From 6f2c54181855bc9116f2112a4c9d3f67cd3b2273 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Mon, 19 Oct 2026 11:15:09 -0500
Subject: [PATCH 01/10] Add tests for zero-inflation rows in glmmTMB bootstrap
 output

---
 tests/testthat/test-bootstrap_parameters.R | 132 +++++++++++++++++++++
 1 file changed, 132 insertions(+)

diff --git a/tests/testthat/test-bootstrap_parameters.R b/tests/testthat/test-bootstrap_parameters.R
index cfd43299f..4cccaf0a0 100644
--- a/tests/testthat/test-bootstrap_parameters.R
+++ b/tests/testthat/test-bootstrap_parameters.R
@@ -403,3 +403,135 @@ test_that("bootstrap_model parametric errors for responses that are not a data c
     )
   )
 })
+
+.fit_zi_glmmTMB <- function(ziformula = ~mined, ...) {
+  data(Salamanders, package = "glmmTMB")
+  glmmTMB::glmmTMB(
+    count ~ mined + (1 | site),
+    ziformula = ziformula,
+    family = poisson,
+    data = Salamanders,
+    ...
+  )
+}
+
+.fit_zi_disp_glmmTMB <- function() {
+  data(Salamanders, package = "glmmTMB")
+  glmmTMB::glmmTMB(
+    count ~ mined + (1 | site),
+    ziformula = ~mined,
+    dispformula = ~mined,
+    family = glmmTMB::nbinom2,
+    data = Salamanders
+  )
+}
+
+test_that("bootstrap_model names zero-inflation columns of glmmTMB models", {
+  skip_if_not_installed("glmmTMB")
+  skip_if_not_installed("lme4")
+  zi_names <- c("(Intercept)", "minedno", "(Intercept)_zi", "minedno_zi")
+
+  set.seed(123)
+  expect_named(bootstrap_model(.fit_zi_glmmTMB(), iterations = 5), zi_names)
+  set.seed(123)
+  expect_named(bootstrap_model(.fit_zi_disp_glmmTMB(), iterations = 5), zi_names)
+  set.seed(123)
+  expect_named(
+    bootstrap_model(.fit_zi_glmmTMB(ziformula = ~cover), iterations = 5),
+    c("(Intercept)", "minedno", "(Intercept)_zi", "cover_zi")
+  )
+
+  m_cond <- .fit_zi_glmmTMB(ziformula = ~0)
+  set.seed(123)
+  expect_named(
+    bootstrap_model(m_cond, iterations = 5),
+    insight::find_parameters(m_cond, effects = "fixed")$conditional
+  )
+  data(sleepstudy, package = "lme4")
+  m_lmer <- lme4::lmer(Reaction ~ Days + (1 | Subject), data = sleepstudy)
+  set.seed(123)
+  expect_named(
+    bootstrap_model(m_lmer, iterations = 5),
+    insight::find_parameters(m_lmer, effects = "fixed")$conditional
+  )
+})
+
+test_that("bootstrap_parameters returns components of glmmTMB models", {
+  skip_if_not_installed("glmmTMB")
+  for (m in list(.fit_zi_glmmTMB(), .fit_zi_disp_glmmTMB())) {
+    params <- insight::get_parameters(m)
+    params <- params[params$Component != "dispersion", ]
+    set.seed(123)
+    out <- list(
+      bootstrap_parameters(m, iterations = 20),
+      model_parameters(m, bootstrap = TRUE, iterations = 20, effects = "fixed"),
+      model_parameters(
+        m,
+        bootstrap = TRUE,
+        iterations = 20,
+        effects = "fixed",
+        exponentiate = TRUE
+      )
+    )
+    for (x in out) {
+      expect_identical(x$Parameter, params$Parameter)
+      expect_identical(x$Component, params$Component)
+      expect_false(anyNA(x$Coefficient))
+    }
+  }
+
+  set.seed(123)
+  mp <- model_parameters(
+    .fit_zi_glmmTMB(),
+    bootstrap = TRUE,
+    iterations = 20,
+    effects = "fixed"
+  )
+  printed <- capture.output(print(mp))
+  zi_start <- grep("# Zero-Inflation", printed, fixed = TRUE)
+  expect_length(zi_start, 1)
+  zi_rows <- printed[seq_along(printed) > min(zi_start, Inf)]
+  expect_length(grep("^\\(Intercept\\)\\s+\\|", zi_rows), 1)
+  expect_length(grep("^mined \\[no\\]\\s+\\|", zi_rows), 1)
+})
+
+test_that("bootstrap_parameters matches each glmmTMB draw to its parameter", {
+  skip_if_not_installed("glmmTMB")
+  m <- .fit_zi_glmmTMB(ziformula = ~cover)
+  estimates <- insight::get_parameters(m)$Estimate
+  set.seed(123)
+  out <- bootstrap_parameters(m, iterations = 50)
+  distances <- abs(outer(out$Coefficient, estimates, "-"))
+  closest <- apply(distances, 1, function(d) which.min(d)[1])
+  expect_identical(closest, seq_along(estimates))
+})
+
+test_that("model_parameters with bootstrap uses component for glmmTMB", {
+  skip_if_not_installed("glmmTMB")
+  m <- .fit_zi_glmmTMB()
+  for (comp in c("conditional", "zi")) {
+    expected <- model_parameters(m, component = comp, effects = "fixed")
+    set.seed(123)
+    out <- model_parameters(
+      m,
+      bootstrap = TRUE,
+      iterations = 20,
+      component = comp,
+      effects = "fixed"
+    )
+    expect_identical(out$Parameter, expected$Parameter)
+    expect_identical(out$Component, expected$Component)
+  }
+})
+
+test_that("model_parameters with bootstrap prints a bootstrap footer for glmmTMB", {
+  skip_if_not_installed("glmmTMB")
+  for (m in list(.fit_zi_glmmTMB(), .fit_zi_glmmTMB(ziformula = ~0))) {
+    set.seed(123)
+    mp <- model_parameters(m, bootstrap = TRUE, iterations = 20, effects = "fixed")
+    messages <- capture_messages(printed <- capture.output(print(mp)))
+    printed <- paste(c(printed, messages), collapse = " ")
+    expect_match(printed, "bootstrap", fixed = TRUE)
+    expect_no_match(printed, "Wald", fixed = TRUE)
+  }
+})

