Fixes for tests

DESCRIPTION

@@ -80,4 +80,3 @@ NeedsCompilation: yes
 URL: https://mc-stan.org/rstanarm/, https://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/rstanarm/issues
 RoxygenNote: 7.3.1
-Config/testthat/parallel: true

tests/testthat/test_methods.R

@@ -20,7 +20,7 @@ library(lme4)
 library(MASS)
 SEED <- 12345
 set.seed(SEED)
-ITER <- 10
+ITER <- 100
 CHAINS <- 2
 REFRESH <- 0
 
@@ -719,7 +719,7 @@ 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),
+  expect_error(predictive_error(stan_glm1, draws = 500),
                "'draws' should be <= posterior sample size")
   expect_error(predictive_error(stan_polr1),
                "not currently available for stan_polr")
@@ -748,7 +748,7 @@ test_that("predictive_error works", {
   expect_equal(dim(err3), c(5, 2))
 })
 test_that("predictive_interval works", {
-  expect_error(predictive_interval(stan_glm1, draws = 100),
+  expect_error(predictive_interval(stan_glm1, draws = 500),
                "'draws' should be <= posterior sample size")
   expect_error(predictive_interval(stan_glm1, prob = c(0.25, 0.76)),
                "'prob' should be a single number greater than 0 and less than 1")
@@ -786,7 +786,7 @@ test_that("predictive_error stanreg and ppd methods return the same thing", {
   preds <- posterior_predict(stan_betareg1, seed = 123)
   expect_equal(
     predictive_error(stan_betareg1, seed = 123),
-    predictive_error(preds, y = stan_betareg1$y)
+    predictive_error(preds, y = stan_betareg2$y)
   )
 })
 test_that("predictive_interval stanreg and ppd methods return the same thing", {

tests/testthat/test_stan_betareg.R

@@ -41,39 +41,39 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
   # sparse currently not used in stan_betareg
   test_that("sparse = TRUE errors", {
     expect_error(
-      stan_betareg(y ~ x, link = "logit", seed = SEED, sparse = TRUE, data = dat),
+      stan_betareg(y ~ x, link = "logit", sparse = TRUE, data = dat),
       "unknown arguments: sparse"
     )
   })
 
   # test QR 
   test_that("QR errors when number of x and/or z predictors is <= 1", {
     expect_error(
-      stan_betareg(y ~ x, link = "logit", seed = SEED, QR = TRUE, data = dat),
+      stan_betareg(y ~ x, link = "logit", QR = TRUE, data = dat),
       "'QR' can only be specified when there are multiple predictors"
     )
     expect_error(
-      stan_betareg(y ~ x | z, link = "logit", seed = SEED, QR = TRUE, data = dat),
+      stan_betareg(y ~ x | z, link = "logit", QR = TRUE, data = dat),
       "'QR' can only be specified when there are multiple predictors"
     )
   })
 
   test_that("QR works when number of x and/or z predictors is >= 1", {
-    SW(fit1 <- stan_betareg(y ~ x + z, link = "logit", seed = SEED, QR = TRUE,
+    SW(fit1 <- stan_betareg(y ~ x + z, link = "logit", QR = TRUE,
                             prior = NULL, prior_intercept = NULL, refresh = 0,
                             data = dat, algorithm = "optimizing"))
     expect_stanreg(fit1)
     expect_output(print(prior_summary(fit1)), "Q-space")
 
-    SW(fit2 <- stan_betareg(y ~ x + z | z, link = "logit", seed = SEED, QR = TRUE,
+    SW(fit2 <- stan_betareg(y ~ x + z | z, link = "logit", QR = TRUE,
                             prior = NULL, prior_intercept = NULL, refresh = 0,
                             data = dat, algorithm = "optimizing"))
     expect_stanreg(fit2)
   })
 
   test_that("stan_betareg returns expected result when modeling x and dispersion", {
     for (i in 1:length(link1)) {
-      SW(fit <- stan_betareg(y ~ x, link = link1[i], seed = SEED,
+      SW(fit <- stan_betareg(y ~ x, link = link1[i],
                              prior = NULL, prior_intercept = NULL,
                              prior_phi = NULL, refresh = 0,
                              data = dat, algorithm = "optimizing"))
@@ -85,7 +85,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
   })
 
   test_that("stan_betareg works with QR = TRUE and algorithm = 'optimizing'", {
-    SW(fit <- stan_betareg(y ~ x + z, link = "logit", seed = SEED, QR = TRUE,
+    SW(fit <- stan_betareg(y ~ x + z, link = "logit", QR = TRUE,
                            prior = NULL, prior_intercept = NULL,
                            prior_phi = NULL, refresh = 0,
                            data = dat, algorithm = "optimizing"))
@@ -185,7 +185,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
 
