bcgov · joethorley · Jan 31, 2025 · Jan 31, 2025 · Jan 31, 2025 · Feb 19, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ssdtools
 Title: Species Sensitivity Distributions
-Version: 2.2.0.9000
+Version: 2.2.0.9002
 Authors@R: c(
     person("Joe", "Thorley", , "joe@poissonconsulting.ca", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7683-4592")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,21 @@
 <!-- NEWS.md is maintained by https://fledge.cynkra.com, contributors should not edit this file -->
 
+# ssdtools 2.2.0.9002
+
+- Added valid column to dist_data to indicate the "invpareto" has invalid likelihood.
+- Modified `ssd_fit_dists()` so fits distributions with invalid likelihoods in isolation.
+- Modified `ssd_hc()` and `ssd_hp()` so does not average if just one distribution.
+
+# ssdtools 2.2.0.9001
+
+- Update citations.
+
+
 # ssdtools 2.2.0.9000
 
 - House-keeping on Github actions.
 
+
 # ssdtools 2.2.0
 
 - Added `ssd_label_comma_hc()` function to label numbers with significant digits and comma and offset hazard concentration value if present in breaks.

diff --git a/R/augment.R b/R/augment.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/autoplot.R b/R/autoplot.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/bcanz.R b/R/bcanz.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/boot.R b/R/boot.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/burrlioz.R b/R/burrlioz.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/burrrIII3.R b/R/burrrIII3.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/censor.R b/R/censor.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,7 +16,7 @@
 #    limitations under the License.
 
 #' Censor Data
-#' 
+#'
 #' Censors data to a specified range based on the `censoring` argument.
 #' The function is useful for creating test data sets.
 #'
@@ -70,7 +70,7 @@ censor_data <- function(data, censoring) {
   if (!.is_censored(censoring)) {
     return(data)
   }
-  
+
   data$right[data$left < censoring[1]] <- min(censoring)
   data$left[data$left < censoring[1]] <- 0
   data$left[data$right > censoring[2]] <- max(censoring)

diff --git a/R/censored.R b/R/censored.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/chk.R b/R/chk.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/cis.R b/R/cis.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/coef.R b/R/coef.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/convergence.R b/R/convergence.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/d.R b/R/d.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/data.R b/R/data.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");
@@ -30,9 +30,9 @@
 #' @family boron
 #' @examples
 #' \dontrun{
-#'  fits <- ssd_fit_dists(ssddata::ccme_boron)
-#'  set.seed(99)
-#'  boron_pred <- predict(fits, ci = TRUE)
+#' fits <- ssd_fit_dists(ssddata::ccme_boron)
+#' set.seed(99)
+#' boron_pred <- predict(fits, ci = TRUE)
 #' }
 #' head(boron_pred)
 "boron_pred"
@@ -43,10 +43,10 @@
 #'
 #' \describe{
 #'   \item{dist}{The distribution (chr).}
-#'   \item{npars}{The number of parameters (int).}
-#'   \item{tails}{Whether the distribution has both tails (flag).}
-#'   \item{stable}{Whether the distribution is numerically stable (flag).}
 #'   \item{bcanz}{Whether the distribution belongs to the set of distributions approved by BC, Canada, Australia and New Zealand for official guidelines (flag).}
+#'   \item{tails}{Whether the distribution has both tails (flag).}
+#'   \item{npars}{The number of parameters (int).}
+#'   \item{valid}{Whether the distribution has a valid likelihood that allows it to be fit with other distributions for modeling averaging (flag).}
 #' }
 #' @family dists
 #' @examples

diff --git a/R/devtools-helpers.R b/R/devtools-helpers.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/dist.R b/R/dist.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/dists.R b/R/dists.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");
@@ -29,10 +29,11 @@
 #' ssd_dists(bcanz = TRUE)
 #' ssd_dists(tails = FALSE)
 #' ssd_dists(npars = 5)
-ssd_dists <- function(bcanz = NULL, tails = NULL, npars = 2:5) {
+ssd_dists <- function(bcanz = NULL, tails = NULL, npars = 2:5, valid = TRUE) {
   chk_null_or(bcanz, vld = vld_flag)
   chk_null_or(tails, vld = vld_flag)
-
+  chk_null_or(valid, vld = vld_flag)
+
   chk_whole_numeric(npars)
   chk_not_any_na(npars)
   chk_range(npars, c(2L, 5L))
@@ -44,23 +45,26 @@ ssd_dists <- function(bcanz = NULL, tails = NULL, npars = 2:5) {
   if (!is.null(tails)) {
     dists <- dists[dists$tails == tails, ]
   }
+  if (!is.null(valid)) {
+    dists <- dists[dists$valid == valid, ]
+  }
   dists <- dists[dists$npars %in% npars, ]
-
   dists$dist
 }
 