From 18dcde34f8c462d0620d788071af1764f1beb926 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Mon, 19 Oct 2026 11:26:38 -0500
Subject: [PATCH 02/10] Name zero-inflation parameters of glmmTMB models in
 bootstrap output (#1284)

---
 DESCRIPTION                                |  2 +-
 NEWS.md                                    | 11 ++++++++
 R/bootstrap_model.R                        |  7 ++++-
 R/bootstrap_parameters.R                   | 21 +++++++++++++++
 R/methods_glmmTMB.R                        | 31 +++++++++++++++++++---
 tests/testthat/test-bootstrap_parameters.R | 19 +++++++++----
 6 files changed, 80 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c8a9b7ab6..fab3d0b69 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.30.0.10
+Version: 0.30.0.11
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
diff --git a/NEWS.md b/NEWS.md
index 5f719ab10..779f1e7fd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -39,6 +39,17 @@
   per row. In the second kind, the response in the formula is not one column
   of the data, for example `log(y)` or `cbind()`.
 
+* `bootstrap_model()`, `bootstrap_parameters()` and `model_parameters()` with
+  `bootstrap = TRUE` now name the zero-inflation parameters of *glmmTMB*
+  models and show them in their own component. Before this fix, these rows
+  were named `NA` or had no name. In `bootstrap_model()`, the columns of the
+  zero-inflation parameters get the suffix `_zi`, as in `simulate_model()`.
+  `model_parameters()` with `bootstrap = TRUE` now uses the `component`
+  argument, and `component = "dispersion"` gives an error. Its output no longer
+  has a dispersion row, because the bootstrap draws have no dispersion
+  parameters. The footer now says that the intervals are bootstrap intervals
+  (#1284).
+
 * The `p_adjust` argument in `model_parameters()` now accepts the methods from
   `stats::p.adjust.methods` in any letter case, for example `"bh"`. Before,
   this failed with an error. An invalid value for `p_adjust` no longer shows the
diff --git a/R/bootstrap_model.R b/R/bootstrap_model.R
index f985572ee..9539612ec 100644
--- a/R/bootstrap_model.R
+++ b/R/bootstrap_model.R
@@ -552,7 +552,12 @@ bootstrap_model.merMod <- function(
   out <- as.data.frame(results$t)
   out <- out[stats::complete.cases(out), ]
 
-  names(out) <- insight::find_parameters(model, effects = "fixed")$conditional
+  # zero-inflation parameters get the suffix "_zi", as in simulate_model()
+  fixed_names <- insight::find_parameters(model, effects = "fixed")
+  names(out) <- c(
+    fixed_names$conditional,
+    if (length(fixed_names$zero_inflated)) paste0(fixed_names$zero_inflated, "_zi")
+  )
   class(out) <- unique(c("bootstrap_model", "see_bootstrap_model", class(out)))
   attr(out, "original_model") <- model
   out
diff --git a/R/bootstrap_parameters.R b/R/bootstrap_parameters.R
index c5c529d62..a3758b69b 100644
--- a/R/bootstrap_parameters.R
+++ b/R/bootstrap_parameters.R
@@ -98,6 +98,7 @@ bootstrap_parameters.bootstrap_model <- function(
     ci_method = ci_method,
     ...
   )
+  out <- .add_component_bootstrap_glmmTMB(out, attr(model, "original_model"))
 
   class(out) <- c("bootstrap_parameters", "parameters_model", class(out))
   attr(out, "boot_samples") <- model
@@ -111,6 +112,26 @@ model_parameters.bootstrap_model <- bootstrap_parameters.bootstrap_model
 
