Context

New York has presented the most cases compared to all states across the U.S..There have also been critiques regarding how much more unnoticed impact the flu has caused. My dataset allows us to compare whether or not this is true according to the most recent data.

Content

This COVID-19 data is from Kaggle whereas the New York influenza data comes from the U.S. government health data website. I merged the two datasets by county and FIPS code and listed the most recent reports of 2020 COVID-19 cases and deaths alongside the 2019 known influenza cases for comparison.

Acknowledgements

I am thankful to Kaggle and the U.S. government for making the data that made this possible openly available.

Inspiration

This data can be extended to answer the common misconceptions of the scale of the COVID-19 and common flu. My inspiration stems from supporting conclusions with data rather than simply intuition.

I would like my data to help answer how we can make U.S. citizens realize what diseases are most impactful.

Note: On April 30, 2024, the Federal mandate for COVID-19 and influenza associated hospitalization data to be reported to CDC’s National Healthcare Safety Network (NHSN) expired. Hospitalization data beyond April 30, 2024, will not be updated on the Open Data Portal. Hospitalization and ICU admission data collected from summer 2020 to May 10, 2023, are sourced from the California Hospital Association (CHA) Survey. Data collected on or after May 11, 2023, are sourced from CDC's National Healthcare Safety Network (NHSN).

Data is from the California Department of Public Health (CDPH) Respiratory Virus State Dashboard at https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/Respiratory-Viruses/RespiratoryDashboard.aspx.

Data are updated each Friday around 2 pm.

For COVID-19 death data: As of January 1, 2023, data was sourced from the California Department of Public Health, California Comprehensive Death File (Dynamic), 2023–Present. Prior to January 1, 2023, death data was sourced from the COVID-19 case registry. The change in data source occurred in July 2023 and was applied retroactively to all 2023 data to provide a consistent source of death data for the year of 2023. Influenza death data was sourced from the California Department of Public Health, California Comprehensive Death File (Dynamic), 2020–Present.

COVID-19 testing data represent data received by CDPH through electronic laboratory reporting of test results for COVID-19 among residents of California. Testing date is the date the test was administered, and tests have a 1-day lag (except for the Los Angeles County, which has an additional 7-day lag). Influenza testing data represent data received by CDPH from clinical sentinel laboratories in California. These laboratories report the aggregate number of laboratory-confirmed influenza virus detections and total tests performed on a weekly basis. These data do not represent all influenza testing occurring in California and are available only at the state level.

Deaths counts for influenza, pneumonia, and COVID-19 reported to NCHS by week ending date, by state and HHS region, and age group.

This dataset is a per-state amalgamation of demographic, public health and other relevant predictors for COVID-19.

Deaths, Infections and Tests by State

The COVID Tracking Project: https://covidtracking.com/data/api

Used positive, death and totalTestResults from the API for, respectively, Infected, Deaths and Tested in this dataset. Please read the documentation of the API for more context on those columns

Predictor Data and Sources

Population (2020)

Density is people per meter squared https://worldpopulationreview.com/states/

ICU Beds and Age 60+

https://khn.org/news/as-coronavirus-spreads-widely-millions-of-older-americans-live-in-counties-with-no-icu-beds/

GDP

https://worldpopulationreview.com/states/gdp-by-state/

Income per capita (2018)

https://worldpopulationreview.com/states/per-capita-income-by-state/

Gini

https://en.wikipedia.org/wiki/List_of_U.S._states_by_Gini_coefficient

Unemployment (2020)

Rates from Feb 2020 and are percentage of labor force
https://www.bls.gov/web/laus/laumstrk.htm

Sex (2017)

Ratio is Male / Female
https://www.kff.org/other/state-indicator/distribution-by-gender/

Smoking Percentage (2020)

https://worldpopulationreview.com/states/smoking-rates-by-state/

Influenza and Pneumonia Death Rate (2018)

Death rate per 100,000 people
https://www.cdc.gov/nchs/pressroom/sosmap/flu_pneumonia_mortality/flu_pneumonia.htm

Chronic Lower Respiratory Disease Death Rate (2018)

Death rate per 100,000 people
https://www.cdc.gov/nchs/pressroom/sosmap/lung_disease_mortality/lung_disease.htm

