BD.Rev, sub_JC.Rev, clock_global.Rev 4b. IQ-TREE 2: fasta_to_iqtree_code.sh 5. Run Final_Figures.R to visualize the results.

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

A. SUMMARY Medical provider confirmed COVID-19 cases and confirmed COVID-19 related deaths in San Francisco, CA aggregated by several different geographic areas and normalized by 2016-2020 American Community Survey (ACS) 5-year estimates for population data to calculate rate per 10,000 residents.

On September 12, 2021, a new case definition of COVID-19 was introduced that includes criteria for enumerating new infections after previous probable or confirmed infections (also known as reinfections). A reinfection is defined as a confirmed positive PCR lab test more than 90 days after a positive PCR or antigen test. The first reinfection case was identified on December 7, 2021.

Cases and deaths are both mapped to the residence of the individual, not to where they were infected or died. For example, if one was infected in San Francisco at work but lives in the East Bay, those are not counted as SF Cases or if one dies in Zuckerberg San Francisco General but is from another county, that is also not counted in this dataset.

Dataset is cumulative and covers cases going back to 3/2/2020 when testing began.

Geographic areas summarized are: 1. Analysis Neighborhoods 2. Census Tracts 3. Census Zip Code Tabulation Areas

B. HOW THE DATASET IS CREATED Addresses from medical data are geocoded by the San Francisco Department of Public Health (SFDPH). Those addresses are spatially joined to the geographic areas. Counts are generated based on the number of address points that match each geographic area. The 2016-2020 American Community Survey (ACS) population estimates provided by the Census are used to create a rate which is equal to ([count] / [acs_population]) * 10000) representing the number of cases per 10,000 residents.

C. UPDATE PROCESS Geographic analysis is scripted by SFDPH staff and synced to this dataset daily at 7:30 Pacific Time.

D. HOW TO USE THIS DATASET San Francisco population estimates for geographic regions can be found in a view based on the San Francisco Population and Demographic Census dataset. These population estimates are from the 2016-2020 5-year American Community Survey (ACS).

Privacy rules in effect To protect privacy, certain rules are in effect: 1. Case counts greater than 0 and less than 10 are dropped - these will be null (blank) values 2. Death counts greater than 0 and less than 10 are dropped - these will be null (blank) values 3. Cases and deaths dropped altogether for areas where acs_population < 1000

Rate suppression in effect where counts lower than 20 Rates are not calculated unless the case count is greater than or equal to 20. Rates are generally unstable at small numbers, so we avoid calculating them directly. We advise you to apply the same approach as this is best practice in epidemiology.

A note on Census ZIP Code Tabulation Areas (ZCTAs) ZIP Code Tabulation Areas are special boundaries created by the U.S. Census based on ZIP Codes developed by the USPS. They are not, however, the same thing. ZCTAs are areal representations of routes. Read how the Census develops ZCTAs on their website.

Row included for Citywide case counts, incidence rate, and deaths A single row is included that has the Citywide case counts and incidence rate. This can be used for comparisons. Citywide will capture all cases regardless of address quality. While some cases cannot be mapped to sub-areas like Census Tracts, ongoing data quality efforts result in improved mapping on a rolling basis.

E. CHANGE LOG

• 9/11/2023 - data on COVID-19 cases and deaths summarized by geography are no longer being updated. This data is currently through 9/6/2023 and will not include any new data after this date.
• 4/6/2023 - the State implemented system updates to improve the integrity of historical data.
• 2/21/2023 - system updates to improve reliability and accuracy of cases data were implemented.
• 1/31/2023 - updated “acs_population” column to reflect the 2020 Census Bureau American Community Survey (ACS) San Francisco Population estimates.
• 1/31/2023 - implemented system updates to streamline and improve our geo-coded data, resulting in small shifts in our case and death data by geography.
• 1/31/2023 - renamed column “last_updated_at” to “data_as_of”.
• 2/23/2022 - the New Cases Map dashboard began pulling from this dataset. To access Cases by Geography Over Time, please refer to this dataset.
• 1/22/2022 - system updates to improve timeliness and accuracy of cases and deaths data were implemented.
• 7/15/2022 - reinfections added to cases dataset. See section SUMMARY for more information on how reinfections are identified.
• 4/16/2021 - dataset updated to refresh with a five-day data lag.

