diff --git a/DESCRIPTION b/DESCRIPTION index e894f099..4f330b20 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: epiprocess Type: Package Title: Tools for basic signal processing in epidemiology -Version: 0.10.0 +Version: 0.10.1 Authors@R: c( person("Jacob", "Bien", role = "ctb"), person("Logan", "Brooks", , "lcbrooks+github@andrew.cmu.edu", role = c("aut", "cre")), @@ -37,13 +37,13 @@ Description: This package introduces common data structures for working with License: MIT + file LICENSE URL: https://cmu-delphi.github.io/epiprocess/ Depends: + epidatasets, R (>= 3.6) Imports: checkmate, cli, data.table, dplyr (>= 1.1.0), - epidatasets, genlasso, ggplot2, glue, diff --git a/NAMESPACE b/NAMESPACE index 1f5180fb..e8b77b6d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -51,19 +51,14 @@ S3method(ungroup,epi_df) S3method(ungroup,grouped_epi_archive) S3method(unnest,epi_df) export("%>%") -export(archive_cases_dv_subset) export(arrange) export(arrange_canonical) export(as_epi_archive) export(as_epi_df) export(as_tsibble) export(autoplot) -export(cases_deaths_subset) export(clone) export(complete) -export(covid_case_death_rates_extended) -export(covid_incidence_county_subset) -export(covid_incidence_outliers) export(deprecated_quo_is_present) export(detect_outlr) export(detect_outlr_rm) diff --git a/NEWS.md b/NEWS.md index ba6826da..47db7024 100644 --- a/NEWS.md +++ b/NEWS.md @@ -6,6 +6,25 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat ## Breaking changes + +## Improvements + + +## Bug fixes + + +## Cleanup + +- Moved example datasets from being reexported in the package to being fetched + from `epidatasets`. The `epidatasets` package is now auto-loaded as a + dependency of `epiprocess`. The datasets can still be accessed, after loading + the package, with `data()` or the name of the dataset alone, or with + `epidatasets::` (#577). + +# epiprocess 0.10 + +## Breaking changes + - Moved example datasets from being hosted in the package to being reexported from the `epidatasets` package. The datasets can no longer be loaded with `data()` but can be accessed with `epiprocess::` or, after loading the diff --git a/R/reexports.R b/R/reexports.R index 9a33e94b..00ac83c2 100644 --- a/R/reexports.R +++ b/R/reexports.R @@ -75,40 +75,3 @@ tidyr::full_seq #' @importFrom ggplot2 autoplot #' @export ggplot2::autoplot - - -# epidatasets ------------------------------------------------------------------- - -#' @rdname epidatasets_reexports -#' -#' @title Selected example data sets from `epidatasets` -#' -#' @description Data sets re-exported from `epidatasets`; please see -#' documentation for each of these objects in `epidatasets`. -#' -#' A brief description of the format of each of the objects above are described -#' in matching order below. -#' -#' @keywords internal -#' @export -delayedAssign("cases_deaths_subset", epidatasets::cases_deaths_subset) - -#' @rdname epidatasets_reexports -#' @keywords internal -#' @export -delayedAssign("covid_incidence_county_subset", epidatasets::covid_incidence_county_subset) - -#' @rdname epidatasets_reexports -#' @keywords internal -#' @export -delayedAssign("covid_incidence_outliers", epidatasets::covid_incidence_outliers) - -#' @rdname epidatasets_reexports -#' @keywords internal -#' @export -delayedAssign("archive_cases_dv_subset", epidatasets::archive_cases_dv_subset) - -#' @rdname epidatasets_reexports -#' @keywords internal -#' @export -delayedAssign("covid_case_death_rates_extended", epidatasets::covid_case_death_rates_extended) diff --git a/man/epidatasets_reexports.Rd b/man/epidatasets_reexports.Rd deleted file mode 100644 index 3dc809e4..00000000 --- a/man/epidatasets_reexports.Rd +++ /dev/null @@ -1,40 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/reexports.R -\docType{data} -\name{cases_deaths_subset} -\alias{cases_deaths_subset} -\alias{covid_incidence_county_subset} -\alias{covid_incidence_outliers} -\alias{archive_cases_dv_subset} -\alias{covid_case_death_rates_extended} -\title{Selected example data sets from \code{epidatasets}} -\format{ -An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 4026 rows