 # utilities --------------------------------------------------------------------
 
+# bootstrap_model() names the zero-inflation draws of glmmTMB models
+# "<name>_zi". Restore the names and add the component, as in model_parameters()
+.add_component_bootstrap_glmmTMB <- function(params, model) {
+  if (!inherits(model, "glmmTMB")) {
+    return(params)
+  }
+  fixed_names <- insight::find_parameters(model, effects = "fixed")
+  if (!length(fixed_names$zero_inflated)) {
+    return(params)
+  }
+  draw_names <- c(fixed_names$conditional, paste0(fixed_names$zero_inflated, "_zi"))
+  idx <- match(params$Parameter, draw_names)
+  params$Parameter <- c(fixed_names$conditional, fixed_names$zero_inflated)[idx]
+  params$Component <- rep(
+    c("conditional", "zero_inflated"),
+    c(length(fixed_names$conditional), length(fixed_names$zero_inflated))
+  )[idx]
+  params
+}
+
 #' @keywords internal
 .summary_bootstrap <- function(data, test, centrality, ci, ci_method, ...) {
   # Is the p-value requested?
diff --git a/R/methods_glmmTMB.R b/R/methods_glmmTMB.R
index a5c8fdaea..c76015420 100644
--- a/R/methods_glmmTMB.R
+++ b/R/methods_glmmTMB.R
@@ -262,8 +262,21 @@ model_parameters.glmmTMB <- function(
 
   if (effects %in% c("fixed", "all")) {
     if (bootstrap) {
+      if (component == "dispersion") {
+        insight::format_error(
+          "Bootstrapping does not return dispersion parameters. Use `component = \"all\"`, `\"conditional\"` or `\"zi\"`." # nolint
+        )
+      }
       # bootstrapped parameters
       params <- bootstrap_parameters(model, iterations = iterations, ci = ci, ...)
+      # keep requested component, and drop the component column for
+      # the conditional component, as for the regular parameters
+      if (!is.null(params$Component)) {
+        params <- .filter_component(params, component)
+        if (component == "conditional") {
+          params$Component <- NULL
+        }
+      }
       if (effects != "fixed") {
         effects <- "fixed"
         if (verbose) {
@@ -297,10 +310,13 @@ model_parameters.glmmTMB <- function(
       params <- do.call(".extract_parameters_generic", fun_args)
     }
 
-    # add dispersion parameter
-    out <- .add_dispersion_param_glmmTMB(model, params, effects, component, ci, verbose)
-    params <- out$params
-    dispersion_param <- out$dispersion_param
+    # add dispersion parameter. bootstrapped draws have no dispersion
+    # parameters, so we don't add a row with Wald intervals for them
+    if (!bootstrap) {
+      out <- .add_dispersion_param_glmmTMB(model, params, effects, component, ci, verbose)
+      params <- out$params
+      dispersion_param <- out$dispersion_param
+    }
 
     # exponentiate coefficients and SE/CI, if requested
     params <- .exponentiate_parameters(params, model, exponentiate)
@@ -344,11 +360,18 @@ model_parameters.glmmTMB <- function(
     attributes(params) <- utils::modifyList(att, attributes(params))
   }
 
+  # bootstrapped intervals are quantiles of the draws
+  if (bootstrap) {
+    ci_method <- "quantile"
+  }
+
   params <- .add_model_parameters_attributes(
     params,
     model,
     ci = ci,
     exponentiate,
+    bootstrap = bootstrap,
+    iterations = iterations,
     ci_method = ci_method,
     p_adjust = p_adjust,
     verbose = verbose,
diff --git a/tests/testthat/test-bootstrap_parameters.R b/tests/testthat/test-bootstrap_parameters.R
index 4cccaf0a0..d4112be78 100644
--- a/tests/testthat/test-bootstrap_parameters.R
+++ b/tests/testthat/test-bootstrap_parameters.R
@@ -498,12 +498,17 @@ test_that("bootstrap_parameters returns components of glmmTMB models", {
 test_that("bootstrap_parameters matches each glmmTMB draw to its parameter", {
   skip_if_not_installed("glmmTMB")
   m <- .fit_zi_glmmTMB(ziformula = ~cover)
-  estimates <- insight::get_parameters(m)$Estimate
+  params <- insight::get_parameters(m)
   set.seed(123)
   out <- bootstrap_parameters(m, iterations = 50)
-  distances <- abs(outer(out$Coefficient, estimates, "-"))
+  own <- match(
+    paste(out$Parameter, out$Component),
+    paste(params$Parameter, params$Component)
+  )
+  distances <- abs(outer(out$Coefficient, params$Estimate, "-"))
   closest <- apply(distances, 1, function(d) which.min(d)[1])
-  expect_identical(closest, seq_along(estimates))
+  expect_identical(closest, own)
+  expect_false(anyNA(own))
 })
 
 test_that("model_parameters with bootstrap uses component for glmmTMB", {
@@ -522,6 +527,10 @@ test_that("model_parameters with bootstrap uses component for glmmTMB", {
     expect_identical(out$Parameter, expected$Parameter)
     expect_identical(out$Component, expected$Component)
   }
+  expect_error(
+    model_parameters(m, bootstrap = TRUE, iterations = 5, component = "dispersion"),
+    "Bootstrapping\\s+does\\s+not\\s+return\\s+dispersion\\s+parameters"
+  )
 })
 
 test_that("model_parameters with bootstrap prints a bootstrap footer for glmmTMB", {
@@ -529,8 +538,8 @@ test_that("model_parameters with bootstrap prints a bootstrap footer for glmmTMB
   for (m in list(.fit_zi_glmmTMB(), .fit_zi_glmmTMB(ziformula = ~0))) {
     set.seed(123)
     mp <- model_parameters(m, bootstrap = TRUE, iterations = 20, effects = "fixed")
-    messages <- capture_messages(printed <- capture.output(print(mp)))
-    printed <- paste(c(printed, messages), collapse = " ")
+    printed <- evaluate_promise(print(mp))
+    printed <- paste(c(printed$output, printed$messages), collapse = " ")
     expect_match(printed, "bootstrap", fixed = TRUE)
     expect_no_match(printed, "Wald", fixed = TRUE)
   }

