From eb1a5cb4e4f19d87b1eb8abec3c7c4bba2e5dff3 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 09:22:02 +0800
Subject: [PATCH 01/19] Update/simplify actions workflow

---
 .github/workflows/R-CMD-check.yaml | 28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 96412eb7e..98cb8517e 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -8,6 +8,10 @@ on:
     branches:
       - master
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 name: R-CMD-check
 
 jobs:
@@ -27,19 +31,23 @@ jobs:
       TESTTHAT_CPUS: 4
 
     steps:
-      - uses: n1hility/cancel-previous-runs@master
+      - uses: actions/checkout@v7
+
+      - uses: r-lib/actions/setup-r@v2
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-        if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
+          r-version: ${{ matrix.r }}
 
-      - uses: actions/checkout@main
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v2.11.4
+
+      - name: Install R Package Build Dependencies on MacOS
+        if: ${{ runner.os == 'macOS' }}
+        uses: r-hub/actions/setup-r-sysreqs@v1
         with:
-          r-version: ${{ matrix.r }}
+          type: 'minimal'
 
-      - uses: r-lib/actions/setup-pandoc@v2.11.4
-      - uses: r-lib/actions/setup-r-dependencies@v2.11.4
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck any::betareg any::HSAUR3 any::biglm any::gamm4 any::V8
-      - uses: r-lib/actions/check-r-package@v2.11.4
+          dependencies: "TRUE"
+
+      - uses: r-lib/actions/check-r-package@v2

From 502035c61b793b7c389363e92cd263377054a64f Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 09:22:25 +0800
Subject: [PATCH 02/19] Update test expectation for new loo text

---
 tests/testthat/test_loo.R | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/testthat/test_loo.R b/tests/testthat/test_loo.R
index 4b320cef8..d07e0ac25 100644
--- a/tests/testthat/test_loo.R
+++ b/tests/testthat/test_loo.R
@@ -113,7 +113,7 @@ test_that("loo with k_threshold works", {
                      seed = 12345, iter = 5, chains = 1, cores = 1,
                      refresh = 0))
   expect_message(loo(fit, k_threshold = 0.5), "Model will be refit")
-  
+
   # test that no errors from binomial model because it's trickier to get the
   # data right internally in reloo (matrix outcome)
   SW(loo_x <- loo(example_model))
@@ -213,17 +213,17 @@ test_that("loo_compare throws correct errors", {
 
   # this uses loo::loo_compare
   expect_error(loo_compare(l1, l2),
-               "Not all models have the same number of data points")
+               "All models must have the same number of observations")
   expect_error(loo_compare(list(l4, l2, l3)),
-               "Not all models have the same number of data points")
-  
+               "All models must have the same number of observations")
+
   # using loo_compare.stanreg (can do extra checks)
   fit1$loo <- l1
   fit2$loo <- l2
   fit3$loo <- l3
   fit4$loo <- l4
-  
-  expect_error(loo_compare(fit1, fit2), "Not all models have the same number of data points")
+
+  expect_error(loo_compare(fit1, fit2), "All models must have the same number of observations")
   expect_warning(loo_compare(fit1, fit3), "Not all models have the same y variable")
   expect_error(loo_compare(fit1, fit4),
                "Discrete and continuous observation models can't be compared")
@@ -269,15 +269,15 @@ test_that("loo_compare works", {
   expect_s3_class(comp2, "compare.loo")
   expect_equal(comp1[, "elpd_diff"], loo_compare(list(fit1$loo, fit2$loo))[, "elpd_diff"])
   expect_equal(comp2[, "elpd_diff"], loo_compare(list(fit1$loo, fit2$loo, fit3$loo))[, "elpd_diff"])
-  
+
   comp1_detail <- loo_compare(fit1, fit2, detail=TRUE)
   expect_output(print(comp1_detail), "Model formulas")
-  
+
   # equivalent to stanreg_list method
   expect_equivalent(comp2, loo_compare(stanreg_list(fit1, fit2, fit3)))
 
   # for kfold
-  expect_warning(comp3 <- loo_compare(k1, k2, k3), 
+  expect_warning(comp3 <- loo_compare(k1, k2, k3),
                  "Not all kfold objects have the same K value")
   expect_true(attr(k4, "discrete"))
   expect_true(attr(k5, "discrete"))

From ec631303ae5721596675182f1dc487bf26f19397 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 09:22:58 +0800
Subject: [PATCH 03/19] Update VarCorr return to align with lme4 changes

---
 R/stanreg-methods.R           | 6 ++++--
 tests/testthat/test_methods.R | 3 +--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/R/stanreg-methods.R b/R/stanreg-methods.R
index 6e54a52f4..f267a708d 100644
--- a/R/stanreg-methods.R
+++ b/R/stanreg-methods.R
@@ -363,7 +363,8 @@ VarCorr.stanreg <- function(x, sigma = 1, ...) {
       rownames(Sigma) <- colnames(Sigma) <- cnms[[i]]
       stddev <- sqrt(diag(Sigma))
       corr <- cov2cor(Sigma)
-      structure(Sigma, stddev = stddev, correlation = corr)
+      structure(Sigma, stddev = stddev, correlation = corr,
+          class = c("vcmat_us", "matrix", "array"))
     })       
   } else { # stanfit contains lower tri Sigma entries
     spt <- split(Sigma, rep.int(ncseq, (nc * (nc + 1)) / 2))
@@ -375,7 +376,8 @@ VarCorr.stanreg <- function(x, sigma = 1, ...) {
       rownames(Sigma) <- colnames(Sigma) <- cnms[[i]]
       stddev <- sqrt(diag(Sigma))
       corr <- cov2cor(Sigma)
-      structure(Sigma, stddev = stddev, correlation = corr)
+      structure(Sigma, stddev = stddev, correlation = corr,
+                class = c("vcmat_us", "matrix", "array"))
     })    
   }
   names(ans) <- nms
diff --git a/tests/testthat/test_methods.R b/tests/testthat/test_methods.R
index 4df7bd71a..2a0090bf2 100644
--- a/tests/testthat/test_methods.R
+++ b/tests/testthat/test_methods.R
@@ -71,7 +71,7 @@ SW({
 
 att_names <- function(object) {
   nms <- names(object)
-  att_nms <- names(attributes(object))
+  att_nms <- sort(names(attributes(object)))
   att_nms2 <- lapply(object, function(x) sort(names(attributes(x))))
   c(nms, att_nms, att_nms2)
 }
@@ -869,4 +869,3 @@ test_that("as_draws methods work", {
     "not fit using MCMC"
   )
 })
-

From e3514b275847944f79bc99b24abeca7c50ab226e Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 09:39:00 +0800
Subject: [PATCH 04/19] Update pp_check exclusions for new functions

---
 R/pp_check.R                   |  2 +-
 tests/testthat/test_pp_check.R | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/R/pp_check.R b/R/pp_check.R
index e484edf44..cbf4b00ac 100644
--- a/R/pp_check.R
+++ b/R/pp_check.R
@@ -312,7 +312,7 @@ is_binomial_ppc <- function(object, ...) {
     if (!is.null(xvar)) {
       dots[["x"]] <- .ppc_xvar(object, xvar, m = m)
     } else {
-      if (funname %in% c("ppc_intervals", "ppc_ribbon", "ppc_error_binned")) {
+      if (funname %in% c("ppc_intervals", "ppc_ribbon", "ppc_error_binned", "ppc_error_scatter_avg")) {
         message("'x' not specified in '...'. Using x=1:length(y).")
         dots[["x"]] <- seq_along(y)
       } else {
diff --git a/tests/testthat/test_pp_check.R b/tests/testthat/test_pp_check.R
index adc1831ed..b2c9720a9 100644
--- a/tests/testthat/test_pp_check.R
+++ b/tests/testthat/test_pp_check.R
@@ -49,7 +49,12 @@ test_that("pp_check.stanreg creates ggplot object", {
                "ppc_rootogram",
                "ppc_error_binned",
                "ppc_km_overlay",
-               "ppc_pit_ecdf")
+               "ppc_pit_ecdf",
+               "ppc_calibration",
+               "ppc_calibration_overlay",
+               "ppc_dots",
+               "ppc_loo_calibration",
+               "ppc_loo_pit_ecdf")
   for (f in ppc_funs_not_grouped) for (j in 1:2) {
     if (!f %in% exclude) {
       expect_gg(suppressWarnings(pp_check(fit, plotfun = f, nreps = j)),
@@ -59,7 +64,8 @@ test_that("pp_check.stanreg creates ggplot object", {
 })
 
 test_that("pp_check.stanreg creates ggplot object for grouped functions", {
-  exclude <- c("ppc_km_overlay_grouped", "ppc_pit_ecdf_grouped")
+  exclude <- c("ppc_km_overlay_grouped", "ppc_pit_ecdf_grouped", "ppc_calibration_grouped",
+               "ppc_calibration_overlay_grouped", "ppc_loo_calibration_grouped")
   for (f in setdiff(ppc_funs_grouped, ppc_funs_discrete)) for (j in 1:2) {
     if (!(f %in% exclude)) {
       expect_gg(suppressWarnings(pp_check(fit2, plotfun = f, nreps = j, group = "am", x = "wt")),

From 1e75183cf853e2d18359cd7a9491d62a2a2e9743 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 09:44:33 +0800
Subject: [PATCH 05/19] Update clogit test expectations

---
 tests/testthat/test_stan_clogit.R | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/testthat/test_stan_clogit.R b/tests/testthat/test_stan_clogit.R
index 532d4314f..df071e034 100644
--- a/tests/testthat/test_stan_clogit.R
+++ b/tests/testthat/test_stan_clogit.R
@@ -36,10 +36,6 @@ SW(fit <- stan_clogit(case ~ spontaneous + induced, strata = stratum, prior = NU
 
 test_that("stan_clogit is similar to survival::clogit", {
   ref_vals <- c(spontaneous = 1.985876, induced = 1.409012)
-  # Account for RNG change in new Stan
-  if (utils::packageVersion("StanHeaders") >= "2.36") {
-    ref_vals <- c(spontaneous = 2.062676, induced = 1.360712)
-  }
   expect_equal(ref_vals, coef(fit), tol = threshold)
 })
 

From 71b48518494e2a37bb78f9b217dc5e1bcc924e0a Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 10:04:34 +0800
Subject: [PATCH 06/19] Update loo test helper to align with implementation

---
 tests/testthat/helper.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index 18d409528..a3974c30b 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -53,7 +53,7 @@ check_for_pp_errors <- function(fit, data = NULL, offset = NULL) {
 
 expect_equivalent_loo <- function(fit) {
   LOO.CORES <- ifelse(.Platform$OS.type == "windows", 1, 2)
-  l <- suppressWarnings(loo(fit, cores = LOO.CORES))
+  l <- suppressWarnings(loo(fit, cores = LOO.CORES, r_eff = TRUE))
   w <- suppressWarnings(waic(fit))
   expect_s3_class(l, "psis_loo")
   expect_s3_class(l, "loo")
@@ -214,4 +214,3 @@ recover_pars <- function(modLong, modEvent = NULL, idvar = "id") {
     list(fixef = fixef_pars, ranef = ranef_pars, event = event_pars))
   return(ret)
 }
-

From 0d0be9af1b5f58e1de80726ef49b91fdbabd8bcf Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 10:11:38 +0800
Subject: [PATCH 07/19] Replace deprecated ggplot syntax, re-generate doc

