Merge pull request #509 from banfai/508-fix-mising-levs

Fix ref_grid with missing levels
rvlenth · Sep 26, 2024 · ca91c9c · ca91c9c
2 parents a39b44b + 3d69943
commit ca91c9c
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diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,7 @@ title: "NEWS for the emmeans package"
 
 ## emmeans 1.10.4.90xxxx
   * Fix for long-standing `weights` bug in `lme()` (#356)
+  * Fix for inconsistent contrasts in case of missing levels (#508)
 
 
 ## emmeans 1.10.4

diff --git a/R/0nly-internal.R b/R/0nly-internal.R
@@ -59,7 +59,7 @@
 ### Internal function to implement 'allow.na.levs' option
 .chk.fac = function(x) {
     if(get_emm_option("allow.na.levs"))
-        x
+        factor(x, exclude = NULL)
     else
         factor(x)
 }

diff --git a/tests/testthat/test-ref_grid.R b/tests/testthat/test-ref_grid.R
@@ -72,3 +72,13 @@ MOats.emm = emmeans(MOats.lm, ~ Variety * rep.meas)
 test_that("We get same predictions with and without nuisance specs", {
     expect_equal(predict(MOats.rgn), predict(MOats.emm), 0.001)
 })
+
+# Missing and NA levels
+miss.df = data.frame(x = factor(c("a", "a", "b", NA), levels = c("a", "b", "c", NA)), y = 1:4)
+miss.lm = lm(y ~ x, data = miss.df)
+miss.rg1 = ref_grid(miss.lm)
+miss.rg2 = ref_grid(miss.lm, data = miss.df)
+test_that("Reference grid handles missing values", {
+    expect_equal(length(miss.rg1@levels$x), 2)
+    expect_equal(length(miss.rg2@levels$x), 2)
+})