Rename <epidist> with <epiparameter>

DESCRIPTION

@@ -30,6 +30,7 @@ Imports:
     distcrete,
     distributional,
     graphics,
+    lifecycle,
     pillar,
     rlang,
     stats,
@@ -53,4 +54,4 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1,62 +1,64 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(as.data.frame,epidist)
-S3method(as.data.frame,multi_epidist)
-S3method(as.function,epidist)
-S3method(as_epidist,data.frame)
-S3method(cdf,epidist)
+S3method(as.data.frame,epiparameter)
+S3method(as.data.frame,multi_epiparameter)
+S3method(as.function,epiparameter)
+S3method(as_epiparameter,data.frame)
+S3method(cdf,epiparameter)
 S3method(convert_params_to_summary_stats,character)
-S3method(convert_params_to_summary_stats,epidist)
+S3method(convert_params_to_summary_stats,epiparameter)
 S3method(convert_summary_stats_to_params,character)
-S3method(convert_summary_stats_to_params,epidist)
-S3method(density,epidist)
+S3method(convert_summary_stats_to_params,epiparameter)
+S3method(density,epiparameter)
 S3method(discretise,default)
-S3method(discretise,epidist)
-S3method(family,epidist)
-S3method(format,epidist)
-S3method(generate,epidist)
-S3method(get_citation,epidist)
-S3method(get_citation,multi_epidist)
-S3method(get_parameters,epidist)
-S3method(is_parameterised,epidist)
-S3method(is_parameterised,multi_epidist)
-S3method(mean,epidist)
-S3method(plot,epidist)
-S3method(print,epidist)
-S3method(print,multi_epidist)
+S3method(discretise,epiparameter)
+S3method(family,epiparameter)
+S3method(format,epiparameter)
+S3method(generate,epiparameter)
+S3method(get_citation,epiparameter)
+S3method(get_citation,multi_epiparameter)
+S3method(get_parameters,epiparameter)
+S3method(is_parameterised,epiparameter)
+S3method(is_parameterised,multi_epiparameter)
+S3method(mean,epiparameter)
+S3method(plot,epiparameter)
+S3method(print,epiparameter)
+S3method(print,multi_epiparameter)
 S3method(print,parameter_tbl)
-S3method(quantile,epidist)
+S3method(quantile,epiparameter)
 S3method(tbl_sum,p_tbl)
-export(as_epidist)
+export(as_epiparameter)
 export(calc_disc_dist_quantile)
 export(cdf)
 export(convert_params_to_summary_stats)
 export(convert_summary_stats_to_params)
-export(create_epidist_citation)
-export(create_epidist_metadata)
-export(create_epidist_method_assess)
-export(create_epidist_prob_dist)
-export(create_epidist_region)
-export(create_epidist_summary_stats)
-export(create_epidist_uncertainty)
+export(create_citation)
+export(create_metadata)
+export(create_method_assess)
+export(create_prob_dist)
+export(create_region)
+export(create_summary_stats)
+export(create_uncertainty)
 export(discretise)
 export(discretize)
-export(epidist)
 export(epidist_db)
+export(epiparameter)
+export(epiparameter_db)
 export(extract_param)
 export(generate)
 export(get_citation)
 export(get_parameters)
 export(is_continuous)
-export(is_epidist)
-export(is_epidist_params)
+export(is_epiparameter)
+export(is_epiparameter_params)
 export(is_parameterised)
 export(is_parameterized)
 export(is_truncated)
 export(parameter_tbl)
-export(validate_epidist)
+export(validate_epiparameter)
 importFrom(distributional,cdf)
 importFrom(distributional,generate)
+importFrom(lifecycle,deprecated)
 importFrom(pillar,tbl_sum)
 importFrom(stats,density)
 importFrom(stats,family)

R/accessors.R

@@ -10,29 +10,30 @@ get_parameters <- function(x, ...) {
   UseMethod("get_parameters")
 }
 