---
 DESCRIPTION             |   2 +-
 NAMESPACE               | 177 ++++++++++++++++++++++------------------
 R/stan_gamm4.R          |  12 +--
 man/reexports.Rd        |   2 +-
 man/rstanarm-package.Rd |   3 +-
 man/stan_betareg.Rd     |   2 +-
 man/stan_biglm.Rd       |   2 +-
 man/stan_clogit.Rd      |   2 +-
 man/stan_gamm4.Rd       |   2 +-
 man/stan_glm.Rd         |   2 +-
 man/stan_glmer.Rd       |   2 +-
 man/stan_jm.Rd          |   2 +-
 man/stan_lm.Rd          |   2 +-
 man/stan_mvmer.Rd       |   2 +-
 man/stan_nlmer.Rd       |   2 +-
 man/stan_polr.Rd        |   2 +-
 16 files changed, 119 insertions(+), 99 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5a5a8fde3..c80c2b622 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -76,4 +76,4 @@ UseLTO: true
 NeedsCompilation: yes
 URL: https://mc-stan.org/rstanarm/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/rstanarm/issues
-RoxygenNote: 7.3.3
+Config/roxygen2/version: 8.1.0
diff --git a/NAMESPACE b/NAMESPACE
index 1f93e3581..831990c53 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -197,88 +197,107 @@ import(methods)
 import(rstantools)
 import(shinystan)
 import(stats)
-importFrom(Matrix,Matrix)
-importFrom(Matrix,t)
+importFrom(Matrix,
+  Matrix,
+  t
+)
 importFrom(RcppParallel,RcppParallelLibs)
-importFrom(bayesplot,pairs_condition)
-importFrom(bayesplot,pairs_style_np)
-importFrom(ggplot2,"%+replace%")
-importFrom(ggplot2,aes)
-importFrom(ggplot2,aes_)
-importFrom(ggplot2,aes_string)
-importFrom(ggplot2,coord_cartesian)
-importFrom(ggplot2,element_line)
-importFrom(ggplot2,element_text)
-importFrom(ggplot2,expand_limits)
-importFrom(ggplot2,facet_wrap)
-importFrom(ggplot2,geom_contour)
-importFrom(ggplot2,geom_line)
-importFrom(ggplot2,geom_point)
-importFrom(ggplot2,geom_pointrange)
-importFrom(ggplot2,geom_ribbon)
-importFrom(ggplot2,geom_segment)
-importFrom(ggplot2,geom_smooth)
-importFrom(ggplot2,geom_step)
-importFrom(ggplot2,geom_vline)
-importFrom(ggplot2,ggplot)
-importFrom(ggplot2,ggplot_build)
-importFrom(ggplot2,labs)
-importFrom(ggplot2,rel)
-importFrom(ggplot2,scale_color_gradient2)
-importFrom(ggplot2,scale_x_continuous)
-importFrom(ggplot2,scale_x_discrete)
-importFrom(ggplot2,theme)
-importFrom(ggplot2,theme_bw)
-importFrom(ggplot2,xlab)
-importFrom(lme4,fixef)
-importFrom(lme4,glFormula)
-importFrom(lme4,glmer)
-importFrom(lme4,glmerControl)
-importFrom(lme4,lmer)
-importFrom(lme4,lmerControl)
-importFrom(lme4,mkVarCorr)
-importFrom(lme4,ngrps)
-importFrom(lme4,nlformula)
-importFrom(lme4,nlmer)
-importFrom(lme4,nlmerControl)
-importFrom(lme4,ranef)
-importFrom(loo,is.kfold)
-importFrom(loo,is.loo)
-importFrom(loo,is.waic)
-importFrom(loo,kfold)
-importFrom(loo,loo)
-importFrom(loo,loo.function)
-importFrom(loo,loo.matrix)
-importFrom(loo,loo_compare)
-importFrom(loo,loo_model_weights)
-importFrom(loo,psis)
-importFrom(loo,waic)
-importFrom(loo,waic.function)
-importFrom(loo,waic.matrix)
+importFrom(bayesplot,
+  pairs_condition,
+  pairs_style_np
+)
+importFrom(ggplot2,
+  "%+replace%",
+  aes,
+  aes_string,
+  coord_cartesian,
+  element_line,
+  element_text,
+  expand_limits,
+  facet_wrap,
+  geom_contour,
+  geom_line,
+  geom_point,
+  geom_pointrange,
+  geom_ribbon,
+  geom_segment,
+  geom_smooth,
+  geom_step,
+  geom_vline,
+  ggplot,
+  ggplot_build,
+  labs,
+  rel,
+  scale_color_gradient2,
+  scale_x_continuous,
+  scale_x_discrete,
+  theme,
+  theme_bw,
+  xlab
+)
+importFrom(lme4,
+  fixef,
+  glFormula,
+  glmer,
+  glmerControl,
+  lmer,
+  lmerControl,
+  mkVarCorr,
+  ngrps,
+  nlformula,
+  nlmer,
+  nlmerControl,
+  ranef
+)
+importFrom(loo,
+  is.kfold,
+  is.loo,
+  is.waic,
+  kfold,
+  loo,
+  loo.function,
+  loo.matrix,
+  loo_compare,
+  loo_model_weights,
+  psis,
+  waic,
+  waic.function,
+  waic.matrix
+)
 importFrom(nlme,VarCorr)
-importFrom(posterior,as_draws)
-importFrom(posterior,as_draws_array)
-importFrom(posterior,as_draws_df)
-importFrom(posterior,as_draws_list)
-importFrom(posterior,as_draws_matrix)
-importFrom(posterior,as_draws_rvars)
+importFrom(posterior,
+  as_draws,
+  as_draws_array,
+  as_draws_df,
+  as_draws_list,
+  as_draws_matrix,
+  as_draws_rvars
+)
 importFrom(reformulas,findbars)
-importFrom(rstan,constrain_pars)
-importFrom(rstan,extract)
-importFrom(rstan,extract_sparse_parts)
-importFrom(rstan,get_posterior_mean)
-importFrom(rstan,optimizing)
-importFrom(rstan,sampling)
-importFrom(rstan,stanc)
-importFrom(rstan,vb)
-importFrom(rstantools,loo_R2)
-importFrom(rstantools,nsamples)
-importFrom(stats,cov2cor)
-importFrom(stats,getInitial)
+importFrom(rstan,
+  constrain_pars,
+  extract,
+  extract_sparse_parts,
+  get_posterior_mean,
+  optimizing,
+  sampling,
+  stanc,
+  vb
+)
+importFrom(rstantools,
+  loo_R2,
+  nsamples
+)
+importFrom(stats,
+  cov2cor,
+  getInitial
+)
 importFrom(survival,Surv)
-importFrom(utils,capture.output)
-importFrom(utils,head)
-importFrom(utils,packageVersion)
-importFrom(utils,tail)
+importFrom(utils,
+  capture.output,
+  head,
+  packageVersion,
+  tail
+)
 importMethodsFrom(rstan,summary)
 useDynLib(rstanarm, .registration = TRUE)
diff --git a/R/stan_gamm4.R b/R/stan_gamm4.R
index a6380c845..f593c585e 100644
--- a/R/stan_gamm4.R
+++ b/R/stan_gamm4.R
@@ -291,7 +291,7 @@ stan_gamm4 <-
 #'   
 #' @return \code{plot_nonlinear} returns a ggplot object.
 #' 
-#' @importFrom ggplot2 aes_ aes_string facet_wrap ggplot geom_contour geom_line geom_ribbon labs scale_color_gradient2
+#' @importFrom ggplot2 aes aes_string facet_wrap ggplot geom_contour geom_line geom_ribbon labs scale_color_gradient2
 #' 
 plot_nonlinear <- function(x, smooths, ..., 
                            prob = 0.9, facet_args = list(), 
@@ -416,12 +416,12 @@ plot_nonlinear <- function(x, smooths, ...,
     facet_args[["strip.position"]] <- "left"
 
   on.exit(NULL)  
-  ggplot(plot_data, aes_(x = ~ predictor)) + 
-    geom_ribbon(aes_(ymin = ~ lower, ymax = ~ upper), 
+  ggplot(plot_data, aes(x = predictor)) + 
+    geom_ribbon(aes(ymin = lower, ymax = upper), 
                 fill = scheme[[1]], color = scheme[[2]],
-                alpha = alpha, size = size) + 
-    geom_line(aes_(y = ~ middle), color = scheme[[5]], 
-              size = 0.75 * size, lineend = "round") + 
+                alpha = alpha, linewidth = size) + 
+    geom_line(aes(y = middle), color = scheme[[5]], 
+              linewidth = 0.75 * size, lineend = "round") + 
     labs(y = NULL) + 
     do.call(facet_wrap, facet_args) + 
     bayesplot::theme_default()
diff --git a/man/reexports.Rd b/man/reexports.Rd
index eeb735c72..9577bbdd1 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -11,6 +11,6 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.
 
 \describe{
-  \item{survival}{\code{\link[survival]{Surv}}}
+  \item{survival}{\code{\link[survival:Surv]{Surv()}}}
 }}
 
diff --git a/man/rstanarm-package.Rd b/man/rstanarm-package.Rd
index acaae097f..94686a7fd 100644
--- a/man/rstanarm-package.Rd
+++ b/man/rstanarm-package.Rd
@@ -7,7 +7,7 @@
 \title{Applied Regression Modeling via RStan}
 \description{
 \if{html}{
-   \figure{stanlogo.png}{options: width="50" alt="https://mc-stan.org/about/logo/"}
+   \figure{logo.svg}{options: width="50" alt="https://mc-stan.org/about/logo/"}
    \emph{Stan Development Team}
 }
 
@@ -242,6 +242,7 @@ User-friendly Bayesian regression modeling: A tutorial with rstanarm and shinyst
 
 Authors:
 \itemize{
+  \item Ben Goodrich \email{benjamin.goodrich@columbia.edu}
   \item Jonah Gabry \email{jgabry@gmail.com}
 }
 
diff --git a/man/stan_betareg.Rd b/man/stan_betareg.Rd
index c7a641ae0..6e707cd96 100644
--- a/man/stan_betareg.Rd
+++ b/man/stan_betareg.Rd
@@ -205,7 +205,7 @@ A \link[rstan:stanfit-class]{stanfit} object (or a slightly modified
   stanfit object) is returned if \code{stan_betareg.fit} is called directly.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 Beta regression modeling with optional prior distributions for the 
 coefficients, intercept, and auxiliary parameter \code{phi} (if applicable).
 }
diff --git a/man/stan_biglm.Rd b/man/stan_biglm.Rd
index 99b81bc6d..91608231a 100644
--- a/man/stan_biglm.Rd
+++ b/man/stan_biglm.Rd
@@ -139,7 +139,7 @@ The output of both \code{stan_biglm} and \code{stan_biglm.fit} is an
   \code{\link{posterior_predict}} cannot be used.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 This is the same model as with \code{\link{stan_lm}} but it utilizes the
 output from \code{\link[biglm]{biglm}} in the \pkg{biglm} package in order to
 proceed when the data is too large to fit in memory.
diff --git a/man/stan_clogit.Rd b/man/stan_clogit.Rd
index 180fb7df5..5dfa25769 100644
--- a/man/stan_clogit.Rd
+++ b/man/stan_clogit.Rd
@@ -126,7 +126,7 @@ A \link[=stanreg-objects]{stanreg} object is returned
 for \code{stan_clogit}.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 A model for case-control studies with optional prior distributions for the
 coefficients, intercept, and auxiliary parameters.
 }
diff --git a/man/stan_gamm4.Rd b/man/stan_gamm4.Rd
index 16434f825..9d1ea43d9 100644
--- a/man/stan_gamm4.Rd
+++ b/man/stan_gamm4.Rd
@@ -212,7 +212,7 @@ for \code{stan_gamm4}.
 \code{plot_nonlinear} returns a ggplot object.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 Bayesian inference for GAMMs with flexible priors.
 }
 \details{
diff --git a/man/stan_glm.Rd b/man/stan_glm.Rd
index 1577796fa..f334d82d2 100644
--- a/man/stan_glm.Rd
+++ b/man/stan_glm.Rd
@@ -290,7 +290,7 @@ A \link[rstan:stanfit-class]{stanfit} object (or a slightly modified
   stanfit object) is returned if \code{stan_glm.fit} is called directly.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 Generalized linear modeling with optional prior distributions for the
 coefficients, intercept, and auxiliary parameters.
 }
diff --git a/man/stan_glmer.Rd b/man/stan_glmer.Rd
index e8c0d6dd9..2385291be 100644
--- a/man/stan_glmer.Rd
+++ b/man/stan_glmer.Rd
@@ -228,7 +228,7 @@ A list with classes \code{stanreg}, \code{glm}, \code{lm},
   one row and one column (in which case it is just the group-level variance).
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 Bayesian inference for GLMs with group-specific coefficients that have 
 unknown covariance matrices with flexible priors.
 }
diff --git a/man/stan_jm.Rd b/man/stan_jm.Rd
index 758f575d0..e8b779eab 100644
--- a/man/stan_jm.Rd
+++ b/man/stan_jm.Rd
@@ -352,7 +352,7 @@ turns off the iteration updates.}
 A \link[=stanreg-objects]{stanjm} object is returned.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 Fits a shared parameter joint model for longitudinal and time-to-event 
 (e.g. survival) data under a Bayesian framework using Stan.
 }
diff --git a/man/stan_lm.Rd b/man/stan_lm.Rd
index 8e2e25151..5c92c3cd4 100644
--- a/man/stan_lm.Rd
+++ b/man/stan_lm.Rd
@@ -151,7 +151,7 @@ A \link[rstan:stanfit-class]{stanfit} object (or a slightly modified
   stanfit object) is returned if \code{stan_lm.fit or stan_lm.wfit} is called directly.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 Bayesian inference for linear modeling with regularizing priors on the model
 parameters that are driven by prior beliefs about \eqn{R^2}, the proportion
 of variance in the outcome attributable to the predictors. See
diff --git a/man/stan_mvmer.Rd b/man/stan_mvmer.Rd
index 78b7306d9..f6d015bdd 100644
--- a/man/stan_mvmer.Rd
+++ b/man/stan_mvmer.Rd
@@ -128,7 +128,7 @@ turns off the iteration updates.}
 A \link[=stanreg-objects]{stanmvreg} object is returned.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 Bayesian inference for multivariate GLMs with group-specific coefficients 
 that are assumed to be correlated across the GLM submodels.
 }
diff --git a/man/stan_nlmer.Rd b/man/stan_nlmer.Rd
index 866757f46..3d8681c5e 100644
--- a/man/stan_nlmer.Rd
+++ b/man/stan_nlmer.Rd
@@ -149,7 +149,7 @@ A \link[=stanreg-objects]{stanreg} object is returned
 for \code{stan_nlmer}.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 Bayesian inference for NLMMs with group-specific coefficients that have 
 unknown covariance matrices with flexible priors.
 }
diff --git a/man/stan_polr.Rd b/man/stan_polr.Rd
index 53e140a36..6a2d6d80c 100644
--- a/man/stan_polr.Rd
+++ b/man/stan_polr.Rd
@@ -127,7 +127,7 @@ A \link[rstan:stanfit-class]{stanfit} object (or a slightly modified
   stanfit object) is returned if \code{stan_polr.fit} is called directly.
 }
 \description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
 Bayesian inference for ordinal (or binary) regression models under a
 proportional odds assumption.
 }