From 251e764677b6dfe2234d3ac114a584abc0cdeb98 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Mon, 19 Oct 2026 11:29:12 -0500
Subject: [PATCH 03/10] Make the NEWS entry for glmmTMB bootstrap output more
 exact

---
 NEWS.md | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 779f1e7fd..48cb9f620 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -42,13 +42,15 @@
 * `bootstrap_model()`, `bootstrap_parameters()` and `model_parameters()` with
   `bootstrap = TRUE` now name the zero-inflation parameters of *glmmTMB*
   models and show them in their own component. Before this fix, these rows
-  were named `NA` or had no name. In `bootstrap_model()`, the columns of the
-  zero-inflation parameters get the suffix `_zi`, as in `simulate_model()`.
+  were named `NA` or `NA.1` or had no name, and one zero-inflation estimate
+  was missing. In `bootstrap_model()`, the columns of the zero-inflation
+  parameters get the suffix `_zi`, as in `simulate_model()`.
   `model_parameters()` with `bootstrap = TRUE` now uses the `component`
-  argument, and `component = "dispersion"` gives an error. Its output no longer
-  has a dispersion row, because the bootstrap draws have no dispersion
-  parameters. The footer now says that the intervals are bootstrap intervals
-  (#1284).
+  argument. For models with a zero-inflation or dispersion formula,
+  `component = "dispersion"` gives an error, because the bootstrap draws have
+  no dispersion parameters. For the same reason, the output no longer has a
+  dispersion row with Wald intervals. The footer now says that the intervals
+  are bootstrap intervals (#1284).
 
 * The `p_adjust` argument in `model_parameters()` now accepts the methods from
   `stats::p.adjust.methods` in any letter case, for example `"bh"`. Before,

From 07d342bb5e4432431824da93c4a61695182f131f Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Mon, 19 Oct 2026 11:39:15 -0500
Subject: [PATCH 04/10] Keep added columns in glmmTMB bootstrap summaries and
 document the dispersion limit

---
 R/bootstrap_parameters.R                   | 10 +++++++---
 R/methods_glmmTMB.R                        |  4 ++++
 man/model_parameters.glmmTMB.Rd            |  4 ++++
 tests/testthat/test-bootstrap_parameters.R | 19 +++++++++++++++++++
 4 files changed, 34 insertions(+), 3 deletions(-)

diff --git a/R/bootstrap_parameters.R b/R/bootstrap_parameters.R
index a3758b69b..a059b1d6f 100644
--- a/R/bootstrap_parameters.R
+++ b/R/bootstrap_parameters.R
@@ -123,12 +123,16 @@ model_parameters.bootstrap_model <- bootstrap_parameters.bootstrap_model
     return(params)
   }
   draw_names <- c(fixed_names$conditional, paste0(fixed_names$zero_inflated, "_zi"))
+  # columns that users added to the draws, like linear combinations, keep
+  # their names
   idx <- match(params$Parameter, draw_names)
-  params$Parameter <- c(fixed_names$conditional, fixed_names$zero_inflated)[idx]
-  params$Component <- rep(
+  found <- !is.na(idx)
+  params$Parameter[found] <- c(fixed_names$conditional, fixed_names$zero_inflated)[idx[found]]
+  params$Component <- "conditional"
+  params$Component[found] <- rep(
     c("conditional", "zero_inflated"),
     c(length(fixed_names$conditional), length(fixed_names$zero_inflated))
-  )[idx]
+  )[idx[found]]
   params
 }
 
diff --git a/R/methods_glmmTMB.R b/R/methods_glmmTMB.R
index c76015420..604b6f3cb 100644
--- a/R/methods_glmmTMB.R
+++ b/R/methods_glmmTMB.R
@@ -132,6 +132,10 @@
 #' For models where the dispersion parameter and the residual variance are
 #' the same, only the residual variance is shown in the output.
 #'
+#' With `bootstrap = TRUE`, the output has no dispersion parameters, because
+#' the bootstrapped draws include only the conditional and zero-inflation
+#' parameters. `component = "dispersion"` then gives an error.
+#'
 #' @seealso [insight::standardize_names()] to
 #'   rename columns into a consistent, standardized naming scheme.
 #'
diff --git a/man/model_parameters.glmmTMB.Rd b/man/model_parameters.glmmTMB.Rd
index ec60d4f7d..fb9cb4189 100644
--- a/man/model_parameters.glmmTMB.Rd
+++ b/man/model_parameters.glmmTMB.Rd
@@ -305,6 +305,10 @@ sigma(model)^2         # 0.09902987
 
