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‎.Rbuildignore‎

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^.*\.Rproj$
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^\.Rproj\.user$
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^data-raw$
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^LICENSE\.md$

‎.gitignore‎

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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.DS_Store

‎DESCRIPTION‎

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Type: Package
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Package: epidatasets
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Title: Epidemiological Data for Delphi Tooling Examples
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Version: 0.0.1
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Authors@R:
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person(c("Daniel", "J."), "McDonald", , "[email protected]", role = c("cre", "aut"))
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Description: This package contains data sets used to compile vignettes and
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other documentation in Delphi R Packages. The goal is to avoid calls
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to the Delphi Epidata API, and deposit some examples here for easy
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offline use.
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License: MIT + file LICENSE
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Depends:
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R (>= 2.10)
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Suggests:
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covidcast,
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dplyr,
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epidatr,
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epipredict,
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here,
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lubridate,
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magrittr,
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purrr,
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readr
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Remotes:
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cmu-delphi/epidatr,
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cmu-delphi/epipredict,
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cmu-delphi/epiprocess
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.2.3

‎LICENSE‎

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YEAR: 2023
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COPYRIGHT HOLDER: epidatasets authors

‎LICENSE.md‎

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# MIT License
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Copyright (c) 2023 epidatasets authors
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎NAMESPACE‎

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# Generated by roxygen2: do not edit by hand
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‎R/epipredict-data.R‎

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#' Subset of JHU daily state cases and deaths
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#'
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#' This data source of confirmed COVID-19 cases and deaths
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#' is based on reports made available by the Center for
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#' Systems Science and Engineering at Johns Hopkins University.
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#' This example data ranges from Dec 31, 2020 to Dec 31, 2021,
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#' and includes all states.
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#'
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#' @format A tibble with 20,496 rows and 4 variables:
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#' \describe{
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#' \item{geo_value}{the geographic value associated with each row
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#' of measurements.}
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#' \item{time_value}{the time value associated with each row of measurements.}
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#' \item{case_rate}{7-day average signal of number of new
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#' confirmed COVID-19 cases per 100,000 population, daily}
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#' \item{death_rate}{7-day average signal of number of new confirmed
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#' deaths due to COVID-19 per 100,000 population, daily}
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#' }
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#' @source This object contains a modified part of the
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#' \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University}
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#' as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}.
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#' This data set is licensed under the terms of the
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#' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
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#' by the Johns Hopkins University on behalf of its Center for Systems Science
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#' in Engineering. Copyright Johns Hopkins University 2020.
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#'
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#' Modifications:
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#' * \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}:
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#' These signals are taken directly from the JHU CSSE
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#' \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository}
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#' without changes. The 7-day average signals are computed by Delphi by
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#' calculating moving averages of the preceding 7 days, so the signal for
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#' June 7 is the average of the underlying data for June 1 through 7,
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#' inclusive.
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"covid_case_death_rates"
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#' State population data
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#'
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#' Data set on state populations, from the 2019 US Census.
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#'
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#' @format Data frame with 57 rows (including one for the United States as a
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#' whole, plus the District of Columbia, Puerto Rico Commonwealth,
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#' American Samoa, Guam, the U.S. Virgin Islands, and the Northern Mariana,
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#' Islands).
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#'
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#' \describe{
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#' \item{fips}{FIPS code}
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#' \item{name}{Full name of the state or territory}
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#' \item{pop}{Estimate of the location's resident population in
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#' 2019.}
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#' \item{abbr}{Postal abbreviation for the location}
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#' }
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#'
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#' @source United States Census Bureau, at
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#' \url{https://www2.census.gov/programs-surveys/popest/datasets/2010-2019/counties/totals/co-est2019-alldata.pdf},
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#' \url{https://www.census.gov/data/tables/time-series/demo/popest/2010s-total-puerto-rico-municipios.html},
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#' and \url{https://www.census.gov/data/tables/2010/dec/2010-island-areas.html}
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"state_census"
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# Epipredict Vignette Data ----------------------------------------------------
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#' CTIS COVID Behaviours
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#'
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#' Data set for a handful of states on masking and distancing behaviours
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#' during the COVID-19 Pandemic and downloaded from the CMU Delphi COVIDcast
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#' Epidata API. This data set covers the period from
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#' June to December 2021.
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"ctis_covid_behaviours"
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#' COVID-19 Incident Cases and Deaths
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#'
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#' Data set for 5 states containing COVID-19 Incident Cases and Deaths as
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#' reported
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#' by JHU-CSSE and downloaded from the CMU Delphi COVIDcast Epidata API.
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#' This data set covers the period from June 2021 to December 2021, and is
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#' used in the [epipredict] Vignette on ... .
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#'
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#' @source This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the
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#' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
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#' by the Johns Hopkins University on behalf of its Center for Systems Science in Engineering.
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#' Copyright Johns Hopkins University 2020.
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"counts_subset"