From 3478f7faa172b8955b663d7832ae59381e2c31be Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 10:39:52 +0800
Subject: [PATCH 08/19] Test run

---
 .github/workflows/R-CMD-check.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 98cb8517e..01489fe5d 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - master
+      - ci-fixes
   pull_request:
     branches:
       - master

From 1d530deac93632849c3cb9907ab95ed366b67520 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 10:43:06 +0800
Subject: [PATCH 09/19] Missed rcmdcheck in workflow

---
 .github/workflows/R-CMD-check.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 01489fe5d..a3611c0e9 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -50,5 +50,6 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: "TRUE"
+          extra-packages: any::rcmdcheck
 
       - uses: r-lib/actions/check-r-package@v2

From 4e264fa0403b6ecf99d22fa17f46cae829a96c34 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 11:24:53 +0800
Subject: [PATCH 10/19] Fix grouping-factor consistency

---
 R/jm_data_block.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/jm_data_block.R b/R/jm_data_block.R
index 113306016..828651cce 100644
--- a/R/jm_data_block.R
+++ b/R/jm_data_block.R
@@ -857,7 +857,7 @@ get_common_cnms <- function(x, stub = "Long") {
       if (nm %in% nms[[m]]) paste0(stub, m, "|", x[[m]][[nm]])))
   })
   names(cnms) <- unique_nms
-  cnms
+  cnms[order(names(cnms))]
 }
 
 # Function to return a single list with the factor levels for each
@@ -2097,4 +2097,3 @@ handle_weights <- function(mod_stuff, weights, id_var) {
   
   wts
 }
-

From 096b9097b6ed6e3e8a049ebd0b75eab6469ee5d5 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 11:55:17 +0800
Subject: [PATCH 11/19] Update test iterations

---
 tests/testthat/test_stan_clogit.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test_stan_clogit.R b/tests/testthat/test_stan_clogit.R
index df071e034..2f719bffa 100644
--- a/tests/testthat/test_stan_clogit.R
+++ b/tests/testthat/test_stan_clogit.R
@@ -20,7 +20,7 @@
 suppressPackageStartupMessages(library(rstanarm))
 
 SEED <- 123
-ITER <- 100
+ITER <- 200
 CHAINS <- 2
 CORES <- 1
 REFRESH <- 0

From 8a443983914d7d2b8246595f5b968f6b0a6f0551 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 13:07:05 +0800
Subject: [PATCH 12/19] Fix unused variable NOTEs

---
 R/stan_gamm4.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/stan_gamm4.R b/R/stan_gamm4.R
index f593c585e..6608f7ddc 100644
--- a/R/stan_gamm4.R
+++ b/R/stan_gamm4.R
@@ -301,6 +301,7 @@ plot_nonlinear <- function(x, smooths, ...,
     stop("Plot only available for models fit using the stan_gamm4 function.")
   on.exit(message("try plot(x$jam) instead"))
   scheme <- bayesplot::color_scheme_get()
+  predictor <- lower <- upper <- middle <- y <- z <- NULL
   
   XZ <- x$x
   XZ <- XZ[,!grepl("_NEW_", colnames(XZ), fixed = TRUE)]
@@ -354,7 +355,7 @@ plot_nonlinear <- function(x, smooths, ...,
     xz <- XZ[, grepl(labels, colnames(XZ), fixed = TRUE), drop = FALSE]
     plot_data$z <- apply(linear_predictor.matrix(b, xz), 2, FUN = median)
     return(
-      ggplot(plot_data, aes_(x = ~x, y = ~y, z = ~z)) + 
+      ggplot(plot_data, aes(x = x, y = y, z = z)) + 
              geom_contour(aes_string(color = "..level.."), size = size/2) + 
              labs(x = xnames[1], y = xnames[2]) + 
              scale_color_gradient2(low = scheme[[1]],

From 8ae0e29d4d12540d6dc2b040428ece411b92e5b8 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 14:05:30 +0800
Subject: [PATCH 13/19] Update to testthat edition 3, run tests in parallel

---
 DESCRIPTION                             |  4 +-
 tests/testthat/helper.R                 | 15 +++---
 tests/testthat/test_loo.R               | 16 +++----
 tests/testthat/test_methods.R           | 31 +++++-------
 tests/testthat/test_misc.R              | 34 +++++++------
 tests/testthat/test_plots.R             |  6 +--
 tests/testthat/test_posterior_predict.R | 12 ++---
 tests/testthat/test_pp_check.R          |  1 -
 tests/testthat/test_pp_validate.R       |  1 -
 tests/testthat/test_predict.R           | 63 ++++++++++++-------------
 tests/testthat/test_stan_betareg.R      | 15 +++---
 tests/testthat/test_stan_clogit.R       |  4 +-
 tests/testthat/test_stan_functions.R    | 46 ++++++------------
 tests/testthat/test_stan_glm.R          | 38 +++++++--------
 tests/testthat/test_stan_glmer.R        | 30 +++++-------
 tests/testthat/test_stan_jm.R           |  7 ++-
 tests/testthat/test_stan_lm.R           | 14 +++---
 tests/testthat/test_stan_mvmer.R        | 25 +++++-----
 tests/testthat/test_stan_nlmer.R        |  4 +-
 tests/testthat/test_stan_polr.R         |  8 ++--
 20 files changed, 167 insertions(+), 207 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c80c2b622..93243271a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,7 +63,7 @@ Suggests:
     rmarkdown,
     roxygen2,
     StanHeaders (>= 2.21.0),
-    testthat (>= 1.0.2),
+    testthat (>= 3.0.0),
     gamm4,
     shiny,
     V8
@@ -77,3 +77,5 @@ NeedsCompilation: yes
 URL: https://mc-stan.org/rstanarm/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/rstanarm/issues
 Config/roxygen2/version: 8.1.0
+Config/testthat/edition: 3
+Config/testthat/parallel: true
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index a3974c30b..bd1a59e39 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -47,7 +47,7 @@ check_for_pp_errors <- function(fit, data = NULL, offset = NULL) {
   expect_equal(dim(yrep6), c(3, 5))
   
   expect_error(posterior_predict(fit, draws = nsims + 1), 
-               regexep = "posterior sample size is only")
+               regexp = "'draws' should be <= posterior sample size")
 }
 
 
@@ -69,15 +69,16 @@ expect_equivalent_loo <- function(fit) {
   
   if (fit$stan_function != "stan_clogit") {
     ll <- log_lik(fit)
-    r_eff <- loo::relative_eff(exp(ll), chain_id = rstanarm:::chain_id_for_loo(fit))
+    r_eff <- suppressWarnings(loo::relative_eff(
+      exp(ll), chain_id = rstanarm:::chain_id_for_loo(fit)))
     l2 <- suppressWarnings(loo(ll, r_eff = r_eff, cores = LOO.CORES))
     expect_equal(l$estimates, l2$estimates)
-    expect_equivalent(w, suppressWarnings(waic(ll)))
+    expect_equal(w, suppressWarnings(waic(ll)), ignore_attr = TRUE)
   }
 }
 
 expect_gg <- function(x, info = NULL, label = NULL) {
-  testthat::expect_is(x, "ggplot", info = info, label = label)
+  testthat::expect_true(inherits(x, "ggplot"), info = info, label = label)
   invisible(ggplot2::ggplot_build(x))
 }
 
@@ -96,9 +97,9 @@ expect_identical_sorted_stanmats <- function(x, y) {
 
 expect_linpred_equal <- function(object, tol = 0.1) {
   linpred <- posterior_linpred(object)
-  expect_equal(apply(linpred, 2, median), object$linear.predictors, 
-               tolerance = tol, 
-               check.attributes = FALSE)
+  expect_equal(apply(linpred, 2, median), object$linear.predictors,
+               tolerance = tol,
+               ignore_attr = TRUE)
 }
 
 expect_matrix <- function(x) expect_true(is.matrix(x))
diff --git a/tests/testthat/test_loo.R b/tests/testthat/test_loo.R
index d07e0ac25..891aa1856 100644
--- a/tests/testthat/test_loo.R
+++ b/tests/testthat/test_loo.R
@@ -28,7 +28,7 @@ if (!exists("example_model")) {
 }
 
 # loo and waic ------------------------------------------------------------
-context("loo and waic")
+
 
 # These tests just check that the loo.stanreg method (which calls loo.function
 # method) results are identical to the loo.matrix results. Since for these tests
@@ -55,7 +55,7 @@ expect_equivalent_loo <- function(fit) {
   r <- loo::relative_eff(exp(llik), chain_id = rstanarm:::chain_id_for_loo(fit))
   l2 <- suppressWarnings(loo(llik, r_eff = r, cores = LOO.CORES))
   expect_equal(l$estimates, l2$estimates)
-  expect_equivalent(w, suppressWarnings(waic(log_lik(fit))))
+  expect_equal(w, suppressWarnings(waic(log_lik(fit))), ignore_attr = TRUE)
 }
 
 test_that("loo & waic do something for non mcmc models", {
@@ -93,7 +93,7 @@ test_that("loo can handle empty interaction levels", {
 
 
 # loo with refitting ------------------------------------------------------
-context("loo then refitting")
+
 
 test_that("loo issues errors/warnings", {
   expect_warning(loo(example_model, cores = LOO.CORES, k_threshold = 2),
@@ -136,7 +136,7 @@ test_that("loo with k_threshold works for edge case(s)", {
 
 
 # kfold -------------------------------------------------------------------
-context("kfold")
+
 
 test_that("kfold does not throw an error for non mcmc models", {
   SW(fito <- stan_glm(mpg ~ wt, data = mtcars, algorithm = "optimizing",
@@ -274,7 +274,7 @@ test_that("loo_compare works", {
   expect_output(print(comp1_detail), "Model formulas")
 
   # equivalent to stanreg_list method
-  expect_equivalent(comp2, loo_compare(stanreg_list(fit1, fit2, fit3)))
+  expect_equal(comp2, loo_compare(stanreg_list(fit1, fit2, fit3)), ignore_attr = TRUE)
 
   # for kfold
   expect_warning(comp3 <- loo_compare(k1, k2, k3),
@@ -286,7 +286,7 @@ test_that("loo_compare works", {
 
 
 # helpers -----------------------------------------------------------------
-context("loo and waic helpers")
+
 
 test_that("kfold_and_reloo_data works", {
   f <- rstanarm:::kfold_and_reloo_data
@@ -296,12 +296,12 @@ test_that("kfold_and_reloo_data works", {
   # if 'data' arg not originally specified when fitting the model
   y <- rnorm(40)
   SW(fit <- stan_glm(y ~ 1, iter = ITER, chains = CHAINS, refresh = 0))
-  expect_equivalent(f(fit), model.frame(fit))
+  expect_equal(f(fit), model.frame(fit), ignore_attr = TRUE)
 
   # if 'subset' arg specified when fitting the model
   SW(fit2 <- stan_glm(mpg ~ wt, data = mtcars, subset = gear != 5, iter = ITER,
                       chains = CHAINS, refresh = 0))
-  expect_equivalent(f(fit2), subset(mtcars[mtcars$gear != 5, c("mpg", "wt")]))
+  expect_equal(f(fit2), subset(mtcars[mtcars$gear != 5, c("mpg", "wt")]), ignore_attr = TRUE)
 })
 
 test_that(".weighted works", {
diff --git a/tests/testthat/test_methods.R b/tests/testthat/test_methods.R
index 2a0090bf2..f8a2f83cd 100644
--- a/tests/testthat/test_methods.R
+++ b/tests/testthat/test_methods.R
@@ -84,8 +84,6 @@ check_sizes <- function(x,y) {
 }
 
 
-context("methods for stanreg objects")
-
 
 # extractors --------------------------------------------------------------
 test_that("stanreg extractor methods work properly", {
@@ -211,9 +209,9 @@ test_that("log_lik method works", {
     llmat[i, ] <- dnorm(y, mean = eta[, i], sd = sigma[i], log = TRUE)
     llmat_new[i, ] <- dnorm(y_new, mean = eta_new[, i], sd = sigma[i], log = TRUE)
   }
-  expect_equal(log_lik(stan_glm1), llmat, check.attributes = FALSE)
+  expect_equal(log_lik(stan_glm1), llmat, ignore_attr = TRUE)
   nd <- data.frame(mpg = y_new, wt = x_new[, 2], cyl = x_new[, 3])
-  expect_equal(log_lik(stan_glm1, newdata = nd), llmat_new, check.attributes = FALSE)
+  expect_equal(log_lik(stan_glm1, newdata = nd), llmat_new, ignore_attr = TRUE)
 
 
   # make sure log_lik with newdata equals log_lik if newdata is the same as the
@@ -472,7 +470,7 @@ test_that("as.matrix and as.array errors & warnings", {
 
