monkeypox-data

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This repository contains data on the Monkeypox (Orthopoxvirus) virus in New York City (NYC), from the NYC Department of Health and Mental Hygiene.

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# NYC mpox (Orthopoxvirus) Data

__Note:__  With the end of the federal public health emergency on January 31, 2023, NYC DOHMH will no longer update this GitHub repository. Please visit the NYC DOHMH website for a summary of the mpox outbreak in NYC from May 2022 to December 2022: https://www.nyc.gov/site/doh/health/health-topics/monkeypox.page

***

This repository contains an archive of data on the mpox (Orthopoxvirus) virus in New York City (NYC), from the NYC Department of Health and Mental Hygiene.

## This Readme includes:
- [How to use this repository](#How-to-use-this-repository)
- [Key Technical notes](#Key-Technical-Notes)
- [Repository Contents](#Repository-Contents)

***

# How to use this repository
This repository contains CSV (comma separated values) files of data, and Readme files with important documentation of the data. If you are unfamiliar with Github, you may find these instructions helpful:

**To download data**, scroll up to the green button labelled "Code." Clicking this button will start a download of a ZIP file of the entire contents of this repository.

Alternatively, you can download a single file. Click on a file you would like to download. Next, click the "Raw" button. Right click and save as a CSV file.

**For help understanding a file**, you can consult the documentation we have provided in the Readme files for each folder of data. To find  Readme files, just click on a folder name, above, and scroll down. Documentation is organized by file name, so you can scroll through the Readme, find the name of the file you are using for, and read documentation on it. Additionally, some universal documentation is provided in the [Key Technical Notes](https://github.com/nychealth/coronavirus-data/blob/master/README.md#key-technical-notes).

**Questions and custom requests**: We will try to answer questions about the data in this repository as we are able to. If you have a question, please search the [Issues](https://github.com/nychealth/coronavirus-data/issues?q=) to see if it’s already been addressed. Please understand that we are responding to a pandemic and we might not be able to address all questions in a timely manner.  We are not able to accommodate custom data requests placed via Github.

***

# Key Technical Notes

## Public health reporting 
### Reporting lag

Case trend data are updated weekly with a three-day lag, meaning the most recent data are from three days prior. Data lags are due to standard delays in reporting a new test or case to the Health Department and are a common limitation of surveillance data. Given the delay, our counts of what has happened in the most recent days are artificially small.

### Date of report versus date of diagnosis

Due to lags common with surveillance data, we receive reports of diagnoses that happened on past days. We publish citywide trend data using the date of diagnosis, not the date of report. The date of diagnosis reflects the earliest specimen collection associated with a positive lab result. This approach may differ from the data published by other state and local health departments. However, publishing data by the date of diagnosis better reflects when things happened (for example, when a person went to the doctor to get tested), as opposed to when the Health Department learned about them.

### Reportable disease surveillance

The Health Department receives electronic laboratory reports for a number of infectious diseases, as required by law in the [NYC Health Code](https://www1.nyc.gov/site/doh/providers/reporting-and-services/notifiable-diseases-and-conditions-reporting-central.page). When a specimen is collected from a patient for mpox laboratory testing, the lab must report all results, — whether positive, negative or inconclusive — to the Health Department. The lab must also report limited demographic information on the person being tested, such as name, address and date of birth.

### Case definitions
The Health Department uses national standard case definitions developed by the Centers for Disease Control and Prevention [CDC] (https://www.cdc.gov/poxvirus/monkeypox/clinicians/case-definition.html).
### Case reporting

Data include confirmed and probable cases of people who live in NYC. Any person who primarily resides outside of NYC is not included.

## Demographic groups
Differences in health outcomes among demographic groups are due to long-term structural biases, not biological or personal traits. People who experience bias or stigma based on one or more aspect of their identity (race/ethnicity, gender identity, sexual orientation, class/income) are more likely to experience health inequities based on historical and ongoing systemic oppression.
Structural biases — centuries of discriminatory policies and practices across institutions, including government agencies, and society — prevents historically disadvantaged communities from accessing vital resources (such as health care, housing and food) and opportunities (such as employment and education), and negatively affects overall health and well-being.

### Gender
The Health Department collects information about people’s current gender identity and sex assigned at birth, when available. People who identify as transgender women, transgender men, gender queer or non-binary, or whose current gender identity differs from their sex assigned at birth, are considered transgender/gender non-conforming/non-binary. Sex and gender information are collected from people’s self-reports, the diagnosing provider or electronic lab reporting. Self-reported gender is prioritized over other sources, but if this information is not available, a person’s reported gender may not reflect their current self-identification.

### Sexual Orientation
The Health Department collects self-reported information on people’s sexual orientation during case investigations. People who identify as gay, lesbian, bisexual or queer are considered to be LGBQ+. LGBQ+ also includes people who identify with other sexual identities that are not noted here but would be considered part of the LGBQ+ community, such as pansexual. The number of cases whose sexual orientation is unknown may be high due to the time needed to gather these data through case investigations.

### Race and ethnicity

Race/ethnicity information is often missing in reportable disease surveillance. Information on race/ethnicity typically comes from electronic laboratory reports, and race/ethnicity data are often missing in these reports. The Health Department collects race/ethnicity information through case investigations. However, this information is often incomplete or not immediately available for analysis.

The Health Department classifies race/ethnicity into the following mutually exclusive categories: Asian/Pacific-Islander, Black/African-American, Hispanic/Latino and White. The Hispanic/Latino category includes people of any race, and all other categories exclude those who identify as Hispanic/Latino.

# Repository Contents
***

### totals/ 
This folder contains files with cumulative totals since the start of the mpox virus in New York City (NYC), which the Health Department defines as the diagnosis of the first confirmed mpox case on May 19, 2022. The Health Department recommends against interpreting daily changes to these files as one day’s worth of data, due to the difference between date of diagnosis and date of report. See this folder’s Readme for a detailed description of its contents.

### trends/ 
This folder contains files with daily data shown across time. Note that these trend data are published by date of diagnosis, not by date of report. The Health Department recommends against interpreting daily changes to these files as one day’s worth of data, due to the difference between date of diagnosis and date of report. See this folder’s Readme for a detailed description of its contents.

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