Merge pull request #315 from cmu-delphi/docs/add-nchs

Release NCHS Mortality

Author: krivard

docs/api/covidcast-signals/nchs-mortality.md

@@ -0,0 +1,101 @@
+---
+title: NCHS Mortality Data
+parent: Data Sources and Signals
+grand_parent: COVIDcast Epidata API
+---
+
+# NCHS Mortality Data
+{: .no_toc}
+
+* **Source name:** `nchs-mortality`
+* **First issued:** Epiweek 50 2020 (6-12 December 2020)
+* **Number of data revisions since 19 May 2020:** 0
+* **Date of last change:** Never
+* **Available for:** state (see [geography coding docs](../covidcast_geography.md))
+* **License:** [NCHS Data Use Agreement](https://www.cdc.gov/nchs/data_access/restrictions.htm)
+
+This data source of national provisional death counts is based on death
+certificate data received and coded by the National Center for Health Statistics
+[(NCHS)](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm).
+
+| Signal | Description |
+| --- | --- |
+| `deaths_covid_incidence_num` | Number of weekly new deaths with confirmed or presumed COVID-19 |
+| `deaths_covid_incidence_prop` | Number of weekly new deaths with confirmed or presumed COVID-19, per 100,000 population |
+| `deaths_allcause_incidence_num` | Number of weekly new deaths from all causes |
+| `deaths_allcause_incidence_prop` | Number of weekly new deaths from all causes, per 100,000 population |
+| `deaths_flu_incidence_num` | Number of weekly new deaths involving Influenza and at least one of (Pneumonia, COVID-19)|
+| `deaths_flu_incidence_prop` | Number of weekly new deaths involving Influenza and at least one of (Pneumonia, COVID-19), per 100,000 population |
+| `deaths_pneumonia_notflu_incidence_num` | Number of weekly new deaths involving Pneumonia, excluding Influenza deaths |
+| `deaths_pneumonia_notflu_incidence_prop` | Number of weekly new deaths involving Pneumonia, excluding Influenza deaths, per 100,000 population |
+| `deaths_covid_and_pneumonia_notflu_incidence_num`| Number of weekly new deaths involving COVID-19 and Pneumonia, excluding Influenza |
+| `deaths_covid_and_pneumonia_notflu_incidence_prop`| Number of weekly new deaths involving COVID-19 and Pneumonia, excluding Influenza, per 100,000 population |
+|`deaths_pneumonia_or_flu_or_covid_incidence_num`| Number of weekly new deaths involving Pneumonia, Influenza, or COVID-19|
+|`deaths_pneumonia_or_flu_or_covid_incidence_prop`| Number of weekly new deaths involving Pneumonia, Influenza, or COVID-19, per 100,000 population|
+|`deaths_percent_of_expected`| Number of weekly new deaths for all causes in 2020 compared to the average number across the same week in 2017–2019|
+
+These signals are taken directly from [Table
+1](https://www.cdc.gov/nchs/nvss/vsrr/COVID19/index.htm) without
+changes. National provisional death counts include deaths occurring within the
+50 states and the District of Columbia that have been received and coded as of
+the date specified during a given time period. The deaths are classified based
+on a new ICD-10 code. (Note that the classification is based on all the codes on
+the death certificate, not just the primary cause of death). The codes that are
+considered for each signals are described in detail
+[here](https://github.com/cmu-delphi/covidcast-indicators/blob/nchs_mortality/nchs_mortality/DETAILS.md#metrics-level-1-m1). We
+export the state-level data as-is in a weekly format.
+
+## Table of contents
+{: .no_toc .text-delta}
+
+1. TOC
+{:toc}
+
+## Geographical Exceptions
+
+New York City is listed as its own region in the NCHS Mortality data, but
+we don't consider NYC separately. The death counts for NYC are included in New
+York State in our reports.
+
+## Report Using Epiweeks
+
+We report the NCHS Mortality data in a weekly format (`time_type=week` \&
+`time_value=\{YYYYWW\}`, where `YYYYWW` refers to an epiweek). The CDC defines
+the [epiweek](https://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf) as
+seven days, from Sunday to Saturday. We check the week-ending dates provided in
+the NCHS morality data and use Python package
+[epiweeks](https://pypi.org/project/epiweeks/) to convert them into epiweek
+format.
+
+## Missingness
+
+NCHS suppresses some data to protect individual privacy and avoid publishing
+low-confidence figures. This includes data for jurisdictions where counts are
+between 1 and 9, and data for weeks where the counts are less than 50% of the
+expected number, since these provisional counts are highly incomplete and
+potentially misleading.
+
+## Lag and Backfill
+
+There is a lag in time between when the death occurred and when the death
+certificate is completed, submitted to NCHS, and processed for reporting
+purposes. The death counts for earlier weeks are continually revised and may
+increase or decrease as new and updated death certificate data are received from
+the states by NCHS. This delay can range from 1 to 8 weeks or even more.
+Some states report deaths on a daily basis, while other states report deaths weekly
+or monthly. State vital record reporting may also be affected or delayed by
+COVID-19 related response activities which make death counts not comparable
+across states. We check for updates reported by NCHS every weekday but will
+report the signals weekly (on Monday).
+
+## Source and Licensing
+
+This data was originally published by the National Center for Health Statistics,
+and is made available here as a convenience to the forecasting community under
+the terms of the original license. The NCHS places restrictions on how this
+dataset may be used: you may not attempt to identify any individual included in
+the data, whether by itself or through linking to other
+individually=identifiable data; you may only use the dataset for statistical
+reporting and analysis. The full text of the [NCHS Data Use
+Agreement](https://www.cdc.gov/nchs/data_access/restrictions.htm) is available
+from their website.