Merge branch 'master' into export-helpers

NEWS.md

@@ -2,8 +2,17 @@
 
 ### Enhancements
 
-* Add `pareto_smooth` option to `weight_draws`, to Pareto smooth
+* Add `exclude` option to `subset_draws()`, which can be used to exclude
+  the matched selection.
+* Add `are_log_weights` option to `pareto_smooth()`, which is necessary
+  for correct Pareto smoothing computation if the input vector
+  consists of log weights.
+* Add `pareto_smooth` option to `weight_draws()`, to Pareto smooth
   weights before adding to a draws object.
+* Add individual Pareto diagnostic functions (`pareto_khat()`,
+  `pareto_khat_threshold()`, `pareto_min_ss()`, `pareto_convergence_rate()`)
+* `thin_draws()` now automatically thins draws based on ESS by default,
+  and non-integer thinning is possible.
 * Matrix multiplication of `rvar`s can now be done with the base matrix 
   multiplication operator (`%*%`) instead of `%**%` in R >= 4.3.
 * `variables()`, `variables<-()`, `set_variables()`, and `nvariables()` now

R/pareto_smooth.R

@@ -250,7 +250,7 @@ pareto_smooth.rvar <- function(x, return_k = FALSE, extra_diags = FALSE, ...) {
 #' @export
 pareto_smooth.default <- function(x,
                                   tail = c("both", "right", "left"),
-                                  r_eff = 1,
+                                  r_eff = NULL,
                                   ndraws_tail = NULL,
                                   return_k = FALSE,
                                   extra_diags = FALSE,

R/rvar-.R

@@ -800,6 +800,13 @@ drop_chain_dim <- function(x) {
 #' (first one is draws), etc.
 #' @noRd
 cleanup_rvar_draws <- function(x) {
+  assert(
+    check_numeric(x),
+    check_logical(x),
+    check_factor(x),
+    check_character(x)
+  )
+
   if (length(x) == 0) {
     # canonical NULL rvar is at least 1 draw of nothing
     # this ensures that (e.g.) extending a null rvar

man-roxygen/args-pareto.R

@@ -15,7 +15,7 @@
 #'   al. (2024)).
 #' @param r_eff (numeric) relative effective sample size estimate. If
 #'   `r_eff` is NULL, it will be calculated assuming the draws are
-#'   from MCMC. Default is 1.
+#'   from MCMC. Default is NULL.
 #' @param verbose (logical) Should diagnostic messages be printed? If
 #'   `TRUE`, messages related to Pareto diagnostics will be
 #'   printed. Default is `FALSE`.