Merge branch 'develop'

# Conflicts:
#	README.md (fixed)

.Rbuildignore

@@ -2,8 +2,8 @@
 ^\.Rproj\.user$
 LICENSE
 ^\.travis\.yml$
-^NEWS\.md$
 ^README\.md$
 .gitignore
 ^cran-comments\.md$
 ^revdep$
+man-roxygen/*

.gitignore

@@ -1,20 +1,14 @@
-# History files
 .Rhistory
 .Rapp.history
-
-# Example code in package build process
 *-Ex.R
-# R data files from past sessions
 .Rdata
-# RStudio files
-.Rproj.user/
-shinyStan.Rproj
-# For the Mac
-*.DS_Store
 .Rproj.user
+shinystan.Rproj
+
+*.DS_Store
 inst/doc
 ^cran-comments\.md$
-
 cran-comments.md
 
+revdep/
 *.swf

.travis.yml

@@ -1,33 +1,9 @@
 language: r
-sudo: required
+r: devel
+cache: packages
 
-cran: http://cran.rstudio.com/
-r_check_revdep: false
-pandoc: false
+r_github_packages:
+  - jimhester/covr
 
-env:
-  global:
-    - _R_CHECK_FORCE_SUGGESTS_=false
-
-r_binary_packages:
-  - coda
-  - dygraphs
-  - ggplot2
-  - gtools
-  - httpuv
-  - inline
-  - jsonlite
-  - knitr
-  - markdown
-  - reshape2
-  - Rcpp
-  - RUnit
-  - shiny
-  - testthat
-  - xts
-  - yaml
-
-notifications:
-  email:
-  on_success: change
-  on_failure: change
+after_success:
+  - Rscript -e 'covr::codecov(function_exclusions = c("launch$", "launch_shinystan_demo"), line_exclusions = list("R/zzz.R"))'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: shinystan
 Title: Interactive Visual and Numerical Diagnostics and Posterior Analysis for
     Bayesian Models
-Version: 2.1.0
-Date: 2016-01-06
+Version: 2.2.0
+Date: 2016-05-23
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
     email = "[email protected]"),
       person(family = "Stan Development Team", role = "ctb"),
@@ -16,12 +16,12 @@ Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
       person("Dongying", "Song", role = "ctb"),
       person("Rob", "Trangucci", role = "ctb"))
 Maintainer: Jonah Gabry <[email protected]>
-Description: We provide a graphical user interface for interactive Markov chain
-    Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a
-    posterior sample. The interface is powered by RStudio's Shiny web application
-    framework and works with the output of MCMC programs written in any programming
-    language (and has extended functionality for Stan models fit using the rstan
-    package and the No-U-Turn sampler).
+Description: A graphical user interface for interactive Markov chain Monte
+    Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a
+    posterior sample. The interface is powered by RStudio's Shiny web
+    application framework and works with the output of MCMC programs written
+    in any programming language (and has extended functionality for Stan models
+    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/
 Depends:
@@ -32,18 +32,20 @@ LazyData: true
 Suggests:
     coda,
     knitr (>= 1.9),
-    rstan (>= 2.7),
     rmarkdown (>= 0.8.1),
+    rstanarm (>= 2.9.0-3),
     testthat
 Imports:
     DT (>= 0.1),
     dygraphs (>= 0.4.5),
-    ggplot2 (>= 2.0.0),
+    ggplot2 (>= 2.1.0),
     gridExtra,
     gtools,
     markdown (>= 0.7.4),
     methods,
     reshape2,
+    rsconnect (>= 0.4.2),
+    rstan (>= 2.9.0-3),
     stats,
     shinyjs (>= 0.1.0),
     shinythemes (>= 1.0.1),

NAMESPACE

@@ -2,10 +2,13 @@
 
 export(as.shinystan)
 export(deploy_shinystan)
+export(drop_parameters)
 export(generate_quantity)
+export(is.shinystan)
 export(launch_shinystan)
 export(launch_shinystan_demo)
 export(model_code)
+export(model_name)
 export(notes)
 export(rename_model)
 export(retrieve)
@@ -24,12 +27,12 @@ importFrom(gridExtra,grid.arrange)
 importFrom(gtools,mixedsort)
 importFrom(markdown,markdownToHTML)
 importFrom(reshape2,melt)
+importFrom(rsconnect,deployApp)
 importFrom(shinyjs,colourInput)
 importFrom(shinyjs,useShinyjs)
 importFrom(shinythemes,shinytheme)
 importFrom(stats,acf)
-importFrom(stats,model.frame)
-importFrom(stats,model.response)
+importFrom(stats,na.omit)
 importFrom(stats,quantile)
 importFrom(stats,time)
 importFrom(stats,var)

NEWS.md

@@ -1,4 +1,19 @@
-# `shinystan news`
+### Version 2.2.0
+* Add optional argument `pars` to the `as.shinystan` method for stanfit objects,
+allowing a subset of parameters to be selected for inclusion in the resulting
+shinystan object.
+* Introduce `drop_parameters` function for removing parameters from a shinystan 
+object (useful for very large objects when you only want to look at a subset of
+parameters).
+* Add **rstanarm** to Suggests (in the DESCRIPTION file) so `rstanarm::pp_check`
+can be called.
+* Allow selecting `yrep` from global environment for PPcheck
+* Change `as.shinystan` to S4 generic with methods
+* Add **rsconnect** to `Imports` in `DESCRIPTION`.
+* Rename some of the slots in shinystan objects. The `update_sso` function can
+be used to ensure that old shinystan objects have an internal structure
+compatible with this release.
+* Improve line coverage of api tests
 
 ### Version 2.1.0
 * Compatibility with recent ggplot2 update
@@ -16,13 +31,12 @@ plot ('Estimate' page)
 Version 2.0.0 has a new look, a new(ish) name, and a lot of new functionality. 
 Many bugs have also been fixed (see GitHub issue tracker). 
 
-[Available on CRAN](https://cran.rstudio.com/web/packages/shinystan/index.html).
 
 ### New names
 * The name of the R package is **shinystan** and the app/GUI is **ShinyStan**. 
 
 ### Deploy ShinyStan apps to shinyapps.io (RStudio's ShinyApps service)
-* The 'deploy_shinystan' function lets you easily deploy ShinyStan apps 
+* The `deploy_shinystan` function lets you easily deploy ShinyStan apps 
 to RStudio's shinyapps.io for any of your models. Each of your apps 
 (i.e. each of your models) will have a unique url.