Update {epiparameter} usage

R/sim_contacts.R

@@ -18,14 +18,14 @@
 #'
 #' # to simulate more realistic contact tracing data load epiparameters from
 #' # {epiparameter}
-#' contact_distribution <- epiparameter::epidist(
+#' contact_distribution <- epiparameter::epiparameter(
 #'   disease = "COVID-19",
 #'   epi_dist = "contact distribution",
 #'   prob_distribution = "pois",
 #'   prob_distribution_params = c(mean = 2)
 #' )
 #'
-#' infectious_period <- epiparameter::epidist(
+#' infectious_period <- epiparameter::epiparameter(
 #'   disease = "COVID-19",
 #'   epi_dist = "infectious period",
 #'   prob_distribution = "gamma",
@@ -52,8 +52,8 @@ sim_contacts <- function(contact_distribution = function(x) stats::dpois(x = x,
                          config = create_config()) {
   # check and convert distribution to func if needed before .check_sim_input()
   stopifnot(
-    "Input delay distributions need to be either functions or <epidist>" =
-      inherits(infectious_period, c("function", "epidist"))
+    "Input delay distributions need to be either functions or <epiparameter>" =
+      inherits(infectious_period, c("function", "epiparameter"))
   )
   contact_distribution <- as.function(
     contact_distribution, func_type = "density"

R/sim_linelist.R

@@ -20,8 +20,8 @@
 #' * `proportion`: a column with the proportion of the population that are in
 #' that age group. Proportions must sum to one.
 #'
-#' @param contact_distribution A `function` or an `<epidist>` object to generate
-#' the number of contacts per infection.
+#' @param contact_distribution A `function` or an `<epiparameter>` object to
+#' generate the number of contacts per infection.
 #'
 #' The function can be defined or anonymous. The function must have a single
 #' argument in the form of an `integer` vector with elements representing the
@@ -33,13 +33,13 @@
 #' of observing zero contacts, the second element is the probability of
 #' observing one contact, etc.
 #'
-#' An `<epidist>` can be provided. This will be converted into a probability
-#' mass function internally.
+#' An `<epiparameter>` can be provided. This will be converted into a
+#' probability mass function internally.
 #'
 #' The default is an anonymous function with a Poisson probability mass function
 #' ([dpois()]) with a mean (\eqn{\lambda}) of 2 contacts per infection.
 #'
-#' @param infectious_period A `function` or an `<epidist>` object for the
+#' @param infectious_period A `function` or an `<epiparameter>` object for the
 #' infectious period. This defines the duration from becoming infectious to
 #' no longer infectious. In the simulation, individuals are assumed to
 #' become infectious immediately after being infected (the latency period is
@@ -52,42 +52,42 @@
 #' The function must have a single argument, the number of random infectious
 #' periods to generate.
 #'
-#' An `<epidist>` can be provided. This will be converted into random number
-#' generator internally.
+#' An `<epiparameter>` can be provided. This will be converted into random
+#' number generator internally.
 #'
 #' The default is an anonymous function with a lognormal distribution random
 #' number generator ([rlnorm()]) with `meanlog = 2` and `sdlog = 0.5`.
 #'
 #' @param prob_infection A single `numeric` for the probability of a secondary
 #' contact being infected by an infected primary contact.
 #'
-#' @param onset_to_hosp A `function` or an `<epidist>` object for the
+#' @param onset_to_hosp A `function` or an `<epiparameter>` object for the
 #' onset-to-hospitalisation delay distribution. `onset_to_hosp` can also be
 #' set to `NULL` to not simulate hospitalisation (admission) dates.
 #'
 #' The function can be defined or anonymous. The function must return a vector
 #' of `numeric`s for the length of the onset-to-hospitalisation delay. The
 #' function must have a single argument.
 #'
-#' An `<epidist>` can be provided. This will be converted into a random number
-#' generator internally.
+#' An `<epiparameter>` can be provided. This will be converted into a random
+#' number generator internally.
 #'
 #' The default is an anonymous function with a lognormal distribution random
 #' number generator ([rlnorm()]) with `meanlog = 1.5` and `sdlog = 0.5`.
 #'
 #' If `onset_to_hosp` is set to `NULL` then `hosp_risk` and `hosp_death_risk`
 #' will be automatically set to `NULL` if not manually specified.
 #'
-#' @param onset_to_death A `function` or an `<epidist>` object for the
+#' @param onset_to_death A `function` or an `<epiparameter>` object for the
 #' onset-to-death delay distribution. `onset_to_death` can also be set to
 #' `NULL` to not simulate dates for individuals that died.
 #'
 #' The function can be defined or anonymous. The function must return a vector
 #' of `numeric`s for the length of the onset-to-death delay. The function must
 #' have a single argument.
 #'
-#' An `<epidist>` can be provided. This will be converted into a random number
-#' generator internally.
+#' An `<epiparameter>` can be provided. This will be converted into a random
+#' number generator internally.
 #'
 #' The default is an anonymous function with a lognormal distribution random
 #' number generator ([rlnorm()]) with `meanlog = 2.5` and `sdlog = 0.5`.
@@ -96,16 +96,16 @@
 #' `hosp_death_risk` will be automatically set to `NULL` if not manually
 #' specified.
 #'
-#' @param onset_to_recovery A `function` or an `<epidist>` object for the
+#' @param onset_to_recovery A `function` or an `<epiparameter>` object for the
 #' onset-to-recovery delay distribution. `onset_to_recovery` can also be `NULL`
 #' to not simulate dates for individuals that recovered.
 #'
 #' The function can be defined or anonymous. The function must return a vector
 #' of `numeric`s for the length of the onset-to-recovery delay. The function
 #' must have a single argument.
 #'
-#' An `<epidist>` can be provided. This will be converted into a random number
-#' generator internally.
+#' An `<epiparameter>` can be provided. This will be converted into a random
+#' number generator internally.
 #'
 #' The default is `NULL` so by default cases that recover get an `NA` in the
 #' `$date_outcome` line list column.
@@ -180,32 +180,32 @@
 #'
 #' # to simulate a more realistic line list load epiparameters from
 #' # {epiparameter}
-#' contact_distribution <- epiparameter::epidist(
+#' contact_distribution <- epiparameter::epiparameter(
 #'   disease = "COVID-19",
 #'   epi_dist = "contact distribution",
 #'   prob_distribution = "pois",
 #'   prob_distribution_params = c(mean = 2)
 #' )
 #'
-#' infectious_period <- epiparameter::epidist(
+#' infectious_period <- epiparameter::epiparameter(
 #'   disease = "COVID-19",
 #'   epi_dist = "infectious period",
 #'   prob_distribution = "gamma",
 #'   prob_distribution_params = c(shape = 1, scale = 1)
 #' )
 #'
 #' # get onset to hospital admission from {epiparameter} database
-#' onset_to_hosp <- epiparameter::epidist_db(
+#' onset_to_hosp <- epiparameter::epiparameter_db(
 #'   disease = "COVID-19",
 #'   epi_dist = "onset to hospitalisation",
-#'   single_epidist = TRUE
+#'   single_epiparameter = TRUE
 #' )
 #'
 #' # get onset to death from {epiparameter} database
-#' onset_to_death <- epiparameter::epidist_db(
+#' onset_to_death <- epiparameter::epiparameter_db(
 #'   disease = "COVID-19",
 #'   epi_dist = "onset to death",
-#'   single_epidist = TRUE
+#'   single_epiparameter = TRUE
 #' )
 #' # example with single hospitalisation risk for entire population
 #' linelist <- sim_linelist(

