Fix get_parameters/find_parameters for glmmTMB 1.1.10 (#934)

* Fix get_parameters/find_parameters for glmmTMB 1.1.10 * find_params * test on R > 4.3
easystats · Sep 27, 2024 · 27dc704 · 27dc704
1 parent fca4b12
commit 27dc704
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: insight
 Title: Easy Access to Model Information for Various Model Objects
-Version: 0.20.4.5
+Version: 0.20.4.6
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",

diff --git a/R/find_parameters_mixed.R b/R/find_parameters_mixed.R
@@ -32,6 +32,8 @@
 #' - `zero_inflated_random`, the "random effects" part from the zero-inflation
 #'   component of the model.
 #' - `dispersion`, the dispersion parameters (auxiliary parameter)
+#' - `dispersion_random`, the "random effects" part from the dispersion
+#'   parameters (auxiliary parameter)
 #' - `nonlinear`, the parameters from the nonlinear formula.
 #'
 #' @examples
@@ -66,7 +68,8 @@ find_parameters.glmmTMB <- function(x,
       random = lapply(lme4::ranef(x)$cond, colnames),
       zero_inflated = names(lme4::fixef(x)$zi),
       zero_inflated_random = lapply(lme4::ranef(x)$zi, colnames),
-      dispersion = names(lme4::fixef(x)$disp)
+      dispersion = names(lme4::fixef(x)$disp),
+      dispersion_random = names(lme4::ranef(x)$disp)
     ))
   }
 

diff --git a/R/get_parameters_mixed.R b/R/get_parameters_mixed.R
@@ -465,7 +465,8 @@ get_parameters.glmmTMB <- function(x,
       random = lme4::ranef(x)$cond,
       zero_inflated = lme4::fixef(x)$zi,
       zero_inflated_random = lme4::ranef(x)$zi,
-      dispersion = lme4::fixef(x)$disp
+      dispersion = lme4::fixef(x)$disp,
+      dispersion_random = lme4::ranef(x)$disp
     ))
   }
 
@@ -517,10 +518,15 @@ get_parameters.glmmTMB <- function(x,
     text_remove_backticks(out)
   } else if (effects == "random") {
     switch(component,
-      all = compact_list(list(random = l$random, zero_inflated_random = l$zero_inflated_random)),
+      all = compact_list(list(
+        random = l$random,
+        zero_inflated_random = l$zero_inflated_random,
+        dispersion_random = l$dispersion_random
+      )),
       conditional = l$random,
       zi = ,
-      zero_inflated = l$zero_inflated_random
+      zero_inflated = l$zero_inflated_random,
+      dispersion_random = l$dispersion_random
     )
   }
 }

diff --git a/R/helper_functions.R b/R/helper_functions.R
@@ -224,12 +224,12 @@
   c(
     "conditional", "conditional1", "conditional2", "conditional3", "precision",
     "nonlinear", "random", "zi", "zero_inflated", "zero_inflated_random", "shape",
-    "dispersion", "instruments", "interactions", "simplex", "smooth_terms",
-    "sigma", "nu", "tau", "correlation", "slopes", "cluster", "extra", "scale",
-    "marginal", "alpha", "beta", "survival", "infrequent_purchase", "auxiliary",
-    "mix", "shiftprop", "phi", "ndt", "hu", "xi", "coi", "zoi", "aux", "dist",
-    "selection", "outcome", "time_dummies", "sigma_random", "beta_random", "car",
-    "nominal"
+    "dispersion", "dispersion_random", "instruments", "interactions", "simplex",
+    "smooth_terms", "sigma", "nu", "tau", "correlation", "slopes", "cluster",
+    "extra", "scale", "marginal", "alpha", "beta", "survival", "infrequent_purchase",
+    "auxiliary", "mix", "shiftprop", "phi", "ndt", "hu", "xi", "coi", "zoi",
+    "aux", "dist", "selection", "outcome", "time_dummies", "sigma_random",
+    "beta_random", "car", "nominal"
   )
 }
 
@@ -240,7 +240,7 @@
     "aux", "dist",
 
     # random parameters
-    "sigma_random", "beta_random"
+    "dispersion_random", "sigma_random", "beta_random"
   )
 }
 
@@ -255,7 +255,7 @@
   auxiliary_parameters <- .aux_elements()
 