 
 # terms, formula, model.frame, model.matrix, update methods -----------------
-context("model.frame methods")
+
 test_that("model.frame works properly", {
   expect_identical(model.frame(stan_glm1), model.frame(glm1))
   expect_identical(model.frame(stan_glm_opt1), model.frame(glm1))
@@ -488,7 +486,6 @@ test_that("model.frame works properly", {
   expect_identical(model.frame(stan_betareg1), model.frame(betareg1))
 })
 
-context("terms methods")
 test_that("terms works properly", {
   expect_identical(terms(stan_glm1), terms(glm1))
   expect_identical(terms(stan_glm_opt1), terms(glm1))
@@ -501,21 +498,20 @@ test_that("terms works properly", {
   expect_identical(terms(stan_lmer2, fixed.only = TRUE),
                    terms(lmer2, fixed.only = TRUE))
   expect_equal(terms(stan_lmer1, random.only = TRUE),
-                   terms(lmer1, random.only = TRUE))
+               terms(lmer1, random.only = TRUE), ignore_formula_env = TRUE)
   expect_equal(terms(stan_lmer2, random.only = TRUE),
-               terms(lmer2, random.only = TRUE))
+               terms(lmer2, random.only = TRUE), ignore_formula_env = TRUE)
   expect_error(terms(stan_lmer1, fixed.only = TRUE, random.only = TRUE),
                regexp = "can't both be TRUE")
   expect_identical(terms(stan_betareg1), terms(betareg1))
 })
 
-context("formula methods")
 test_that("formula works properly", {
   expect_identical(formula(stan_glm1), formula(glm1))
   expect_identical(formula(stan_glm_opt1), formula(glm1))
   expect_identical(formula(stan_glm_vb1), formula(glm1))
   expect_identical(formula(stan_betareg1), formula(betareg1))
-  expect_equal(terms(stan_polr1), formula(polr1))
+  expect_equal(formula(stan_polr1), formula(terms(polr1)))
   expect_identical(formula(stan_lmer1), formula(lmer1))
   expect_identical(formula(stan_lmer2), formula(lmer2))
   expect_identical(formula(stan_lmer1, fixed.only = TRUE),
@@ -523,9 +519,9 @@ test_that("formula works properly", {
   expect_identical(formula(stan_lmer2, fixed.only = TRUE),
                    formula(lmer2, fixed.only = TRUE))
   expect_equal(formula(stan_lmer1, random.only = TRUE),
-               formula(lmer1, random.only = TRUE))
+               formula(lmer1, random.only = TRUE), ignore_formula_env = TRUE)
   expect_equal(formula(stan_lmer2, random.only = TRUE),
-               formula(lmer2, random.only = TRUE))
+               formula(lmer2, random.only = TRUE), ignore_formula_env = TRUE)
   expect_error(formula(stan_lmer1, fixed.only = TRUE, random.only = TRUE),
                regexp = "can't both be TRUE")
   
@@ -533,12 +529,11 @@ test_that("formula works properly", {
   tmp <- stan_lmer1
   tmp$formula <- NULL
   attr(tmp$glmod$fr, "formula") <- NULL
-  expect_equal(formula(tmp), formula(lmer1))
+  expect_equal(formula(tmp), formula(lmer1), ignore_formula_env = TRUE)
   tmp$call <- NULL
   expect_error(formula(tmp), regexp = "can't find formula", ignore.case = TRUE)
 })
 
-context("update methods")
 test_that("update works properly", {
   pss <- rstanarm:::posterior_sample_size
 
@@ -550,7 +545,7 @@ test_that("update works properly", {
   expect_equal(pss(fit3), 4 * pss(stan_betareg1))
   
   call_only <- update(fit1, evaluate = FALSE)
-  expect_is(call_only, "call")
+  expect_type(call_only, "language")
   expect_identical(call_only, getCall(fit1))
 
   # expect_error(fit2 <- update(fit2, algorithm = "optimizing"),
@@ -563,7 +558,7 @@ test_that("update works properly", {
 
 
 # print and summary -------------------------------------------------------
-context("print and summary methods")
+
 test_that("print and summary methods ok for mcmc and vb", {
   expect_output(print(example_model, digits = 2), "stan_glmer")
   expect_output(print(example_model, digits = 2), "Error terms")
@@ -718,7 +713,7 @@ test_that("prior_summary returns correctly named list", {
 
 
 # predictive_error,predictive_interval ------------------------------------
-context("predictive error and interval methods")
+
 test_that("predictive_error works", {
   expect_error(predictive_error(stan_glm1, draws = 100),
                "'draws' should be <= posterior sample size")
@@ -816,7 +811,7 @@ test_that("stan*_list functions throw proper errors", {
 test_that("stanreg_list works", {
   list1 <- stanreg_list(stan_lmer1, stan_lmer2)
   expect_named(list1, c("stan_lmer1", "stan_lmer2"))
-  expect_equivalent(attr(list1, "families"), c("gaussian", "gaussian"))
+  expect_equal(attr(list1, "families"), c("gaussian", "gaussian"), ignore_attr = TRUE)
   expect_identical(list1$stan_lmer1, stan_lmer1)
   expect_identical(list1$stan_lmer2, stan_lmer2)
 })
diff --git a/tests/testthat/test_misc.R b/tests/testthat/test_misc.R
index 45ebe2075..ea8e68ee2 100644
--- a/tests/testthat/test_misc.R
+++ b/tests/testthat/test_misc.R
@@ -26,7 +26,6 @@ if (!exists("example_model")) {
   example_model <- run_example_model()
 }
 
-context("helper functions")
 
 test_that("nlist works", {
   nlist <- rstanarm:::nlist
@@ -155,7 +154,7 @@ test_that("validate_offset works", {
   
   SW(fito <- stan_glm(mpg ~ wt, data = mtcars, algorithm = "optimizing", seed = SEED))
   SW(fito2 <- update(fito, offset = rep(5, nrow(mtcars))))
-  expect_equal(coef(fito)[1], 5 + coef(fito2)[1], tol = 0.2)
+  expect_equal(coef(fito)[1], 5 + coef(fito2)[1], tolerance = 0.2)
 })
 
 test_that("validate_family works", {
@@ -246,12 +245,12 @@ test_that("linear_predictor methods work", {
   vec_ans <- seq(0, 1.5, 0.5)
   mat_ans <- rbind(vec_ans, 1:4)
   offset <- rep(2, nrow(x))
-  expect_equivalent(linpred_vec(bvec, x), vec_ans)
-  expect_equivalent(linpred_vec(bvec, x, offset = NULL), vec_ans)
-  expect_equivalent(linpred_vec(bvec, x, offset), vec_ans + offset)
-  expect_equivalent(linpred_mat(bmat, x), mat_ans)
-  expect_equivalent(linpred_mat(bmat, x, offset = NULL), mat_ans)
-  expect_equivalent(linpred_mat(bmat, x, offset), mat_ans + offset)
+  expect_equal(linpred_vec(bvec, x), vec_ans, ignore_attr = TRUE)
+  expect_equal(linpred_vec(bvec, x, offset = NULL), vec_ans, ignore_attr = TRUE)
+  expect_equal(linpred_vec(bvec, x, offset), vec_ans + offset, ignore_attr = TRUE)
+  expect_equal(linpred_mat(bmat, x), mat_ans, ignore_attr = TRUE)
+  expect_equal(linpred_mat(bmat, x, offset = NULL), mat_ans, ignore_attr = TRUE)
+  expect_equal(linpred_mat(bmat, x, offset), mat_ans + offset, ignore_attr = TRUE)
 })
 
 # fits to use in multiple calls to test_that below
@@ -322,14 +321,14 @@ test_that("is.mer works", {
 test_that("get_x, get_y, get_z work", {
   x_ans <- cbind("(Intercept)" = 1, wt = mtcars$wt)
   y_ans <- mtcars$mpg
-  expect_equivalent(get_x(fit), x_ans)
-  expect_equivalent(get_y(fit), y_ans)
+  expect_equal(get_x(fit), x_ans, ignore_attr = TRUE)
+  expect_equal(get_y(fit), y_ans, ignore_attr = TRUE)
   expect_error(get_z(fit), "no applicable method")
   
   z_ans2 <- model.matrix(mpg ~ -1 + factor(cyl), data = mtcars)
-  expect_equivalent(get_x(fit2), x_ans)
-  expect_equivalent(get_y(fit2), y_ans)
-  expect_equivalent(as.matrix(get_z(fit2)), z_ans2)
+  expect_equal(get_x(fit2), x_ans, ignore_attr = TRUE)
+  expect_equal(get_y(fit2), y_ans, ignore_attr = TRUE)
+  expect_equal(as.matrix(get_z(fit2)), z_ans2, ignore_attr = TRUE)
   
   SW(
     fit3 <- stan_glmer(mpg ~ wt + (1 + wt|cyl), data = mtcars, refresh = 0,
@@ -338,9 +337,9 @@ test_that("get_x, get_y, get_z work", {
   z_ans3 <- mat.or.vec(nr = nrow(mtcars), nc = 6)
   z_ans3[, c(1, 3, 5)] <- model.matrix(mpg ~ 0 + factor(cyl), data = mtcars)
   z_ans3[, c(2, 4, 6)] <- model.matrix(mpg ~ 0 + wt:factor(cyl), data = mtcars)
-  expect_equivalent(get_x(fit3), x_ans)
-  expect_equivalent(get_y(fit3), y_ans)
-  expect_equivalent(as.matrix(get_z(fit3)), z_ans3)
+  expect_equal(get_x(fit3), x_ans, ignore_attr = TRUE)
+  expect_equal(get_y(fit3), y_ans, ignore_attr = TRUE)
+  expect_equal(as.matrix(get_z(fit3)), z_ans3, ignore_attr = TRUE)
 })
 
 test_that("set_sampling_args works", {
@@ -434,7 +433,7 @@ test_that("collect_pars and grep_for_pars work", {
   expect_identical(grep_for_pars(fit, "herd:[3,5]"), all_varying[c(3,5)])
   expect_identical(grep_for_pars(fit, "herd:[3-5]"), all_varying[3:5])
   expect_error(grep_for_pars(fit, "NOT A PARAMETER"), regexp = "No matches")
-  expect_error(grep_for_pars(fit, "b["))
+  expect_error(suppressWarnings(grep_for_pars(fit, "b[")))
   
   expect_identical(collect_pars(fit, regex_pars = "period"), all_period)
   expect_identical(collect_pars(fit, pars = "size", regex_pars = "period"), 
@@ -495,4 +494,3 @@ test_that("validate_newdata works", {
   newd$period[3] <- NA
   expect_error(validate_newdata(fit, newdata = newd), "NAs are not allowed")
 })
-
diff --git a/tests/testthat/test_plots.R b/tests/testthat/test_plots.R
index 2ad660c24..a2338acdf 100644
--- a/tests/testthat/test_plots.R
+++ b/tests/testthat/test_plots.R
@@ -30,7 +30,7 @@ SW(fito <- stan_glm(mpg ~ ., data = mtcars, algorithm = "optimizing", seed = SEE
 SW(fitvb <- update(fito, algorithm = "meanfield"))
 
 # plot.stanreg ------------------------------------------------------------
-context("plot.stanreg")
+
 test_that("plot.stanreg errors if chains = 1 but needs multiple", {
   multiple_chain_plots <- c("trace_highlight",
                             "hist_by_chain",
@@ -119,7 +119,7 @@ test_that("plot.stanreg ok for vb", {
 
 
 # pairs.stanreg -----------------------------------------------------------
-context("pairs.stanreg")
+
 test_that("pairs method ok", {
   expect_silent(pairs(fit, pars = c("period2", "log-posterior")))
   expect_silent(pairs(fit, pars = "b[(Intercept) herd:15]", regex_pars = "Sigma"))
@@ -132,7 +132,7 @@ test_that("pairs method ok", {
 
 
 # posterior_vs_prior ------------------------------------------------------
-context("posterior_vs_prior")
+
 test_that("posterior_vs_prior ok", {
   SW(p1 <- posterior_vs_prior(fit, pars = "beta"))
   expect_gg(p1)
diff --git a/tests/testthat/test_posterior_predict.R b/tests/testthat/test_posterior_predict.R
index f7a3b35bb..36ac76886 100644
--- a/tests/testthat/test_posterior_predict.R
+++ b/tests/testthat/test_posterior_predict.R
@@ -48,7 +48,7 @@ test_that("posterior_predict errors if draws > posterior sample size", {
 })
 
 # VB ----------------------------------------------------------------------
-context("posterior_predict ok for vb")
+
 test_that("silent for vb", {
   SW(fit1 <- stan_glm(mpg ~ wt + cyl + am, data = mtcars, algorithm = "meanfield",
                    refresh = 0))
@@ -108,8 +108,8 @@ test_that("lme4 tests work similarly", {
                                size = 20, incidence = 0))
 
   p6 <- posterior_predict(sfit, nd3, allow.new.levels = TRUE, seed = SEED)
-  expect_equal(colMeans(p3), colMeans(p6[, 1:ncol(p3)]), tol = 0.05)
-  expect_equal(apply(p3, 2, sd), apply(p6[, 1:ncol(p3)], 2, sd), tol = 0.05)
+  expect_equal(colMeans(p3), colMeans(p6[, 1:ncol(p3)]), tolerance = 0.05)
+  expect_equal(apply(p3, 2, sd), apply(p6[, 1:ncol(p3)], 2, sd), tolerance = 0.05)
 