R/sim_outbreak.R

@@ -23,32 +23,32 @@
 #'
 #' # to simulate a more realistic outbreak load epiparameters from
 #' # {epiparameter}
-#' contact_distribution <- epiparameter::epidist(
+#' contact_distribution <- epiparameter::epiparameter(
 #'   disease = "COVID-19",
 #'   epi_dist = "contact distribution",
 #'   prob_distribution = "pois",
 #'   prob_distribution_params = c(mean = 2)
 #' )
 #'
-#' infectious_period <- epiparameter::epidist(
+#' infectious_period <- epiparameter::epiparameter(
 #'   disease = "COVID-19",
 #'   epi_dist = "infectious period",
 #'   prob_distribution = "gamma",
 #'   prob_distribution_params = c(shape = 1, scale = 1)
 #' )
 #'
 #' # get onset to hospital admission from {epiparameter} database
-#' onset_to_hosp <- epiparameter::epidist_db(
+#' onset_to_hosp <- epiparameter::epiparameter_db(
 #'   disease = "COVID-19",
 #'   epi_dist = "onset to hospitalisation",
-#'   single_epidist = TRUE
+#'   single_epiparameter = TRUE
 #' )
 #'
 #' # get onset to death from {epiparameter} database
-#' onset_to_death <- epiparameter::epidist_db(
+#' onset_to_death <- epiparameter::epiparameter_db(
 #'   disease = "COVID-19",
 #'   epi_dist = "onset to death",
-#'   single_epidist = TRUE
+#'   single_epiparameter = TRUE
 #' )
 #'
 #' outbreak <- sim_outbreak(

R/simulist-package.R

@@ -10,6 +10,6 @@ NULL
 # nocov start
 # fix for R CMD check from https://github.com/hadley/r-pkgs/issues/828
 ignore_unused_imports <- function() {
-  epiparameter::epidist
+  epiparameter::epiparameter
 }
 # nocov end