       SW(fit <- stan_betareg(y ~ x | 1, link = link1[i], link.phi = "sqrt", 
                              data = dat, chains = 1, iter = 1, refresh = 0, 
-                             algorithm = "sampling", seed = SEED)) 
+                             algorithm = "sampling")) 
       expect_stanreg(fit)
     }
   })
@@ -199,7 +199,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
     mu <- binomial(link="logit")$linkinv(1+0.2*dat$x)
     phi <- 20
     dat$y <- rbeta(N, mu * phi, (1 - mu) * phi)
-    SW(fit <- stan_betareg(y ~ x, link = "logit", seed = SEED,
+    SW(fit <- stan_betareg(y ~ x, link = "logit",
                            prior = NULL, prior_intercept = NULL, prior_phi = NULL,
                            data = dat, weights = weights, offset = offset, 
                            algorithm = "optimizing", iter = 2000, refresh = 0))
@@ -240,7 +240,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
   test_that("compatible with stan_betareg with z", {
     data("GasolineYield", package = "betareg")
     SW(fit <- stan_betareg(yield ~ pressure + temp | temp, data = GasolineYield,
-                           iter = ITER*5, chains = 2*CHAINS, seed = SEED, 
+                           iter = ITER*5, chains = 2*CHAINS, 
                            refresh = 0))
     check_for_pp_errors(fit)
     # expect_linpred_equal(fit)
@@ -249,7 +249,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
   test_that("compatible with stan_betareg without z", {
     data("GasolineYield", package = "betareg")
     SW(fit <- stan_betareg(yield ~ temp, data = GasolineYield, 
-                           iter = ITER, chains = CHAINS, seed = SEED, refresh = 0))
+                           iter = ITER, chains = CHAINS, refresh = 0))
     check_for_pp_errors(fit)
     # expect_linpred_equal(fit)
   })
@@ -258,9 +258,9 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
     GasolineYield2 <- GasolineYield
     GasolineYield2$offs <- runif(nrow(GasolineYield2))
     SW(fit <- stan_betareg(yield ~ temp, data = GasolineYield2, offset = offs,
-                           iter = ITER*5, chains = CHAINS, seed = SEED, refresh = 0))
+                           iter = ITER*5, chains = CHAINS, refresh = 0))
     SW(fit2 <- stan_betareg(yield ~ temp + offset(offs), data = GasolineYield2,
-                            iter = ITER*5, chains = CHAINS, seed = SEED, refresh = 0))
+                            iter = ITER*5, chains = CHAINS, refresh = 0))
 
     expect_warning(posterior_predict(fit, newdata = GasolineYield), 
                    "offset")
@@ -284,7 +284,7 @@ if (.Platform$OS.type != "windows" && require(betareg)) {
     betaregfit <- betareg(y ~ x | z, data = dat)
     SW(capture.output(
       stanfit <- stan_betareg(y ~ x | z, data = dat, chains = CHAINS,
-                              iter = ITER, seed = SEED, refresh = 0)
+                              iter = ITER, refresh = 0)
     ))
 
     pb <- predict(betaregfit, type = "response")

tests/testthat/test_stan_clogit.R

@@ -20,7 +20,7 @@
 suppressPackageStartupMessages(library(rstanarm))
 
 SEED <- 123
-ITER <- 100
+ITER <- 500
 CHAINS <- 2
 CORES <- 1
 REFRESH <- 0
@@ -30,9 +30,8 @@ threshold <- 0.03
 context("stan_clogit")
 
 SW(fit <- stan_clogit(case ~ spontaneous + induced, strata = stratum, prior = NULL,
-                   data = infert[order(infert$stratum), ], 
-                   QR = TRUE, init_r = 0.5,
-                   chains = CHAINS, iter = ITER, seed = SEED, refresh = 0))
+                   data = infert[order(infert$stratum), ],
+                   chains = CHAINS, iter = ITER, refresh = 0))
 
 test_that("stan_clogit is similar to survival::clogit", {
   expect_equal(c(spontaneous = 1.985876, induced = 1.409012), coef(fit), tol = threshold)
@@ -47,9 +46,8 @@ test_that("stan_clogit works when y is a factor", {
   d$case <- factor(d$case, labels = c("A", "B"))
   SW(fit_factor <- stan_clogit(case ~ spontaneous + induced, strata = stratum, prior = NULL,
                         data = infert[order(infert$stratum), ], 
-                        QR = TRUE, init_r = 0.5,
-                        chains = CHAINS, iter = ITER, seed = SEED, refresh = 0))
-  expect_equal(coef(fit_factor), coef(fit))
+                        chains = CHAINS, iter = ITER, refresh = 0))
+  expect_equal(coef(fit_factor), coef(fit), tolerance = threshold)
 })
 
 test_that("stan_clogit throws error if data are not sorted", {

tests/testthat/test_stan_functions.R

@@ -18,8 +18,8 @@
 Sys.setenv(USE_CXX17 = 1)
 set.seed(12345)
 
-MODELS_HOME <- "../../inst/stan"
-INCLUDE_DIR <- "../../inst/include"
+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", {