Simple glms no longer supported? (#660)

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: performance
 Title: Assessment of Regression Models Performance
-Version: 0.10.8.5
+Version: 0.10.8.6
 Authors@R: 
     c(person(given = "Daniel",
              family = "Lüdecke",

NEWS.md

@@ -1,8 +1,15 @@
 # performance 0.10.9
 
+## Changes
+
 * `r2()` for models of class `glmmTMB` without random effects now returns the
   correct r-squared value for non-mixed models.
 
+## Bug fixes
+
+* Fixed issue in `binned_residuals()` for models with binary outcome, where
+  in rare occasions empty bins could occur.
+
 # performance 0.10.8
 
 ## Changes

R/binned_residuals.R

@@ -143,17 +143,22 @@ binned_residuals <- function(model,
     n <- length(items)
     sdev <- stats::sd(y[items], na.rm = TRUE)
 
-    conf_int <- switch(ci_type,
-      gaussian = stats::qnorm(c((1 - ci) / 2, (1 + ci) / 2), mean = ybar, sd = sdev / sqrt(n)),
-      exact = {
-        out <- stats::binom.test(sum(y0[items]), n)$conf.int
-        # center CIs around point estimate
-        out <- out - (min(out) - ybar) - (diff(out) / 2)
-        out
-      },
-      boot = .boot_binned_ci(y[items], ci, iterations)
-    )
-    names(conf_int) <- c("CI_low", "CI_high")
+    # sanity check - do we have any data in our bin?
+    if (n == 0) {
+      conf_int <- stats::setNames(c(NA, NA), c("CI_low", "CI_high"))
+    } else {
+      conf_int <- switch(ci_type,
+        gaussian = stats::qnorm(c((1 - ci) / 2, (1 + ci) / 2), mean = ybar, sd = sdev / sqrt(n)),
+        exact = {
+          out <- stats::binom.test(sum(y0[items]), n)$conf.int
+          # center CIs around point estimate
+          out <- out - (min(out) - ybar) - (diff(out) / 2)
+          out
+        },
+        boot = .boot_binned_ci(y[items], ci, iterations)
+      )
+      names(conf_int) <- c("CI_low", "CI_high")
+    }
 
     d0 <- data.frame(
       xbar = xbar,

tests/testthat/test-binned_residuals.R

@@ -164,7 +164,7 @@ test_that("binned_residuals, msg for non-bernoulli", {
 
   dat <- data.frame(tot, suc)
   dat$prop <- suc / tot
-  dat$x1 <- as.factor(sample(1:5, 100, replace = TRUE))
+  dat$x1 <- as.factor(sample.int(5, 100, replace = TRUE))
 
   mod <- glm(prop ~ x1,
     family = binomial,
@@ -175,3 +175,69 @@ test_that("binned_residuals, msg for non-bernoulli", {
   expect_message(binned_residuals(mod), regex = "Using `ci_type = \"gaussian\"`")
   expect_silent(binned_residuals(mod, verbose = FALSE))
 })
+
+test_that("binned_residuals, empty bins", {
+  eel <- data.frame(
+    cured_bin = c(
+      1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0,
+      0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0,
+      0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,
+      0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0,
+      0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1,
+      0, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0
+    ),
+    intervention = c(
+      "No treatment",
+      "No treatment", "No treatment", "No treatment", "Intervention",
+      "No treatment", "Intervention", "Intervention", "No treatment",
+      "No treatment", "Intervention", "No treatment", "No treatment",
+      "Intervention", "No treatment", "No treatment", "Intervention",
+      "Intervention", "Intervention", "Intervention", "No treatment",
+      "Intervention", "Intervention", "No treatment", "Intervention",
+      "Intervention", "No treatment", "No treatment", "Intervention",
+      "Intervention", "No treatment", "No treatment", "Intervention",
+      "Intervention", "Intervention", "No treatment", "No treatment",
+      "Intervention", "No treatment", "Intervention", "No treatment",
+      "Intervention", "Intervention", "Intervention", "No treatment",
+      "No treatment", "No treatment", "Intervention", "Intervention",
+      "No treatment", "Intervention", "Intervention", "Intervention",
+      "No treatment", "No treatment", "Intervention", "Intervention",
+      "No treatment", "Intervention", "Intervention", "No treatment",
+      "No treatment", "No treatment", "Intervention", "Intervention",
+      "No treatment", "No treatment", "No treatment", "No treatment",
+      "No treatment", "Intervention", "No treatment", "Intervention",
+      "Intervention", "Intervention", "No treatment", "Intervention",
+      "Intervention", "No treatment", "Intervention", "No treatment",
+      "No treatment", "Intervention", "Intervention", "Intervention",
+      "Intervention", "No treatment", "Intervention", "Intervention",
+      "No treatment", "Intervention", "No treatment", "Intervention",
+      "Intervention", "Intervention", "Intervention", "No treatment",
+      "No treatment", "No treatment", "Intervention", "No treatment",
+      "No treatment", "Intervention", "No treatment", "No treatment",
+      "No treatment", "No treatment", "No treatment", "Intervention",
+      "Intervention", "No treatment", "No treatment", "Intervention"
+    ), duration = c(
+      7L, 7L, 6L, 8L, 7L, 6L, 7L, 7L, 8L, 7L, 7L, 7L,
+      5L, 9L, 6L, 7L, 8L, 7L, 7L, 9L, 7L, 9L, 8L, 7L, 6L, 8L, 7L, 6L,
+      7L, 6L, 7L, 6L, 5L, 6L, 7L, 7L, 8L, 7L, 5L, 7L, 9L, 10L, 7L,
+      8L, 5L, 8L, 4L, 7L, 8L, 6L, 6L, 6L, 7L, 7L, 8L, 7L, 7L, 7L, 7L,
+      8L, 7L, 9L, 7L, 8L, 8L, 7L, 7L, 7L, 8L, 7L, 8L, 7L, 8L, 8L, 9L,
+      7L, 10L, 5L, 7L, 8L, 9L, 5L, 10L, 8L, 7L, 6L, 5L, 6L, 7L, 7L,
+      7L, 7L, 7L, 7L, 8L, 5L, 6L, 7L, 6L, 7L, 7L, 9L, 6L, 6L, 7L, 7L,
+      6L, 7L, 8L, 9L, 4L, 6L, 9L
+    ),
+    stringsAsFactors = FALSE
+  )
+  m_eel <- glm(cured_bin ~ intervention + duration, data = eel, family = binomial())
+  out <- binned_residuals(m_eel)
+  expect_equal(
+    out$xbar,
+    c(0.27808, 0.28009, 0.28167, 0.28326, 0.48269, 0.56996, 0.57188, 0.57456),
+    tolerance = 1e-4
+  )
+  expect_equal(
+    out$CI_low,
+    c(-0.42552, -0.45162, -0.10819, -0.7339, -0.28086, -0.52599, 0.02795, -0.44023),
+    tolerance = 1e-4
+  )
+})