v2.3.0

Author: jgabry

.Rbuildignore

@@ -7,3 +7,4 @@ LICENSE
 ^cran-comments\.md$
 ^revdep$
 man-roxygen/*
+images/*

.gitignore

@@ -3,7 +3,6 @@
 *-Ex.R
 .Rdata
 .Rproj.user
-shinystan.Rproj
 
 *.DS_Store
 inst/doc

.travis.yml

@@ -3,7 +3,6 @@ r: devel
 cache: packages
 
 r_github_packages:
-  - HenrikBengtsson/matrixStats@develop
   - jimhester/covr
 
 after_success:

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: shinystan
 Title: Interactive Visual and Numerical Diagnostics and Posterior Analysis for
     Bayesian Models
-Version: 2.2.1-2
-Date: 2016-08-31
+Version: 2.3.0
+Date: 2017-01-31
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
     email = "[email protected]"),
       person(family = "Stan Development Team", role = "ctb"),
@@ -24,35 +24,36 @@ Description: A graphical user interface for interactive Markov chain Monte
     fit using the rstan and rstanarm packages).
 URL: https://github.com/stan-dev/shinystan/, http://mc-stan.org/
 BugReports: https://github.com/stan-dev/shinystan/issues/
+License: GPL (>=3)
 Depends:
     R (>= 3.1.0),
     shiny (>= 0.12.1)
-License: GPL (>=3)
-LazyData: true
-Suggests:
-    coda,
-    knitr (>= 1.9),
-    rmarkdown (>= 0.8.1),
-    rstanarm (>= 2.9.0-3),
-    testthat
 Imports:
+    bayesplot (>= 1.1.0),
     colourpicker,
     DT (>= 0.2),
-    dygraphs (>= 0.4.5),
-    ggplot2 (>= 2.1.0),
+    dygraphs (>= 1.1.1.2),
+    ggplot2 (>= 2.1.1),
     gridExtra,
     gtools,
     markdown (>= 0.7.4),
     methods,
     reshape2,
     rsconnect (>= 0.4.2),
-    rstan (>= 2.9.0-3),
+    rstan (>= 2.14.1),
     stats,
     shinyjs (>= 0.6.0),
     shinythemes (>= 1.0.1),
     threejs (>= 0.2.1),
     utils,
     xtable,
     xts (>= 0.9-7)
+Suggests:
+    coda,
+    knitr (>= 1.9),
+    rmarkdown (>= 0.8.1),
+    rstanarm (>= 2.14.1),
+    testthat
+LazyData: true
 VignetteBuilder: knitr
 RoxygenNote: 5.0.1

NAMESPACE

@@ -14,6 +14,7 @@ export(rename_model)
 export(retrieve)
 export(sso_info)
 export(update_sso)
+import(bayesplot)
 import(dygraphs)
 import(ggplot2)
 import(methods)

NEWS.md

@@ -1,7 +1,20 @@
-### Version 2.2.1-2
-* Fix various issues resulting in errors for models fit using static HMC (thanks to @colemonnahan)
+### Version 2.3.0
+
+#### Fixes 
+* Fix various issues resulting in errors for models fit using static HMC (thanks
+to Cole Monnahan).
+* Deprecate `burnin` argument to `as.shinystan`. Use `warmup` instead. Only 
+relevant for models _not_ fit using Stan.
+
+#### New features
+* Add NUTS energy diagnostic plots to Diagnose page
+* Allowing passing `sampler_params` to `as.shinystan`. This makes it possible to
+display sampler diagnositcs for HMC/NUTS even if not using Stan's implementation
+of those algorithms (thanks to Cole Monnahan)
+>>>>>>> develop
 
 ### Version 2.2.1
+
 * Better compatibility with latest releases of 'shinyjs' and 'DT' packages
 * `shinystan::launch_shinystan_demo()` now works without first having to load 
 the package with a call to `library`

R/deploy_shinystan.R

@@ -88,6 +88,7 @@ deploy_shinystan <- function(sso, appName, account = NULL, ..., deploy = TRUE) {
   ui_pkgs <- c(
     server_pkgs,
     "ggplot2",
+    "bayesplot",
     "gtools",
     "reshape2",
     "dygraphs",

R/generate_quantity.R

@@ -54,12 +54,6 @@ generate_quantity <- function(sso, param1, param2, fun, new_name) {
     if (two_params)
       y_samp <- posterior[, , param2]
   }
-  if (ndim == 2) {
-    # i.e. only 1 chain
-    x_samp <- posterior[, param1]
-    if (two_params)
-      y_samp <- posterior[, param2]
-  }
 
   arglist <- if (two_params)
     list(x_samp, y_samp) else list(x_samp)
@@ -79,7 +73,7 @@ generate_quantity <- function(sso, param1, param2, fun, new_name) {
   sso_new <- as.shinystan(
     posterior,
     model_name = slot(sso, "model_name"),
-    burnin = slot(sso, "n_warmup"),
+    warmup = slot(sso, "n_warmup"),
     param_dims = param_dims_new
   )
   slot(sso_new, "summary") <-

R/misc.R

@@ -58,8 +58,10 @@ grepl_ic <- function(pattern, x, ignore.case = TRUE) {
 # release reminders (for devtools)
 release_questions <- function() {
   c(
-    "Have you updated version numbers in the citation?",
-    "Have you updated NEWS.md? and inst/NEWS?"
+    "Have you updated version numbers in inst/CITATION?",
+    "Have you updated version numbers in the citation on the About page?",
+    "Have you updated version numbers in the citation on the Stan website?",
+    "Have you updated NEWS.md?"
   )
 }
 # nocov end