‎R/epiprocess-data.R‎

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#' Subset of JHU daily state cases and deaths
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#'
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#' This data source of confirmed COVID-19 cases and deaths
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#' is based on reports made available by the Center for
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#' Systems Science and Engineering at Johns Hopkins University.
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#' This example data ranges from Mar 1, 2020 to Dec 31, 2021, and is limited to
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#' California, Florida, Texas, New York, Georgia, and Pennsylvania.
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#'
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#' @format A tibble with 4026 rows and 6 variables:
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#' \describe{
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#' \item{geo_value}{the geographic value associated with each row
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#' of measurements.}
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#' \item{time_value}{the time value associated with each row of measurements.}
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#' \item{case_rate_7d_av}{7-day average signal of number of new
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#' confirmed COVID-19 cases per 100,000 population, daily}
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#' \item{death_rate_7d_av}{7-day average signal of number of new confirmed
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#' deaths due to COVID-19 per 100,000 population, daily}
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#' \item{cases}{Number of new confirmed COVID-19 cases, daily}
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#' \item{cases_7d_av}{7-day average signal of number of new confirmed
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#' COVID-19 cases, daily}
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#' }
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#' @source This object contains a modified part of the
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#' \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University}
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#' as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}.
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#' This data set is licensed under the terms of the
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#' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
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#' by the Johns Hopkins University on behalf of its Center for Systems Science
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#' in Engineering. Copyright Johns Hopkins University 2020.
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#'
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#' Modifications:
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#' * \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}:
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#' These signals are taken directly from the JHU CSSE
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#' \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository}
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#' without changes. The 7-day average signals are computed by Delphi by
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#' calculating moving averages of the preceding 7 days, so the signal for
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#' June 7 is the average of the underlying data for June 1 through 7,
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#' inclusive.
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#' * Furthermore, the data has been limited to a very small number of rows,
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#' the signal names slightly altered, and formatted into a tibble.
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# Named "jhu_csse_daily_subset" in {epiprocess}
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"cases_deaths_subset"
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#' Subset of daily doctor visits and cases in archive format
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#'
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#' This data source is based on information about outpatient visits,
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#' provided to us by health system partners, and also contains confirmed
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#' COVID-19 cases based on reports made available by the Center for
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#' Systems Science and Engineering at Johns Hopkins University.
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#' This example data ranges from June 1, 2020 to Dec 1, 2021, and
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#' is also limited to California, Florida, Texas, and New York.
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#'
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#' @format An `epi_archive$DT` data format. The data table DT has 129,638 rows and 5 columns:
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#' \describe{
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#' \item{geo_value}{the geographic value associated with each row of measurements.}
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#' \item{time_value}{the time value associated with each row of measurements.}
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#' \item{version}{the time value specifying the version for each row of measurements. }
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#' \item{percent_cli}{percentage of doctor’s visits with CLI (COVID-like illness) computed from medical insurance claims}
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#' \item{case_rate_7d_av}{7-day average signal of number of new confirmed deaths due to COVID-19 per 100,000 population, daily}
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#' }
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#' @source
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#' This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the
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#' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
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#' by Johns Hopkins University on behalf of its Center for Systems Science in Engineering.
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#' Copyright Johns Hopkins University 2020.
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#'
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#' Modifications:
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#' * \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/doctor-visits.html}{From the COVIDcast Doctor Visits API}: The signal `percent_cli` is taken directly from the API without changes.
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#' * \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: `case_rate_7d_av` signal was computed by Delphi from the original JHU-CSSE data by calculating moving averages of the preceding 7 days, so the signal for June 7 is the average of the underlying data for June 1 through 7, inclusive.
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#' * Furthermore, the data is a subset of the full dataset, the signal names slightly altered, and formatted into a tibble.
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# This is named "archive_cases_dv_subset" in {epiprocess}
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"archive_cases_dv_subset_dt"
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#' Subset of JHU daily cases from California and Florida
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#'
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#' This data source of confirmed COVID-19 cases
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#' is based on reports made available by the Center for