Active Physicians (2019)

https://www.kff.org/other/state-indicator/total-active-physicians/

Hospitals (2018)

https://www.kff.org/other/state-indicator/total-hospitals

Health spending per capita

Includes spending for all health care services and products by state of residence. Hospital spending is included and reflects the total net revenue. Costs such as insurance, administration, research, and construction expenses are not included.
https://www.kff.org/other/state-indicator/avg-annual-growth-per-capita/

Pollution (2019)

Pollution: Average exposure of the general public to particulate matter of 2.5 microns or less (PM2.5) measured in micrograms per cubic meter (3-year estimate)
https://www.americashealthrankings.org/explore/annual/measure/air/state/ALL

Medium and Large Airports

For each state, number of medium and large airports https://en.wikipedia.org/wiki/List_of_the_busiest_airports_in_the_United_States

Temperature (2019)

Note that FL was incorrect in the table, but is corrected in the Hottest States paragraph
https://worldpopulationreview.com/states/average-temperatures-by-state/
District of Columbia temperature computed as the average of Maryland and Virginia

Urbanization (2010)

Urbanization as a percentage of the population https://www.icip.iastate.edu/tables/population/urban-pct-states

Age Groups (2018)

https://www.kff.org/other/state-indicator/distribution-by-age/

School Closure Dates

Schools that haven't closed are marked NaN https://www.edweek.org/ew/section/multimedia/map-coronavirus-and-school-closures.html

Note that some datasets above did not contain data for District of Columbia, this missing data was found via Google searches manually entered.

Demographic Trends and Health Outcomes in the U.S

Inequalities,Risk Factors and Access to Care

By Data Society [source]

About this dataset

This dataset contains key demographic, health status indicators and leading cause of death data to help us understand the current trends and health outcomes in communities across the United States. By looking at this data, it can be seen how different states, counties and populations have changed over time. With this data we can analyze levels of national health services use such as vaccination rates or mammography rates; review leading causes of death to create public policy initiatives; as well as identify risk factors for specific conditions that may be associated with certain populations or regions. The information from these files includes State FIPS Code, County FIPS Code, CHSI County Name, CHSI State Name, CHSI State Abbreviation, Influenza B (FluB) report count & expected cases rate per 100K population , Hepatitis A (HepA) Report Count & expected cases rate per 100K population , Hepatitis B (HepB) Report Count & expected cases rate per 100K population , Measles (Meas) Report Count & expected cases rate per 100K population , Pertussis(Pert) Report Count & expected case rate per 100K population , CRS report count & expected case rate per 100K population , Syphilis report count and expected case rate per 100k popuation. We also look at measures related to preventive care services such as Pap smear screen among women aged 18-64 years old check lower/upper confidence intervals seperately ; Mammogram checks among women aged 40-64 years old specified lower/upper conifence intervals separetly ; Colonosopy/ Proctoscpushy among men aged 50+ measured in lower/upper limits ; Pneumonia Vaccination amongst 65+ with loewr/upper confidence level detail Additionally we have some interesting trend indicating variables like measures of birth adn death which includes general fertility ratye ; Teen Birth Rate by Mother's age group etc Summary Measures covers mortality trend following life expectancy by sex&age categories Vressionable populations access info gives us insight into disablilty ratio + access to envtiromental issues due to poor quality housing facilities Finally Risk Factors cover speicfic hoslitic condtiions suchs asthma diagnosis prevelance cancer diabetes alcholic abuse smoking trends All these information give a good understanding on Healthy People 2020 target setings demograpihcally speaking hence will aid is generating more evience backed policies