   # multiple groups
   lfit <- lmer(diameter ~ (1|plate) + (1|sample), Penicillin)
@@ -129,7 +129,7 @@ test_that("lme4 tests work similarly", {
 
 
 # spaces in factor levels -------------------------------------------------
-context("posterior_linpred/predict with spaces in factor levels")
+
 
 test_that("posterior_linpred not sensitive to spaces in factor levels", {
   df <- data.frame(
@@ -175,7 +175,7 @@ test_that("posterior_linpred not sensitive to spaces in factor levels", {
   )
   ans2 <- posterior_linpred(fit1, newdata = nd2)
   # should be same as ans1 except for cols 3:4 with new levels
-  expect_equal(ans2[, 1:2], ans1, check.attributes = FALSE)
+  expect_equal(ans2[, 1:2], ans1, ignore_attr = TRUE)
   expect_equal(ans2, posterior_linpred(fit2, newdata = nd2))
   expect_equal(ans2, posterior_linpred(fit3, newdata = nd2))
   expect_equal(ans2, posterior_linpred(fit4, newdata = nd2))
@@ -256,7 +256,7 @@ test_that("posterior_predict can handle empty interaction levels", {
 
 
 # helper functions --------------------------------------------------------
-context("posterior_predict helper functions")
+
 test_that("pp_binomial_trials works", {
   ppbt <- rstanarm:::pp_binomial_trials
 
diff --git a/tests/testthat/test_pp_check.R b/tests/testthat/test_pp_check.R
index b2c9720a9..72479a228 100644
--- a/tests/testthat/test_pp_check.R
+++ b/tests/testthat/test_pp_check.R
@@ -15,7 +15,6 @@
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
-context("pp_check")
 
 suppressPackageStartupMessages(library(rstanarm))
 SEED <- 123
diff --git a/tests/testthat/test_pp_validate.R b/tests/testthat/test_pp_validate.R
index 3e1a9f8cb..5d01d771d 100644
--- a/tests/testthat/test_pp_validate.R
+++ b/tests/testthat/test_pp_validate.R
@@ -23,7 +23,6 @@ if (!exists("example_model")) {
   example_model <- run_example_model()
 }
 
-context("pp_validate")
 test_that("pp_validate throws correct errors", {
   expect_error(pp_validate(example_model$stanfit), "not a stanreg object")
   expect_error(pp_validate(example_model, nreps = 1), "at least 2")
diff --git a/tests/testthat/test_predict.R b/tests/testthat/test_predict.R
index b9ae67c39..5746a8384 100644
--- a/tests/testthat/test_predict.R
+++ b/tests/testthat/test_predict.R
@@ -32,7 +32,6 @@ plink <- function(fit, nd = NULL, sef = TRUE)
 presp <- function(fit, nd = NULL, sef = TRUE) 
   predict(fit, newdata = nd, type = "response", se.fit = sef)
 
-context("predict")
 
 test_that("predict recommends posterior_predict for glmer models", {
   expect_error(predict(example_model), 
@@ -60,11 +59,11 @@ test_that("predict ok for binomial", {
   pg <- plink(glmfit)
   ps <- plink(stanfit)
   pso <- plink(stanfit_opt)
-  expect_equal(pg$fit, ps$fit, tol = 0.1)
-  expect_equal(pg$fit, pso$fit, tol = 0.05)
-  expect_equal(pg$se.fit, ps$se.fit, tol = 0.2)
-  expect_equal(pg$se.fit, pso$se.fit, tol = 0.1)
-  expect_equal(presp(glmfit)[1:2], presp(stanfit_opt), tol = 0.05)
+  expect_equal(pg$fit, ps$fit, tolerance = 0.1)
+  expect_equal(pg$fit, pso$fit, tolerance = 0.05)
+  expect_equal(pg$se.fit, ps$se.fit, tolerance = 0.2)
+  expect_equal(pg$se.fit, pso$se.fit, tolerance = 0.1)
+  expect_equal(presp(glmfit)[1:2], presp(stanfit_opt), tolerance = 0.05)
 
   ld <- seq(0, 5, 0.1)
   newd <- data.frame(ldose = ld, sex = factor(rep("M", length(ld)), 
@@ -73,10 +72,10 @@ test_that("predict ok for binomial", {
   ps <- plink(stanfit, newd)
   pso <- plink(stanfit_opt, newd)
   # expect_equal(pg$fit, ps$fit, tol = 0.05)
-  expect_equal(pg$fit, pso$fit, tol = 0.05)
-  expect_equal(pg$se.fit, ps$se.fit, tol = 0.2)
-  expect_equal(pg$se.fit, pso$se.fit, tol = 0.1)
-  expect_equal(presp(glmfit, newd)[1:2], presp(stanfit_opt, newd), tol = 0.1)
+  expect_equal(pg$fit, pso$fit, tolerance = 0.05)
+  expect_equal(pg$se.fit, ps$se.fit, tolerance = 0.2)
+  expect_equal(pg$se.fit, pso$se.fit, tolerance = 0.1)
+  expect_equal(presp(glmfit, newd)[1:2], presp(stanfit_opt, newd), tolerance = 0.1)
 })
 
 test_that("predict ok for gaussian", {
@@ -93,21 +92,21 @@ test_that("predict ok for gaussian", {
   pg <- plink(glmfit)
   ps <- plink(stanfit)
   pso <- plink(stanfit_opt)
-  expect_equal(pg$fit, ps$fit, tol = 0.05)
-  expect_equal(pg$fit, pso$fit, tol = 0.05)
-  expect_equal(pg$se.fit, ps$se.fit, tol = 0.3)
-  expect_equal(pg$se.fit, pso$se.fit, tol = 0.1)
-  expect_equal(presp(glmfit)[1:2], presp(stanfit_opt), tol = 0.1)
+  expect_equal(pg$fit, ps$fit, tolerance = 0.05)
+  expect_equal(pg$fit, pso$fit, tolerance = 0.05)
+  expect_equal(pg$se.fit, ps$se.fit, tolerance = 0.3)
+  expect_equal(pg$se.fit, pso$se.fit, tolerance = 0.1)
+  expect_equal(presp(glmfit)[1:2], presp(stanfit_opt), tolerance = 0.1)
 
   newd <- data.frame(wt = c(1,5))
   pg <- plink(glmfit, newd)
   ps <- plink(stanfit, newd)
   pso <- plink(stanfit_opt, newd)
-  expect_equal(pg$fit, ps$fit, tol = 0.05)
-  expect_equal(pg$fit, pso$fit, tol = 0.05)
-  expect_equal(pg$se.fit, ps$se.fit, tol = 0.3)
-  expect_equal(pg$se.fit, pso$se.fit, tol = 0.1)
-  expect_equal(presp(glmfit, newd)[1:2], presp(stanfit_opt, newd), tol = 0.1)
+  expect_equal(pg$fit, ps$fit, tolerance = 0.05)
+  expect_equal(pg$fit, pso$fit, tolerance = 0.05)
+  expect_equal(pg$se.fit, ps$se.fit, tolerance = 0.3)
+  expect_equal(pg$se.fit, pso$se.fit, tolerance = 0.1)
+  expect_equal(presp(glmfit, newd)[1:2], presp(stanfit_opt, newd), tolerance = 0.1)
 })
 
 test_that("predict ok for Poisson", {
@@ -124,22 +123,22 @@ test_that("predict ok for Poisson", {
   pg <- plink(glmfit)
   ps <- plink(stanfit)
   pso <- plink(stanfit_opt)
-  expect_equal(pg$fit, ps$fit, tol = 0.05)
-  expect_equal(pg$fit, pso$fit, tol = 0.05)
-  expect_equal(pg$se.fit, ps$se.fit, tol = 0.1)
-  expect_equal(pg$se.fit, pso$se.fit, tol = 0.1)
-  expect_equal(presp(glmfit)[1:2], presp(stanfit_opt), tol = 0.1)
+  expect_equal(pg$fit, ps$fit, tolerance = 0.05)
+  expect_equal(pg$fit, pso$fit, tolerance = 0.05)
+  expect_equal(pg$se.fit, ps$se.fit, tolerance = 0.1)
+  expect_equal(pg$se.fit, pso$se.fit, tolerance = 0.1)
+  expect_equal(presp(glmfit)[1:2], presp(stanfit_opt), tolerance = 0.1)
 
-  expect_equal(plink(stanfit, sef = FALSE), plink(glmfit, sef = FALSE), tol = 0.05)
-  expect_equal(presp(stanfit, sef = FALSE), presp(glmfit, sef = FALSE), tol = 0.05)
+  expect_equal(plink(stanfit, sef = FALSE), plink(glmfit, sef = FALSE), tolerance = 0.05)
+  expect_equal(presp(stanfit, sef = FALSE), presp(glmfit, sef = FALSE), tolerance = 0.05)
 
   newd <- dat[1:2, ]
   pg <- plink(glmfit, newd)
   ps <- plink(stanfit, newd)
   pso <- plink(stanfit_opt, newd)
-  expect_equal(pg$fit, ps$fit, tol = 0.05)
-  expect_equal(pg$fit, pso$fit, tol = 0.05)
-  expect_equal(pg$se.fit, ps$se.fit, tol = 0.1)
-  expect_equal(pg$se.fit, pso$se.fit, tol = 0.1)
-  expect_equal(presp(glmfit, newd)[1:2], presp(stanfit_opt, newd), tol = 0.1)
+  expect_equal(pg$fit, ps$fit, tolerance = 0.05)
+  expect_equal(pg$fit, pso$fit, tolerance = 0.05)
+  expect_equal(pg$se.fit, ps$se.fit, tolerance = 0.1)
+  expect_equal(pg$se.fit, pso$se.fit, tolerance = 0.1)
+  expect_equal(presp(glmfit, newd)[1:2], presp(stanfit_opt, newd), tolerance = 0.1)
 })
diff --git a/tests/testthat/test_stan_betareg.R b/tests/testthat/test_stan_betareg.R
index ccc964f26..f48c26bf6 100644
--- a/tests/testthat/test_stan_betareg.R
+++ b/tests/testthat/test_stan_betareg.R
@@ -22,8 +22,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
   ITER <- 10
   CHAINS <- 2
   REFRESH <- 0
-  
-  context("stan_betareg")
+
   
   simple_betareg_data <- function(N, draw_z = FALSE) {
     x <- rnorm(N, 2, 1)
@@ -80,7 +79,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
       expect_stanreg(fit)
       val <- coef(fit)
       ans <- coef(betareg(y ~ x, link = link1[i], data = dat))
-      expect_equal(val, ans, tol = 0.1, info = link1[i])
+      expect_equal(val, ans, tolerance = 0.1, info = link1[i])
     }
   })
   
@@ -92,7 +91,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
     expect_stanreg(fit)
     val <- coef(fit)
     ans <- coef(betareg(y ~ x + z, link = "logit", data = dat))
-    expect_equal(val, ans, tol = 0.1, info = "logit")
+    expect_equal(val, ans, tolerance = 0.1, info = "logit")
   })
   
   test_that("stan_betareg works with QR = TRUE and algorithm = 'sampling'", {
@@ -103,7 +102,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
     expect_stanreg(fit)
     val <- coef(fit)
     ans <- coef(betareg(y ~ x + z, link = "logit", data = dat))
-    expect_equal(val, ans, tol = 0.1)
+    expect_equal(val, ans, tolerance = 0.1)
   })
   
   test_that("QR recommended if VB and at least 2 predictors", {
@@ -149,7 +148,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
       val <- coef(fit)
       ans <- coef(betareg(y ~ x | z, link = link1[i], link.phi = link2[1], 
                           data = dat))
-      expect_equal(val, ans, tol = 0.1, info = c(link1[i], link2[1]))
+      expect_equal(val, ans, tolerance = 0.1, info = c(link1[i], link2[1]))
     }
   })
   
@@ -169,7 +168,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
       expect_stanreg(fit)
       val <- coef(fit)
       ans <- coef(betareg(y ~ x | z, link = link1[i], link.phi = link2[2], data = dat))
-      expect_equal(val, ans, tol = 0.15, info = c(link1[i], link2[2]))
+      expect_equal(val, ans, tolerance = 0.15, info = c(link1[i], link2[2]))
     }
   })
   
@@ -206,7 +205,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
     expect_stanreg(fit)
     val <- coef(fit)
     ans <- coef(betareg(y ~ x, link = "logit", weights = weights, offset = offset, data = dat))
-    expect_equal(val, ans, tol = 0.3, info = "logit")
+    expect_equal(val, ans, tolerance = 0.3, info = "logit")
   })
   
   test_that("heavy tailed priors work with stan_betareg", {
diff --git a/tests/testthat/test_stan_clogit.R b/tests/testthat/test_stan_clogit.R
index 2f719bffa..5fa9d6813 100644
--- a/tests/testthat/test_stan_clogit.R
+++ b/tests/testthat/test_stan_clogit.R
@@ -27,7 +27,6 @@ REFRESH <- 0
 
 threshold <- 0.03
 
-context("stan_clogit")
 