 For models where the dispersion parameter and the residual variance are
 the same, only the residual variance is shown in the output.
+
+With \code{bootstrap = TRUE}, the output has no dispersion parameters, because
+the bootstrapped draws include only the conditional and zero-inflation
+parameters. \code{component = "dispersion"} then gives an error.
 }
 
 \section{Model components}{
diff --git a/tests/testthat/test-bootstrap_parameters.R b/tests/testthat/test-bootstrap_parameters.R
index d4112be78..0efc584d0 100644
--- a/tests/testthat/test-bootstrap_parameters.R
+++ b/tests/testthat/test-bootstrap_parameters.R
@@ -480,6 +480,8 @@ test_that("bootstrap_parameters returns components of glmmTMB models", {
     }
   }
 
+  skip_if_not_installed("withr")
+  withr::local_options(width = 300)
   set.seed(123)
   mp <- model_parameters(
     .fit_zi_glmmTMB(),
@@ -495,6 +497,23 @@ test_that("bootstrap_parameters returns components of glmmTMB models", {
   expect_length(grep("^mined \\[no\\]\\s+\\|", zi_rows), 1)
 })
 
+test_that("bootstrap_parameters keeps added columns of glmmTMB draws", {
+  skip_if_not_installed("glmmTMB")
+  set.seed(123)
+  b <- bootstrap_model(.fit_zi_glmmTMB(), iterations = 5)
+  b$lin_comb <- b$minedno - b$minedno_zi
+  out <- bootstrap_parameters(b)
+  expect_identical(
+    out$Parameter,
+    c("(Intercept)", "minedno", "(Intercept)", "minedno", "lin_comb")
+  )
+  expect_identical(
+    out$Component,
+    c("conditional", "conditional", "zero_inflated", "zero_inflated", "conditional")
+  )
+  expect_equal(out$Coefficient[5], median(b$lin_comb), tolerance = 1e-10)
+})
+
 test_that("bootstrap_parameters matches each glmmTMB draw to its parameter", {
   skip_if_not_installed("glmmTMB")
   m <- .fit_zi_glmmTMB(ziformula = ~cover)

From 95a57fecb1afeda1128442d0dbe29bfac4134ee9 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Mon, 19 Oct 2026 13:58:23 -0500
Subject: [PATCH 05/10] Shorten a line in the glmmTMB bootstrap summary for air

---
 R/bootstrap_parameters.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/bootstrap_parameters.R b/R/bootstrap_parameters.R
index a059b1d6f..f11b880c0 100644
--- a/R/bootstrap_parameters.R
+++ b/R/bootstrap_parameters.R
@@ -127,7 +127,8 @@ model_parameters.bootstrap_model <- bootstrap_parameters.bootstrap_model
   # their names
   idx <- match(params$Parameter, draw_names)
   found <- !is.na(idx)
-  params$Parameter[found] <- c(fixed_names$conditional, fixed_names$zero_inflated)[idx[found]]
+  fixed_parameters <- c(fixed_names$conditional, fixed_names$zero_inflated)
+  params$Parameter[found] <- fixed_parameters[idx[found]]
   params$Component <- "conditional"
   params$Component[found] <- rep(
     c("conditional", "zero_inflated"),

From ddaaa4bb121b868c7c26fdaa5db954ed86e60433 Mon Sep 17 00:00:00 2001
From: "Mattan S. Ben-Shachar" <35330040+mattansb@users.noreply.github.com>
Date: Tue, 20 Oct 2026 09:01:47 +0300
Subject: [PATCH 06/10] Apply suggestion from @mattansb

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fab3d0b69..582502ba3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.30.0.11
+Version: 0.30.0.12
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",

From 99c2ce39178b8680292e9f7cf80e73889b687cd1 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Wed, 21 Oct 2026 13:39:11 -0500
Subject: [PATCH 07/10] shorten NEWS entry, docs and comments

---
 NEWS.md                         | 16 ++++------------
 R/bootstrap_parameters.R        |  6 ++----
 R/methods_glmmTMB.R             |  8 +++-----
 man/model_parameters.glmmTMB.Rd |  5 ++---
 4 files changed, 11 insertions(+), 24 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index e1198d892..984f7d7dd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -48,18 +48,10 @@
   per row. In the second kind, the response in the formula is not one column
   of the data, for example `log(y)` or `cbind()`.
 
-* `bootstrap_model()`, `bootstrap_parameters()` and `model_parameters()` with
-  `bootstrap = TRUE` now name the zero-inflation parameters of *glmmTMB*
-  models and show them in their own component. Before this fix, these rows
-  were named `NA` or `NA.1` or had no name, and one zero-inflation estimate
-  was missing. In `bootstrap_model()`, the columns of the zero-inflation
-  parameters get the suffix `_zi`, as in `simulate_model()`.
-  `model_parameters()` with `bootstrap = TRUE` now uses the `component`
-  argument. For models with a zero-inflation or dispersion formula,
-  `component = "dispersion"` gives an error, because the bootstrap draws have
-  no dispersion parameters. For the same reason, the output no longer has a
-  dispersion row with Wald intervals. The footer now says that the intervals
-  are bootstrap intervals (#1284).
+* Fixed issue where `bootstrap_parameters()` and `model_parameters()` with
+  `bootstrap = TRUE` mislabeled the zero-inflation parameters of *glmmTMB*
+  models. `bootstrap_model()` now adds the suffix `_zi` to these parameters,
+  and bootstrapped output no longer includes dispersion parameters (#1284).
 
