minor edits

Author: jgabry

R/fit.R

@@ -858,8 +858,10 @@ CmdStanMCMC <- R6::R6Class(
       } else {
         if (self$runset$args$validate_csv) {
           fixed_param <- runset$args$method_args$fixed_param
-          private$read_csv_(variables = "",
-                           sampler_diagnostics = if (!fixed_param) c("treedepth__", "divergent__", "energy__") else "")
+          private$read_csv_(
+            variables = "",
+            sampler_diagnostics = if (!fixed_param) c("treedepth__", "divergent__", "energy__") else ""
+          )
           if (!fixed_param) {
             check_divergences(private$sampler_diagnostics_)
             check_sampler_transitions_treedepth(private$sampler_diagnostics_, private$metadata_)

R/utils.R

@@ -282,9 +282,9 @@ ebfmi <- function(post_warmup_sampler_diagnostics) {
   efbmi_val <- NULL
   if (!is.null(post_warmup_sampler_diagnostics)) {
     if (!("energy__" %in% posterior::variables(post_warmup_sampler_diagnostics))) {
-      warning("E-BFMI not computed as the 'energy__' diagnostic could not be located.", call. = FALSE)
+      warning("E-BFMI not computed because the 'energy__' diagnostic could not be located.", call. = FALSE)
     } else if (posterior::niterations(post_warmup_sampler_diagnostics) < 3) {
-      warning("E-BFMI is undefined for posterior chains of length less than 3.", call. = FALSE)
+      warning("E-BFMI not computed because it is undefined for posterior chains of length less than 3.", call. = FALSE)
     } else {
       energy <- posterior::extract_variable_matrix(post_warmup_sampler_diagnostics, "energy__")
       if (any(is.na(energy))) {
@@ -302,9 +302,12 @@ ebfmi <- function(post_warmup_sampler_diagnostics) {
 check_ebfmi <- function(post_warmup_sampler_diagnostics, threshold = 0.2) {
   efbmi_val <- ebfmi(post_warmup_sampler_diagnostics)
   if (any(efbmi_val < threshold)) {
-    message(paste0(sum(efbmi_val < threshold), " of ", length(efbmi_val), " chains had energy-based Bayesian fraction ",
-    "of missing information (E-BFMI) less than ", threshold, ", which may indicate poor exploration of the ", 
-    "posterior."))
+    message(
+      "Warning: ", sum(efbmi_val < threshold), " of ", length(efbmi_val),
+      " chains had energy-based Bayesian fraction of missing information (E-BFMI)",
+      " less than ", threshold, ".",
+      "\nThis may indicate poor exploration of the posterior."
+    )
   }
   invisible(NULL)
 }

tests/testthat/test-utils.R

@@ -190,12 +190,12 @@ test_that("check_ebfmi and computing ebfmi works", {
   expect_equal(as.numeric(ebfmi(posterior::as_draws_list(energy_df))), check_val)
   expect_equal(as.numeric(ebfmi(posterior::as_draws_matrix(energy_df))), check_val)
   energy_df <- posterior::as_draws(data.frame("energy__" = 0))
-  expect_warning(check_ebfmi(energy_df), "E-BFMI is undefined for posterior chains of length less than 3.")
-  expect_warning(ebfmi(energy_df), "E-BFMI is undefined for posterior chains of length less than 3.")
+  expect_warning(check_ebfmi(energy_df), "E-BFMI not computed because it is undefined for posterior chains of length less than 3.")
+  expect_warning(ebfmi(energy_df), "E-BFMI not computed because it is undefined for posterior chains of length less than 3.")
 
   energy_df <- posterior::as_draws(data.frame("somethingelse" = 0))
-  expect_warning(check_ebfmi(energy_df), "E-BFMI not computed as the 'energy__' diagnostic could not be located.")
-  expect_warning(ebfmi(energy_df), "E-BFMI not computed as the 'energy__' diagnostic could not be located.")
+  expect_warning(check_ebfmi(energy_df), "E-BFMI not computed because the 'energy__' diagnostic could not be located.")
+  expect_warning(ebfmi(energy_df), "E-BFMI not computed because the 'energy__' diagnostic could not be located.")
 
 })