update variable names used in documentation

R/accessors.R

@@ -27,12 +27,12 @@ get_parameters <- function(x, ...) {
 #' @export
 #'
 #' @examples
-#' edist <- epiparameter_db(
+#' ep <- epiparameter_db(
 #'   disease = "COVID-19",
 #'   epi_dist = "serial interval",
 #'   single_epiparameter = TRUE
 #' )
-#' get_parameters(edist)
+#' get_parameters(ep)
 get_parameters.epiparameter <- function(x, ...) {
   chkDots(...)
   # extract parameters depending on prob distribution class
@@ -88,12 +88,12 @@ get_citation <- function(x, ...) {
 #'
 #' @examples
 #' # example with <epiparameter>
-#' edist <- epiparameter_db(single_epiparameter = TRUE)
-#' get_citation(edist)
+#' ep <- epiparameter_db(single_epiparameter = TRUE)
+#' get_citation(ep)
 #'
 #' # example returning bibtex format
-#' edist <- epiparameter_db(disease = "COVID-19", single_epiparameter = TRUE)
-#' cit <- get_citation(edist)
+#' ep <- epiparameter_db(disease = "COVID-19", single_epiparameter = TRUE)
+#' cit <- get_citation(ep)
 #' format(cit, style = "bibtex")
 get_citation.epiparameter <- function(x, ...) {
   chkDots(...)
@@ -119,8 +119,8 @@ get_citation.epiparameter <- function(x, ...) {
 #'
 #' @examples
 #' # example with list of <epiparameter>
-#' edist <- epiparameter_db()
-#' get_citation(edist)
+#' db <- epiparameter_db()
+#' get_citation(db)
 get_citation.multi_epiparameter <- function(x, ...) {
   chkDots(...)
   # dispatches to get_citation.epiparameter method

R/checkers.R

@@ -13,24 +13,24 @@
 #'
 #' @examples
 #' # parameterised <epiparameter>
-#' edist <- 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 <epiparameter>
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation"
 #' )
-#' is_parameterised(edist)
+#' is_parameterised(ep)
 #'
 #' # list of <epiparameter>
-#' edist <- epiparameter_db()
-#' is_parameterised(edist)
+#' db <- epiparameter_db()
+#' is_parameterised(db)
 is_parameterised <- function(x, ...) {
   UseMethod("is_parameterised")
 }

R/epiparameter.R

@@ -457,23 +457,23 @@ format.epiparameter <- function(x, ...) {
 #' @export
 #'
 #' @examples
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "serial_interval",
 #'   prob_distribution = "gamma",
 #'   prob_distribution_params = c(shape = 1, scale = 1)
 #' )
 #'
-#' is_epiparameter(edist)
+#' is_epiparameter(ep)
 #'
-#' false_edist <- list(
+#' false_ep <- list(
 #'   disease = "ebola",
 #'   epi_dist = "serial_interval",
 #'   prob_distribution = "gamma",
 #'   prob_distribution_params = c(shape = 1, scale = 1)
 #' )
 #'
-#' is_epiparameter(false_edist)
+#' is_epiparameter(false_ep)
 is_epiparameter <- function(x) {
   inherits(x, "epiparameter")
 }
@@ -501,18 +501,18 @@ is_epiparameter <- function(x) {
 #' @keywords epiparameter_distribution_functions
 #'
 #' @examples
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation_period",
 #'   prob_distribution = "gamma",
 #'   prob_distribution_params = c(shape = 1, scale = 1)
 #' )
 #'
 #' # example of each distribution method for an `epiparameter` object
-#' stats::density(edist, at = 1)
-#' distributional::cdf(edist, q = 1)
-#' stats::quantile(edist, p = 0.2)
-#' distributional::generate(edist, times = 10)
+#' stats::density(ep, at = 1)
+#' distributional::cdf(ep, q = 1)
+#' stats::quantile(ep, p = 0.2)
+#' distributional::generate(ep, times = 10)
 NULL
 
