deprecate get functions for delay distributions

R/get.R

@@ -158,10 +158,10 @@ get_regional_results <- function(regional_output,
 #' Get a Literature Distribution
 #'
 #'
-#' @description `r lifecycle::badge("stable")`
-#' Search a data frame for a distribution and return it in the format expected
-#' by `delay_opts()` and the `generation_time` argument of `epinow` and
-#' `estimate_infections`.
+#' @description `r lifecycle::badge("deprecated")`
+#'
+#' This function has been deprecated. Please specify a distribution
+#' using `dist_spec` instead
 #'
 #' @param data A `data.table` in the format of `generation_times`.
 #'
@@ -177,12 +177,13 @@ get_regional_results <- function(regional_output,
 #' @return A list defining a distribution
 #'
 #' @author Sam Abbott
+#' @seealso dist_spec
 #' @export
-#' @examples
-#' get_dist(
-#'  EpiNow2::generation_times, disease = "SARS-CoV-2", source = "ganyani"
-#' )
 get_dist <- function(data, disease, source, max_value = 14, fixed = FALSE) {
+  lifecycle::deprecate_warn(
+    "2.0.0", "get_dist()", "dist_spec()",
+    "The function will be removed completely in version 2.1.0."
+  )
   target_disease <- disease
   target_source <- source
   data <- data[disease == target_disease][source == target_source]
@@ -195,19 +196,25 @@ get_dist <- function(data, disease, source, max_value = 14, fixed = FALSE) {
   }
   return(do.call(dist_spec, dist))
 }
-#'  Get a Literature Distribution for the Generation Time
+#' Get a Literature Distribution for the Generation Time
+#'
+#' @description `r lifecycle::badge("deprecated")`
 #'
-#' @description `r lifecycle::badge("stable")`
 #' Extracts a literature distribution from `generation_times`.
+#' This function has been deprecated. Please specify a distribution
+#' using `dist_spec` instead
 #'
 #' @inheritParams get_dist
 #' @inherit get_dist
 #' @export
+#' @seealso dist_spec
 #' @author Sam Abbott
-#' @examples
-#' get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
 get_generation_time <- function(disease, source, max_value = 14,
                                 fixed = FALSE) {
+  lifecycle::deprecate_warn(
+    "2.0.0", "get_generation_time()", "dist_spec()",
+    "The function will be removed completely in version 2.1.0."
+  )
   dist <- get_dist(EpiNow2::generation_times,
     disease = disease, source = source,
     max_value = max_value, fixed = fixed
@@ -217,17 +224,23 @@ get_generation_time <- function(disease, source, max_value = 14,
 }
 #'  Get a Literature Distribution for the Incubation Period
 #'
-#' @description `r lifecycle::badge("stable")`
-#' Extracts a literature distribution from `incubation_periods`.
+#' @description `r lifecycle::badge("deprecated")`
+#'
+#' Extracts a literature distribution from `generation_times`.
+#' This function has been deprecated. Please specify a distribution
+#' using `dist_spec` instead
 #'
 #' @inheritParams get_dist
 #' @inherit get_dist
 #' @author Sam Abbott
 #' @export
-#' @examples
-#' get_incubation_period(disease = "SARS-CoV-2", source = "lauer")
+#' @seealso dist_spec
 get_incubation_period <- function(disease, source, max_value = 14,
                                   fixed = FALSE) {
+  lifecycle::deprecate_warn(
+    "2.0.0", "get_incubation_period()", "dist_spec()",
+    "The function will be removed completely in version 2.1.0."
+  )
   dist <- get_dist(EpiNow2::incubation_periods,
     disease = disease, source = source,
     max_value = max_value, fixed = fixed

