diff --git a/DESCRIPTION b/DESCRIPTION index 552b8b3a..9d30c46f 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,9 +15,10 @@ Authors@R: c( person("Dmitry", "Shemetov", role = "ctb"), person("Ryan", "Tibshirani", , "ryantibs@cmu.edu", role = c("aut", "cre")) ) -Description: This package introduces a common data structure for - epidemiological data sets measured over space and time, and offers - associated utilities to perform basic signal processing tasks. +Description: This package introduces a common data structure for epidemiological + data reported by location and time, provides another data structure to + work with revisions to these data sets over time, and offers associated + utilities to perform basic signal processing tasks. License: MIT + file LICENSE Imports: data.table, diff --git a/man/archive_cases_dv_subset.Rd b/man/archive_cases_dv_subset.Rd index 3a44ed04..1c6b9eb9 100644 --- a/man/archive_cases_dv_subset.Rd +++ b/man/archive_cases_dv_subset.Rd @@ -3,7 +3,7 @@ \docType{data} \name{archive_cases_dv_subset} \alias{archive_cases_dv_subset} -\title{Subset of daily doctor visits and cases from California, Florida, Texas, and New York in archive format} +\title{Subset of daily doctor visits and cases in archive format} \format{ An \code{epi_archive} data format. The data table DT has 129,638 rows and 5 columns: \describe{ @@ -35,6 +35,7 @@ This data source is based on information about outpatient visits, provided to us by health system partners, and also contains confirmed COVID-19 cases based on reports made available by the Center for Systems Science and Engineering at Johns Hopkins University. -This example data ranges from June 1, 2020 to Dec 1, 2021, and is also limited to California, Florida, Texas, and New York. +This example data ranges from June 1, 2020 to Dec 1, 2021, and +is also limited to California, Florida, Texas, and New York. } \keyword{datasets} diff --git a/man/incidence_num_outlier_example.Rd b/man/incidence_num_outlier_example.Rd index 23afdf51..90275099 100644 --- a/man/incidence_num_outlier_example.Rd +++ b/man/incidence_num_outlier_example.Rd @@ -32,7 +32,8 @@ incidence_num_outlier_example This data source of confirmed COVID-19 cases is based on reports made available by the Center for Systems Science and Engineering at Johns Hopkins University. -This example data is a snapshot as of Oct 28, 2021 and captures the cases from June 1, 2020 to May 31, 2021 +This example data is a snapshot as of Oct 28, 2021 and captures the cases +from June 1, 2020 to May 31, 2021 and is limited to California and Florida. } \keyword{datasets} diff --git a/man/jhu_csse_county_level_subset.Rd b/man/jhu_csse_county_level_subset.Rd index 6ab47a12..dfe8ef8a 100644 --- a/man/jhu_csse_county_level_subset.Rd +++ b/man/jhu_csse_county_level_subset.Rd @@ -33,6 +33,7 @@ jhu_csse_county_level_subset This data source of confirmed COVID-19 cases and deaths is based on reports made available by the Center for Systems Science and Engineering at Johns Hopkins University. -This example data ranges from Mar 1, 2020 to Dec 31, 2021, and is limited to Massachusetts and Vermont. +This example data ranges from Mar 1, 2020 to Dec 31, 2021, +and is limited to Massachusetts and Vermont. } \keyword{datasets} diff --git a/man/jhu_csse_daily_subset.Rd b/man/jhu_csse_daily_subset.Rd index 20c4d909..626bf545 100644 --- a/man/jhu_csse_daily_subset.Rd +++ b/man/jhu_csse_daily_subset.Rd @@ -3,28 +3,42 @@ \docType{data} \name{jhu_csse_daily_subset} \alias{jhu_csse_daily_subset} -\title{Subset of JHU daily cases and deaths from California, Florida, Texas, New York, Georgia, and Pennsylvania} +\title{Subset of JHU daily state cases and deaths} \format{ A tibble with 4026 rows and 6 variables: \describe{ -\item{geo_value}{the geographic value associated with each row of measurements.} +\item{geo_value}{the geographic value associated with each row +of measurements.} \item{time_value}{the time value associated with each row of measurements.} -\item{case_rate_7d_av}{7-day average signal of number of new confirmed COVID-19 cases per 100,000 population, daily} -\item{death_rate_7d_av}{7-day average signal of number of new confirmed deaths due to COVID-19 per 100,000 population, daily} +\item{case_rate_7d_av}{7-day average signal of number of new +confirmed COVID-19 cases per 100,000 population, daily} +\item{death_rate_7d_av}{7-day average signal of number of new confirmed +deaths due to COVID-19 per 100,000 population, daily} \item{cases}{Number of new confirmed COVID-19 cases, daily} -\item{cases_7d_av}{7-day average signal of number of new confirmed COVID-19 cases, daily} +\item{cases_7d_av}{7-day average signal of number of new confirmed +COVID-19 cases, daily} } } \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 +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 \href{https://creativecommons.org/licenses/by/4.0/}{Creative Commons Attribution 4.0 International license} -by the Johns Hopkins University on behalf of its Center for Systems Science in Engineering. -Copyright Johns Hopkins University 2020. +by the Johns Hopkins University on behalf of its Center for Systems Science +in Engineering. Copyright Johns Hopkins University 2020. Modifications: \itemize{ -\item \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. -\item Furthermore, the data has been limited to a very small number of rows, the signal names slightly altered, and formatted into a tibble. +\item \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. +\item Furthermore, the data has been limited to a very small number of rows, +the signal names slightly altered, and formatted into a tibble. } } \usage{ @@ -34,6 +48,7 @@ jhu_csse_daily_subset This data source of confirmed COVID-19 cases and deaths is based on reports made available by the Center for Systems Science and Engineering at Johns Hopkins University. -This example data ranges from Mar 1, 2020 to Dec 31, 2021, and is limited to California, Florida, Texas, New York, Georgia, and Pennsylvania. +This example data ranges from Mar 1, 2020 to Dec 31, 2021, and is limited to +California, Florida, Texas, New York, Georgia, and Pennsylvania. } \keyword{datasets}