-#' Get parameters from an `<epidist>` object
+#' Get parameters from an `<epiparameter>` object
 #'
-#' Extract the parameters of the distribution stored in an `<epidist>` object.
+#' Extract the parameters of the distribution stored in an `<epiparameter>`
+#' object.
 #'
-#' @details The `<epidist>` object can be unparameterised in which it lacks
+#' @details The `<epiparameter>` object can be unparameterised in which it lacks
 #' a probability distribution or parameters of a probability distribution,
-#' in this case the `get_parameters.epidist()` method will return `NA`.
+#' in this case the `get_parameters.epiparameter()` method will return `NA`.
 #'
-#' @inheritParams print.epidist
+#' @inheritParams print.epiparameter
 #' @param ... [dots] Not used, extra arguments supplied will cause a warning.
 #'
-#' @return A named vector of parameters or `NA` when the `<epidist>` object is
-#' unparameterised.
+#' @return A named vector of parameters or `NA` when the `<epiparameter>`
+#' object is unparameterised.
 #' @export
 #'
 #' @examples
-#' edist <- epidist_db(
+#' ep <- epiparameter_db(
 #'   disease = "COVID-19",
 #'   epi_dist = "serial interval",
-#'   single_epidist = TRUE
+#'   single_epiparameter = TRUE
 #' )
-#' get_parameters(edist)
-get_parameters.epidist <- function(x, ...) {
+#' get_parameters(ep)
+get_parameters.epiparameter <- function(x, ...) {
   chkDots(...)
   # extract parameters depending on prob distribution class
   if (inherits(x$prob_dist, "distcrete")) {
@@ -51,7 +52,7 @@ get_parameters.epidist <- function(x, ...) {
     }
 
     # convert to meanlog and sdlog names
-    params <- .clean_epidist_params(
+    params <- .clean_params(
       prob_dist = family(x),
       prob_dist_params = params
     )
@@ -75,26 +76,26 @@ get_citation <- function(x, ...) {
   UseMethod("get_citation")
 }
 
-#' Get citation from an `<epidist>` object
+#' Get citation from an `<epiparameter>` object
 #'
-#' Extract the citation stored in an `<epidist>` object.
+#' Extract the citation stored in an `<epiparameter>` object.
 #'
-#' @inheritParams print.epidist
+#' @inheritParams print.epiparameter
 #' @param ... [dots] Not used, extra arguments supplied will cause a warning.
 #'
 #' @return A `<bibentry>` object.
 #' @export
 #'
 #' @examples
-#' # example with <epidist>
-#' edist <- epidist_db(single_epidist = TRUE)
-#' get_citation(edist)
+#' # example with <epiparameter>
+#' ep <- epiparameter_db(single_epiparameter = TRUE)
+#' get_citation(ep)
 #'
 #' # example returning bibtex format
-#' edist <- epidist_db(disease = "COVID-19", single_epidist = TRUE)
-#' cit <- get_citation(edist)
+#' ep <- epiparameter_db(disease = "COVID-19", single_epiparameter = TRUE)
+#' cit <- get_citation(ep)
 #' format(cit, style = "bibtex")
-get_citation.epidist <- function(x, ...) {
+get_citation.epiparameter <- function(x, ...) {
   chkDots(...)
   if (!inherits(x$citation, "bibentry")) {
     stop("Citation should be a <bibentry>", call. = FALSE)
@@ -104,25 +105,25 @@ get_citation.epidist <- function(x, ...) {
   x$citation
 }
 
