Fix current test errors, update to testthat 3rd edition

.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 +31,24 @@ 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"
+          extra-packages: any::rcmdcheck, rstan?source
+
+      - uses: r-lib/actions/check-r-package@v2

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"),
@@ -63,7 +64,7 @@ Suggests:
     rmarkdown,
     roxygen2,
     StanHeaders (>= 2.21.0),
-    testthat (>= 1.0.2),
+    testthat (>= 3.0.0),
     gamm4,
     shiny,
     V8
@@ -76,4 +77,6 @@ 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
+Config/testthat/edition: 3
+Config/testthat/parallel: true

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)

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
 }
-

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 {

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(), 
@@ -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]],
@@ -416,12 +417,12 @@ 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()

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