From c5c7277ad2d3667f6c56be2aaa130aa2cf743e63 Mon Sep 17 00:00:00 2001
From: Ben Bolker <bbolker@gmail.com>
Date: Tue, 24 Oct 2023 09:20:01 -0400
Subject: [PATCH 1/2] binom CI hack for binned_performance

---
 R/binned_residuals.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/R/binned_residuals.R b/R/binned_residuals.R
index 355ab63c4..9df75e74e 100644
--- a/R/binned_residuals.R
+++ b/R/binned_residuals.R
@@ -67,7 +67,8 @@ binned_residuals <- function(model, term = NULL, n_bins = NULL, ...) {
     pred <- mf[[term]]
   }
 
-  y <- .recode_to_zero(insight::get_response(model, verbose = FALSE)) - fv
+  y0 <- .recode_to_zero(insight::get_response(model, verbose = FALSE))
+  y <- y0 - fv
 
   if (is.null(n_bins)) n_bins <- round(sqrt(length(pred)))
 
@@ -84,6 +85,7 @@ binned_residuals <- function(model, term = NULL, n_bins = NULL, ...) {
     n <- length(items)
     sdev <- stats::sd(y[items], na.rm = TRUE)
 
+    bt <- binom.test(sum(y0[items]), n)
     data.frame(
       xbar = xbar,
       ybar = ybar,
@@ -91,7 +93,9 @@ binned_residuals <- function(model, term = NULL, n_bins = NULL, ...) {
       x.lo = model.range[1],
       x.hi = model.range[2],
       se = stats::qnorm(0.975) * sdev / sqrt(n),
-      ci_range = sdev / sqrt(n)
+      ci_range = sdev / sqrt(n),
+      CI_low = bt$conf.int[1] - fv,
+      CI_high = bt$conf.int[2] - fv
     )
   }))
 
@@ -99,8 +103,6 @@ binned_residuals <- function(model, term = NULL, n_bins = NULL, ...) {
   d <- d[stats::complete.cases(d), ]
 
   # CIs
-  d$CI_low <- d$ybar - stats::qnorm(0.975) * d$ci_range
-  d$CI_high <- d$ybar + stats::qnorm(0.975) * d$ci_range
 
   gr <- abs(d$ybar) > abs(d$se)
   d$group <- "yes"

From 2fb679acf97c7b978031e4c60f3191c15dcd0ad5 Mon Sep 17 00:00:00 2001
From: Ben Bolker <bbolker@gmail.com>
Date: Tue, 24 Oct 2023 10:06:58 -0400
Subject: [PATCH 2/2] still hacking on binned_residuals

---
 R/binned_residuals.R | 31 ++++++++++++++++++++++---------
 1 file changed, 22 insertions(+), 9 deletions(-)

diff --git a/R/binned_residuals.R b/R/binned_residuals.R
index eb45aee82..402f68788 100644
--- a/R/binned_residuals.R
+++ b/R/binned_residuals.R
@@ -62,7 +62,9 @@
 #' }
 #'
 #' @export
-binned_residuals <- function(model, term = NULL, n_bins = NULL, show_dots = NULL, ...) {
+binned_residuals <- function(model, term = NULL, n_bins = NULL, show_dots = NULL, resids = c("gaussian", "exact", "boot"), level = 0.95, ...) {
+
+  resids <- match.arg(resids)
   fv <- stats::fitted(model)
   mf <- insight::get_data(model, verbose = FALSE)
 
@@ -78,8 +80,9 @@ binned_residuals <- function(model, term = NULL, n_bins = NULL, show_dots = NULL
     show_dots <- is.null(n) || n <= 1e5
   }
 
-  y <- .recode_to_zero(insight::get_response(model, verbose = FALSE)) - fv
->>>>>>> upstream/main
+
+  y0 <- .recode_to_zero(insight::get_response(model, verbose = FALSE))
+  y <- y0 - fv
 
   if (is.null(n_bins)) n_bins <- round(sqrt(length(pred)))
 
@@ -96,18 +99,28 @@ binned_residuals <- function(model, term = NULL, n_bins = NULL, show_dots = NULL
     n <- length(items)
     sdev <- stats::sd(y[items], na.rm = TRUE)
 
-    bt <- binom.test(sum(y0[items]), n)
-    data.frame(
+    ci_fun <- function() {
+        r <- switch(resids,
+               gaussian = qnorm(c((1-level)/2, (1+level)/2),
+                                mean = ybar, sd = sdev/sqrt(n)),
+               exact = stats:::binom.test(sum(y0[items]), n)$conf.int - fv,
+               boot = Hmisc::smean.cl.boot(y[items], conf.int = level)[c("Lower", "Upper")]
+               )
+        names(r) <- c("CI_low", "CI_high")
+        r
+    }
+
+    d0 <- data.frame(
       xbar = xbar,
       ybar = ybar,
       n = n,
       x.lo = model.range[1],
       x.hi = model.range[2],
-      se = stats::qnorm(0.975) * sdev / sqrt(n),
-      ci_range = sdev / sqrt(n),
-      CI_low = bt$conf.int[1] - fv,
-      CI_high = bt$conf.int[2] - fv
+      se = stats::qnorm((1+level)/2) * sdev / sqrt(n),
+      ci_range = sdev / sqrt(n)
     )
+    cbind(d0, rbind(ci_fun()))
+          
   }))
 
   d <- do.call(rbind, d)