report.compare.loo: minor edits (#427)

* edits

* Adding reference for all the things meme

#428

* fix errors, wordlist, styler, lints

---------

Co-authored-by: Daniel <[email protected]>
Co-authored-by: Rémi Thériault <[email protected]>

R/report.compare.loo.R

@@ -3,8 +3,8 @@
 #' Automatically report the results of Bayesian model comparison using the `loo` package.
 #'
 #' @param x An object of class [brms::loo_compare].
-#' @param index type if index to report - expected log pointwise predictive
-#'   density (ELPD) or information criteria (IC).
+#' @param include_IC Whether to include the information criteria (IC).
+#' @param include_ENP Whether to include the effective number of parameters (ENP).
 #' @param ... Additional arguments (not used for now).
 #'
 #' @examplesIf require("brms", quietly = TRUE)
@@ -13,24 +13,33 @@
 #'
 #' m1 <- brms::brm(mpg ~ qsec, data = mtcars)
 #' m2 <- brms::brm(mpg ~ qsec + drat, data = mtcars)
+#' m3 <- brms::brm(mpg ~ qsec + drat + wt, data = mtcars)
 #'
-#' x <- brms::loo_compare(brms::add_criterion(m1, "loo"),
+#' x <- brms::loo_compare(
+#'   brms::add_criterion(m1, "loo"),
 #'   brms::add_criterion(m2, "loo"),
-#'   model_names = c("m1", "m2")
+#'   brms::add_criterion(m3, "loo"),
+#'   model_names = c("m1", "m2", "m3")
 #' )
 #' report(x)
+#' report(x, include_IC = FALSE)
+#' report(x, include_ENP = TRUE)
 #' }
 #'
 #' @details
 #' The rule of thumb is that the models are "very similar" if |elpd_diff| (the
 #' absolute value of elpd_diff) is less than 4 (Sivula, Magnusson and Vehtari, 2020).
 #' If superior to 4, then one can use the SE to obtain a standardized difference
 #' (Z-diff) and interpret it as such, assuming that the difference is normally
-#' distributed.
+#' distributed. The corresponding p-value is then calculated as `2 * pnorm(-abs(Z-diff))`.
+#' However, note that if the raw ELPD difference is small (less than 4), it doesn't
+#' make much sense to rely on its standardized value: it is not very useful to
+#' conclude that a model is much better than another if both models make very
+#' similar predictions.
 #'
 #' @return Objects of class [report_text()].
 #' @export
-report.compare.loo <- function(x, index = c("ELPD", "IC"), ...) {
+report.compare.loo <- function(x, include_IC = TRUE, include_ENP = FALSE, ...) {
   # nolint start
   # https://stats.stackexchange.com/questions/608881/how-to-interpret-elpd-diff-of-bayesian-loo-estimate-in-bayesian-logistic-regress
   # nolint end
@@ -40,72 +49,89 @@ report.compare.loo <- function(x, index = c("ELPD", "IC"), ...) {
   # The difference in expected log predictive density (elpd) between each model
   # and the best model as well as the standard error of this difference (assuming
   # the difference is approximately normal).
-  index <- match.arg(index)
-  x <- as.data.frame(x)
+
   # The values in the first row are 0s because the models are ordered from best to worst according to their elpd.
+  x <- as.data.frame(x)
   modnames <- rownames(x)
 
   elpd_diff <- x[["elpd_diff"]]
+  se_elpd_diff <- x[["se_diff"]]
   ic_diff <- -2 * elpd_diff
 
-  z_elpd_diff <- elpd_diff / x[["se_diff"]]
+  z_elpd_diff <- elpd_diff / se_elpd_diff
+  p_elpd_diff <- 2 * stats::pnorm(-abs(z_elpd_diff))
   z_ic_diff <- -z_elpd_diff
 
   if ("looic" %in% colnames(x)) {
-    type <- "LOO"
-    ENP <- x[["p_loo"]]
+    elpd <- x[["elpd_loo"]]
+    enp <- x[["p_loo"]]
+    index_label <- "ELPD-LOO"
+    ic <- x[["looic"]]
+    index_ic <- "LOOIC"
   } else {
-    type <- "WAIC"
-    ENP <- x[["p_waic"]]
+    elpd <- x[["elpd_waic"]]
+    enp <- x[["p_waic"]]
+    index_label <- "ELPD-WAIC"
+    ic <- x[["waic"]]
+    index_ic <- "WAIC"
   }
 
-  if (index == "ELPD") {
-    index_label <- sprintf("Expected Log Predictive Density (ELPD-%s)", type)
-  } else if (type == "LOO") {
-    index_label <- "Leave-One-Out CV Information Criterion (LOOIC)"
-  } else {
-    index_label <- "Widely Applicable Information Criterion (WAIC)"
-  }
+  # TODO: The above indices-computation and name-matching should be implemented
+  # in a parameters.compare.loo() function which would be run here.
 