and 6 columns. - -An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 16212 rows and 5 columns. - -An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 730 rows and 3 columns. - -An object of class \code{epi_archive} of length 6. - -An object of class \code{epi_df} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 37576 rows and 4 columns. -} -\usage{ -cases_deaths_subset - -covid_incidence_county_subset - -covid_incidence_outliers - -archive_cases_dv_subset - -covid_case_death_rates_extended -} -\description{ -Data sets re-exported from \code{epidatasets}; please see -documentation for each of these objects in \code{epidatasets}. - -A brief description of the format of each of the objects above are described -in matching order below. -} -\keyword{internal} diff --git a/vignettes/correlation.Rmd b/vignettes/correlation.Rmd index 8d5054bc..bfcbeb14 100644 --- a/vignettes/correlation.Rmd +++ b/vignettes/correlation.Rmd @@ -24,7 +24,8 @@ library(epiprocess) library(dplyr) ``` -The data is included in this package (via the [`epidatasets` package](https://cmu-delphi.github.io/epidatasets/)) and can be loaded with: +The data is included in the [`epidatasets` package](https://cmu-delphi.github.io/epidatasets/), +which is loaded along with `epiprocess`, and can be accessed with: ```{r} x <- covid_case_death_rates_extended %>% arrange(geo_value, time_value) diff --git a/vignettes/epi_archive.Rmd b/vignettes/epi_archive.Rmd index 6d8749cc..34f5a74b 100644 --- a/vignettes/epi_archive.Rmd +++ b/vignettes/epi_archive.Rmd @@ -37,8 +37,8 @@ signal is subject to very heavy and regular revision; you can read more about it on its [API documentation page](https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/doctor-visits.html). -The data is included in this package (via the [`epidatasets` -package](https://cmu-delphi.github.io/epidatasets/)) and can be loaded with: +The data is included in the [`epidatasets` package](https://cmu-delphi.github.io/epidatasets/), +which is loaded along with `epiprocess`, and can be accessed with: ```{r, message = FALSE, warning = FALSE} library(epiprocess) diff --git a/vignettes/epi_df.Rmd b/vignettes/epi_df.Rmd index de10b9af..15f76338 100644 --- a/vignettes/epi_df.Rmd +++ b/vignettes/epi_df.Rmd @@ -32,8 +32,8 @@ library(epiprocess) library(dplyr) ``` -The data is included in this package (via the [`epidatasets` -package](https://cmu-delphi.github.io/epidatasets/)) and can be loaded with: +The data is included in the [`epidatasets` package](https://cmu-delphi.github.io/epidatasets/), +which is loaded along with `epiprocess`, and can be accessed with: ```{r} edf <- cases_deaths_subset %>% @@ -276,8 +276,8 @@ edf_missing %>% We can also use the `tsibble` package to detect and fill time gaps. We'll work with county-level reported COVID-19 cases in MA and VT. -The data is included in this package (via the [`epidatasets` -package](https://cmu-delphi.github.io/epidatasets/)) and can be loaded with: +The data is included in the [`epidatasets` package](https://cmu-delphi.github.io/epidatasets/), +which is loaded along with `epiprocess`, and can be accessed with: ```{r, warning = FALSE, message = FALSE} library(epiprocess) diff --git a/vignettes/epiprocess.Rmd b/vignettes/epiprocess.Rmd index b9648e00..7435f704 100644 --- a/vignettes/epiprocess.Rmd +++ b/vignettes/epiprocess.Rmd @@ -37,7 +37,6 @@ object, which we prepared by downloading the data using `epidatr::pub_covidcast()`. ```{r, results=FALSE, warning=FALSE, message=FALSE} -library(epidatasets) library(epidatr) library(epiprocess) library(dplyr) diff --git a/vignettes/growth_rate.Rmd b/vignettes/growth_rate.Rmd index 8f332de3..ec073876 100644 --- a/vignettes/growth_rate.Rmd +++ b/vignettes/growth_rate.Rmd @@ -24,7 +24,8 @@ library(dplyr) library(tidyr) ``` -The data is included in this package (via the [`epidatasets` package](https://cmu-delphi.github.io/epidatasets/)) and can be loaded with: +The data is included in the [`epidatasets` package](https://cmu-delphi.github.io/epidatasets/), +which is loaded along with `epiprocess`, and can be accessed with: ```{r} x <- cases_deaths_subset %>%