Merge pull request #363 from poissonconsulting/dev

- Combine `multi_ci = TRUE` and `weight = TRUE` into `ci_method = "weighted_samples"

NAMESPACE

@@ -95,6 +95,7 @@ export(ssd_hc)
 export(ssd_hc_bcanz)
 export(ssd_hc_burrlioz)
 export(ssd_hp)
+export(ssd_hp_bcanz)
 export(ssd_is_censored)
 export(ssd_match_moments)
 export(ssd_pal)

R/bcanz.R

@@ -51,13 +51,7 @@ ssd_dists_bcanz <- function(npars = c(2L, 5L)) {
 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
+                dists = dists
   )
 }
 
@@ -66,7 +60,7 @@ ssd_fit_bcanz <- function(data, left = "Conc", dists = ssd_dists_bcanz()) {
 #' Gets hazard concentrations with confidence intervals that protect
 #' 1, 5, 10 and 20% of species using settings adopted by
 #' BC, Canada, Australia and New Zealand for official guidelines.
-#' This function can take several minutes to run with required 10,000 iterations.
+#' This function can take several minutes to run with recommended 10,000 iterations.
 #'
 #' @inheritParams params
 #' @return A tibble of corresponding hazard concentrations.
@@ -76,15 +70,34 @@ ssd_fit_bcanz <- function(data, left = "Conc", dists = ssd_dists_bcanz()) {
 #' @examples
 #' fits <- ssd_fit_bcanz(ssddata::ccme_boron)
 #' ssd_hc_bcanz(fits, nboot = 100)
-ssd_hc_bcanz <- function(x, nboot = 10000, delta = 10, min_pboot = 0.95) {
+ssd_hc_bcanz <- function(x, nboot = 10000, 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
+         min_pboot = min_pboot
+  )
+}
+
+#' BCANZ Hazard Proportion
+#'
+#' Gets  proportion of species affected at specified concentration(s)
+#' using settings adopted by BC, Canada, Australia and New Zealand for official guidelines.
+#' This function can take several minutes to run with recommended 10,000 iterations.
+#'
+#' @inheritParams params
+#' @return A tibble of corresponding hazard concentrations.
+#' @seealso [`ssd_hp()`].
+#' @family BCANZ
+#' @export
+#' @examples
+#' fits <- ssd_fit_bcanz(ssddata::ccme_boron)
+#' ssd_hp_bcanz(fits, nboot = 100)
+ssd_hp_bcanz <- function(x, conc = 1, nboot = 10000, min_pboot = 0.95) {
+  ssd_hp(x,
+         conc = conc,
+         ci = TRUE,
+         nboot = nboot,
+         min_pboot = min_pboot
   )
 }

R/hc.R

@@ -123,8 +123,7 @@ ssd_hc.fitdists <- function(
     nboot = 1000,
     min_pboot = 0.95,
     multi_est = TRUE,
-    multi_ci = TRUE,
-    weighted = TRUE,
+    ci_method = "weighted_samples",
     parametric = TRUE, 
     delta = 9.21, 
     samples = FALSE,
@@ -146,6 +145,11 @@ ssd_hc.fitdists <- function(
   chk_vector(proportion)
   chk_numeric(proportion)
   chk_range(proportion)
+  chk_string(ci_method)
+  chk_subset(ci_method, c("weighted_samples", "weighted_arithmetic", "multi_free", "multi_fixed"))
+
+  fix_weights <- ci_method %in% c("weighted_samples", "multi_fixed")
+  multi_ci <- ci_method %in% c("multi_free", "multi_fixed")
 
   hcp <- ssd_hcp_fitdists(
     x = x, 
@@ -159,7 +163,7 @@ ssd_hc.fitdists <- function(
     min_pboot = min_pboot,
     parametric = parametric,
     multi_ci = multi_ci,
-    fix_weights = weighted,
+    fix_weights = fix_weights,
     control = control,
     samples = samples,
     save_to = save_to,