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How to use the dataset

What the Dataset Contains

This dataset contains valuable information about public health relevant to each county in the United States, broken down into 9 indicator domains: Demographics, Leading Causes of Death, Summary Measures of Health, Measures of Birth and Death Rates, Relative Health Importance, Vulnerable Populations and Environmental Health Conditions, Preventive Services Use Data from BRFSS Survey System Data , Risk Factors and Access to Care/Health Insurance Coverage & State Developed Types of Measurements such as CRS with Multiple Categories Identified for Each Type . The data includes indicators such as percentages or rates for influenza (FLU), hepatitis (HepA/B), measles(MEAS) pertussis(PERT), syphilis(Syphilis) , cervical cancer (CI_Min_Pap_Smear - CI_Max\Pap \Smear), breast cancer (CI\Min Mammogram - CI \Max \Mammogram ) proctoscopy (CI Min Proctoscopy - CI Max Proctoscopy ), pneumococcal vaccinations (Ci min Pneumo Vax - Ci max Pneumo Vax )and flu vaccinations (Ci min Flu Vac - Ci Max Flu Vac). Additionally , it provides information on leading causes of death at both county levels & national level including age-adjusted mortality rates due to suicide among teens aged between 15-19 yrs per 100000 population etc.. Furthermore , summary measures such as age adjusted percentage who consider their physical health fair or poor are provided; vulnerable populations related indicators like relative importance score for disabled adults ; preventive service use related ones ranging from self reported vaccination coverage among men40-64 yrs old against hepatitis B virus etc...

Getting Started With The Dataset

To get started with exploring this dataset first your need to understand what each column in the table represents: State FIPS Code identifies a unique identifier used by various US government agencies which denote states . County FIPS code denotes counties wi...

This dataset represents preliminary estimates of cumulative U.S. COVID-19 disease burden for the 2024-2025 period, including illnesses, outpatient visits, hospitalizations, and deaths. The weekly COVID-19-associated burden estimates are preliminary and based on continuously collected surveillance data from patients hospitalized with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. The data come from the Coronavirus Disease 2019 (COVID-19)-Associated Hospitalization Surveillance Network (COVID-NET), a surveillance platform that captures data from hospitals that serve about 10% of the U.S. population. Each week CDC estimates a range (i.e., lower estimate and an upper estimate) of COVID-19 -associated burden that have occurred since October 1, 2024.

Note: Data are preliminary and subject to change as more data become available. Rates for recent COVID-19-associated hospital admissions are subject to reporting delays; as new data are received each week, previous rates are updated accordingly.

References

1. Reed C, Chaves SS, Daily Kirley P, et al. Estimating influenza disease burden from population-based surveillance data in the United States. PLoS One. 2015;10(3):e0118369. https://doi.org/10.1371/journal.pone.0118369 
2. Rolfes, MA, Foppa, IM, Garg, S, et al. Annual estimates of the burden of seasonal influenza in the United States: A tool for strengthening influenza surveillance and preparedness. Influenza Other Respi Viruses. 2018; 12: 132– 137. https://doi.org/10.1111/irv.12486
3. Tokars JI, Rolfes MA, Foppa IM, Reed C. An evaluation and update of methods for estimating the number of influenza cases averted by vaccination in the United States. Vaccine. 2018;36(48):7331-7337. doi:10.1016/j.vaccine.2018.10.026 
4. Collier SA, Deng L, Adam EA, Benedict KM, Beshearse EM, Blackstock AJ, Bruce BB, Derado G, Edens C, Fullerton KE, Gargano JW, Geissler AL, Hall AJ, Havelaar AH, Hill VR, Hoekstra RM, Reddy SC, Scallan E, Stokes EK, Yoder JS, Beach MJ. Estimate of Burden and Direct Healthcare Cost of Infectious Waterborne Disease in the United States. Emerg Infect Dis. 2021 Jan;27(1):140-149. doi: 10.3201/eid2701.190676. PMID: 33350905; PMCID: PMC7774540.
5. Reed C, Kim IK, Singleton JA,  et al. Estimated influenza illnesses and hospitalizations averted by vaccination–United States, 2013-14 influenza season. MMWR Morb Mortal Wkly Rep. 2014 Dec 12;63(49):1151-4. https://www.cdc.gov/mmwr/preview/mmwrhtml/mm6349a2.htm 
6. Reed C, Angulo FJ, Swerdlow DL, et al. Estimates of the Prevalence of Pandemic (H1N1) 2009, United States, April–July 2009. Emerg Infect Dis. 2009;15(12):2004-2007. https://dx.doi.org/10.3201/eid1512.091413  
7. Devine O, Pham H, Gunnels B, et al. Extrapolating Sentinel Surveillance Information to Estimate National COVID-19 Hospital Admission Rates: A Bayesian Modeling Approach. Influenza and Other Respiratory Viruses. https://onlinelibrary.wiley.com/doi/10.1111/irv.70026. Volume18, Issue10. October 2024.
8. https://www.cdc.gov/covid/php/covid-net/index.html">COVID-NET | COVID-19 | CDC 
9. https://www.cdc.gov/covid/hcp/clinical-care/systematic-review-process.html 
10. https://academic.oup.com/pnasnexus/article/1/3/pgac079/6604394?login=false">Excess natural-cause deaths in California by cause and setting: March 2020 through February 2021 | PNAS Nexus | Oxford Academic (oup.com)
11. Kruschke, J. K. 2011. Doing Bayesian data analysis: a tutorial with R and BUGS. Elsevier, Amsterdam, Section 3.3.5.

