fixes for CRAN

.Rbuildignore

@@ -4,6 +4,7 @@ LICENSE
 ^\.travis\.yml$
 ^README\.md$
 .gitignore
+.github/*
 ^cran-comments\.md$
 ^revdep$
 man-roxygen/*

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: shinystan
 Title: Interactive Visual and Numerical Diagnostics and Posterior Analysis for
     Bayesian Models
-Version: 2.5.0
-Date: 2018-04-29
+Version: 2.6.0
+Date: 2021-03-30
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
     email = "[email protected]"),
       person(family = "Stan Development Team", role = "ctb"),

NAMESPACE

@@ -31,7 +31,6 @@ importFrom(gridExtra,grid.arrange)
 importFrom(gtools,mixedsort)
 importFrom(markdown,markdownToHTML)
 importFrom(reshape2,melt)
-importFrom(rsconnect,deployApp)
 importFrom(shinyjs,useShinyjs)
 importFrom(shinythemes,shinytheme)
 importFrom(stats,acf)

NEWS.md

@@ -1,3 +1,8 @@
+# shinystan 2.6.0
+
+* Moved rsconnect package from Imports to Suggests as requested by CRAN
+* Initial support for CmdStanMCMC objects from CmdStanR
+
 # shinystan 2.5.0
 
 * New website with online documentation: http://mc-stan.org/shinystan

R/deploy_shinystan.R

@@ -48,7 +48,7 @@
 #'
 #'   \url{http://www.shinyapps.io/} to sign up for a free or paid 'ShinyApps'
 #'   account and for details on how to configure your account on your local
-#'   system using the \pkg{\link[rsconnect]{rsconnect}} package from 'RStudio'.
+#'   system using the \pkg{rsconnect} package from 'RStudio'.
 #'
 #' @examples
 #' \dontrun{
@@ -64,8 +64,6 @@
 #' deploy_shinystan(sso, appName = "my-model")
 #' }
 #'
-#' @importFrom rsconnect deployApp
-#'
 deploy_shinystan <- function(sso, appName, account = NULL, ..., deploy = TRUE) {
   sso_check(sso)
   if (missing(appName))
@@ -133,6 +131,9 @@ deploy_shinystan <- function(sso, appName, account = NULL, ..., deploy = TRUE) {
   if (!deploy)
     return(invisible(deployDir))
 
+  if (!requireNamespace("rsconnect", quietly = TRUE)) {
+    stop("Please install the 'rsconnect' package.", call. = FALSE)
+  }
   rsconnect::deployApp(
     appDir = deployDir,
     appName = appName,

R/shinystan-objects.R

@@ -911,7 +911,7 @@ setMethod(
       note = note,
       sampler_params = sampler_params, 
       algorithm = "NUTS",
-      max_treedepth = fit$metadata()$max_treedepth
+      max_treedepth = X$metadata()$max_treedepth
     )
   }
 )

tests/testthat/test_creating_sso.R

@@ -1,7 +1,6 @@
 library(shinystan)
-suppressPackageStartupMessages(library(rstan))
-suppressPackageStartupMessages(library(rstanarm))
 library(coda)
+suppressPackageStartupMessages(library(rstan))
 
 sso <- eight_schools
 array1 <- array(rnorm(300), dim = c(25, 4, 3))
@@ -13,11 +12,15 @@ data(line, package = "coda")
 mcmc1 <- line
 mcmc2 <- line[[1L]]
 
-suppressWarnings(capture.output(
-  stanreg1 <- stan_glmer(mpg ~ wt + (1 + wt|cyl), data = mtcars, 
-                         seed = 12345, iter = 200, chains = 2, refresh = 0)
-))
-stanfit1 <- stanreg1$stanfit
+if (requireNamespace("rstanarm", quietly = TRUE)) {
+  suppressPackageStartupMessages(library(rstanarm))
+  suppressWarnings(capture.output(
+    stanreg1 <- stan_glmer(mpg ~ wt + (1 + wt|cyl), data = mtcars, 
+                           seed = 12345, iter = 200, chains = 2, refresh = 0)
+  ))
+  stanfit1 <- stanreg1$stanfit
+}
+
 
 # load 'old_sso', a shinystan object created by previous shinystan version
 load("old_sso_for_tests.rda")
@@ -39,6 +42,7 @@ test_that("sso_check throws errors", {
 
 # is.shinystan ------------------------------------------------------------
 test_that("is.shinystan, is.stanfit, is.stanreg work", {
+  skip_if_not_installed("rstanarm")
   expect_true(is.shinystan(sso))
   expect_false(is.shinystan(sso@posterior_sample))
 
@@ -53,6 +57,7 @@ test_that("is.shinystan, is.stanfit, is.stanreg work", {
 context("Creating shinystan objects")
 # as.shinystan helpers ----------------------------------------------------
 test_that("as.shinystan stanfit helpers work", {
+  skip_if_not_installed("rstanarm")
   expect_is(.rstan_max_treedepth(stanfit1), "integer")
   expect_equal(.rstan_warmup(stanfit1), 0)
   expect_equal(length(.rstan_sampler_params(stanfit1)), ncol(stanfit1))
@@ -68,7 +73,7 @@ test_that("as.shinystan stanfit helpers work", {
   expect_identical(.rstan_sampler_params(stanfit1), list(NA))
 
   stanfit1@stan_args[[1]]$control$max_treedepth <- NULL
-  expect_equal(.rstan_max_treedepth(stanfit1), 11)
+  expect_equal(.rstan_max_treedepth(stanfit1), 10)
 })
 
 
@@ -127,6 +132,7 @@ test_that("as.shinystan (list of matrices) creates sso", {
   expect_s4_class(x, "shinystan")
 })
 test_that("as.shinystan (stanreg) creates sso", {
+  skip_if_not_installed("rstanarm")
   expect_message(x <- as.shinystan(stanreg1, model_name = "test"), 
                  "preparing graphical posterior predictive checks")
   expect_is(x, "shinystan")
@@ -141,6 +147,7 @@ test_that("as.shinystan (stanreg) creates sso", {
   expect_null(x@misc$pp_check_plots)
 })
 test_that("as.shinystan (stanfit) creates sso", {
+  skip_if_not_installed("rstanarm")
   expect_is(x <- as.shinystan(stanfit1, model_name = "test", note = "test"), "shinystan")
   expect_identical(sso_version(x), utils::packageVersion("shinystan"))
 })
@@ -151,6 +158,7 @@ test_that("as.shinystan throws errors", {
 })
 
 test_that("as.shinystan arguments works with rstanarm example", {
+  skip_if_not_installed("rstanarm")
   sso1 <- as.shinystan(stanreg1)
   sso2 <- as.shinystan(stanreg1, ppd = FALSE)
   expect_is(sso1, "shinystan")

tests/testthat/test_misc.R

@@ -10,6 +10,7 @@ test_that("options set when package loads", {
 })
 
 test_that("Can work with CSV files created by RStan", {
+  skip_if_not_installed("rstanarm")
   test_data <- data.frame(Y = rnorm(10))
   samples_tmp <- tempfile()
   fit <- rstanarm::stan_glm(Y ~ 1, data = test_data, sample_file = samples_tmp, chains = 1, iter = 10, sample_file = samples_tmp)