R/hp.R

@@ -42,8 +42,7 @@ ssd_hp.fitdists <- function(
     nboot = 1000,
     min_pboot = 0.95,
     multi_est = TRUE,
-    multi_ci = TRUE,
-    weighted = TRUE,
+    ci_method = "weighted_samples",
     parametric = TRUE, 
     delta = 9.21, 
     samples = FALSE,
@@ -54,7 +53,13 @@ ssd_hp.fitdists <- function(
 
   chk_vector(conc)
   chk_numeric(conc)
+  chk_subset(ci_method, c("weighted_samples", "weighted_arithmetic", "multi_free", "multi_fixed"))
+
   chk_unused(...)
+
+
+  fix_weights <- ci_method %in% c("weighted_samples", "multi_fixed")
+  multi_ci <- ci_method %in% c("multi_free", "multi_fixed")
 
   hcp <- ssd_hcp_fitdists(
     x = x, 
@@ -68,11 +73,11 @@ ssd_hp.fitdists <- function(
     min_pboot = min_pboot,
     parametric = parametric, 
     multi_ci = multi_ci, 
+    fix_weights = fix_weights,
     control = control, 
     save_to = save_to, 
     samples = samples, 
-    hc = FALSE,  
-    fix_weights = weighted,
+    hc = FALSE
   )
   hcp <- dplyr::rename(hcp, conc = "value")
   hcp

R/params.R

@@ -62,7 +62,8 @@
 #' @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 ci_method A string specifying which method to use for estimating the bootstrap values. 
+#' Possible values are "multi_free" and "multi_fixed" which treat the distributions as constituting a single distribution but differ in whether the model weights are fixed and "weighted_samples" and "weighted_arithmetic" take bootstrap samples from each distribution proportional to its weight versus calculating the weighted arithmetic means of the lower and upper confidence limits.
 #' @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.
 #' @param na.rm A flag specifying whether to silently remove missing values or 
 #' remove them with a warning.
@@ -105,10 +106,6 @@
 #' @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
-#' whether to take bootstrap samples from each distribution proportional to 
-#' its weight versus calculating the weighted arithmetic means of the lower 
-#' and upper confidence limits.
 #' @param x The object.
 #' @param xbreaks The x-axis breaks as one of:
 #'   - `NULL` for no breaks

R/predict.R

@@ -38,8 +38,7 @@ predict.fitdists <- function(
     nboot = 1000,
     min_pboot = 0.95,
     multi_est = TRUE,
-    multi_ci = TRUE,
-    weighted = TRUE,
+    ci_method = "weighted_samples",
     parametric = TRUE, 
     delta = 9.21, 
     control = NULL,
@@ -69,9 +68,7 @@ predict.fitdists <- function(
     average = average, 
     delta = delta, 
     parametric = parametric,
-    multi_ci = multi_ci, 
-    multi_est = multi_est,
-    weighted = weighted, 
+    ci_method = ci_method,
     control = control
   )
 }

_pkgdown.yml

@@ -3,14 +3,12 @@ template:
 authors:
   Joe Thorley:
     href: "https://github.com/joethorley"
-  Carl Schwarz:
-    href: "https://www.sfu.ca/stat-actsci/department/profiles/carl-schwarz.html"
-  David Fox:
-    href: "https://training.ecotox.science/who-we-are/"
   Rebecca Fisher:
     href: "https://www.aims.gov.au/about/our-people/dr-rebecca-fisher"
-  Angeline Tillmans:
-    href: "https://www.linkedin.com/in/angeline-tillmanns-5b7999a/"
+  David Fox:
+    href: "https://training.ecotox.science/who-we-are/"
+  Carl Schwarz:
+    href: "https://www.sfu.ca/stat-actsci/department/profiles/carl-schwarz.html"
   Province of British Columbia:
     href: "https://www2.gov.bc.ca/"
   Environment and Climate Change Canada:
@@ -21,55 +19,42 @@ authors:
 destination: docs
 