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#' Systems Science and Engineering at Johns Hopkins University.
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#' This example data is a snapshot as of Oct 28, 2021 and captures the cases
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#' from June 1, 2020 to May 31, 2021
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#' and is limited to California and Florida.
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#'
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#' @format A tibble with 730 rows and 3 variables:
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#' \describe{
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#' \item{geo_value}{the geographic value associated with each row of measurements.}
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#' \item{time_value}{the time value associated with each row of measurements.}
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#' \item{cases}{Number of new confirmed COVID-19 cases, daily}
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#' }
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#' @source This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the
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#' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
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#' by the Johns Hopkins University on behalf of its Center for Systems Science in Engineering.
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#' Copyright Johns Hopkins University 2020.
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#'
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#' Modifications:
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#' * \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}:
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#' These signals are taken directly from the JHU CSSE \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} without changes.
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#' * Furthermore, the data has been limited to a very small number of rows, the signal names slightly altered, and formatted into a tibble.
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"covid_incidence_outliers"
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#' Subset of JHU daily cases from counties in Massachusetts and Vermont
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#'
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#' This data source of confirmed COVID-19 cases and deaths
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#' is based on reports made available by the Center for
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#' Systems Science and Engineering at Johns Hopkins University.
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#' This example data ranges from Mar 1, 2020 to Dec 31, 2021,
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#' and is limited to Massachusetts and Vermont.
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#'
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#' @format A tibble with 16,212 rows and 5 variables:
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#' \describe{
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#' \item{geo_value}{the geographic value associated with each row of measurements.}
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#' \item{time_value}{the time value associated with each row of measurements.}
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#' \item{cases}{Number of new confirmed COVID-19 cases, daily}
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#' \item{county_name}{the name of the county}
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#' \item{state_name}{the full name of the state}
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#' }
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#' @source This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the
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#' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
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#' by the Johns Hopkins University on behalf of its Center for Systems Science in Engineering.
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#' Copyright Johns Hopkins University 2020.
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#'
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#' Modifications:
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#' * \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{From the COVIDcast Epidata API}: These signals are taken directly from the JHU CSSE \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 GitHub repository} without changes. The 7-day average signals are computed by Delphi by calculating moving averages of the preceding 7 days, so the signal for June 7 is the average of the underlying data for June 1 through 7, inclusive.
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#' * Furthermore, the data has been limited to a very small number of rows, the signal names slightly altered, and formatted into a tibble.
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# This is named "jhu_csse_county_level_subset" in {epiprocess}
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"covid_incidence_county_subset"
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#' COVID Incident Cases Outlier Example
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#'
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#' Data set for 2 states containing COVID-19 Incident Cases as reported
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#' by JHU-CSSE and Downloaded from the CMU Delphi COVIDcast Epidata API.
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#' This data set covers the period from June 2020 to May 2021, and is
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#' used in the [epiprocess] Vignette on Outliers.
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#'
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#' @source This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the
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#' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
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#' by the Johns Hopkins University on behalf of its Center for Systems Science in Engineering.
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#' Copyright Johns Hopkins University 2020.
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"covid_incidence_outliers"
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#' COVID Cumulative Cases Example
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#'
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#' Data set for 4 states containing COVID-19 Cumulative Cases as reported
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#' by JHU-CSSE and downloaded from the CMU Delphi COVIDcast Epidata API.
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#' This data set covers the period from March 2020 to January 2022, and is
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#' used in the [epiprocess] Vignette on ... .
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#'
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#' @source This object contains a modified part of the \href{https://github.com/CSSEGISandData/COVID-19}{COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University} as \href{https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/jhu-csse.html}{republished in the COVIDcast Epidata API}. This data set is licensed under the terms of the
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#' \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license}
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#' by the Johns Hopkins University on behalf of its Center for Systems Science in Engineering.
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#' Copyright Johns Hopkins University 2020.
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"jhu_confirmed_cumulative_num"
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