 * The `p_adjust` argument in `model_parameters()` now accepts the methods from
   `stats::p.adjust.methods` in any letter case, for example `"bh"`. Before,
diff --git a/R/bootstrap_parameters.R b/R/bootstrap_parameters.R
index f11b880c0..607d3d66b 100644
--- a/R/bootstrap_parameters.R
+++ b/R/bootstrap_parameters.R
@@ -112,8 +112,7 @@ model_parameters.bootstrap_model <- bootstrap_parameters.bootstrap_model
 
 # utilities --------------------------------------------------------------------
 
-# bootstrap_model() names the zero-inflation draws of glmmTMB models
-# "<name>_zi". Restore the names and add the component, as in model_parameters()
+# restore names of zero-inflation parameters ("_zi" suffix) and add component
 .add_component_bootstrap_glmmTMB <- function(params, model) {
   if (!inherits(model, "glmmTMB")) {
     return(params)
@@ -123,8 +122,7 @@ model_parameters.bootstrap_model <- bootstrap_parameters.bootstrap_model
     return(params)
   }
   draw_names <- c(fixed_names$conditional, paste0(fixed_names$zero_inflated, "_zi"))
-  # columns that users added to the draws, like linear combinations, keep
-  # their names
+  # user-added columns (e.g. linear combinations) keep their names
   idx <- match(params$Parameter, draw_names)
   found <- !is.na(idx)
   fixed_parameters <- c(fixed_names$conditional, fixed_names$zero_inflated)
diff --git a/R/methods_glmmTMB.R b/R/methods_glmmTMB.R
index 604b6f3cb..7a03a3e9d 100644
--- a/R/methods_glmmTMB.R
+++ b/R/methods_glmmTMB.R
@@ -132,9 +132,8 @@
 #' For models where the dispersion parameter and the residual variance are
 #' the same, only the residual variance is shown in the output.
 #'
-#' With `bootstrap = TRUE`, the output has no dispersion parameters, because
-#' the bootstrapped draws include only the conditional and zero-inflation
-#' parameters. `component = "dispersion"` then gives an error.
+#' With `bootstrap = TRUE`, dispersion parameters are not included in the
+#' output.
 #'
 #' @seealso [insight::standardize_names()] to
 #'   rename columns into a consistent, standardized naming scheme.
@@ -314,8 +313,7 @@ model_parameters.glmmTMB <- function(
       params <- do.call(".extract_parameters_generic", fun_args)
     }
 
-    # add dispersion parameter. bootstrapped draws have no dispersion
-    # parameters, so we don't add a row with Wald intervals for them
+    # add dispersion parameter (not for bootstrapped draws, which have none)
     if (!bootstrap) {
       out <- .add_dispersion_param_glmmTMB(model, params, effects, component, ci, verbose)
       params <- out$params
diff --git a/man/model_parameters.glmmTMB.Rd b/man/model_parameters.glmmTMB.Rd
index d340312e9..9b8c0f394 100644
--- a/man/model_parameters.glmmTMB.Rd
+++ b/man/model_parameters.glmmTMB.Rd
@@ -306,9 +306,8 @@ sigma(model)^2         # 0.09902987
 For models where the dispersion parameter and the residual variance are
 the same, only the residual variance is shown in the output.
 
-With \code{bootstrap = TRUE}, the output has no dispersion parameters, because
-the bootstrapped draws include only the conditional and zero-inflation
-parameters. \code{component = "dispersion"} then gives an error.
+With \code{bootstrap = TRUE}, dispersion parameters are not included in the
+output.
 }
 
 \section{Model components}{

From d9376b33ceae267a2de5fcf9de82ba65ca869091 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Wed, 21 Oct 2026 21:20:35 -0500
Subject: [PATCH 08/10] Trim tests

---
 tests/testthat/test-bootstrap_parameters.R | 171 ++++++---------------
 1 file changed, 47 insertions(+), 124 deletions(-)

diff --git a/tests/testthat/test-bootstrap_parameters.R b/tests/testthat/test-bootstrap_parameters.R
index 0efc584d0..d5a6e1a51 100644
--- a/tests/testthat/test-bootstrap_parameters.R
+++ b/tests/testthat/test-bootstrap_parameters.R
@@ -19,8 +19,26 @@ test_that("bootstrap_model intercept-only", {
   expect_equal(
     as.numeric(out),
     c(
-      6.3, 4.8, 7, 6, 6.3, 6.7, 6.6, 6.6, 6.1, 6.1, 6.3, 6.3, 6.1,
-      7.2, 5.9, 5.6, 5.7, 6.8, 6.7, 6.4
+      6.3,
+      4.8,
+      7,
+      6,
+      6.3,
+      6.7,
+      6.6,
+      6.6,
+      6.1,
+      6.1,
+      6.3,
+      6.3,
+      6.1,
+      7.2,
+      5.9,
+      5.6,
+      5.7,
+      6.8,
+      6.7,
+      6.4
     ),
     tolerance = 1e-2
   )
@@ -404,103 +422,18 @@ test_that("bootstrap_model parametric errors for responses that are not a data c
   )
 })
 