-  out_text <- sprintf(
-    paste(
-      "The difference in predictive accuracy, as index by %s, suggests that '%s' ",
-      "is the best model (effective number of parameters (ENP) = %.2f), followed by"
+  # Starting text -----
+  text1 <- sprintf(
+    paste0(
+      "The difference in predictive accuracy, as indexed by Expected Log ",
+      "Predictive Density (%s), suggests that '%s' is the best model ("
     ),
-    index_label, modnames[1], ENP[1]
+    index_label, modnames[1]
   )
-
-  if (index == "ELPD") {
-    other_texts <- sprintf(
-      "'%s' (diff = %.2f, ENP = %.2f, z-diff = %.2f)",
-      modnames[-1],
-      elpd_diff[-1],
-      ENP[-1],
-      z_elpd_diff[-1]
-    )
+  if (all(c(include_IC, include_ENP))) {
+    if (include_IC) {
+      text1 <- sprintf(paste0(text1, "%s = %.2f"), index_ic, ic[1])
+    }
+    if (include_ENP) {
+      if (include_IC) {
+        text1 <- sprintf(paste0(text1, ", ENP = %.2f)"), enp[1])
+      } else {
+        text1 <- sprintf(paste0(text1, "ENP = %.2f)"), enp[1])
+      }
+    } else {
+      text1 <- paste0(text1, ")")
+    }
   } else {
-    other_texts <- sprintf(
-      "'%s' (diff = %.2f, ENP = %.2f, z-diff = %.2f)",
-      modnames[-1],
-      ic_diff[-1],
-      ENP[-1],
-      z_ic_diff[-1]
-    )
+    text1 <- sprintf(paste0(text1, "ELPD = %.2f)"), elpd[1])
   }
 
-  sep <- "."
-  nothermods <- length(other_texts)
-  if (nothermods > 1L) {
-    if (nothermods == 2L) {
-      sep <- c(" and ", sep)
+  # Other models ---
+  text_models <- sprintf(
+    "'%s' (diff-ELPD = %.2f +- %.2f, %s",
+    modnames[-1],
+    elpd_diff[-1],
+    se_elpd_diff[-1],
+    insight::format_p(p_elpd_diff[-1])
+  )
+
+  if (all(c(include_IC, include_ENP))) {
+    if (include_IC) {
+      text_models <- sprintf(paste0(text_models, ", %s = %.2f"), index_ic, ic[-1])
+    }
+    if (include_ENP) {
+      if (include_IC) {
+        text_models <- sprintf(paste0(text_models, ", ENP = %.2f)"), enp[-1])
+      } else {
+        text_models <- sprintf(paste0(text_models, "ENP = %.2f)"), enp[-1])
+      }
     } else {
-      sep <- c(rep(", ", length = nothermods - 2), ", and ", sep)
+      text_models <- sprintf(paste0(text_models, ")"))
     }
+  } else {
+    text_models <- paste0(text_models, ")")
   }
 
-  other_texts <- paste0(other_texts, sep, collapse = "")
 
-  out_text <- paste(out_text, other_texts, collapse = "")
-  class(text) <- c("report_text", class(text))
-  out_text
+  text1 <- paste0(text1, ", followed by ", datawizard::text_concatenate(text_models))
+  class(text1) <- c("report_text", class(text1))
+  text1
 }

README.Rmd

@@ -79,7 +79,7 @@ The package documentation can be found [**here**](https://easystats.github.io/re
 
 ## Report all the things 
 
-<a href=https://easystats.github.io/report/><img src="man/figures/allthethings.jpg" height="60"></a>
+<a href=https://easystats.github.io/report/><img src="man/figures/allthethings.jpg" height="60" alt="All the things meme by Allie Brosh" ></a>
 
 ### General Workflow
 

inst/WORDLIST

@@ -6,6 +6,7 @@ CMD
 CSL
 Dom
 ELPD
+ENP
 ESS
 Gabry
 Hotfix