- Update to testthat3

DESCRIPTION

@@ -6,6 +6,8 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-7683-4592")),
     person("Kirill", "Müller", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0002-1416-3412")),
+    person("Nicole", "Hill", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-7623-2153")),
     person("Ayla", "Pearson", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0001-7388-1222")),
     person("Nadine", "Hussein", , "[email protected]", role = "ctb",
@@ -51,7 +53,7 @@ Suggests:
     cli,
     covr,
     jmbr,
-    testthat
+    testthat (>= 3.0.0)
 RdMacros: 
     lifecycle
 Remotes: 
@@ -64,3 +66,4 @@ Remotes:
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
+Config/testthat/edition: 3

R/plot-data.R

@@ -20,7 +20,7 @@ ggplot_data <- function(x, y, x_name, y_name) {
   height <- if (is.numeric(y)) 0 else 0.2
 
   gp <- ggplot2::ggplot(data = data) +
-    ggplot2::aes_string(x = "x", y = "y") +
+    ggplot2::aes(x = "x", y = "y") +
     ggplot2::xlab(x_name) +
     ggplot2::ylab(y_name) +
     ggplot2::geom_jitter(alpha = 1 / 3, width = width, height = height)

R/residuals.R

@@ -28,7 +28,7 @@ plot_residuals <- function(x, ...) {
 
 ggplot_residuals_histogram <- function(data, name) {
   gp <- ggplot2::ggplot(data = data) +
-    ggplot2::aes_string(x = "residuals") +
+    ggplot2::aes(x = "residuals") +
     suppressWarnings(ggplot2::geom_histogram()) +
     ggplot2::expand_limits(x = 0) +
     ggplot2::xlab("residual")
@@ -37,7 +37,7 @@ ggplot_residuals_histogram <- function(data, name) {
 
 ggplot_residuals <- function(data, name) {
   gp <- ggplot2::ggplot(data = data) +
-    ggplot2::aes_string(x = "x", y = "residuals") +
+    ggplot2::aes(x = "x", y = "residuals") +
     ggplot2::geom_hline(yintercept = 0) +
     ggplot2::expand_limits(y = 0) +
     ggplot2::xlab(name) +

tests/testthat/test-mb-code.R

@@ -1,7 +1,7 @@
 test_that("mb_code", {
   expect_warning(mb_code("blah blah"), "template type is unrecognised")
-  expect_is(mb_code(.tmb_template), "tmb_code")
-  expect_is(mb_code("function() dpois()"), "lmb_code")
+  expect_s3_class(mb_code(.tmb_template), "tmb_code")
+  expect_s3_class(mb_code("function() dpois()"), "lmb_code")
 })
 
 test_that("template", {

tests/testthat/test-mb-null-analysis.R

@@ -3,17 +3,17 @@ test_that("mb_null_analysis", {
   class(analysis) <- c("mb_null_analysis", "mb_analysis")
 
   coef <- coef(analysis)
-  expect_is(coef, "tbl")
+  expect_s3_class(coef, "tbl")
   expect_identical(colnames(coef), c("term", "estimate", "sd", "zscore", "lower", "upper", "pvalue"))
   expect_identical(nrow(coef), 0L)
 
   glance <- glance(analysis)
-  expect_is(glance, "tbl")
+  expect_s3_class(glance, "tbl")
   expect_identical(colnames(glance), c("n", "K", "logLik", "IC", "converged"))
   expect_identical(nrow(glance), 1L)
 
   tidy <- tidy(analysis)
-  expect_is(tidy, "tbl")
+  expect_s3_class(tidy, "tbl")
   expect_identical(colnames(tidy), c("term", "estimate", "lower", "upper"))
   expect_identical(nrow(tidy), 0L)
 

tests/testthat/test-new-expr-update.R

@@ -59,7 +59,7 @@ test_that("update new expr string expression", {
           residual <- res_lnorm(Density, fit, exp(log_sDensity))
       }"
   )
-  expect_warning(analysis <- analyse(model, data = data, glance = FALSE))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = FALSE)))
 
   expect_identical(pars(analysis, "derived"), "eDensity")
   expect_identical(pars(analysis, "random"), "bSiteYear")
@@ -143,11 +143,11 @@ test_that("update new expr bare expression", {
       residual <- res_lnorm(Density, fit, exp(log_sDensity))
     }
   )
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = FALSE)))
 
   year <- predict(analysis, new_data = "Year")
 
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",
@@ -223,11 +223,11 @@ test_that("add new_expr_vec argument to update model", {
       }",
     new_expr_vec = FALSE
   )
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = FALSE)))
 
   year <- predict(analysis, new_data = "Year")
 