-.fit_zi_glmmTMB <- function(ziformula = ~mined, ...) {
-  data(Salamanders, package = "glmmTMB")
-  glmmTMB::glmmTMB(
-    count ~ mined + (1 | site),
-    ziformula = ziformula,
-    family = poisson,
-    data = Salamanders,
-    ...
-  )
-}
-
-.fit_zi_disp_glmmTMB <- function() {
+test_that("bootstrap_parameters returns zero-inflation components of glmmTMB models", {
+  skip_if_not_installed("glmmTMB")
   data(Salamanders, package = "glmmTMB")
-  glmmTMB::glmmTMB(
+  m <- glmmTMB::glmmTMB(
     count ~ mined + (1 | site),
     ziformula = ~mined,
-    dispformula = ~mined,
-    family = glmmTMB::nbinom2,
+    family = poisson,
     data = Salamanders
   )
-}
-
-test_that("bootstrap_model names zero-inflation columns of glmmTMB models", {
-  skip_if_not_installed("glmmTMB")
-  skip_if_not_installed("lme4")
-  zi_names <- c("(Intercept)", "minedno", "(Intercept)_zi", "minedno_zi")
-
   set.seed(123)
-  expect_named(bootstrap_model(.fit_zi_glmmTMB(), iterations = 5), zi_names)
-  set.seed(123)
-  expect_named(bootstrap_model(.fit_zi_disp_glmmTMB(), iterations = 5), zi_names)
-  set.seed(123)
-  expect_named(
-    bootstrap_model(.fit_zi_glmmTMB(ziformula = ~cover), iterations = 5),
-    c("(Intercept)", "minedno", "(Intercept)_zi", "cover_zi")
-  )
-
-  m_cond <- .fit_zi_glmmTMB(ziformula = ~0)
-  set.seed(123)
-  expect_named(
-    bootstrap_model(m_cond, iterations = 5),
-    insight::find_parameters(m_cond, effects = "fixed")$conditional
-  )
-  data(sleepstudy, package = "lme4")
-  m_lmer <- lme4::lmer(Reaction ~ Days + (1 | Subject), data = sleepstudy)
-  set.seed(123)
-  expect_named(
-    bootstrap_model(m_lmer, iterations = 5),
-    insight::find_parameters(m_lmer, effects = "fixed")$conditional
-  )
-})
-
-test_that("bootstrap_parameters returns components of glmmTMB models", {
-  skip_if_not_installed("glmmTMB")
-  for (m in list(.fit_zi_glmmTMB(), .fit_zi_disp_glmmTMB())) {
-    params <- insight::get_parameters(m)
-    params <- params[params$Component != "dispersion", ]
-    set.seed(123)
-    out <- list(
-      bootstrap_parameters(m, iterations = 20),
-      model_parameters(m, bootstrap = TRUE, iterations = 20, effects = "fixed"),
-      model_parameters(
-        m,
-        bootstrap = TRUE,
-        iterations = 20,
-        effects = "fixed",
-        exponentiate = TRUE
-      )
-    )
-    for (x in out) {
-      expect_identical(x$Parameter, params$Parameter)
-      expect_identical(x$Component, params$Component)
-      expect_false(anyNA(x$Coefficient))
-    }
-  }
-
-  skip_if_not_installed("withr")
-  withr::local_options(width = 300)
-  set.seed(123)
-  mp <- model_parameters(
-    .fit_zi_glmmTMB(),
-    bootstrap = TRUE,
-    iterations = 20,
-    effects = "fixed"
-  )
-  printed <- capture.output(print(mp))
-  zi_start <- grep("# Zero-Inflation", printed, fixed = TRUE)
-  expect_length(zi_start, 1)
-  zi_rows <- printed[seq_along(printed) > min(zi_start, Inf)]
-  expect_length(grep("^\\(Intercept\\)\\s+\\|", zi_rows), 1)
-  expect_length(grep("^mined \\[no\\]\\s+\\|", zi_rows), 1)
-})
-
-test_that("bootstrap_parameters keeps added columns of glmmTMB draws", {
-  skip_if_not_installed("glmmTMB")
-  set.seed(123)
-  b <- bootstrap_model(.fit_zi_glmmTMB(), iterations = 5)
+  b <- bootstrap_model(m, iterations = 5)
+  expect_named(b, c("(Intercept)", "minedno", "(Intercept)_zi", "minedno_zi"))
   b$lin_comb <- b$minedno - b$minedno_zi
   out <- bootstrap_parameters(b)
   expect_identical(
@@ -511,55 +444,45 @@ test_that("bootstrap_parameters keeps added columns of glmmTMB draws", {
     out$Component,
     c("conditional", "conditional", "zero_inflated", "zero_inflated", "conditional")
   )
-  expect_equal(out$Coefficient[5], median(b$lin_comb), tolerance = 1e-10)
-})
-
-test_that("bootstrap_parameters matches each glmmTMB draw to its parameter", {
-  skip_if_not_installed("glmmTMB")
-  m <- .fit_zi_glmmTMB(ziformula = ~cover)
-  params <- insight::get_parameters(m)
-  set.seed(123)
-  out <- bootstrap_parameters(m, iterations = 50)
-  own <- match(
-    paste(out$Parameter, out$Component),
-    paste(params$Parameter, params$Component)
-  )
-  distances <- abs(outer(out$Coefficient, params$Estimate, "-"))
-  closest <- apply(distances, 1, function(d) which.min(d)[1])
-  expect_identical(closest, own)
-  expect_false(anyNA(own))
+  estimates <- insight::get_parameters(m)$Estimate
+  expect_lt(max(abs(out$Coefficient[1:4] - estimates)), 0.5)
 })
 