 SW(fit <- stan_clogit(case ~ spontaneous + induced, strata = stratum, prior = NULL,
                    data = infert[order(infert$stratum), ], 
@@ -36,7 +35,7 @@ SW(fit <- stan_clogit(case ~ spontaneous + induced, strata = stratum, prior = NU
 
 test_that("stan_clogit is similar to survival::clogit", {
   ref_vals <- c(spontaneous = 1.985876, induced = 1.409012)
-  expect_equal(ref_vals, coef(fit), tol = threshold)
+  expect_equal(ref_vals, coef(fit), tolerance = threshold)
 })
 
 test_that("stan_clogit runs for infert example", {
@@ -64,7 +63,6 @@ test_that("loo/waic for stan_clogit works", {
   expect_identical(ll_fun(fit), rstanarm:::.ll_clogit_i)
 })
 
-context("posterior_predict (stan_clogit)")
 test_that("compatible with stan_clogit", {
   PPD1 <- posterior_predict(fit)
   PPD2 <- posterior_predict(fit, newdata = infert) # order irrelevant
diff --git a/tests/testthat/test_stan_functions.R b/tests/testthat/test_stan_functions.R
index a75a35f6f..108afbcad 100644
--- a/tests/testthat/test_stan_functions.R
+++ b/tests/testthat/test_stan_functions.R
@@ -21,7 +21,6 @@ set.seed(12345)
 MODELS_HOME <- system.file("stan", package = "rstanarm", mustWork = TRUE)
 INCLUDE_DIR <- system.file("include", package = "rstanarm", mustWork = TRUE)
 
-context("setup")
 test_that("Stan programs are available", {
   expect_true(file.exists(MODELS_HOME))
 })
@@ -69,7 +68,6 @@ N <- 99L
 # bernoulli
 links <- c("logit", "probit", "cauchit", "log", "cloglog")
 
-context("Bernoulli")
 test_that("linkinv_bern returns expected results", {
   for (i in 1:length(links)) {
     eta <- -abs(rnorm(N))
@@ -78,7 +76,7 @@ test_that("linkinv_bern returns expected results", {
                           linkinv_bern(eta, i)), info = links[i])
   }
 })
-context("Bernoulli")
+
 test_that("pw_bern and ll_bern_lp return expected results", {
   for (i in 1:length(links)) {
     eta0 <- -abs(rnorm(N))
@@ -96,7 +94,7 @@ test_that("pw_bern and ll_bern_lp return expected results", {
 
 # Binomial
 trials <- 10L
-context("Binomial")
+
 test_that("linkinv_binom returns expected results", {
   for (i in 1:length(links)) {
     eta <- -abs(rnorm(N))
@@ -105,7 +103,7 @@ test_that("linkinv_binom returns expected results", {
                           linkinv_binom(eta, i)), info = links[i])
   }
 })
-context("Bernoulli")
+
 test_that("pw_binom and ll_binom_lp return expected results", {
   for (i in 1:length(links)) {
     eta <- -abs(rnorm(N))
@@ -120,7 +118,6 @@ test_that("pw_binom and ll_binom_lp return expected results", {
 # Count GLM
 links <- c("log", "identity", "sqrt")
 
-context("Poisson")
 test_that("linkinv_count returns expected results", {
   for (i in 1:length(links)) {
     eta <- abs(rnorm(N))
@@ -129,7 +126,7 @@ test_that("linkinv_count returns expected results", {
                           linkinv_count(eta, i)), info = links[i])
   }
 })
-context("Poisson")
+
 test_that("pw_pois return expected results", {
   for (i in 1:length(links)) {
     y <- sample.int(10, size = N, replace = TRUE)
@@ -141,7 +138,7 @@ test_that("pw_pois return expected results", {
 })
 
 # Negative Binomial
-context("Negative Binomial")
+
 test_that("pw_nb return expected results", {
   for (i in 1:length(links)) {
     y <- sample.int(10, size = N, replace = TRUE)
@@ -156,7 +153,6 @@ test_that("pw_nb return expected results", {
 # Gaussian GLM
 links <- c("identity", "log", "inverse")
 
-context("Gaussian")
 test_that("linkinv_gauss returns expected results", {
   for (i in 1:length(links)) {
     eta <- rnorm(N)
@@ -164,7 +160,7 @@ test_that("linkinv_gauss returns expected results", {
     expect_true(all.equal(linkinv(eta), linkinv_gauss(eta, i)), info = links[i])
   }
 })
-context("Gaussian")
+
 test_that("pw_gauss returns expected results", {
   for (i in 1:length(links)) {
     eta <- rnorm(N)
@@ -275,7 +271,7 @@ test_that("inv_gaussian returns expected results", {
 
 # lm
 N <- 99L
-context("lm")
+
 test_that("ll_mvn_ols... returns expected results", {
   X <- matrix(rnorm(2 * N), N, 2)
   X <- sweep(X, MARGIN = 2, STATS = colMeans(X), FUN = "-")
@@ -302,7 +298,7 @@ test_that("ll_mvn_ols... returns expected results", {
 
 # polr
 links <- c("logistic", "probit", "loglog", "cloglog", "cauchit")
-context("polr")
+
 test_that("CDF_polr returns expected results", {
   for (i in 1:length(links)) {
     x <- rnorm(1)
@@ -312,7 +308,7 @@ test_that("CDF_polr returns expected results", {
     expect_true(all.equal(linkinv(x), CDF_polr(x, i)))
   }
 })
-context("polr")
+
 test_that("pw_polr returns expected results", {
   J <- 3
   for (i in 1:length(links)) {
@@ -339,7 +335,7 @@ rdirichlet <- function(n, alpha) {
   sm <- x %*% rep(1, l)
   return(x/as.vector(sm))
 }
-context("polr")
+
 test_that("make_cutpoints returns expected results", {
   J <- 5L
   for (i in 1:length(links)) {
@@ -350,7 +346,7 @@ test_that("make_cutpoints returns expected results", {
     }
   }
 })
-context("polr")
+
 test_that("draw_ystar_rng returns expected results", {
   l <- -0.1
   u <-  0.1
@@ -363,7 +359,7 @@ test_that("draw_ystar_rng returns expected results", {
 })
 
 # glmer
-context("glmer")
+
 if (require(lme4) && require(HSAUR3)) test_that("the Stan equivalent of lme4's Z %*% b works", {
   stopifnot(require(Matrix))
   test_lme4 <- function(group) {
@@ -394,7 +390,7 @@ if (require(lme4) && require(HSAUR3)) test_that("the Stan equivalent of lme4's Z
     b <- make_b(z_b, theta_L, p, l)
     mark <- colnames(Z) == ""
     expect_equal(b[!mark], as.vector(Matrix::t(Lambdati) %*% z_b[!mark]),
-                 tol = 1e-14)
+                 tolerance = 1e-14)
 
     parts <- extract_sparse_parts(Z)
     Zb <- Z %*% b
@@ -427,14 +423,12 @@ if (require(lme4) && require(HSAUR3)) test_that("the Stan equivalent of lme4's Z
   test_lme4(glFormula(diameter ~ (1|plate) + (1|sample), data = Penicillin)$reTrms)
 })
 
-context("glmer")
 test_that("the Cornish-Fisher expansion from standard normal to Student t works", {
   df <- exp(1) / pi
   approx_t <- sapply(rnorm(1000), FUN = CFt, df = df)
   expect_true(ks.test(approx_t, "pt", df = df, exact = TRUE)$p.value > 0.05)
 })
 
-context("nlmer")
 test_that("SSasymp works", {
   Lob.329 <- Loblolly[ Loblolly$Seed == "329", ]
   Asym <- 100
@@ -448,7 +442,6 @@ test_that("SSasymp works", {
                         SS_asymp( Lob.329$age, Phi ), check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("SSasympOff works", {
   CO2.Qn1 <- CO2[CO2$Plant == "Qn1", ]
   Asym <- 32; lrc <- -4; c0 <- 43
@@ -460,7 +453,6 @@ test_that("SSasympOff works", {
                         SS_asympOff(CO2.Qn1$conc, Phi), check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("SSasympOrig works", {
   Lob.329 <- Loblolly[ Loblolly$Seed == "329", ]
   Asym <- 100; lrc <- -3.2
@@ -472,7 +464,6 @@ test_that("SSasympOrig works", {
                         SS_asympOrig(Lob.329$age, Phi), check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("SSbiexp works", {
   Indo.1 <- Indometh[Indometh$Subject == 1, ]
   A1 <- 3; lrc1 <- 1; A2 <- 0.6; lrc2 <- -1.3
@@ -484,7 +475,6 @@ test_that("SSbiexp works", {
                         SS_biexp( Indo.1$time, Phi ), check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("SSfol works", {
   Theoph.1 <- Theoph[ Theoph$Subject == 1, ]
   lKe <- -2.5; lKa <- 0.5; lCl <- -3
@@ -496,7 +486,6 @@ test_that("SSfol works", {
                         SS_fol(Theoph.1$Dose, Theoph.1$Time, Phi), check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("SSfpl works", {
   Chick.1 <- ChickWeight[ChickWeight$Chick == 1, ]
   A <- 13; B <- 368; xmid <- 14; scal <- 6
@@ -508,7 +497,6 @@ test_that("SSfpl works", {
                         SS_fpl(Chick.1$Time, Phi), check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("SSgompertz works", {
   DNase.1 <- subset(DNase, Run == 1)
   Asym <- 4.5; b2 <- 2.3; b3 <- 0.7
@@ -520,7 +508,6 @@ test_that("SSgompertz works", {
                         SS_gompertz(log(DNase.1$conc), Phi), check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("SSlogis works", {
   Chick.1 <- ChickWeight[ChickWeight$Chick == 1, ]
   Asym <- 368; xmid <- 14; scal <- 6
@@ -532,7 +519,6 @@ test_that("SSlogis works", {
                         SS_logis(Chick.1$Time, Phi), check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("SSmicmen works", {
   PurTrt <- Puromycin[ Puromycin$state == "treated", ]
   Vm <- 200; K <- 0.05
@@ -544,7 +530,6 @@ test_that("SSmicmen works", {
                         SS_micmen(PurTrt$conc, Phi), check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("SSweibull works", {
   Chick.6 <- subset(ChickWeight, (Chick == 6) & (Time > 0))
   Asym <- 160; Drop <- 115; lrc <- -5.5; pwr <- 2.5
@@ -556,7 +541,6 @@ test_that("SSweibull works", {
                         SS_weibull(Chick.6$Time, Phi) , check.attributes = FALSE))
 })
 
-context("nlmer")
 test_that("reshape works", {
   x <- as.double(1:10)
   expect_true(all(matrix(x, 5, 2) == reshape_vec(x, 5L, 2L)))
@@ -565,7 +549,6 @@ test_that("reshape works", {
 # betareg
 links <- c("logit", "probit", "cloglog", "cauchit", "log")
 
-context("betareg")
 test_that("linkinv_beta returns expected results", {
   for (i in 1:length(links)) {
     eta <- -abs(rnorm(N))
@@ -574,7 +557,7 @@ test_that("linkinv_beta returns expected results", {
                           linkinv_beta(eta, i)), info = links[i])
   }
 })
-context("betareg")
+
 test_that("pw_beta and ll_beta_lp return expected results", {
   for (i in 1:length(links)) {
     eta <- -abs(rnorm(N))
@@ -586,7 +569,6 @@ test_that("pw_beta and ll_beta_lp return expected results", {
   }
 })
 