Motivation

Why did I create this dataset? This is my first time creating a notebook in Kaggle and I am interested in learning more about COVID-19 and how different countries are affected by it and why. It might be useful to compare different metrics between different countries. And I also wanted to participate in a challenge, and I've decided to join the COVID-19 datasets challenge. While looking through the projects, I noticed https://www.kaggle.com/koryto/countryinfo and it inspired me to start this project.

Method

My approach is to scour the Internet and Kaggle looking for country data that can potentially have an impact on how the COVID-19 pandemic spreads. In the end, I ended up with the following for each country:

• Monthly temperature and precipitation from Worldbank
• Latitude and longitude
• Population, density, gender and age
• Airport traffic from Worldbank
• COVID-19 date of first case and number of cases and deaths as of March 26, 2020
• 2009 H1N1 flu pandemic cases and deaths obtained from Wikipedia
• Property affordability index and Health care index from Numbeo
• Number of hospital beds and ICU beds from Wikipedia
• Flu and pneumonia death rate from Worldlifeexpectancy.com (Age Adjusted Death Rate Estimates: 2017)
• School closures due to COVID-19
• Number of COVID-19 tests done
• Number of COVID-19 genetic strains
• US Social Distancing Policies from COVID19StatePolicy’s SocialDistancing repository on GitHub
• DHL Global Connectedness Index 2018 (People Breadth scores)
• Datasets have been merged by country name whenever possible. I needed to rename some countries by hand, e.g. US to United Sates, etc. but it's possible that I might have missed some. See the output file covid19_merged.csv for the merged result.

See covid19_data - data_sources.csv for data source details.

Notebook: https://www.kaggle.com/bitsnpieces/covid19-data

Caveats

Since I did not personally collect each datapoint, and because each datasource is different with different objectives, collected at different times, measured in different ways, any inferences from this dataset will need further investigation.

Other interesting sources of information

• IMF Policy Tracker
• nCov strain analysis across the globe!
• Google Mobility Report
• Oxford government response tracker
• Impact on aviation
• Impact on restaurants
• Harvard
• Tableau datahub
• Unemployment outlook from ILO

Acknowledgements

I want to acknowledge the authors of the datasets that made their data publicly available which has made this project possible. Banner image is by Brian.

I hope that the community finds this dataset useful. Feel free to recommend other datasets that you think will be useful / relevant! Thanks for looking.

ObjectivesThe aim of this study is to describe, visualize, and compare the trends and epidemiological features of the mortality rates of 10 notifiable respiratory infectious diseases in China from 2004 to 2020.SettingData were obtained from the database of the National Infectious Disease Surveillance System (NIDSS) and reports released by the National and local Health Commissions from 2004 to 2020. Spearman correlations and Joinpoint regression models were used to quantify the temporal trends of RIDs by calculating annual percentage changes (APCs) in the rates of mortality.ResultsThe overall mortality rate of RIDs was stable across China from 2004 to 2020 (R = −0.38, P = 0.13), with an APC per year of −2.2% (95% CI: −4.6 to 0.3; P = 0.1000). However, the overall mortality rate of 10 RIDs in 2020 decreased by 31.80% (P = 0.006) compared to the previous 5 years before the COVID-19 pandemic. The highest mortality occurred in northwestern, western, and northern China. Tuberculosis was the leading cause of RID mortality, and mortality from tuberculosis was relatively stable throughout the 17 years (R = −0.36, P = 0.16), with an APC of −1.9% (95% CI −4.1 to 0.4, P = 0.1000). Seasonal influenza was the only disease for which mortality significantly increased (R = 0.73, P = 0.00089), with an APC of 29.70% (95% CI 16.60–44.40%; P = 0.0000). The highest yearly case fatality ratios (CFR) belong to avian influenza A H5N1 [687.5 per 1,000 (33/48)] and epidemic cerebrospinal meningitis [90.5748 per 1,000 (1,010/11,151)]. The age-specific CFR of 10 RIDs was highest among people over 85 years old [13.6551 per 1,000 (2,353/172,316)] and was lowest among children younger than 10 years, particularly in 5-year-old children [0.0552 per 1,000 (58/1,051,178)].ConclusionsThe mortality rates of 10 RIDs were relatively stable from 2004 to 2020 with significant differences among Chinese provinces and age groups. There was an increased mortality trend for seasonal influenza and concerted efforts are needed to reduce the mortality rate of seasonal influenza in the future.