 test_that("model_parameters with bootstrap uses component for glmmTMB", {
   skip_if_not_installed("glmmTMB")
-  m <- .fit_zi_glmmTMB()
-  for (comp in c("conditional", "zi")) {
+  data(Salamanders, package = "glmmTMB")
+  m <- glmmTMB::glmmTMB(
+    count ~ mined + (1 | site),
+    ziformula = ~mined,
+    dispformula = ~mined,
+    family = glmmTMB::nbinom2,
+    data = Salamanders
+  )
+  for (comp in c("all", "conditional", "zi")) {
     expected <- model_parameters(m, component = comp, effects = "fixed")
+    if (comp == "all") {
+      expected <- expected[expected$Component != "dispersion", ]
+    }
     set.seed(123)
     out <- model_parameters(
       m,
       bootstrap = TRUE,
-      iterations = 20,
+      iterations = 5,
       component = comp,
       effects = "fixed"
     )
     expect_identical(out$Parameter, expected$Parameter)
     expect_identical(out$Component, expected$Component)
   }
+  printed <- evaluate_promise(print(out))
+  expect_match(paste(printed$messages, collapse = " "), "bootstrap", fixed = TRUE)
   expect_error(
     model_parameters(m, bootstrap = TRUE, iterations = 5, component = "dispersion"),
     "Bootstrapping\\s+does\\s+not\\s+return\\s+dispersion\\s+parameters"
   )
-})
 
-test_that("model_parameters with bootstrap prints a bootstrap footer for glmmTMB", {
-  skip_if_not_installed("glmmTMB")
-  for (m in list(.fit_zi_glmmTMB(), .fit_zi_glmmTMB(ziformula = ~0))) {
-    set.seed(123)
-    mp <- model_parameters(m, bootstrap = TRUE, iterations = 20, effects = "fixed")
-    printed <- evaluate_promise(print(mp))
-    printed <- paste(c(printed$output, printed$messages), collapse = " ")
-    expect_match(printed, "bootstrap", fixed = TRUE)
-    expect_no_match(printed, "Wald", fixed = TRUE)
-  }
+  m <- glmmTMB::glmmTMB(count ~ mined + (1 | site), family = poisson, data = Salamanders)
+  set.seed(123)
+  out <- model_parameters(m, bootstrap = TRUE, iterations = 5, effects = "fixed")
+  expect_identical(out$Parameter, c("(Intercept)", "minedno"))
 })

From d95582e67efe12eb64bd1fb10b10c80fcf36742a Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Wed, 21 Oct 2026 21:20:56 -0500
Subject: [PATCH 09/10] Restore formatting of an unchanged test

---
 tests/testthat/test-bootstrap_parameters.R | 22 ++--------------------
 1 file changed, 2 insertions(+), 20 deletions(-)

diff --git a/tests/testthat/test-bootstrap_parameters.R b/tests/testthat/test-bootstrap_parameters.R
index d5a6e1a51..1ba451bbd 100644
--- a/tests/testthat/test-bootstrap_parameters.R
+++ b/tests/testthat/test-bootstrap_parameters.R
@@ -19,26 +19,8 @@ test_that("bootstrap_model intercept-only", {
   expect_equal(
     as.numeric(out),
     c(
-      6.3,
-      4.8,
-      7,
-      6,
-      6.3,
-      6.7,
-      6.6,
-      6.6,
-      6.1,
-      6.1,
-      6.3,
-      6.3,
-      6.1,
-      7.2,
-      5.9,
-      5.6,
-      5.7,
-      6.8,
-      6.7,
-      6.4
+      6.3, 4.8, 7, 6, 6.3, 6.7, 6.6, 6.6, 6.1, 6.1, 6.3, 6.3, 6.1,
+      7.2, 5.9, 5.6, 5.7, 6.8, 6.7, 6.4
     ),
     tolerance = 1e-2
   )

From d20dca25d7db60b68c634d3ffe56dc3d1016198d Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 29 Oct 2026 11:09:37 +0100
Subject: [PATCH 10/10] Set Version to 0.30.0.13

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d7c30cb7e..f42bc344d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.30.0.12
+Version: 0.30.0.13
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",