move examples to extdata

epiforecasts · sbfnk · Oct 3, 2023 · Sep 19, 2023 · Sep 19, 2023 · Sep 27, 2023
commit fbe2745b757ff1661cfb53dadbe473d43d3aa1ea
diff --git a/R/data.R b/R/data.R
@@ -21,21 +21,3 @@
 #' An example data frame of observed cases
 #' @format A data frame containing cases reported on each date.
 "example_confirmed"
-
-#' Example estimate_infections output
-#'
-#' @description `r lifecycle::badge("stable")`
-#' An example output of `estimate_infections` containing 200 samples.
-#' See here for details:
-#'  https://github.com/epiforecasts/EpiNow2/blob/main/data-raw/estimate_infections.R # nolint
-#' @format An `estimate_infections` object with the results
-"example_estimate_infections"
-
-#' Example regional_epinow output
-#'
-#' @description `r lifecycle::badge("stable")`
-#' An example output of `regional_epinow` containing 200 samples per region.
-#' See here for details:
-#'  https://github.com/epiforecasts/EpiNow2/blob/main/data-raw/estimate_infections.R # nolint
-#' @format A list with the results
-"example_regional_epinow"
diff --git a/R/get.R b/R/get.R
@@ -71,7 +71,10 @@ get_raw_result <- function(file, region, date,
 #' @importFrom data.table rbindlist
 #' @examples
 #' # get example multiregion estimates
-#' regional_out <- example_regional_epinow
+#' regional_out <- readRDS(system.file(
+#'     package = "EpiNow2", "extdata", "example_regional_epinow.rds"
+#' ))
+#'
 #' # from output
 #' results <- get_regional_results(regional_out$regional, samples = FALSE)
 get_regional_results <- function(regional_output,

diff --git a/R/plot.R b/R/plot.R
@@ -80,7 +80,10 @@ plot_CrIs <- function(plot, CrIs, alpha, linewidth) {
 #' @importFrom purrr map
 #' @examples
 #' # get example model results
-#' out <- example_estimate_infections
+#' out <- readRDS(system.file(
+#'     package = "EpiNow2", "extdata", "example_estimate_infections.rds"
+#' ))
+#'
 #' # plot infections
 #' plot_estimates(
 #'   estimate = out$summarised[variable == "infections"],

diff --git a/R/report.R b/R/report.R
@@ -263,7 +263,9 @@ report_summary <- function(summarised_estimates,
 #' @export
 #' @examples
 #' # get example output form estimate_infections
-#' out <- example_estimate_infections
+#' out <- readRDS(system.file(
+#'     package = "EpiNow2", "extdata", "example_estimate_infections.rds"
+#' ))
 #'
 #' # plot infections
 #' plots <- report_plots(

diff --git a/R/summarise.R b/R/summarise.R
@@ -166,10 +166,13 @@ summarise_results <- function(regions,
 #' @importFrom futile.logger flog.info
 #' @examples
 #' # get example output from regional_epinow model
-#' out <- example_regional_epinow
+#' regional_out <- readRDS(system.file(
+#'     package = "EpiNow2", "extdata", "example_regional_epinow.rds"
+#' ))
+#'
 #' regional_summary(
-#'   regional_output = out$regional,
-#'   reported_cases = out$summary$reported_cases
+#'   regional_output = regional_out$regional,
+#'   reported_cases = regional_out$summary$reported_cases
 #' )
 regional_summary <- function(regional_output = NULL,
                              reported_cases,
@@ -501,7 +504,9 @@ summarise_key_measures <- function(regional_results = NULL,
 #' @importFrom data.table data.table fwrite
 #' @importFrom purrr map safely
 #' @examples
-#' regional_out <- example_regional_epinow # get example run outputs
+#' regional_out <- readRDS(system.file(
+#'     package = "EpiNow2", "extdata", "example_regional_epinow.rds"
+#' ))
 #' regional_runtimes(regional_output = regional_out$regional)
 regional_runtimes <- function(regional_output = NULL,
                               target_folder = NULL,

diff --git a/data-raw/estimate-infections.R b/data-raw/estimate-infections.R
@@ -1,4 +1,7 @@
 library("EpiNow2")
+library("here")
+
+options(mc.cores = 4)
 
 # get example case counts
 reported_cases <- example_confirmed[1:60]
@@ -42,5 +45,13 @@ example_regional_epinow <- regional_epinow(
   stan = stan_opts(samples = 200, control = list(adapt_delta = 0.95))
 )
 
-usethis::use_data(example_estimate_infections, overwrite = TRUE)
-usethis::use_data(example_regional_epinow, overwrite = TRUE)
+saveRDS(
+  example_estimate_infections,
+  here("inst", "extdata", "example_estimate_infections.rds"),
+  compress = "xz"
+)
+saveRDS(
+  example_regional_epinow,
+  here("inst", "extdata", "example_regional_epinow.rds"),
+  compress = "xz"
+)
diff --git a/data/example_estimate_infections.rda b/data/example_estimate_infections.rda
diff --git a/data/example_regional_epinow.rda b/data/example_regional_epinow.rda
diff --git a/inst/extdata/example_estimate_infections.rds b/inst/extdata/example_estimate_infections.rds
diff --git a/inst/extdata/example_regional_epinow.rds b/inst/extdata/example_regional_epinow.rds
diff --git a/man/example_estimate_infections.Rd b/man/example_estimate_infections.Rd
diff --git a/man/example_regional_epinow.Rd b/man/example_regional_epinow.Rd
diff --git a/man/get_regional_results.Rd b/man/get_regional_results.Rd
diff --git a/man/plot_estimates.Rd b/man/plot_estimates.Rd
diff --git a/man/regional_runtimes.Rd b/man/regional_runtimes.Rd
diff --git a/man/regional_summary.Rd b/man/regional_summary.Rd
diff --git a/man/report_plots.Rd b/man/report_plots.Rd