Rank, number of deaths, percentage of deaths, and age-specific mortality rates for the leading causes of death, by age group and sex, 2000 to most recent year.

IntroductionWe compared hospitalization outcomes of young children hospitalized with COVID-19 to those hospitalized with influenza in the United States.MethodsPatients aged 0-<5 years hospitalized with an admission diagnosis of acute COVID-19 (April 2021-March 2022) or influenza (April 2019-March 2020) were selected from the PINC AI Healthcare Database Special Release. Hospitalization outcomes included length of stay (LOS), intensive care unit (ICU) admission, oxygen supplementation, and mechanical ventilation (MV). Inverse probability of treatment weighting was used to adjust for confounders in logistic regression analyses.ResultsAmong children hospitalized with COVID-19 (n = 4,839; median age: 0 years), 21.3% had an ICU admission, 19.6% received oxygen supplementation, 7.9% received MV support, and 0.5% died. Among children hospitalized with influenza (n = 4,349; median age: 1 year), 17.4% were admitted to the ICU, 26.7% received oxygen supplementation, 7.6% received MV support, and 0.3% died. Compared to children hospitalized with influenza, those with COVID-19 were more likely to have an ICU admission (adjusted odds ratio [aOR]: 1.34; 95% confidence interval [CI]: 1.21–1.48). However, children with COVID-19 were less likely to receive oxygen supplementation (aOR: 0.71; 95% CI: 0.64–0.78), have a prolonged LOS (aOR: 0.81; 95% CI: 0.75–0.88), or a prolonged ICU stay (aOR: 0.56; 95% CI: 0.46–0.68). The likelihood of receiving MV was similar (aOR: 0.94; 95% CI: 0.81, 1.1).ConclusionsHospitalized children with either SARS-CoV-2 or influenza had severe complications including ICU admission and oxygen supplementation. Nearly 10% received MV support. Both SARS-CoV-2 and influenza have the potential to cause severe illness in young children.

Introduction: Respiratory viruses are among the leading causes of disease and death among children. Co-circulation of influenza and SARS-CoV2 can lead to diagnostic and management difficulties given the similarities in the clinical picture.Methods: This is a cohort of all children hospitalized with SARS-CoV2 infection from March to September 3rd 2020, and all children admitted with influenza throughout five flu-seasons (2013–2018) at a pediatric referral hospital. Patients with influenza were identified from the clinical laboratory database. All hospitalized patients with confirmed SARS-CoV2 infection were followed-up prospectively.Results: A total of 295 patients with influenza and 133 with SARS-CoV2 infection were included. The median age was 3.7 years for influenza and 5.3 years for SARS-CoV2. Comorbidities were frequent in both groups, but they were more common in patients with influenza (96.6 vs. 82.7%, p < 0.001). Fever and cough were the most common clinical manifestations in both groups. Rhinorrhea was present in more than half of children with influenza but was infrequent in those with COVID-19 (53.6 vs. 5.8%, p < 0.001). Overall, 6.4% percent of patients with influenza and 7.5% percent of patients with SARS-CoV2 infection died. In-hospital mortality and the need for mechanical ventilation among symptomatic patients were similar between groups in the multivariate analysis.Conclusions: Influenza and COVID-19 have a similar picture in pediatric patients, which makes diagnostic testing necessary for adequate diagnosis and management. Even though most cases of COVID-19 in children are asymptomatic or mild, the risk of death among hospitalized patients with comorbidities may be substantial, especially among infants.