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 COVID-19 deaths in this report are defined as those for which the death certificate has an ICD-10 code of U07.1 as either a primary (underlying) or a contributing cause of death. More information on COVID-19 mortality can be found at the following link: https://portal.ct.gov/DPH/Health-Information-Systems--Reporting/Mortality/Mortality-Statistics

Data are reported daily, with timestamps indicated in the daily briefings posted at: portal.ct.gov/coronavirus. Data are subject to future revision as reporting changes.

Starting in July 2020, this dataset will be updated every weekday.

Additional notes: Due to an issue with the town-level data dated 1/17/2021, the data was temporarily unavailable; as of 11:19 AM on 1/19/2021 the data has been restored.

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.

A delay in the data pull schedule occurred on 06/23/2020. Data from 06/22/2020 was processed on 06/23/2020 at 3:30 PM. The normal data cycle resumed with the data for 06/23/2020.

A network outage on 05/19/2020 resulted in a change in the data pull schedule. Data from 5/19/2020 was processed on 05/20/2020 at 12:00 PM. Data from 5/20/2020 was processed on 5/20/2020 8:30 PM. The normal data cycle resumed on 05/20/2020 with the 8:30 PM data pull. As a result of the network outage, the timestamp on the datasets on the Open Data Portal differ from the timestamp in DPH's daily PDF reports.

Starting 5/10/2021, the date field will represent the date this data was updated on data.ct.gov. Previously the date the data was pulled by DPH was listed, which typically coincided with the date before the data was published on data.ct.gov. This change was made to standardize the COVID-19 data sets on data.ct.gov.

On 5/16/2022, 8,622 historical cases were included in the data. The date range for these cases were from August 2021 – April 2022.”

Analysis of ‘COVID-19 Tests, Cases, and Deaths (By Town)’ provided by Analyst-2 (analyst-2.ai), based on source dataset retrieved from https://catalog.data.gov/dataset/32a9484b-f6cb-4ba2-ac23-8495915e9e0e on 13 February 2022.

--- Dataset description provided by original source is as follows ---

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 COVID-19 deaths in this report are defined as those for which the death certificate has an ICD-10 code of U07.1 as either a primary (underlying) or a contributing cause of death. More information on COVID-19 mortality can be found at the following link: https://portal.ct.gov/DPH/Health-Information-Systems--Reporting/Mortality/Mortality-Statistics

Data are reported daily, with timestamps indicated in the daily briefings posted at: portal.ct.gov/coronavirus. Data are subject to future revision as reporting changes.

Starting in July 2020, this dataset will be updated every weekday.

Additional notes: Due to an issue with the town-level data dated 1/17/2021, the data was temporarily unavailable; as of 11:19 AM on 1/19/2021 the data has been restored.

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.

A delay in the data pull schedule occurred on 06/23/2020. Data from 06/22/2020 was processed on 06/23/2020 at 3:30 PM. The normal data cycle resumed with the data for 06/23/2020.

A network outage on 05/19/2020 resulted in a change in the data pull schedule. Data from 5/19/2020 was processed on 05/20/2020 at 12:00 PM. Data from 5/20/2020 was processed on 5/20/2020 8:30 PM. The normal data cycle resumed on 05/20/2020 with the 8:30 PM data pull. As