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",
@@ -296,11 +296,11 @@ test_that("add new_expr_vec argument to update model and updates original new_ex
     model,
     new_expr_vec = TRUE
   )
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = TRUE)))
 
   year <- predict(analysis, new_data = "Year")
 
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",
@@ -369,11 +369,11 @@ test_that("cannot undo the vectorization if orignally set in the model", {
     model,
     new_expr_vec = FALSE
   )
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = FALSE)))
 
   year <- predict(analysis, new_data = "Year")
 
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",

tests/testthat/test-new-expr-vec.R

@@ -50,11 +50,11 @@ test_that("vectorize predict string expression", {
     random_effects = list(bSiteYear = c("Site", "YearFactor"))
   )
 
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = TRUE)))
 
   year <- predict(analysis, new_data = "Year")
 
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",
@@ -65,7 +65,7 @@ test_that("vectorize predict string expression", {
 
   ppc <- posterior_predictive_check(analysis)
 
-  expect_is(ppc, "tbl_df")
+  expect_s3_class(ppc, "tbl_df")
   expect_identical(colnames(ppc), c("moment", "observed", "median", "lower", "upper", "svalue"))
   expect_identical(ppc$moment, structure(1:5, .Label = c(
     "zeros", "mean", "variance", "skewness",
@@ -130,11 +130,11 @@ test_that("vectorize predict bare expression", {
     random_effects = list(bSiteYear = c("Site", "YearFactor"))
   )
 
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = FALSE)))
 
   year <- predict(analysis, new_data = "Year")
 
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",
@@ -145,7 +145,7 @@ test_that("vectorize predict bare expression", {
 
   ppc <- posterior_predictive_check(analysis)
 
-  expect_is(ppc, "tbl_df")
+  expect_s3_class(ppc, "tbl_df")
   expect_identical(colnames(ppc), c("moment", "observed", "median", "lower", "upper", "svalue"))
   expect_identical(ppc$moment, structure(1:5, .Label = c(
     "zeros", "mean", "variance", "skewness",
@@ -213,11 +213,11 @@ test_that("two expressions wrapped even when new_expr_vec = TRUE", {
     random_effects = list(bSiteYear = c("Site", "YearFactor"))
   )
 
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = FALSE)))
 
   year <- predict(analysis, new_data = "Year")
 
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",
@@ -228,7 +228,7 @@ test_that("two expressions wrapped even when new_expr_vec = TRUE", {
 
   ppc <- posterior_predictive_check(analysis)
 
-  expect_is(ppc, "tbl_df")
+  expect_s3_class(ppc, "tbl_df")
   expect_identical(colnames(ppc), c("moment", "observed", "median", "lower", "upper", "svalue"))
   expect_identical(ppc$moment, structure(1:5, .Label = c(
     "zeros", "mean", "variance", "skewness",

tests/testthat/test-new-expr.R

@@ -50,11 +50,11 @@ test_that("predict string expression", {
     random_effects = list(bSiteYear = c("Site", "YearFactor"))
   )
 
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = FALSE)))
 
   year <- predict(analysis, new_data = "Year")
 
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",
@@ -65,7 +65,7 @@ test_that("predict string expression", {
 
   ppc <- posterior_predictive_check(analysis)
 
-  expect_is(ppc, "tbl_df")
+  expect_s3_class(ppc, "tbl_df")
   expect_identical(colnames(ppc), c("moment", "observed", "median", "lower", "upper", "svalue"))
   expect_identical(ppc$moment, structure(1:5, .Label = c(
     "zeros", "mean", "variance", "skewness",
@@ -130,11 +130,11 @@ test_that("predict bare expression", {
     random_effects = list(bSiteYear = c("Site", "YearFactor"))
   )
 
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_warning(expect_warning(analysis <- analyse(model, data = data, glance = FALSE)))
 
   year <- predict(analysis, new_data = "Year")
 
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",
@@ -145,7 +145,7 @@ test_that("predict bare expression", {
 
   ppc <- posterior_predictive_check(analysis)
 