R/opts.R

@@ -1,13 +1,10 @@
 #' Generation Time Distribution Options
 #'
 #' @description `r lifecycle::badge("stable")`
-#' Returns generation time parameters in a format for lower level model use. The
-#' generation time can either be given as a \code{disease} and \code{source} to
-#' be passed to [get_generation_time], or as parameters of a distribution to be
-#' passed to [dist_spec].
+#' Returns generation time parameters in a format for lower level model use.
 #'
 #' @param dist A delay distribution or series of delay distributions generated
-#' using [dist_spec()] or [get_generation_time()]. If no distribution is given
+#' using [dist_spec()]. If no distribution is given
 #' a fixed generation time of 1 will be assumed.
 #'
 #' @param ... deprecated; use `dist` instead
@@ -89,8 +86,7 @@ generation_time_opts <- function(dist = dist_spec(mean = 1), ...,
   if (deprecated_options_given) {
     warning(
       "The generation time distribution must be given to ",
-      "`generation_time_opts` using a call to either ",
-      "`dist_spec` or `get_generation_time`. ",
+      "`generation_time_opts` using a call to `dist_spec`. ",
       "This behaviour has changed from previous versions of `EpiNow2` and ",
       "any code using it may need to be updated as any other ways of ",
       "specifying the generation time are deprecated and will be removed in ",

tests/testthat/test-delays.R

@@ -34,29 +34,6 @@ test_that("generation times can be specified in different ways", {
     ), digits = 2),
     c(0.02, 0.11, 0.22, 0.30, 0.35)
   )
-  expect_equal(
-    round(test_stan_delays(
-      generation_time = generation_time_opts(
-        get_generation_time(
-          disease = "SARS-CoV-2", source = "ganyani",
-          max = 9, fixed = TRUE
-        )
-      ),
-      params = delay_params
-    ), digits = 2),
-    c(0.18, 0.20, 0.17, 0.13, 0.10, 0.07, 0.05, 0.04, 0.03, 0.02)
-  )
-  expect_equal(
-    round(test_stan_delays(
-      generation_time = generation_time_opts(
-        get_generation_time(
-          disease = "SARS-CoV-2", source = "ganyani", max = 10
-        )
-      ),
-      params = delay_params
-    ), digits = 2),
-    c(3.64, 0.71, 3.08, 0.77, 10.00)
-  )
 })
 
 test_that("delay parameters can be specified in different ways", {
@@ -136,4 +113,22 @@ test_that("deprecated arguments are caught", {
       params = delay_params
     ), "deprecated"
   )
+  expect_warning(
+    test_stan_delays(
+      generation_time = generation_time_opts(
+        get_generation_time(
+          disease = "SARS-CoV-2", source = "ganyani",
+        )
+      ),
+    ), "deprecated"
+  )
+  expect_warning(
+    test_stan_delays(
+      delays = delay_opts(
+        get_incubation_period(
+          disease = "SARS-CoV-2", source = "lauer"
+        )
+      ),
+    ), "deprecated"
+  )
 })

tests/testthat/test-get_dist.R

@@ -1,18 +1,7 @@
-test_that("get_dist returns distributional definition data in the format expected by EpiNow2", {
+test_that("get_dist is deprecated", {
   data <- data.table::data.table(mean = 1, mean_sd = 1, sd = 1, sd_sd = 1, source = "test", disease = "test", dist = "gamma")
-  dist <- get_dist(data, disease = "test", source = "test")
-  expect_equal(
-    dist[c("mean_mean", "mean_sd", "sd_mean", "sd_sd", "max")],
-    list(mean_mean = array(1), mean_sd = array(1),
-         sd_mean = array(1), sd_sd = array(1), max = array(14))
-  )
-})
-
-test_that("get_dist returns distributional definition data in the format expected by EpiNow2 with no uncertainty", {
-  data <- data.table::data.table(mean = 1, mean_sd = 1, sd = 1, sd_sd = 1, source = "test", disease = "test", dist = "lognormal")
-  dist <- get_dist(data, disease = "test", source = "test", fixed = TRUE)
-  expect_equal(
-    round(dist$np_pmf[1:7], digits = 2),
-    array(c(0.17, 0.23, 0.17, 0.12, 0.08, 0.06, 0.04))
+  expect_warning(
+    get_dist(data, disease = "test", source = "test"),
+    "deprecated"
   )
 })