Fix R2 for multiple (1 | g)

pbs-assess · Nov 16, 2023 · b845a14 · b845a14
1 parent c668805
commit b845a14
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Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/R/r2.R b/R/r2.R
@@ -169,9 +169,9 @@ r2.sdmTMB <- function(model, ...) {
 }
 
 .get_var_re_iid <- function(x) {
-  if (x$tmb_data$nobs_RE > 0) {
+  if (any(x$tmb_data$nobs_RE > 0)) {
     b <- tidy(x, "ran_par")
-    varG <- b$estimate[b$term == "sigma_G"]^2 # random effect variance
+    varG <- sum(b$estimate[b$term == "sigma_G"]^2) # random effect variance
   } else {
     varG <- 0
   }

diff --git a/tests/testthat/test-r2.R b/tests/testthat/test-r2.R
@@ -24,6 +24,15 @@ test_that("r2 function works", {
   p2 <- performance::r2_nakagawa(fit2)
   .compare(p1, p2)
 
+  # multiple random intercepts:
+  set.seed(1)
+  d$g <- as.factor(sample(letters[1:5], size = nrow(d), replace = TRUE))
+  fit <- sdmTMB(density ~ scaled_log_depth + (1 | g) + (1 | fyear), data = d, spatial = "off", family = tweedie())
+  fit2 <- glmmTMB::glmmTMB(density ~ scaled_log_depth + (1 | g) + (1 | fyear), data = d, family = glmmTMB::tweedie())
+  p1 <- r2(fit)
+  p2 <- r2(fit2)
+  .compare(p1, p2)
+
   # no (1 | g)
   fit <- sdmTMB(
     density ~ s(depth),