removed possible_epidist_params() and added info to epidist() doc

NAMESPACE

@@ -74,7 +74,6 @@ export(lnorm_meanlogsdlog2meansd)
 export(lnorm_meansd2meanlogsdlog)
 export(nbinom_meandisp2probdisp)
 export(nbinom_probdisp2meandisp)
-export(possible_epidist_params)
 export(validate_epidist)
 export(validate_vb_epidist)
 export(vb_epidist)

R/check_epidist.R

@@ -19,7 +19,7 @@ check_epidist_params <- function(prob_dist, prob_dist_params) {
 
   stopifnot(
     "distribution parameters must have valid names,
-       use possible_epidist_params() to see valid names" =
+       see epidist() documentation for valid names" =
       is_epidist_params(prob_dist_params)
   )
 

R/epidist.R

@@ -135,6 +135,14 @@ new_epidist <- function(disease = list(),
 #' pipelines. This is where the `epidist()` function can be used to fill out
 #' each field for which information is known.
 #'
+#' @details Accepted `<epidist>` distribution parameterisations are:
+#' - Gamma must be either 'shape' and 'scale' or 'shape' and 'rate'
+#' - Weibull must be 'shape' and 'scale'
+#' - Lognormal must be 'mealog' and 'sdlog' or 'mu' and 'sigma'
+#' - Negative Binomial must be either 'mean' and 'dispersion' or 'n' and 'p'
+#' - Geometric must be either 'mean' or 'prob'
+#' - Poisson must be 'mean'
+#'
 #' @param disease A character string with name of the infectious disease.
 #' @param pathogen A character string with the name of the causative agent of
 #' disease, or NULL if not known.

R/epidist_utils.R

@@ -519,27 +519,6 @@ is_epidist_params <- function(prob_dist_params) {
   is_valid_params
 }
 
-#' Print accepted distribution parameters
-#'
-#' Helper function that prints the distribution parameters accepted by
-#' `epiparameter`
-#'
-#' @return Nothing, prints to console
-#' @export
-#'
-#' @examples
-#' possible_epidist_params()
-possible_epidist_params <- function() {
-  cat(
-    "Gamma or Weibull must be either 'shape' and 'scale' or 'shape' and 'rate'",
-    "Lognormal must be 'mealog' and 'sdlog' or 'mu' and 'sigma'",
-    "Negative Binomial must be 'mean' and 'dispersion'",
-    "Poisson must be 'mean'",
-    "Geometric must be 'prob'",
-    sep = "\n"
-  )
-}
-
 clean_epidist_params <- function(prob_dist_params, ...) {
   UseMethod("clean_epidist_params")
 }

_pkgdown.yml

@@ -109,11 +109,6 @@ reference:
     - clean_disease
     - clean_epidist_name
 
-  - title: Check valid parameterisation
-    desc: Check parameters are valid for `<epidist>`
-    contents:
-    - possible_epidist_params
-
   - title: Utility function
     contents:
     - calc_disc_dist_quantile

tests/testthat/test-epidist_utils.R

@@ -24,10 +24,6 @@ test_that("create_epidist_citation works with PMID", {
   )
 })
 
-test_that("possible_epidist_params works as expected", {
-  expect_output(possible_epidist_params())
-})
-
 test_that("clean_epidist_params fails when gamma parameters are incorrect", {
   gamma_params <- c(meanlog = 1, sdlog = 1)
   class(gamma_params) <- "gamma"