 #' @rdname epiparameter_distribution_functions
@@ -704,23 +704,23 @@ discretise.default <- function(x, ...) {
 #'
 #' @examples
 #' # example with continuous distribution
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation_period",
 #'   prob_distribution = "gamma",
 #'   prob_distribution_params = c(shape = 1, scale = 1)
 #' )
-#' family(edist)
+#' family(ep)
 #'
 #' # example with discretised distribution
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation_period",
 #'   prob_distribution = "lnorm",
 #'   prob_distribution_params = c(meanlog = 1, sdlog = 1),
 #'   discretise = TRUE
 #' )
-#' family(edist)
+#' family(ep)
 family.epiparameter <- function(object, ...) {
   if (inherits(object$prob_dist, "distcrete")) {
     prob_dist <- object$prob_dist$name
@@ -769,22 +769,22 @@ family.epiparameter <- function(object, ...) {
 #' @export
 #'
 #' @examples
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation_period",
 #'   prob_distribution = "lnorm",
 #'   prob_distribution_params = c(meanlog = 1, sdlog = 1)
 #' )
-#' is_truncated(edist)
+#' is_truncated(ep)
 #'
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation_period",
 #'   prob_distribution = "lnorm",
 #'   prob_distribution_params = c(meanlog = 1, sdlog = 1),
 #'   truncation = 10
 #' )
-#' is_truncated(edist)
+#' is_truncated(ep)
 is_truncated <- function(x) {
   stopifnot(
     "is_truncated only works for `<epiparameter> objects`" =
@@ -824,22 +824,22 @@ is_truncated <- function(x) {
 #' @export
 #'
 #' @examples
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation_period",
 #'   prob_distribution = "lnorm",
 #'   prob_distribution_params = c(meanlog = 1, sdlog = 1)
 #' )
-#' is_continuous(edist)
-#' is_continuous(discretise(edist))
+#' is_continuous(ep)
+#' is_continuous(discretise(ep))
 #'
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "offspring distribution",
 #'   prob_distribution = "nbinom",
 #'   prob_distribution_params = c(mean = 2, dispersion = 0.5)
 #' )
-#' is_continuous(edist)
+#' is_continuous(ep)
 is_continuous <- function(x) {
   stopifnot(
     "is_truncated only works for `<epiparameter> objects`" =
@@ -858,12 +858,12 @@ is_continuous <- function(x) {
 #' @export
 #'
 #' @examples
-#' edist <- epiparameter_db(
+#' ep <- epiparameter_db(
 #'   disease = "COVID-19",
 #'   epi_dist = "incubation period",
 #'   single_epiparameter = TRUE
 #' )
-#' mean(edist)
+#' mean(ep)
 mean.epiparameter <- function(x, ...) {
   chkDots(...)
   # extract mean if given

R/plot.R

@@ -23,23 +23,23 @@
 #'
 #' @examples
 #' # plot continuous epiparameter
-#' edist <- epiparameter(
+#' ep <- epiparameter(
 #'   disease = "ebola",
 #'   epi_dist = "incubation_period",
 #'   prob_distribution = "gamma",
 #'   prob_distribution_params = c(shape = 2, scale = 1)
 #' )
-#' plot(edist)
+#' plot(ep)
 #'
 #' # plot different day range (x-axis)
-#' plot(edist, xlim = c(0, 10))
+#' plot(ep, xlim = c(0, 10))
 #'
 #' # plot CDF
-#' plot(edist, cumulative = TRUE)
+#' plot(ep, cumulative = TRUE)
 #'
 #' # plot discrete epiparameter
-#' edist <- discretise(edist)
-#' plot(edist)
+#' ep <- discretise(ep)
+#' plot(ep)
 plot.epiparameter <- function(x,
                               cumulative = FALSE,
                               ...) {