-#' Get citation from a list of `<epidist>` objects
+#' Get citation from a list of `<epiparameter>` objects
 #'
-#' Extract the citation stored in a list of `<epidist>` objects.
+#' Extract the citation stored in a list of `<epiparameter>` objects.
 #'
-#' @inheritParams print.epidist
+#' @inheritParams print.epiparameter
 #' @param ... [dots] Not used, extra arguments supplied will cause a warning.
 #'
 #' @return A `<bibentry>` object containing multiple references. The length of
-#' output `<bibentry>` is equal to the length of the list of `<epidist>`
+#' output `<bibentry>` is equal to the length of the list of `<epiparameter>`
 #' objects supplied.
 #' @export
 #'
 #' @examples
-#' # example with list of <epidist>
-#' edist <- epidist_db()
-#' get_citation(edist)
-get_citation.multi_epidist <- function(x, ...) {
+#' # example with list of <epiparameter>
+#' db <- epiparameter_db()
+#' get_citation(db)
+get_citation.multi_epiparameter <- function(x, ...) {
   chkDots(...)
-  # dispatches to get_citation.epidist method
+  # dispatches to get_citation.epiparameter method
   citation_list <- lapply(x, get_citation)
   # dispatches to c.bibentry method
   multi_bibentry <- Reduce(f = c, x = citation_list)

R/calc_dist_params.R

@@ -22,8 +22,8 @@
 #' provided the lowest value is used for the calculation.
 #' 3. The last method is the extraction using a median and range of the data.
 #'
-#' @inheritParams new_epidist
-#' @inheritParams epidist
+#' @inheritParams new_epiparameter
+#' @inheritParams epiparameter
 #' @param sample_size The sample size of the data. Only needed when falling back
 #' on using the median-range extraction calculation.
 #'

R/checkers.R

@@ -1,35 +1,36 @@
-#' Check if `<epidist>` or list of `<epidist>` objects contains a distribution
-#' and distribution parameters
+#' Check if `<epiparameter>` or list of `<epiparameter>` objects contains a
+#' distribution and distribution parameters
 #'
-#' @param x An `<epidist>` or list of `<epidist>` objects.
+#' @param x An `<epiparameter>` or list of `<epiparameter>` objects.
 #' @param ... [dots] Extra arguments to be passed to the method.
 #'
-#' @return A single boolean `logical` for `<epidist>` or vector of `logical`s
-#' equal in length to the list of `<epidist>` objects input. If the `<epidist>`
-#' object is missing either a probability distribution or parameters for
-#' the probability distribution returns `FALSE`, otherwise it returns `TRUE`.
+#' @return A single boolean `logical` for `<epiparameter>` or vector of
+#' `logical`s equal in length to the list of `<epiparameter>` objects input.
+#' If the `<epiparameter>` object is missing either a probability distribution
+#' or parameters for the probability distribution returns `FALSE`, otherwise it
+#' returns `TRUE`.
 #' @export
 #'
 #' @examples
-#' # parameterised <epidist>
-#' edist <- epidist(
+#' # parameterised <epiparameter>
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation",
 #'   prob_distribution = "gamma",
 #'   prob_distribution_params = c(shape = 1, scale = 1)
 #' )
-#' is_parameterised(edist)
+#' is_parameterised(ep)
 #'
-#' # unparameterised <epidist>
-#' edist <- epidist(
+#' # unparameterised <epiparameter>
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation"
 #' )
-#' is_parameterised(edist)
+#' is_parameterised(ep)
 #'
-#' # list of <epidist>
-#' edist <- epidist_db()
-#' is_parameterised(edist)
+#' # list of <epiparameter>
+#' db <- epiparameter_db()
+#' is_parameterised(db)
 is_parameterised <- function(x, ...) {
   UseMethod("is_parameterised")
 }
@@ -39,14 +40,14 @@ is_parameterised <- function(x, ...) {
 is_parameterized <- is_parameterised
 
 #' @export
-is_parameterised.epidist <- function(x, ...) {
+is_parameterised.epiparameter <- function(x, ...) {
   chkDots(...)
   # probability distribution object
   return(is.object(x$prob_dist))
 }
 
 #' @export
-is_parameterised.multi_epidist <- function(x, ...) {
+is_parameterised.multi_epiparameter <- function(x, ...) {
   chkDots(...)
 
   # return logical vector