Merge pull request #362 from poissonconsulting/dev

- Add `npars` argument to `ssd_dists_bcanz()`.

R/bcanz.R

@@ -17,15 +17,23 @@
 #' Gets a character vector of the names of the distributions
 #' adopted by BC, Canada, Australia and New Zealand for official guidelines.
 #'
+#' @inheritParams params
 #' @return A unique, sorted character vector of the distributions.
 #' @seealso [`ssd_dists()`]
 #' @family dists BCANZ
 #' @export
 #'
 #' @examples
 #' ssd_dists_bcanz()
-ssd_dists_bcanz <- function() {
-  ssd_dists(bcanz = TRUE)
+#' ssd_dists_bcanz(npars = 2)
+ssd_dists_bcanz <- function(npars = c(2L, 5L)) {
+  chk_whole_numeric(npars)
+  chk_not_any_na(npars)
+  chk_unique(npars)
+  check_dim(npars, values = 1:2)
+  chk_subset(npars, c(2L, 5L))
+
+  ssd_dists(bcanz = TRUE, npars = npars)
 }
 
 #' Fit BCANZ Distributions
@@ -42,14 +50,14 @@ ssd_dists_bcanz <- function() {
 #' ssd_fit_bcanz(ssddata::ccme_boron)
 ssd_fit_bcanz <- function(data, left = "Conc", dists = ssd_dists_bcanz()) {
   ssd_fit_dists(data,
-    left = left,
-    dists = dists,
-    nrow = 6L,
-    rescale = FALSE,
-    reweight = FALSE,
-    computable = TRUE,
-    at_boundary_ok = FALSE,
-    min_pmix = 0
+                left = left,
+                dists = dists,
+                nrow = 6L,
+                rescale = FALSE,
+                reweight = FALSE,
+                computable = TRUE,
+                at_boundary_ok = FALSE,
+                min_pmix = 0
   )
 }
 
@@ -70,13 +78,13 @@ ssd_fit_bcanz <- function(data, left = "Conc", dists = ssd_dists_bcanz()) {
 #' ssd_hc_bcanz(fits, nboot = 100)
 ssd_hc_bcanz <- function(x, nboot = 10000, delta = 10, min_pboot = 0.95) {
   ssd_hc(x,
-    proportion = c(0.01, 0.05, 0.1, 0.2),
-    ci = TRUE,
-    level = 0.95,
-    nboot = nboot,
-    average = TRUE,
-    delta = delta,
-    min_pboot = min_pboot,
-    parametric = TRUE
+         proportion = c(0.01, 0.05, 0.1, 0.2),
+         ci = TRUE,
+         level = 0.95,
+         nboot = nboot,
+         average = TRUE,
+         delta = delta,
+         min_pboot = min_pboot,
+         parametric = TRUE
   )
 }

R/dists.R

@@ -16,9 +16,7 @@
 #'
 #' Gets a character vector of the names of the available distributions.
 #'
-#' @param bcanz A flag or NULL specifying whether to only include distributions in the set that is approved by BC, Canada, Australia and New Zealand for official guidelines.
-#' @param tails A flag or NULL specifying whether to only include distributions with both tails.
-#' @param npars A whole numeric vector specifying which distributions to include based on the number of parameters.
+#' @inheritParams params
 #' @return A unique, sorted character vector of the distributions.
 #' @family dists
 #' @export
@@ -31,11 +29,11 @@
 ssd_dists <- function(bcanz = NULL, tails = NULL, npars = 2:5) {
   chk_null_or(bcanz, vld = vld_flag)
   chk_null_or(tails, vld = vld_flag)
-
+  
   chk_whole_numeric(npars)
   chk_not_any_na(npars)
   chk_range(npars, c(2L, 5L))
-
+  
   dists <- ssdtools::dist_data
   if (!is.null(bcanz)) {
     dists <- dists[dists$bcanz == bcanz, ]
@@ -44,7 +42,7 @@ ssd_dists <- function(bcanz = NULL, tails = NULL, npars = 2:5) {
     dists <- dists[dists$tails == tails, ]
   }
   dists <- dists[dists$npars %in% npars, ]
-
+  
   dists$dist
 }
 

R/params.R

@@ -19,6 +19,7 @@
 #' @param at_boundary_ok A flag specifying whether a model with one or more
 #' parameters at the boundary should be considered to have converged (default = FALSE).
 #' @param average A flag specifying whether to provide model averaged values as opposed to a value for each distribution.
+#' @param bcanz A flag or NULL specifying whether to only include distributions in the set that is approved by BC, Canada, Australia and New Zealand for official guidelines. 
 #' @param breaks A character vector
 #' @param bounds A named non-negative numeric vector of the left and right bounds for
 #' uncensored missing (0 and Inf) data in terms of the orders of magnitude
@@ -59,6 +60,7 @@
 #' proportion of bootstrap samples that must successfully fit (return a likelihood) 
 #' to report the confidence intervals.
 #' @param min_pmix A number between 0 and 0.5 specifying the minimum proportion in mixture models.
+#' @param npars A whole numeric vector specifying which distributions to include based on the number of parameters.
 #' @param all_estimates A flag specifying whether to calculate estimates for all implemented distributions.
 #' @param multi_ci A flag specifying whether to treat the distributions as constituting a single distribution which is now the recommended approach (as opposed to taking the mean) when calculating model averaged confidence intervals.
 #' @param multi_est A flag specifying whether to treat the distributions as constituting a single distribution (as opposed to taking the mean) when calculating model averaged estimates.
@@ -100,6 +102,7 @@
 #' @param shift_x The value to multiply the label x values by (after adding `add_x`).
 #' @param silent A flag indicating whether fits should fail silently.
 #' @param size A number for the size of the labels.
+#' @param tails A flag or NULL specifying whether to only include distributions with both tails.
 #' @param trans A string which transformation to use by default `"log10"`.
 #' @param weight A string of the numeric column in data with positive weights less than or equal to 1,000 or NULL.
 #' @param weighted A flag which specifies whether to use the original model weights (as opposed to re-estimating for each bootstrap sample) unless `multi_ci = FALSE` in which case it specifies

tests/testthat/test-dists.R

@@ -39,5 +39,6 @@ test_that("dists 5 pars", {
 })
 
 test_that("dists bcanz", {
-  expect_identical(ssd_dists(bcanz = TRUE), ssd_dists_bcanz())
+  expect_identical(ssd_dists_bcanz(), ssd_dists(bcanz = TRUE))
+  expect_identical(ssd_dists_bcanz(npars = 2L), c("gamma", "lgumbel", "llogis", "lnorm", "weibull"))
 })