-  expect_is(ppc, "tbl_df")
+  expect_s3_class(ppc, "tbl_df")
   expect_identical(colnames(ppc), c("moment", "observed", "median", "lower", "upper", "svalue"))
   expect_identical(ppc$moment, structure(1:5, .Label = c(
     "zeros", "mean", "variance", "skewness",

tests/testthat/test-predict.R

@@ -14,7 +14,7 @@ test_that("lmb", {
   # models <- as.models(models)
   #
   # analyses <- analyse(models, data = data, glance = FALSE, beep = FALSE)
-  # expect_is(analyses, "mb_analyses")
+  # expect_s3_class(analyses, "mb_analyses")
   #
   # feed <- predict(analyses, new_data = "feed")
   # expect_identical(as.character(feed$feed), levels(datasets::chickwts$feed))

tests/testthat/test-residuals.R

@@ -17,5 +17,5 @@ test_that("lmb", {
   #
   # plots <- plot_residuals(analysis)
   # expect_identical(names(plots), c("feed", "fit", "weight"))
-  # expect_is(plots[[1]], "ggplot")
+  # expect_s3_class(plots[[1]], "ggplot")
 })

tests/testthat/test-zzz-analyse.R

@@ -53,7 +53,7 @@ test_that("analyse", {
     new_expr = new_expr
   )
 
-  expect_output(expect_warning(analysis <- analyse(model, data = data)))
+  expect_output(expect_warning(expect_warning(analysis <- analyse(model, data = data))))
 
   expect_equal(as.data.frame(data_set(analysis)), data)
   data2 <- data_set(analysis, marginalize_random_effects = TRUE)
@@ -93,10 +93,10 @@ test_that("analyse", {
     c("bHabitatQuality", "bIntercept", "bSiteYear", "bYear", "eDensity", "log_sDensity", "log_sSiteYear")
   )
 
-  expect_is(as.mcmcr(analysis), "mcmcr")
+  expect_s3_class(as.mcmcr(analysis), "mcmcr")
 
   glance <- glance(analysis)
-  expect_is(glance, "tbl")
+  expect_s3_class(glance, "tbl")
   expect_identical(colnames(glance), c("n", "K", "nchains", "niters", "nthin", "ess", "rhat", "converged"))
   expect_identical(glance$n, 300L)
   expect_identical(glance$nthin, 1L)
@@ -108,7 +108,7 @@ test_that("analyse", {
 
   coef <- coef(analysis, simplify = TRUE)
 
-  expect_is(coef, "tbl")
+  expect_s3_class(coef, "tbl")
   expect_identical(colnames(coef), c("term", "estimate", "lower", "upper", "svalue"))
 
   expect_identical(coef$term, as.term(c(
@@ -127,13 +127,13 @@ test_that("analyse", {
 
   ppc <- posterior_predictive_check(analysis)
 
-  expect_is(ppc, "tbl_df")
+  expect_s3_class(ppc, "tbl_df")
   expect_identical(colnames(ppc), c("moment", "observed", "median", "lower", "upper", "svalue"))
   expect_identical(ppc$moment, structure(1:5, .Label = c(
     "zeros", "mean", "variance", "skewness",
     "kurtosis"
   ), class = "factor"))
-  expect_is(year, "tbl")
+  expect_s3_class(year, "tbl")
   expect_identical(colnames(year), c(
     "Site", "HabitatQuality", "Year", "Visit",
     "Density", "YearFactor",
@@ -145,15 +145,15 @@ test_that("analyse", {
   dd <- mcmc_derive_data(analysis, new_data = c("Site", "Year"), ref_data = TRUE)
   expect_true(mcmcdata::is.mcmc_data(dd))
 
-  expect_warning(
+  expect_warning(expect_warning(expect_warning(
     sensitivity <- sd_priors_by(analysis, by = 10, glance = FALSE),
     "incomplete adaptation"
-  )
+  )))
 
   analyses <- analyses(analysis, sensitivity)
 
   rhat2 <- rhat(analyses)
-  expect_is(rhat2, "list")
+  expect_type(rhat2, "list")
   expect_identical(names(rhat2), c("mcmcr1", "mcmcr2"))
 
   skip_if_not_installed("mcmcr", "0.6.1.9001")
@@ -163,15 +163,15 @@ test_that("analyse", {
     "`rhat.mcmcrs\\(x, bound = TRUE\\)`"
   )
 
-  expect_is(rhat2, "list")
+  expect_type(rhat2, "list")
   expect_identical(names(rhat2), c("mcmcr1", "mcmcr2", "bound"))
 
   lifecycle::expect_deprecated(
     glance <- glance(analyses, bound = TRUE),
     "`rhat.mcmcrs\\(x, bound = TRUE\\)`"
   )
 
-  expect_is(glance, "tbl")
+  expect_s3_class(glance, "tbl")
   expect_identical(nrow(glance), 1L)
   expect_identical(colnames(glance), c("n", "K", "nchains", "niters", "rhat_1", "rhat_2", "rhat_all", "converged"))
 })