   # random parameters
-  random_parameters <- c("random", "zero_inflated_random", "sigma_random", "beta_random", "car")
+  random_parameters <- c("random", "zero_inflated_random", "dispersion_random", "sigma_random", "beta_random", "car")
 
   # conditional component
   conditional_component <- setdiff(

diff --git a/man/find_parameters.glmmTMB.Rd b/man/find_parameters.glmmTMB.Rd
diff --git a/tests/testthat/test-glmmTMB.R b/tests/testthat/test-glmmTMB.R
@@ -1,6 +1,5 @@
 skip_on_os("mac") # error: FreeADFunObject
 skip_if_not(getRversion() >= "4.0.0")
-skip_if(getRversion() > "4.3.3")
 skip_if_not_installed("TMB")
 skip_if_not_installed("glmmTMB")
 
@@ -975,7 +974,6 @@ test_that("model_info, ordered beta", {
 
 
 test_that("model_info, recognize ZI even without ziformula", {
-  skip_if_not_installed("glmmTMB")
   data("fish", package = "insight")
   fish$count <- fish$count + 1
   m1 <- glmmTMB::glmmTMB(
@@ -1010,3 +1008,72 @@ test_that("model_info, recognize ZI even without ziformula", {
 #     expect_equal(out$var.distribution, 1.44250604187634, tolerance = 1e-4)
 #   })
 # )
+
+test_that("get/find_parameters with dispersion-random", {
+  skip_if_not_installed("glmmTMB", minimum_version = "1.1.10")
+  data(Salamanders, package = "glmmTMB")
+  m <- glmmTMB::glmmTMB(
+    count ~ spp + cover + mined + (1 | site),
+    ziformula = ~ spp + mined,
+    dispformula = ~ DOY + (1 | site),
+    data = Salamanders,
+    family = glmmTMB::nbinom2
+  )
+  out <- get_parameters(m)
+  expect_identical(nrow(out), 19L)
+  out <- get_parameters(m, effects = "random")
+  expect_length(out, 2)
+  expect_named(out, c("random", "dispersion_random"))
+
+  expect_equal(
+    find_parameters(m),
+    list(
+      conditional = c(
+        "(Intercept)", "sppPR", "sppDM", "sppEC-A",
+        "sppEC-L", "sppDES-L", "sppDF", "cover", "minedno"
+      ),
+      random = list(site = "(Intercept)"),
+      zero_inflated = c(
+        "(Intercept)", "sppPR",
+        "sppDM", "sppEC-A", "sppEC-L", "sppDES-L", "sppDF", "minedno"
+      ),
+      dispersion = c("(Intercept)", "DOY"),
+      dispersion_random = "site"
+    ),
+    ignore_attr = TRUE
+  )
+  expect_equal(
+    find_parameters(m, effects = "fixed"),
+    list(
+      conditional = c(
+        "(Intercept)", "sppPR", "sppDM", "sppEC-A",
+        "sppEC-L", "sppDES-L", "sppDF", "cover", "minedno"
+      ),
+      zero_inflated = c(
+        "(Intercept)", "sppPR",
+        "sppDM", "sppEC-A", "sppEC-L", "sppDES-L", "sppDF", "minedno"
+      ),
+      dispersion = c("(Intercept)", "DOY")
+    ),
+    ignore_attr = TRUE
+  )
+  expect_equal(
+    find_parameters(m, effects = "random"),
+    list(
+      random = list(site = "(Intercept)"),
+      dispersion_random = "site"
+    ),
+    ignore_attr = TRUE
+  )
+  expect_equal(
+    find_parameters(m, component = "conditional"),
+    list(
+      conditional = c(
+        "(Intercept)", "sppPR", "sppDM", "sppEC-A",
+        "sppEC-L", "sppDES-L", "sppDF", "cover", "minedno"
+      ),
+      random = list(site = "(Intercept)")
+    ),
+    ignore_attr = TRUE
+  )
+})
diff --git a/tests/testthat/test-null_model.R b/tests/testthat/test-null_model.R
@@ -1,4 +1,3 @@
-skip_if(getRversion() > "4.3.3")
 skip_if_not_installed("glmmTMB")
 skip_if_not_installed("lme4")
 skip_if_not_installed("TMB")