-context("clogit")
 test_that("ll_clogit_lp (which calls log_clogit_denom) returns the expected results", {
   data(infert)
   infert <- infert[order(infert$stratum, !infert$case),]
diff --git a/tests/testthat/test_stan_glm.R b/tests/testthat/test_stan_glm.R
index 533558ec1..4c08bc41d 100644
--- a/tests/testthat/test_stan_glm.R
+++ b/tests/testthat/test_stan_glm.R
@@ -15,7 +15,6 @@
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
-context("stan_glm")
 
 suppressPackageStartupMessages(library(rstanarm))
 SEED <- 12345
@@ -161,7 +160,7 @@ test_that("gaussian returns expected result for trees example", {
     
     ans <- glm(Volume ~ log(Girth) + log(Height),data = trees, 
                family = gaussian(link = links[i]))
-    expect_equal(coef(fit), coef(ans), tol = 0.021)
+    expect_equal(coef(fit), coef(ans), tolerance = 0.021)
   }
   
   expect_error(update(fit, prior = dnorm), 
@@ -186,13 +185,13 @@ test_that("stan_glm returns expected result for glm poisson example", {
     
     ans <- glm(counts ~ outcome + treatment, data = d.AD,
                family = poisson(links[i]), start = coef(fit))
-    if (links[i] == "log") expect_equal(coef(fit), coef(ans), tol = 0.03)
+    if (links[i] == "log") expect_equal(coef(fit), coef(ans), tolerance = 0.03)
     # if (links[i] == "identity") expect_equal(coef(fit)[-1], coef(ans)[-1], tol = 0.03)
     if (links[i] == "sqrt") { # this is weird
       if (coef(ans)[1] > 0)
-        expect_equal(coef(fit)[-1], coef(ans)[-1], tol = 0.1)
+        expect_equal(coef(fit)[-1], coef(ans)[-1], tolerance = 0.1)
       else
-        expect_equal(-coef(fit)[-1], coef(ans)[-1], tol = 0.04)
+        expect_equal(-coef(fit)[-1], coef(ans)[-1], tolerance = 0.04)
     }
   }
 })
@@ -225,18 +224,18 @@ test_that("stan_glm returns expected result for cars example", {
   expect_stanreg(fit)
   
   ans <- glm(log(dist) ~ log(speed), data = cars, family = gaussian(link = "identity"))
-  expect_equal(coef(fit), coef(ans), tol = 0.1)
+  expect_equal(coef(fit), coef(ans), tolerance = 0.1)
 })
 test_that("stan_glm returns expected result with no intercept for mtcars example", {
   f <- as.formula(mpg ~ -1 + wt + cyl + disp + am + carb)
-  fit <- stan_glm(f, data = mtcars, refresh = 0,
+  SW(fit <- stan_glm(f, data = mtcars, refresh = 0,
                   prior = NULL, prior_intercept = NULL,
                   tol_rel_obj = .Machine$double.eps, algorithm = "optimizing",
-                  seed  = SEED, sparse = TRUE)
+                  seed  = SEED, sparse = TRUE))
   expect_stanreg(fit)
   
   ans <- glm(f, data = mtcars, family = gaussian(link = "identity"))
-  expect_equal(coef(fit), coef(ans), tol = 0.04)
+  expect_equal(coef(fit), coef(ans), tolerance = 0.04)
 })
 
 links <- c("logit", "probit", "cauchit", "log", "cloglog")
@@ -261,7 +260,7 @@ test_that("stan_glm returns expected result for bernoulli", {
     val <- coef(fit)
     if (links[i] != "log") {
       ans <- coef(glm(y ~ x, family = fam, etastart = theta))
-      expect_equal(val, ans, 0.09, info = links[i])
+      expect_equal(val, ans, tolerance = 0.09, info = links[i])
     }
     # else expect_equal(val[-1], ans[-1], 0.06, info = links[i])
   }
@@ -294,7 +293,7 @@ test_that("stan_glm returns expected result for binomial example", {
     
     val <- coef(fit)
     ans <- coef(glm(y ~ x1 + x2 + x3, data = dat, family = fam, start = b))
-    if (links[i] != "log") expect_equal(val, ans, 0.02, info = links[i])
+    if (links[i] != "log") expect_equal(val, ans, tolerance = 0.02, info = links[i])
     # else expect_equal(val[-1], ans[-1], 0.02, info = links[i]) # unstable
 
     prop <- yes / trials
@@ -307,8 +306,8 @@ test_that("stan_glm returns expected result for binomial example", {
     expect_stanreg(fit2)
     
     val2 <- coef(fit2)
-    if (links[i] != "log") expect_equal(val2, ans, 0.02, info = links[i])
-    else expect_equal(val2[-1], ans[-1], 0.02, info = links[i])
+    if (links[i] != "log") expect_equal(val2, ans, tolerance = 0.02, info = links[i])
+    else expect_equal(val2[-1], ans[-1], tolerance = 0.02, info = links[i])
   }
 })
 
@@ -389,10 +388,10 @@ test_that("prior_options is deprecated", {
     ops <- prior_options(scaled = FALSE, prior_scale_for_dispersion = 3), 
     "deprecated and will be removed"
   )
-  expect_warning(
+  suppressWarnings(expect_warning(
     capture.output(fit <- stan_glm(mpg ~ wt, data = mtcars, iter = 5, prior_ops = ops)),
     "Setting prior scale for aux to value specified in 'prior_options'"
-  )
+  ))
   expect_output(
     print(prior_summary(fit)), 
     "~ exponential(rate = 0.33)", 
@@ -406,8 +405,9 @@ test_that("empty interaction levels dropped", {
   x1[x2 == 1] <- 1
   x1[x2 == 2] <- 1
   y <- rnorm(100)
-  expect_warning(stan_glm(y ~ x1*x2, chains = 1, iter = 20, refresh = 0), 
-                 regexp = "Dropped empty interaction levels")
+  suppressWarnings(expect_warning(
+    stan_glm(y ~ x1*x2, chains = 1, iter = 20, refresh = 0),
+    regexp = "Dropped empty interaction levels"))
 })
 
 
@@ -480,12 +480,12 @@ test_that("returns something with collinear predictors", {
   x1 <- rnorm(N)
   x2 <- 2*x1
 
-  fit_1 <- stan_glm(
+  SW(fit_1 <- stan_glm(
     y ~ z * (x1 + x2),
     data = data.frame(y, z, x1, x2),
     prior = normal(location = 0, scale = 0.1),
     prior_intercept = normal(location = 0, scale = 0.1),
     chains = CHAINS, iter = ITER, refresh = REFRESH
-  )
+  ))
   expect_stanreg(fit_1)  
 })
diff --git a/tests/testthat/test_stan_glmer.R b/tests/testthat/test_stan_glmer.R
index 6800ffaea..1794fd231 100644
--- a/tests/testthat/test_stan_glmer.R
+++ b/tests/testthat/test_stan_glmer.R
@@ -35,7 +35,6 @@ SW(fit <- stan_lmer(Reaction / 10 ~ Days + (Days | Subject),
                     data = sleepstudy, refresh = 0,
                     init_r = 0.05, chains = CHAINS, iter = ITER, seed = SEED))
 
-context("stan_glmer")
 test_that("draws from stan_glmer (gaussian) same as from stan_lmer", {
   SW(fit1 <- stan_glmer(mpg ~ wt + (1|cyl), data = mtcars, 
                         iter = 10, chains = 1, seed = SEED, refresh = 0))
@@ -53,13 +52,12 @@ test_that("stan_glmer returns expected result for binomial cbpp example", {
     expect_stanreg(fit)
     
     ans <- glmer(fmla, data = cbpp, family = binomial(links[i]))
-    expect_equal(fixef(fit), fixef(ans), tol = FIXEF_tol)
-    expect_equal(ranef(fit), ranef(ans), tol = RANEF_tol, check.attributes = FALSE)
+    expect_equal(fixef(fit), fixef(ans), tolerance = FIXEF_tol)
+    expect_equal(ranef(fit), ranef(ans), tolerance = RANEF_tol, ignore_attr = TRUE)
     expect_equal(ngrps(fit), ngrps(ans))
   # }
 })
 
-context("stan_glmer.nb")
 test_that("stan_glmer.nb ok", {
   dd <- expand.grid(f1 = factor(1:3),
                     f2 = LETTERS[1:2], g=1:9, rep=1:15,
@@ -78,13 +76,12 @@ test_that("stan_glmer.nb ok", {
   expect_equal(ngrps(fit), ngrps(ans))
 })
 
-context("stan_lmer")
 test_that("stan_lmer returns expected result for slepstudy example", {
   fmla <- formula(fit)
   expect_stanreg(fit)
   
   ans <- lmer(fmla, data = sleepstudy)
-  expect_equal(fixef(fit), fixef(ans), tol = FIXEF_tol)
+  expect_equal(fixef(fit), fixef(ans), tolerance = FIXEF_tol)
   # expect_equal(ranef(fit), ranef(ans), tol = RANEF_tol)
   expect_equal(ngrps(fit), ngrps(ans))
 })
@@ -95,8 +92,8 @@ test_that("stan_lmer returns expected result for Penicillin example", {
   expect_stanreg(fit)
   
   ans <- lmer(fmla, data = Penicillin)
-  expect_equal(fixef(fit), fixef(ans), tol = FIXEF_tol)
-  expect_equal(ranef(fit), ranef(ans), tol = RANEF_tol, check.attributes = FALSE)
+  expect_equal(fixef(fit), fixef(ans), tolerance = FIXEF_tol)
+  expect_equal(ranef(fit), ranef(ans), tolerance = RANEF_tol, ignore_attr = TRUE)
   expect_identical(ngrps(fit), ngrps(ans))
 })
 test_that("stan_lmer ok if global intercept forced to 0", {
@@ -128,8 +125,6 @@ test_that("error if y is character", {
   )
 })
 
-
-context("stan_gamm4")
 test_that("stan_gamm4 returns stanreg object", {
   skip_if_not_installed("mgcv")
   sleepstudy$y <- sleepstudy$Reaction / 10
@@ -139,7 +134,7 @@ test_that("stan_gamm4 returns stanreg object", {
   expect_stanreg(fit)
   # ans <- gamm4(Reaction / 10 ~ s(Days), data = sleepstudy, 
   #              random = ~(1|Subject))$mer
-  # expect_equal(fixef(fit)[-1], fixef(ans)[-1], tol = FIXEF_tol, check.attributes = FALSE)
+  # expect_equal(fixef(fit)[-1], fixef(ans)[-1], tol = FIXEF_tol, ignore_attr = TRUE)
   # expect_equal(ranef(fit), ranef(ans), tol = RANEF_tol)
   # expect_identical(ngrps(fit), ngrps(ans))
   
@@ -196,7 +191,6 @@ test_that("loo/waic for stan_glmer works", {
   expect_identical(ll_fun(example_model), rstanarm:::.ll_binomial_i)
 })
 
-context("posterior_predict (stan_gamm4)")
 test_that("stan_gamm4 returns expected result for sleepstudy example", {
   skip_if_not_installed("mgcv")
   sleepstudy$y <- sleepstudy$Reaction / 10
@@ -210,8 +204,6 @@ test_that("stan_gamm4 returns expected result for sleepstudy example", {
   expect_silent(posterior_predict(fit, newdata = sleepstudy))
 })
 
-
-context("posterior_predict (stan_(g)lmer)")
 test_that("compatible with stan_lmer", {
   check_for_pp_errors(fit)
   expect_linpred_equal(fit)
@@ -262,7 +254,7 @@ test_that("predition with family mgcv::betar doesn't error", {
 })
 
 # compare to lme4 ---------------------------------------------------------
-context("posterior_predict (compare to lme4)")
+
 test_that("posterior_predict close to predict.merMod for gaussian", {
   mod1 <- as.formula(mpg ~ wt + (1|cyl) + (1|gear))
   mod2 <- as.formula(mpg ~ log1p(wt) + I(disp/100) + (1|cyl))
@@ -290,17 +282,17 @@ test_that("posterior_predict close to predict.merMod for gaussian", {
     expect_equal(
       colMeans(posterior_predict(get(paste0("sfit", j)), newdata = nd, seed = SEED)),
       unname(predict(get(paste0("lfit", j)), newdata = nd)),
-      tol = tol, check.attributes = FALSE)
+      tolerance = tol, ignore_attr = TRUE)
     expect_equal(
       colMeans(posterior_predict(get(paste0("sfit", j)), newdata = nd2, seed = SEED,
                                  allow.new.levels = TRUE)),
       unname(predict(get(paste0("lfit", j)), newdata = nd2, allow.new.levels = TRUE)),
-      tol = tol, check.attributes = FALSE)
+      tolerance = tol, ignore_attr = TRUE)
     expect_equal(
       colMeans(posterior_predict(get(paste0("sfit", j)), newdata = nd3, seed = SEED,
                                  allow.new.levels = TRUE)),
       unname(predict(get(paste0("lfit", j)), newdata = nd3, allow.new.levels = TRUE)),
-      tol = tol, check.attributes = FALSE)
+      tolerance = tol, ignore_attr = TRUE)
   }
 })
 
@@ -320,5 +312,5 @@ test_that("posterior_predict close to predict.merMod for binomial", {
                              seed = SEED)
   spred <- sweep(spred, 2, rowSums(get_y(sfit)), "/")
   expect_equal(colMeans(spred), unname(colMeans(lpred)),
-               tol = .125, check.attributes = FALSE)
+               tolerance = .125, ignore_attr = TRUE)
 })
diff --git a/tests/testthat/test_stan_jm.R b/tests/testthat/test_stan_jm.R
index e5d075fad..6342dc502 100644
--- a/tests/testthat/test_stan_jm.R
+++ b/tests/testthat/test_stan_jm.R
@@ -33,7 +33,6 @@ TOLSCALES <- list(
   event = 0.3        # how many SEs can stan_jm fixefs be from coxph fixefs
 )
 
-context("stan_jm")
 
 #----  Data (for non-Gaussian families)
 
@@ -354,11 +353,11 @@ compare_glmer <- function(fmLong, fam = gaussian, ...) {
   pars <- recover_pars(y1, s1)
   parsjm <- recover_pars(j1)
   for (i in names(tols$fixef))
-    expect_equal(pars$fixef[[i]], parsjm$fixef[[i]], tol = tols$fixef[[i]], info = fam)
+    expect_equal(pars$fixef[[i]], parsjm$fixef[[i]], tolerance = tols$fixef[[i]], info = fam)
   for (i in names(tols$ranef))
-    expect_equal(pars$ranef[[i]], parsjm$ranef[[i]], tol = tols$ranef[[i]], info = fam)
+    expect_equal(pars$ranef[[i]], parsjm$ranef[[i]], tolerance = tols$ranef[[i]], info = fam)
   for (i in names(tols$event))
-    expect_equal(pars$event[[i]], parsjm$event[[i]], tol = tols$event[[i]], info = fam)
+    expect_equal(pars$event[[i]], parsjm$event[[i]], tolerance = tols$event[[i]], info = fam)
 }
 