--- Original source retains full ownership of the source dataset ---

Tropical mountains are global hotspots for birdlife. However, there is a dearth of baseline avifaunal data along eleva-tional gradients, particularly in Africa, limiting our ability to observe and assess changes over time in tropical montane avian communities. In this study, we undertook a multi-year assessment of understory birds along a 1,750 m elevational gradient (1,430-3,186 m) in an Afrotropical moist evergreen montane forest within Ethiopia's Bale Mountains. Analyzing 6 years of systematic bird-banding data from 5 sites, we describe the patterns of species richness, abundance, community composition, and demographic rates over space and time. We found bimodal patterns in observed and estimated species richness across the elevational gradient (peaking at 1,430 and 2,388 m), although no sites reached asymptotic species richness throughout the study. Species turnover was high across the gradient, though forested sites at mid-elevations resembled each other in species composition. We found significant variation across sites in bird abundance in some of the dietary and habitat guilds. However, we did not find any significant trends in species richness or guild abundances over time. For the majority of analyzed species, capture rates did not change over time and there were no changes in species' mean elevations. Population growth rates, recruitment rates, and apparent survival rates averaged 1.02, 0.52, and 0.51 respectively, and there were no elevational patterns in demographic rates. This study establishes a multi-year baseline for Afrotropical birds along an elevational gradient in an under-studied international biodiversity hotspot. These data will be critical in assessing the long-term responses of tropical montane birdlife to climate change and habitat degradation.

Methods Statistical Analyses

Community-level Analyses

To test whether our survey effort had adequately surveyed the local bird community, we calculated rarified species accumulation curves across sampling days for each site, based on observed and expected (sample-based rarefaction) species richness (Colwell et al. 2012) using the “exact” method of the specaccum function from the R package VEGAN (Oksanen et al. 2019). Since our species accumulation curves did not reach asymptotes for species richness, observed species richness likely does not capture true species richness. We, therefore, used sample-size-based rarefaction and extrapolation (R/E) of Hill numbers (the effective number of species, which integrates species richness and relative abundances; Chao et al. 2014). Sample-size-based rarefaction and extrapolation of Hill numbers is an emerging approach used to standardize and compare estimates of diversity between samples (see Cox et al. 2017, Fair et al. 2018, Baumel et al. 2018, Chao et al. 2019, Debela et al. 2020). Specifically, we used this framework to estimate two values of Hill number 0 (i.e. estimated species richness). First, we calculated standardized species richness. We used the function iNEXT from the R package iNEXT (Hsieh et al. 2016) to calculate R/E curves, standardizing our curve parameters to a maximum of 1,000 individual bird captures (endpoint = 1,000), knots = 500, and a bootstrap replication of 1,000 (nboot = 1,000). From these curves, we provide standardized estimates of species richness based on the sampling of 1,000 individuals at each site. We also estimated asymptotic species richness using the function ChaoRichness from the package iNEXT (Hsieh et al. 2016). Although the asymptotic species richness is an estimate of true species richness, in practice, reaching an asymptote can take a long time and a lot of sampling. We then plotted the R/E curves of standardized species richness (i.e. over 1,000 individuals) for each site as a function of sample size using the function ggiNEXT (Hsieh et al. 2016). We also visualized asymptotic species richness by setting the endpoint of the iNEXT function to 10,000 individuals.

Next, we assessed the spatial and temporal patterns in observed species richness and guild-specific captures. For guild-specific captures, we identified the primary diet and habitat association of each species using a global dataset of avian ecological traits (Table 1; see Şekercioğlu et al. 2004, 2019 for a description of the dataset) and summed captures for each separate guild based on either primary diet or habitat. We restricted our analyses to guilds that had ≥40 captures and ≥5 species over the study period and modeled each guild independently. We chose a ≥40 capture threshold as our cutoff between infrequently and frequently encountered species. Most species above this threshold were recorded each year and more than once or twice in each year (the few species that were not recorded each year were recorded multiple times in the other years), whereas individuals under this threshold tended to have few captures across more than one year. We chose a ≥5 species threshold for the guild models to ensure that results for these metrics represented more than a few species.

