Autoload epidatasets as a dependency rather than reexporting epidat…

…asets data (#577) * stop reexporting epidatasets data * import epidatasets in package file * version * docs: document (GHA) --------- Co-authored-by: nmdefries <[email protected]>
cmu-delphi · Dec 13, 2024 · 0613150 · 0613150
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diff --git 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", , "[email protected]", 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
@@ -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
@@ -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
@@ -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
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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 %>%