From b183fffbc14a84fbfd2a4f2ac3b09989d71c83f8 Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Wed, 25 Sep 2024 18:15:21 +0100 Subject: [PATCH] update examples to use new epiparameter function signature --- R/checkers.R | 6 ++- R/epiparameter.R | 88 ++++++++++++++++++++++++-------------- R/plot.R | 6 ++- man/discretise.Rd | 6 ++- man/epiparameter.Rd | 24 +++++++---- man/family.epiparameter.Rd | 14 +++--- man/format.epiparameter.Rd | 6 ++- man/is_continuous.Rd | 12 ++++-- man/is_epiparameter.Rd | 6 ++- man/is_parameterised.Rd | 6 ++- man/is_truncated.Rd | 14 +++--- man/plot.epiparameter.Rd | 6 ++- man/print.epiparameter.Rd | 6 ++- 13 files changed, 130 insertions(+), 70 deletions(-) diff --git a/R/checkers.R b/R/checkers.R index 35139714b..2de76462b 100644 --- a/R/checkers.R +++ b/R/checkers.R @@ -16,8 +16,10 @@ #' ep <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 1, scale = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 1, scale = 1) +#' ) #' ) #' is_parameterised(ep) #' diff --git a/R/epiparameter.R b/R/epiparameter.R index 7fca67868..4c3dac102 100644 --- a/R/epiparameter.R +++ b/R/epiparameter.R @@ -173,17 +173,21 @@ new_epiparameter <- function(disease = character(), #' ebola_incubation <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 1, scale = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 1, scale = 1) +#' ) #' ) #' #' # minimal input required for discrete `epiparameter` #' ebola_incubation <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 1, scale = 1), -#' discretise = TRUE +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 1, scale = 1), +#' discretise = TRUE +#' ) #' ) #' #' # example with more fields filled in @@ -191,8 +195,12 @@ new_epiparameter <- function(disease = character(), #' disease = "ebola", #' pathogen = "ebola_virus", #' epi_dist = "incubation", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 1, scale = 1), +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 1, scale = 1), +#' discretise = FALSE, +#' truncation = NA +#' ), #' uncertainty = create_uncertainty(), #' summary_stats = create_summary_stats(mean = 2, sd = 1), #' citation = create_citation( @@ -211,8 +219,6 @@ new_epiparameter <- function(disease = character(), #' method_assess = create_method_assess( #' censored = TRUE #' ), -#' discretise = FALSE, -#' truncation = NA, #' notes = "No notes" #' ) epiparameter <- function(disease, @@ -381,8 +387,10 @@ test_epiparameter <- function(x) { # nolint cyclocomp_linter #' epiparameter <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 1, scale = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 1, scale = 1) +#' ) #' ) #' epiparameter print.epiparameter <- function(x, ...) { @@ -401,8 +409,10 @@ print.epiparameter <- function(x, ...) { #' epiparameter <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 1, scale = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 1, scale = 1) +#' ) #' ) #' format(epiparameter) format.epiparameter <- function(x, ...) { @@ -463,8 +473,10 @@ format.epiparameter <- function(x, ...) { #' ep <- epiparameter( #' disease = "ebola", #' epi_dist = "serial_interval", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 1, scale = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 1, scale = 1) +#' ) #' ) #' #' is_epiparameter(ep) @@ -615,8 +627,10 @@ generate.epiparameter <- function(x, times, ...) { #' ebola_incubation <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 1, scale = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 1, scale = 1) +#' ) #' ) #' discretise(ebola_incubation) discretise <- function(x, ...) { @@ -710,8 +724,10 @@ discretise.default <- function(x, ...) { #' ep <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 1, scale = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 1, scale = 1) +#' ) #' ) #' family(ep) #' @@ -719,9 +735,11 @@ discretise.default <- function(x, ...) { #' ep <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "lnorm", -#' prob_distribution_params = c(meanlog = 1, sdlog = 1), -#' discretise = TRUE +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "lnorm", +#' prob_distribution_params = c(meanlog = 