R/utils.R

@@ -120,7 +120,7 @@
   out
 }
 
-#' Convert `<epidist>` or `NULL` to function
+#' Convert `<epiparameter>` or `NULL` to function
 #'
 #' @description
 #' An extension to [as.function()], particularly the \pkg{epiparameter}
@@ -132,25 +132,26 @@
 #' If a function is already passed to `as_function` it will be returned
 #' unchanged.
 #'
-#' There is also input checking to error if input is not an `<epidist>`,
+#' There is also input checking to error if input is not an `<epiparameter>`,
 #' `function` ([closure]), or for onset-to-event distributions `NULL`.
 #'
-#' @param x A named list containing either `<epidist>`, `function` or `NULL`.
-#' Named list elements are: `"contact_distribution"`, `"infectious_period"`,
-#' `"onset_to_hosp"`, `"onset_to_death"`, `"onset_to_recovery".`
+#' @param x A named list containing either `<epiparameter>`, `function` or
+#' `NULL`. Named list elements are: `"contact_distribution"`,
+#' `"infectious_period"`, `"onset_to_hosp"`, `"onset_to_death"`,
+#' `"onset_to_recovery".`
 #'
 #' @return A list of `function`s.
 #' @keywords internal
 as_function <- function(x) {
   stopifnot(
-    "Input delay distributions need to be either functions or <epidist>" =
-      inherits(x$contact_distribution, c("function", "epidist")) &&
-      inherits(x$infectious_period, c("function", "epidist")),
+    "Input delay distributions need to be either functions or <epiparameter>" =
+      inherits(x$contact_distribution, c("function", "epiparameter")) &&
+      inherits(x$infectious_period, c("function", "epiparameter")),
     "onset_to_hosp, onset_to_death and onset_to_recovery need to be a function,
-    <epidist> or NULL" =
-      (inherits(x$onset_to_hosp, c("function", "epidist")) ||
+    <epiparameter> or NULL" =
+      (inherits(x$onset_to_hosp, c("function", "epiparameter")) ||
       is.null(x$onset_to_hosp)) &&
-      (inherits(x$onset_to_death, c("function", "epidist")) ||
+      (inherits(x$onset_to_death, c("function", "epiparameter")) ||
       is.null(x$onset_to_death))
   )
   contact_distribution <- as.function(

README.Rmd

@@ -75,33 +75,33 @@ library(epiparameter)
 
 ```{r create-epidists}
 # create COVID-19 contact distribution
-contact_distribution <- epiparameter::epidist(
+contact_distribution <- epiparameter::epiparameter(
   disease = "COVID-19", 
   epi_dist = "contact distribution", 
   prob_distribution = "pois", 
   prob_distribution_params = c(mean = 2)
 )
 
 # create COVID-19 infectious period
-infectious_period <- epiparameter::epidist(
+infectious_period <- epiparameter::epiparameter(
   disease = "COVID-19",
   epi_dist = "infectious period",
   prob_distribution = "gamma",
   prob_distribution_params = c(shape = 1, scale = 1)
 )
 
 # get onset to hospital admission from {epiparameter} database
-onset_to_hosp <- epiparameter::epidist_db(
+onset_to_hosp <- epiparameter::epiparameter_db(
   disease = "COVID-19",
   epi_dist = "onset to hospitalisation",
-  single_epidist = TRUE
+  single_epiparameter = TRUE
 )
 
 # get onset to death from {epiparameter} database
-onset_to_death <- epiparameter::epidist_db(
+onset_to_death <- epiparameter::epiparameter_db(
   disease = "COVID-19",
   epi_dist = "onset to death",
-  single_epidist = TRUE
+  single_epiparameter = TRUE
 )
 ```
 

README.md

@@ -100,7 +100,7 @@ library(epiparameter)
 
 ``` r
 # create COVID-19 contact distribution
-contact_distribution <- epiparameter::epidist(
+contact_distribution <- epiparameter::epiparameter(
   disease = "COVID-19", 
   epi_dist = "contact distribution", 
   prob_distribution = "pois", 
@@ -109,7 +109,7 @@ contact_distribution <- epiparameter::epidist(
 #> Citation cannot be created as author, year, journal or title is missing
 
 # create COVID-19 infectious period
-infectious_period <- epiparameter::epidist(
+infectious_period <- epiparameter::epiparameter(
   disease = "COVID-19",
   epi_dist = "infectious period",
   prob_distribution = "gamma",
@@ -118,10 +118,10 @@ infectious_period <- epiparameter::epidist(
 #> Citation cannot be created as author, year, journal or title is missing
 
 # get onset to hospital admission from {epiparameter} database
-onset_to_hosp <- epiparameter::epidist_db(
+onset_to_hosp <- epiparameter::epiparameter_db(
   disease = "COVID-19",
   epi_dist = "onset to hospitalisation",
-  single_epidist = TRUE
+  single_epiparameter = TRUE
 )
 #> Using Linton N, Kobayashi T, Yang Y, Hayashi K, Akhmetzhanov A, Jung S, Yuan
 #> B, Kinoshita R, Nishiura H (2020). "Incubation Period and Other
@@ -132,10 +132,10 @@ onset_to_hosp <- epiparameter::epidist_db(
 #> To retrieve the citation use the 'get_citation' function
 
 # get onset to death from {epiparameter} database
-onset_to_death <- epiparameter::epidist_db(
+onset_to_death <- epiparameter::epiparameter_db(
   disease = "COVID-19",
   epi_dist = "onset to death",
-  single_epidist = TRUE
+  single_epiparameter = TRUE
 )
 #> Using Linton N, Kobayashi T, Yang Y, Hayashi K, Akhmetzhanov A, Jung S, Yuan
 #> B, Kinoshita R, Nishiura H (2020). "Incubation Period and Other