update max in defaults/examples/tests

R/get.R

@@ -169,7 +169,7 @@ get_regional_results <- function(regional_output,
 #'
 #' @param source A character string indicating the source of interest.
 #'
-#' @param max_value Numeric, the maximum value to allow. Defaults to 15 days.
+#' @param max_value Numeric, the maximum value to allow. Defaults to 14 days.
 #'
 #' @param fixed Logical, defaults to `FALSE`. Should distributions be supplied
 #' as fixed values (vs with uncertainty)?
@@ -182,7 +182,7 @@ get_regional_results <- function(regional_output,
 #' get_dist(
 #'  EpiNow2::generation_times, disease = "SARS-CoV-2", source = "ganyani"
 #' )
-get_dist <- function(data, disease, source, max_value = 15, fixed = FALSE) {
+get_dist <- function(data, disease, source, max_value = 14, fixed = FALSE) {
   target_disease <- disease
   target_source <- source
   data <- data[disease == target_disease][source == target_source]
@@ -204,7 +204,7 @@ get_dist <- function(data, disease, source, max_value = 15, fixed = FALSE) {
 #' @author Sam Abbott
 #' @examples
 #' get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
-get_generation_time <- function(disease, source, max_value = 15,
+get_generation_time <- function(disease, source, max_value = 14,
                                 fixed = FALSE) {
   dist <- get_dist(EpiNow2::generation_times,
     disease = disease, source = source,
@@ -224,7 +224,7 @@ get_generation_time <- function(disease, source, max_value = 15,
 #' @export
 #' @examples
 #' get_incubation_period(disease = "SARS-CoV-2", source = "lauer")
-get_incubation_period <- function(disease, source, max_value = 15,
+get_incubation_period <- function(disease, source, max_value = 14,
                                   fixed = FALSE) {
   dist <- get_dist(EpiNow2::incubation_periods,
     disease = disease, source = source,

R/opts.R

@@ -28,18 +28,18 @@
 #' generation_time_opts()
 #'
 #' # A fixed gamma distributed generation time
-#' generation_time_opts(dist_spec(mean = 3, sd = 2, max = 15))
+#' generation_time_opts(dist_spec(mean = 3, sd = 2, max = 14))
 #'
 #' # An uncertain gamma distributed generation time
 #' generation_time_opts(
-#'  dist_spec(mean = 3, sd = 2, mean_sd = 1, sd_sd = 0.5, max = 15)
+#'  dist_spec(mean = 3, sd = 2, mean_sd = 1, sd_sd = 0.5, max = 14)
 #' )
 #'
 #' # A generation time sourced from the literature
 #' dist <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
 #' generation_time_opts(dist)
 generation_time_opts <- function(dist = dist_spec(mean = 1), ...,
-                                 disease, source, max = 15L, fixed = FALSE,
+                                 disease, source, max = 14, fixed = FALSE,
                                  prior_weight) {
   deprecated_options_given <- FALSE
   dot_options <- list(...)
@@ -120,11 +120,11 @@ generation_time_opts <- function(dist = dist_spec(mean = 1), ...,
 #' delay_opts()
 #'
 #' # A single delay that has uncertainty
-#' delay <- dist_spec(mean = 1, mean_sd = 0.2, sd = 0.5, sd_sd = 0.1, max = 15)
+#' delay <- dist_spec(mean = 1, mean_sd = 0.2, sd = 0.5, sd_sd = 0.1, max = 14)
 #' delay_opts(delay)
 #'
 #' # A single delay without uncertainty
-#' delay <- dist_spec(mean = 1, sd = 0.5, max = 15)
+#' delay <- dist_spec(mean = 1, sd = 0.5, max = 14)
 #' delay_opts(delay)
 #'
 #' # Multiple delays (in this case twice the same)

R/simulate_infections.R

@@ -56,7 +56,7 @@
 #' )
 #' reporting_delay <- dist_spec(
 #'   mean = convert_to_logmean(2, 1), mean_sd = 0.1,
-#'   sd = convert_to_logsd(2, 1), sd_sd = 0.1, max = 15
+#'   sd = convert_to_logsd(2, 1), sd_sd = 0.1, max = 14
 #' )
 #'
 #' # fit model to data to recover Rt estimates

README.Rmd

@@ -100,7 +100,7 @@ For example if data on the delay between onset and infection was available we co
 ```{r, eval = FALSE}
 reporting_delay <- estimate_delay(
   rlnorm(1000, log(2), 1),
-  max_value = 15, bootstraps = 1
+  max_value = 14, bootstraps = 1
 )
 ```
 

tests/testthat/test-delays.R

@@ -29,7 +29,7 @@ test_that("generation times can be specified in different ways", {
   )
   expect_equal(
     round(test_stan_delays(
-      generation_time = generation_time_opts(dist_spec(mean = 3, sd = 1, max = 5)),
+      generation_time = generation_time_opts(dist_spec(mean = 3, sd = 1, max = 4)),
       params = delay_params
     ), digits = 2),
     c(0.02, 0.11, 0.22, 0.30, 0.35)
@@ -39,7 +39,7 @@ test_that("generation times can be specified in different ways", {
       generation_time = generation_time_opts(
         get_generation_time(
           disease = "SARS-CoV-2", source = "ganyani",
-          max = 10, fixed = TRUE
+          max = 9, fixed = TRUE
         )
       ),
       params = delay_params
@@ -69,7 +69,7 @@ test_that("delay parameters can be specified in different ways", {
   )
   expect_equal(
     tail(round(test_stan_delays(
-      delays = delay_opts(dist_spec(mean = 3, sd = 1, max = 5)),
+      delays = delay_opts(dist_spec(mean = 3, sd = 1, max = 4)),
       params = delay_params
     ), digits = 2), n = -2),
     c(0.02, 0.11, 0.22, 0.30, 0.35)
@@ -79,7 +79,7 @@ test_that("delay parameters can be specified in different ways", {
 test_that("truncation parameters can be specified in different ways", {
   expect_equal(
     tail(round(test_stan_delays(
-      truncation = trunc_opts(dist = dist_spec(mean = 3, sd = 1, max = 5)),
+      truncation = trunc_opts(dist = dist_spec(mean = 3, sd = 1, max = 4)),
       params = delay_params
     ), digits = 2), n = -2),
     c(0.02, 0.11, 0.22, 0.30, 0.35)