This dataset represents preliminary estimates of cumulative U.S. RSV –associated disease burden estimates for the 2024-2025 season, including outpatient visits, hospitalizations, and deaths. Real-time estimates are preliminary and based on continuously collected surveillance data from patients hospitalized with laboratory-confirmed respiratory syncytial virus (RSV) infections. The data come from the Respiratory Syncytial Virus Hospitalization Surveillance Network (RSV-NET), a surveillance platform that captures data from hospitals that serve about 8% of the U.S. population. Each week CDC estimates a range (i.e., lower estimate and an upper estimate) of RSV-associated disease burden estimates that have occurred since October 1, 2024.

Note: Data are preliminary and subject to change as more data become available. Rates for recent RSV-associated hospital admissions are subject to reporting delays; as new data are received each week, previous rates are updated accordingly.

Note: Preliminary burden estimates are not inclusive of data from all RSV-NET sites. Due to model limitations, sites with small sample sizes can impact estimates in unpredictable ways and are excluded for the benefit of model stability. CDC is working to address model limitations and include data from all sites in final burden estimates.

References

1. Reed C, Chaves SS, Daily Kirley P, et al. Estimating influenza disease burden from population-based surveillance data in the United States. PLoS One. 2015;10(3):e0118369. https://doi.org/10.1371/journal.pone.0118369 
2. Rolfes, MA, Foppa, IM, Garg, S, et al. Annual estimates of the burden of seasonal influenza in the United States: A tool for strengthening influenza surveillance and preparedness. Influenza Other Respi Viruses. 2018; 12: 132– 137. https://doi.org/10.1111/irv.12486
3. Tokars JI, Rolfes MA, Foppa IM, Reed C. An evaluation and update of methods for estimating the number of influenza cases averted by vaccination in the United States. Vaccine. 2018;36(48):7331-7337. doi:10.1016/j.vaccine.2018.10.026 
4. Collier SA, Deng L, Adam EA, Benedict KM, Beshearse EM, Blackstock AJ, Bruce BB, Derado G, Edens C, Fullerton KE, Gargano JW, Geissler AL, Hall AJ, Havelaar AH, Hill VR, Hoekstra RM, Reddy SC, Scallan E, Stokes EK, Yoder JS, Beach MJ. Estimate of Burden and Direct Healthcare Cost of Infectious Waterborne Disease in the United States. Emerg Infect Dis. 2021 Jan;27(1):140-149. doi: 10.3201/eid2701.190676. PMID: 33350905; PMCID: PMC7774540.
5. Reed C, Kim IK, Singleton JA,  et al. Estimated influenza illnesses and hospitalizations averted by vaccination–United States, 2013-14 influenza season. MMWR Morb Mortal Wkly Rep. 2014 Dec 12;63(49):1151-4. https://www.cdc.gov/mmwr/preview/mmwrhtml/mm6349a2.htm 
6. Reed C, Angulo FJ, Swerdlow DL, et al. Estimates of the Prevalence of Pandemic (H1N1) 2009, United States, April–July 2009. Emerg Infect Dis. 2009;15(12):2004-2007. https://dx.doi.org/10.3201/eid1512.091413  
7. Devine O, Pham H, Gunnels B, et al. Extrapolating Sentinel Surveillance Information to Estimate National COVID-19 Hospital Admission Rates: A Bayesian Modeling Approach. Influenza and Other Respiratory Viruses. https://onlinelibrary.wiley.com/doi/10.1111/irv.70026. Volume18, Issue10. October 2024.
8. https://www.cdc.gov/covid/php/covid-net/index.html">COVID-NET | COVID-19 | CDC 
9. https://www.cdc.gov/covid/hcp/clinical-care/systematic-review-process.html 
10. https://academic.oup.com/pnasnexus/article/1/3/pgac079/6604394?login=false">Excess natural-cause deaths in California by cause and setting: March 2020 through February 2021 | PNAS Nexus | Oxford Academic (oup.com)
11. Kruschke, J. K. 2011. Doing Bayesian data analysis: a tutorial with R and BUGS. Elsevier, Amsterdam, Section 3.3.5.

Characteristics of patients hospitalised for COVID-19 and controls.

Post hoc analysis of specific hospitalisation/mortality outcomes within the mental health and cognitive category.