1, sdlog = 1), +#' discretise = TRUE +#' ) #' ) #' family(ep) family.epiparameter <- function(object, ...) { @@ -775,17 +793,21 @@ family.epiparameter <- function(object, ...) { #' ep <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "lnorm", -#' prob_distribution_params = c(meanlog = 1, sdlog = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "lnorm", +#' prob_distribution_params = c(meanlog = 1, sdlog = 1) +#' ) #' ) #' is_truncated(ep) #' #' ep <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "lnorm", -#' prob_distribution_params = c(meanlog = 1, sdlog = 1), -#' truncation = 10 +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "lnorm", +#' prob_distribution_params = c(meanlog = 1, sdlog = 1), +#' truncation = 10 +#' ) #' ) #' is_truncated(ep) is_truncated <- function(x) { @@ -830,8 +852,10 @@ is_truncated <- function(x) { #' ep <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "lnorm", -#' prob_distribution_params = c(meanlog = 1, sdlog = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "lnorm", +#' prob_distribution_params = c(meanlog = 1, sdlog = 1) +#' ) #' ) #' is_continuous(ep) #' is_continuous(discretise(ep)) @@ -839,8 +863,10 @@ is_truncated <- function(x) { #' ep <- epiparameter( #' disease = "ebola", #' epi_dist = "offspring distribution", -#' prob_distribution = "nbinom", -#' prob_distribution_params = c(mean = 2, dispersion = 0.5) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "nbinom", +#' prob_distribution_params = c(mean = 2, dispersion = 0.5) +#' ) #' ) #' is_continuous(ep) is_continuous <- function(x) { diff --git a/R/plot.R b/R/plot.R index 38836a0f9..bea286975 100644 --- a/R/plot.R +++ b/R/plot.R @@ -26,8 +26,10 @@ #' ep <- epiparameter( #' disease = "ebola", #' epi_dist = "incubation_period", -#' prob_distribution = "gamma", -#' prob_distribution_params = c(shape = 2, scale = 1) +#' prob_distribution = create_prob_distribution( +#' prob_distribution = "gamma", +#' prob_distribution_params = c(shape = 2, scale = 1) +#' ) #' ) #' plot(ep) #' diff --git a/man/discretise.Rd b/man/discretise.Rd index bb0b25ae1..878728996 100644 --- a/man/discretise.Rd +++ b/man/discretise.Rd @@ -35,8 +35,10 @@ discretised distribution (using an object from the \code{{distcrete}} package). ebola_incubation <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 1, scale = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 1, scale = 1) + ) ) discretise(ebola_incubation) } diff --git a/man/epiparameter.Rd b/man/epiparameter.Rd index a302612fa..0a3fccc5d 100644 --- a/man/epiparameter.Rd +++ b/man/epiparameter.Rd @@ -119,17 +119,21 @@ Accepted \verb{} distribution parameterisations are: ebola_incubation <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 1, scale = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 1, scale = 1) + ) ) # minimal input required for discrete `epiparameter` ebola_incubation <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 1, scale = 1), - discretise = TRUE + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 1, scale = 1), + discretise = TRUE + ) ) # example with more fields filled in @@ -137,8 +141,12 @@ ebola_incubation <- epiparameter( disease = "ebola", pathogen = "ebola_virus", epi_dist = "incubation", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 1, scale = 1), + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 1, scale = 1), + discretise = FALSE, + truncation = NA + ), uncertainty = create_uncertainty(), summary_stats = create_summary_stats(mean = 2, sd = 1), citation = create_citation( @@ -157,8 +165,6 @@ ebola_incubation <- epiparameter( method_assess = create_method_assess( censored = TRUE ), - discretise = FALSE, - truncation = NA, notes = "No notes" ) } diff --git a/man/family.epiparameter.Rd b/man/family.epiparameter.Rd index 0417b2251..ab14c2e7e 100644 --- a/man/family.epiparameter.Rd +++ b/man/family.epiparameter.Rd @@ -26,8 +26,10 @@ output irrespective of the internal distribution class. ep <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 1, scale = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 1, scale = 1) + ) ) family(ep) @@ -35,9 +37,11 @@ family(ep) ep <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "lnorm", - prob_distribution_params = c(meanlog = 1, sdlog = 1), - discretise = TRUE + prob_distribution = create_prob_distribution( + prob_distribution = "lnorm", + prob_distribution_params = c(meanlog = 1, sdlog = 1), + discretise = TRUE + ) ) family(ep) } diff --git a/man/format.epiparameter.Rd b/man/format.epiparameter.Rd index 930f74db3..07bf8e618 100644 --- a/man/format.epiparameter.Rd +++ b/man/format.epiparameter.Rd @@ -22,8 +22,10 @@ Format method for \verb{} class epiparameter <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 1, scale = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 1, scale = 1) + ) ) format(epiparameter) } diff --git a/man/is_continuous.Rd b/man/is_continuous.Rd index 0ce293433..8743e0f5a 100644 --- a/man/is_continuous.Rd +++ b/man/is_continuous.Rd @@ -26,8 +26,10 @@ binomial), and all \verb{} objects are discrete. ep <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "lnorm", - prob_distribution_params = c(meanlog = 1, sdlog = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "lnorm", + prob_distribution_params = c(meanlog = 1, sdlog = 1) + ) ) is_continuous(ep) is_continuous(discretise(ep)) @@ -35,8 +37,10 @@ is_continuous(discretise(ep)) ep <- epiparameter( disease = "ebola", epi_dist = "offspring distribution", - prob_distribution = "nbinom", - prob_distribution_params = c(mean = 2, dispersion = 0.5) + prob_distribution = create_prob_distribution( + prob_distribution = "nbinom", + prob_distribution_params = c(mean = 2, dispersion = 0.5) + ) ) is_continuous(ep) } diff --git a/man/is_epiparameter.Rd b/man/is_epiparameter.Rd index 489a357c0..37bca1ec2 100644 --- a/man/is_epiparameter.Rd +++ b/man/is_epiparameter.Rd @@ -20,8 +20,10 @@ Check object is an \verb{} ep <- epiparameter( disease = "ebola", epi_dist = "serial_interval", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 1, scale = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 1, scale = 1) + ) ) is_epiparameter(ep) diff --git a/man/is_parameterised.Rd b/man/is_parameterised.Rd index 3ca83db4c..c34eaaa06 100644 --- a/man/is_parameterised.Rd +++ b/man/is_parameterised.Rd @@ -31,8 +31,10 @@ distribution and distribution parameters ep <- epiparameter( disease = "ebola", epi_dist = "incubation", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 1, scale = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 1, scale = 1) + ) ) is_parameterised(ep) diff --git a/man/is_truncated.Rd b/man/is_truncated.Rd index d86c81f36..546784b00 100644 --- a/man/is_truncated.Rd +++ b/man/is_truncated.Rd @@ -26,17 +26,21 @@ return \code{FALSE} by default. ep <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "lnorm", - prob_distribution_params = c(meanlog = 1, sdlog = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "lnorm", + prob_distribution_params = c(meanlog = 1, sdlog = 1) + ) ) is_truncated(ep) ep <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "lnorm", - prob_distribution_params = c(meanlog = 1, sdlog = 1), - truncation = 10 + prob_distribution = create_prob_distribution( + prob_distribution = "lnorm", + prob_distribution_params = c(meanlog = 1, sdlog = 1), + truncation = 10 + ) ) is_truncated(ep) } diff --git a/man/plot.epiparameter.Rd b/man/plot.epiparameter.Rd index d9f32bfe8..49d8ac80a 100644 --- a/man/plot.epiparameter.Rd +++ b/man/plot.epiparameter.Rd @@ -32,8 +32,10 @@ first and last day to plot on the x-axis can be supplied to \code{xlim} ep <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 2, scale = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 2, scale = 1) + ) ) plot(ep) diff --git a/man/print.epiparameter.Rd b/man/print.epiparameter.Rd index ac3b04e75..263d4af00 100644 --- a/man/print.epiparameter.Rd +++ b/man/print.epiparameter.Rd @@ -21,8 +21,10 @@ Print method for \verb{} class epiparameter <- epiparameter( disease = "ebola", epi_dist = "incubation_period", - prob_distribution = "gamma", - prob_distribution_params = c(shape = 1, scale = 1) + prob_distribution = create_prob_distribution( + prob_distribution = "gamma", + prob_distribution_params = c(shape = 1, scale = 1) + ) ) epiparameter }