 # test_that("coefs same for stan_jm and stan_lmer/coxph", {
diff --git a/tests/testthat/test_stan_lm.R b/tests/testthat/test_stan_lm.R
index 49c953232..6a232c25f 100644
--- a/tests/testthat/test_stan_lm.R
+++ b/tests/testthat/test_stan_lm.R
@@ -15,7 +15,6 @@
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
-context("stan_lm|aov|biglm")
 
 suppressPackageStartupMessages(library(rstanarm))
 SEED <- 12345
@@ -43,7 +42,7 @@ test_that("stan_aov returns expected result for npk example", {
   fit_sigma <- fit$stan_summary["sigma", "mean"]
   lm_sigma <- summary(lm(yield ~ block + N*P*K, data = npk,
                          contrasts = contrasts_list))$sigma
-  expect_equal(fit_sigma, lm_sigma, tol = threshold)
+  expect_equal(fit_sigma, lm_sigma, tolerance = threshold)
   expect_output(print(fit), regexp = "stan_aov")
   expect_output(print(fit), regexp = "ANOVA-like table")
 })
@@ -73,7 +72,7 @@ test_that("stan_biglm returns expected result", {
   SW(post <- stan_biglm(biglm, xbar, ybar, s_y, prior = R2(0.5),
                         chains = CHAINS, iter = ITER, seed = SEED, refresh = 0))
   expect_equal(coef(lm(mpg ~ wt + qsec + am, data = mtcars)),
-               rstan::summary(post)$summary[1:4, "mean"], tol = threshold)
+               rstan::summary(post)$summary[1:4, "mean"], tolerance = threshold)
 })
 
 test_that("stan_lm returns expected result for mtcars example", {
@@ -82,7 +81,7 @@ test_that("stan_lm returns expected result for mtcars example", {
 
   fit_sigma <- fit$stan_summary["sigma", "mean"]
   lm_sigma <- summary(lm(mpg ~ ., data = mtcars))$sigma
-  expect_equal(fit_sigma, lm_sigma, tol = threshold)
+  expect_equal(fit_sigma, lm_sigma, tolerance = threshold)
 })
 test_that("stan_lm returns expected result for trees example", {
   # example using trees dataset
@@ -93,7 +92,7 @@ test_that("stan_lm returns expected result for trees example", {
 
   fit_sigma <- fit$stan_summary["sigma", "mean"]
   lm_sigma <- summary(lm(log(Volume) ~ log(Girth) + log(Height),data = trees))$sigma
-  expect_equal(fit_sigma, lm_sigma, tol = threshold)
+  expect_equal(fit_sigma, lm_sigma, tolerance = threshold)
 })
 
 test_that("stan_lm doesn't break with less common priors", {
@@ -158,5 +157,8 @@ test_that("loo/waic for stan_lm works", {
 test_that("posterior_predict compatible with stan_lm", {
   skip_on_os("mac")
   check_for_pp_errors(fit)
-  expect_linpred_equal(fit)
+  # Scale relative error by the posterior medians.
+  expect_true(all.equal(apply(posterior_linpred(fit), 2, median),
+                        fit$linear.predictors, tolerance = 0.1,
+                        check.attributes = FALSE))
 })
diff --git a/tests/testthat/test_stan_mvmer.R b/tests/testthat/test_stan_mvmer.R
index 43cc1b5b0..2275006ea 100644
--- a/tests/testthat/test_stan_mvmer.R
+++ b/tests/testthat/test_stan_mvmer.R
@@ -31,7 +31,6 @@ TOLSCALES <- list(
   glmer_ranef = 0.1 # how many SDs can stan_jm ranefs be from glmer ranefs
 )
 
-context("stan_mvmer")
 
 #----  Data (for non-Gaussian families)
 
@@ -167,14 +166,14 @@ if (interactive()) {
     pars <- recover_pars(y1)
     pars2 <- recover_pars(y2)
     for (i in names(tols$fixef))
-      expect_equal(pars$fixef[[i]], pars2$fixef[[i]], tol = tols$fixef[[i]])     
+      expect_equal(pars$fixef[[i]], pars2$fixef[[i]], tolerance = tols$fixef[[i]])
     for (i in names(tols$ranef))
-      expect_equal(pars$ranef[[i]], pars2$ranef[[i]], tol = tols$ranef[[i]])
+      expect_equal(pars$ranef[[i]], pars2$ranef[[i]], tolerance = tols$ranef[[i]])
     expect_equal(colMeans(log_lik(y1)), 
-                 colMeans(log_lik(y2)), tol = 0.15)
+                 colMeans(log_lik(y2)), tolerance = 0.15)
     nd <- pbcLong[stats::complete.cases(pbcLong), , drop = FALSE]
     expect_equal(colMeans(log_lik(y1, newdata = nd)), 
-                 colMeans(log_lik(y2, newdata = nd)), tol = 0.15)
+                 colMeans(log_lik(y2, newdata = nd)), tolerance = 0.15)
   }
   test_that("coefs same for stan_jm and stan_lmer/coxph", {
     # fails in many cases
@@ -287,14 +286,14 @@ for (j in 1:5) {
     fm <- formula(mod)
     fam <- family(mod)
     sig <- sigma(mod)
-    expect_is(fe, "list"); expect_identical(length(fe), M)
-    expect_is(re, "list"); expect_identical(length(re), M)
-    expect_is(ce, "list"); expect_identical(length(re), M)
-    expect_is(mf, "list"); expect_identical(length(mf), M); lapply(mf, function(x) expect_is(x, "data.frame"))
-    expect_is(tt, "list"); expect_identical(length(tt), M); lapply(tt, function(x) expect_is(x, "terms"))
-    expect_is(fm, "list"); expect_identical(length(fm), M); lapply(fm, function(x) expect_is(x, "formula"))
-    expect_is(fam,"list"); expect_identical(length(fam),M); lapply(fam, function(x) expect_is(x, "family"))
-    expect_is(sig, "numeric");
+    expect_type(fe, "list"); expect_identical(length(fe), M)
+    expect_type(re, "list"); expect_identical(length(re), M)
+    expect_type(ce, "list"); expect_identical(length(re), M)
+    expect_type(mf, "list"); expect_identical(length(mf), M); lapply(mf, function(x) expect_s3_class(x, "data.frame"))
+    expect_type(tt, "list"); expect_identical(length(tt), M); lapply(tt, function(x) expect_s3_class(x, "terms"))
+    expect_type(fm, "list"); expect_identical(length(fm), M); lapply(fm, function(x) expect_s3_class(x, "formula"))
+    expect_type(fam, "list"); expect_identical(length(fam),M); lapply(fam, function(x) expect_s3_class(x, "family"))
+    expect_type(sig, "double");
   })
   
   test_that("these extraction methods are currently disallowed", {
diff --git a/tests/testthat/test_stan_nlmer.R b/tests/testthat/test_stan_nlmer.R
index 5448155d6..e955a2df6 100644
--- a/tests/testthat/test_stan_nlmer.R
+++ b/tests/testthat/test_stan_nlmer.R
@@ -26,7 +26,6 @@ REFRESH <- 0
 
 threshold <- 0.05
 
-context("stan_nlmer")
 
 data("Orange", package = "datasets")
 Orange$circumference <- Orange$circumference / 100
@@ -44,7 +43,7 @@ test_that("stan_nlmer runs for Orange example", {
 })
 
 test_that("stan_nlmer is similar to nlmer on Orange example", {
-  expect_equal(fixef(ml), fixef(fit), tol = threshold)
+  expect_equal(fixef(ml), fixef(fit), tolerance = threshold)
 })
 
 test_that("stan_nlmer throws error if formula includes an unknown function", {
@@ -57,7 +56,6 @@ test_that("loo/waic for stan_nlmer works", {
   expect_equivalent_loo(fit)
 })
 
-context("posterior_predict (stan_nlmer)")
 test_that("compatible with stan_nlmer", {
   check_for_pp_errors(fit)
 })
diff --git a/tests/testthat/test_stan_polr.R b/tests/testthat/test_stan_polr.R
index 89972bf97..796a8da62 100644
--- a/tests/testthat/test_stan_polr.R
+++ b/tests/testthat/test_stan_polr.R
@@ -26,7 +26,6 @@ REFRESH <- 0
 
 threshold <- 0.03
 
-context("stan_polr")
 
 
 f <- tobgp ~ agegp + alcgp
@@ -82,10 +81,10 @@ test_that("gumbel functions ok", {
   # formulas are correct
   # just test a few cases so they're flagged if anything changes by accident
   # maybe should compare to corresponding functions in ordinal package?
-  expect_equal(rstanarm:::dgumbel(0), 0.3678794, tol = 0.00001)
+  expect_equal(rstanarm:::dgumbel(0), 0.3678794, tolerance = 0.00001)
   expect_equal(rstanarm:::qgumbel(0), -Inf)
-  expect_equal(rstanarm:::qgumbel(0.5), 0.3665129, tol = 0.00001)
-  expect_equal(rstanarm:::pgumbel(0.3665129), 0.5, tol = 0.00001)
+  expect_equal(rstanarm:::qgumbel(0.5), 0.3665129, tolerance = 0.00001)
+  expect_equal(rstanarm:::pgumbel(0.3665129), 0.5, tolerance = 0.00001)
   expect_equal(rstanarm:::qgumbel(1), Inf)
 })
 
@@ -101,7 +100,6 @@ test_that("loo/waic for stan_polr works", {
   expect_identical(ll_fun(fit3), rstanarm:::.ll_polr_i)
 })
 
-context("posterior_predict (stan_polr)")
 test_that("compatible with stan_polr", {
   check_for_pp_errors(fit1)
   check_for_pp_errors(fit2)

From 7d643d3206020c34c41c7bd6fba46aaf1e74def5 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Mon, 14 Sep 2026 15:24:20 +0800
Subject: [PATCH 14/19] Test updated action

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index a3611c0e9..51984d4a8 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -34,7 +34,7 @@ jobs:
     steps:
       - uses: actions/checkout@v7
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: andrjohns/actions/setup-r@flang-mac-devel
         with:
           r-version: ${{ matrix.r }}
 

From ab6a99c884c697586a968f0cb2975b6f31dba34a Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Fri, 18 Sep 2026 15:41:31 +0800
Subject: [PATCH 15/19] Force source build

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 51984d4a8..b7dac72b2 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -50,6 +50,6 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: "TRUE"
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, any::rstan=?source
 
       - uses: r-lib/actions/check-r-package@v2

From 5d93d840750d284270c7c9094ce180a928fe2262 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Fri, 18 Sep 2026 15:48:13 +0800
Subject: [PATCH 16/19] Pak syntax

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index b7dac72b2..c681e1c96 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -50,6 +50,6 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: "TRUE"
-          extra-packages: any::rcmdcheck, any::rstan=?source
+          extra-packages: any::rcmdcheck, any::rstan?source
 
       - uses: r-lib/actions/check-r-package@v2

From fd97b84178606d568014cd80c17945dab51b9861 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Fri, 18 Sep 2026 16:08:06 +0800
Subject: [PATCH 17/19] Force source build

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index c681e1c96..bdf4de2bc 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -50,6 +50,6 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: "TRUE"
-          extra-packages: any::rcmdcheck, any::rstan?source
+          extra-packages: any::rcmdcheck, rstan?source
 
       - uses: r-lib/actions/check-r-package@v2

From 5bb077621905357657ac9fd6f921fddd9e4e9dd2 Mon Sep 17 00:00:00 2001
From: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: Sat, 19 Sep 2026 15:54:33 +0800
Subject: [PATCH 18/19] Remove CI testing changes

---
 .github/workflows/R-CMD-check.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index bdf4de2bc..47197c8f2 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master
-      - ci-fixes
   pull_request:
     branches:
       - master
@@ -34,7 +33,7 @@ jobs:
     steps:
       - uses: actions/checkout@v7
 
-      - uses: andrjohns/actions/setup-r@flang-mac-devel
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.r }}
 

From b3a76f09e92fabf7451fcd8b219f8e6ddc7dc043 Mon Sep 17 00:00:00 2001
From: jgabry <jgabry@gmail.com>
Date: Mon, 21 Sep 2026 10:16:20 -0600
Subject: [PATCH 19/19] add @andrjohns to DESCRIPTION

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 93243271a..53d7d7791 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -7,6 +7,7 @@ Encoding: UTF-8
 Authors@R: c(person("Jonah", "Gabry", email = "jgabry@gmail.com", role = "aut"),
              person("Imad", "Ali", role = "ctb"),
              person("Sam", "Brilleman", role = "ctb"),
+             person("Andrew", "Johnson", role = "ctb"),
              person(given = "Jacqueline Buros", family = "Novik",
                     role = "ctb", comment = "R/stan_jm.R"),
              person("AstraZeneca", role = "ctb", comment = "R/stan_jm.R"),