We constructed models comparing each response variable (observed species richness, dietary, and habitat guild-specific captures) as a function of the site, and included the number of survey days per site and year (Table 2) as a covariate to control for the variation in the sampling effort. We used generalized linear models (GLMs) for species richness and guild-specific captures, as these represent count data. Within the GLMs, we used a Poisson error structure for species richness, and for guild-specific captures, we used a quasi-Poisson error structure to account for over-dispersion in the count data. To assess changes in the bird community over time, we ran an additional model for each response variable that contained year and site, with a year * site interaction (error structures were applied as above). We tested the significance of the explanatory variables in the GLMs with an analysis of deviance.

We assessed species dissimilarity between sites along the elevational gradient by calculating the Sørenson dissimilarity index (S8) for pairs of sites adjacent to each other along the elevational gradient, as well as for Chiri-1430 and Dinsho-3186 at either end of the gradient. S8 can range from complete dissimilarity (S8 = 1) to complete similarity (S8 = 0). This dissimilarity can be further decomposed into turnover and nestedness, which we calculated using the function beta.pair in the package betapart (Baselga et al. 2020). Finally, to compare community composition (captures of different species, weighted by abundance), we ran a Principal Coordinate Analysis (PCoA) based on a Bray-Curtis dissimilarity matrix (Legendre and Legendre 2012). A PCoA extracts the greatest orthogonal axes of variation in community composition, plotting them in multidimensional space such that more similar communities are closer to each other in Euclidean space. We extracted the first two axes from the PCoA that represent the greatest variation in community composition.

Species-level Analyses

As a proxy for species abundance (Dulle et al. 2016), we calculated species-specific captures (the number of captured and recaptured individuals of a particular species) per site and year for the most frequently-captured species (≥ 40 captures over the study period). To assess the variation in species’ elevational distributions, we calculated the mean elevation at which each species was detected each year (hereafter “mean elevation”) for frequently-captured species that were detected at least once in every year of the study. Smaller range shifts in tropical birds are more detectable when analyzing mean elevational occurrence rather than the changes in upper or lower range boundaries, as the position of range boundaries is strongly dependent on the sampling effort (Shoo et al. 2006).

We regressed both species-specific captures (in a GLM with a quasi-Poisson error structure) and mean elevation (in a simple linear model) against year. Since the Dinsho-3186 site was located far from the other sites, we decided to re-run the species-level analyses with Dinsho-3186 data removed. The results remained similar with Dinsho-3186 excluded (Supplemental Material Tables S2 and S3) and, therefore, we retained Dinsho-3186 data in the analyses to increase our statistical power. Additionally, we compared our elevational records for banded birds with those reported in the literature for Ethiopia and the Horn of Africa (Ash and Atkins 2009, Dowsett and Dowsett-Lemaire 2015, Rannestad 2016) in order to assess whether any species were detected outside of their recorded elevational distributions. We used an elevational difference of at least 150 m to indicate whether a species had clearly been recorded in our study higher or lower than previously reported in Ethiopia, a distance previously used to signify extralimital records of birds in Ethiopia (Dowsett and Dowsett-Lemaire 2015). A difference of <150 m could result from chance, whereas a difference >150 m is more likely to result from a systematic change in the elevational range.

At the population level, we used Pradel models (Pradel 1996) implemented with the package RMark (Laake and Rexstad 2012) to estimate the rates of apparent survival (φ), recruitment (F), and realized population growth (λ) while controlling for encounter probabilities (p). φ is the rate at which individuals remain in the population; F is the rate at which new individuals join the population via birth or immigration; and λ is the combined effect of survival and recruitment. A population does not change in size when λ = 1, declines when λ <1, and grows when λ >1. These mark-recapture models cannot distinguish movement in and out of a study area (immigration/emigration) from true birth and survival. However, birds living in tropical mountains are known to have small range sizes (Orme et al. 2006), and tropical

Mortality rates (per 10,000 prisoners) and the relative percentage change in prisoner mortality for forty-four states reporting to the NCRP, 2000–2014.