 #' All Species Sensitivity Distributions
 #'
 #' Gets a character vector of the names of all the available distributions.
-#'
+#' 
+#' @inheritParams params
 #' @return A unique, sorted character vector of the distributions.
 #' @family dists
 #' @export
 #'
 #' @examples
 #' ssd_dists_all()
-ssd_dists_all <- function() {
-  ssd_dists(bcanz = NULL, tails = NULL, npars = 2:5)
+ssd_dists_all <- function(valid = TRUE) {
+  ssd_dists(bcanz = NULL, tails = NULL, npars = 2:5, valid = valid)
 }
 
 #' All Shiny Species Sensitivity Distributions
@@ -75,5 +79,5 @@ ssd_dists_all <- function() {
 #' @examples
 #' ssd_dists_shiny()
 ssd_dists_shiny <- function() {
-  ssd_dists(bcanz = NULL, tails = TRUE, npars = 2:5)
+  ssd_dists(bcanz = NULL, tails = TRUE, npars = 2:5, valid = TRUE)
 }
diff --git a/R/estimates.R b/R/estimates.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/exposure.R b/R/exposure.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");
@@ -27,11 +27,11 @@
 #' @export
 #' @examples
 #' \dontrun{
-#'   fits <- ssd_fit_dists(ssddata::ccme_boron, dists = "lnorm")
-#'   set.seed(10)
-#'   ssd_exposure(fits)
-#'   ssd_exposure(fits, meanlog = 1)
-#'   ssd_exposure(fits, meanlog = 1, sdlog = 1)
+#' fits <- ssd_fit_dists(ssddata::ccme_boron, dists = "lnorm")
+#' set.seed(10)
+#' ssd_exposure(fits)
+#' ssd_exposure(fits, meanlog = 1)
+#' ssd_exposure(fits, meanlog = 1, sdlog = 1)
 #' }
 ssd_exposure <- function(x, meanlog = 0, sdlog = 1, nboot = 1000) {
   chk_number(meanlog)

diff --git a/R/fit-burrlioz.R b/R/fit-burrlioz.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/fit.R b/R/fit.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");
@@ -185,7 +185,10 @@ ssd_fit_dists <- function(
   chk_not_any_na(dists)
   chk_unique(dists)
 
-  chk_subset(dists, ssd_dists_all())
+  chk_subset(dists, ssd_dists_all(valid = NULL))
+  if(length(dists) > 1 && any(dists %in% ssd_dists_all(valid = FALSE))) {
+    err("distributions with invalid likelihoods must be fitted in isolation.")
+  }
 
   chk_whole_number(nrow)
   chk_gte(nrow, 4L)

diff --git a/R/gamma.R b/R/gamma.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/getters.R b/R/getters.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/ggplot.R b/R/ggplot.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");
@@ -33,7 +33,7 @@ ssd_pal <- function() {
 }
 
 #' Discrete color-blind scale for SSD Plots
-#' 
+#'
 #' The functions were designed for coloring different groups in a plot of SSD data.
 #'
 #' @param ... Arguments passed to [ggplot2::discrete_scale()].

diff --git a/R/ggproto.R b/R/ggproto.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/glance.R b/R/glance.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/R/gof.R b/R/gof.R
@@ -1,6 +1,6 @@
 # Copyright 2015-2023 Province of British Columbia
 # Copyright 2021 Environment and Climate Change Canada
-# Copyright 2023-2024 Australian Government Department of Climate Change, 
+# Copyright 2023-2024 Australian Government Department of Climate Change,
 # Energy, the Environment and Water
 #
 #    Licensed under the Apache License, Version 2.0 (the "License");