 reference:
-- title: Information
-  desc: Data frames of information
-  contents:
-  - '`boron_pred`'
-  - '`dist_data`'
 - title: Distribution Names
   desc: Functions that return character vectors of distribution names
   contents: 
   - '`ssd_dists`'
   - '`ssd_dists_all`'
   - '`ssd_dists_bcanz`'
-- title: Distributional Functions
-  desc: Distribution, quantile, random functions
-  contents: 
-  - '`ssd_p`'
-  - '`ssd_q`'
-  - '`ssd_r`'
-  - '`ssd_e`'
 - title: Fit
   desc: Functions that fit distributions to data
   contents: 
+  - '`ssd_fit_dists`'
   - '`ssd_fit_bcanz`'
   - '`ssd_fit_burrlioz`'
-  - '`ssd_fit_dists`'
+- title: Hazard Concentrations
+  desc: Functions that calculate hazard concentrations
+  contents:
+  - '`ssd_hc`'
+  - '`ssd_hc_bcanz`'
+  - '`ssd_wqg_bc`'
+  - '`ssd_wqg_burrlioz`'
+- title: Hazard Proportions
+  desc: Functions that calculate hazard proportions
+  contents:
+  - '`ssd_hp`'
+  - '`ssd_hp_bcanz`'
 - title: Manipulate Fits
   desc: Functions that manipulate fits of distributions
   contents:
   - '`augment.fitdists`'
   - '`coef.fitdists`'
   - '`estimates.fitdists`'
   - '`glance.fitdists`'
-  - '`is.fitdists`'
   - '`predict.fitburrlioz`'
   - '`predict.fitdists`'
-  - '`ssd_ecd`'
-  - '`ssd_ecd_data`'
-  - '`ssd_exposure`'
   - '`ssd_gof`'
-  - '`ssd_hp`'
-  - '`ssd_match_moments`'
   - '`subset.fitdists`'
   - '`tidy.fitdists`'
-- title: Hazard Concentrations
-  desc: Functions that calculate hazard concentrations
-  contents:
-  - '`ssd_hc`'
-  - '`ssd_hc_bcanz`'
-  - '`ssd_wqg_bc`'
-  - '`ssd_wqg_burrlioz`'
 - title: Plots
   desc: Functions to Generate Plots
   contents:
@@ -84,14 +69,29 @@ reference:
   - '`ssd_plot_cdf`'
   - '`ssd_plot_data`'
   - '`ssdtools-ggproto`'
+- title: Distributional Functions
+  desc: Distribution, quantile, random functions
+  contents: 
+  - '`ssd_p`'
+  - '`ssd_q`'
+  - '`ssd_r`'
+  - '`ssd_e`'
 - title: Miscellaneous
   desc: Miscellaneous functions and data
   contents:
+  - '`boron_pred`'
   - '`comma_signif`'
+  - '`dist_data`'
+  - '`is.fitdists`'
   - '`licensing_md`'
   - '`npars`'
   - '`ssd_data`'
+  - '`ssd_ecd`'
+  - '`ssd_ecd_data`'
+  - '`ssd_exposure`'
+  - '`ssd_fit_dists`'
   - '`ssd_is_censored`'
+  - '`ssd_match_moments`'
   - '`ssd_sort_data`'
   - '`pearson1000`'
 - title: Deprecated

data-raw/data-raw.R

@@ -36,5 +36,5 @@ use_data(dist_data, overwrite = TRUE)
 fits <- ssd_fit_dists(ssddata::ccme_boron)
 
 set.seed(99)
-boron_pred <- predict(fits, ci = TRUE, multi_ci = FALSE)
+boron_pred <- predict(fits, ci = TRUE, ci_method = "weighted bootstrap")
 use_data(boron_pred, overwrite = TRUE)