updates to web, manual, stan version and release notes and to-do for …

…1.1.0

RELEASE-NOTES.txt

@@ -15,37 +15,59 @@ HOW TO (developer notes on how to release, last column is ordering)
 10.  Announce                                                    > 9
 
 
-v1.0.0
-----------------------------------------------------------------------
-First release.
+v1.1.0
+======================================================================
+-- Backward Compatibility Issue
+   * Categorical distribution recoded to match documentation;  it
+     now has support {1,...,K} rather than {0,...,K-1}.  
+   * (RStan) change default value of permuted flag from FALSE to TRUE for
+     Stan fit S4 extract() method
+-- New Features
+   * Conditional (if-then-else) statements
+   * While statements
+-- New Functions
+   * generalized multiply_lower_tri_self_transpose() to non-square
+     matrices
+   * special functions: log_inv_logit(), log1m_inv_logit()
+   * matrix special functions: cumulative_sum()
+   * probability functions: poisson_log_log() for log-rate 
+     parameterized Poisson
+   * matrix functions: block(), diag_pre_multiply(), diag_post_multiply()
+   * comparison operators (<, >, <=, >=, ==, !=)
+   * boolean operators (!, ||, &&)
+   * allow +/- inf values in variable declaration constraints
+-- RStan Improvements
+   * get_posterior_mean() method for Stan fit objects
+   * replaced RcppEigen dependency with include of Eigen source
+   * added read_stan_csv() to create Stan fit object from CSV files of
+     the form written to disk by the command-line version of Stan
+   * as.data.frame() S3 method for Stan fit objects
+-- Bug Fixes
+   * fixed bug in NUTS diagonal resulting in too small step sizes
+   * fixed bug introduced in 1.0.3 that hid line and column number
+     bug reporting
+   * added checks that data dimensions match as well as sizes
+   * removed non-symmetric versions of eigenvalues() and eigenvectors()
+   * testing identifiers are not reserved words in C++/Stan
+   * trapping/reporting locations of errors in data and init reads
+   * improvements in dump data format reader for more R compatibility
+     and more generality
+   * fix bug in bernoulli logit distro tail density
+-- Code Improvements
+   * templated out matrix libs to reduce code duplication
+   * vectorized auto-dif for tcrossprod() and crossprod()
+   * optimizations in Wishart
+   * vectorization with efficiency improvements in probability distributions
+-- Libraries Updated
+   * Eigen version 3.1.1 replaced with version 3.1.2
+   * Boost version 1.51.0 replaced with version 1.52.0
+-- Manual Improvements
+   * New chapter on univariate and multivariate variable transforms
+   * Many consistency improvements and typo corrections
+   * Information on running command line in parallel from shell
 
-v1.0.1
-----------------------------------------------------------------------
-Patch release.
 
 
-V 1.0.2 Release Notes (28 Sep 2012)
-----------------------------------------------------------------------
-Bug Fixes:
-  -- check ranges for LHS of assignment to prevent seg faults
-  -- added matrix size and shape tests to avoid seg faults
-  -- changed matrix to throw domain_error rather than illegal_argument
-  -- removed template variable names from distribution error msgs
-  -- indexing fixed for arrays of matrix/vector/row_vector
-  -- fixed sd() and variance() to return 0.0 for sequences of size 1
-  -- fixed void return type in auto_covariance
-  -- patch truncation to return -inf for variates out of range
-  -- upgraded BUGS ring model to use constraints plus tan2()
-New Features:
-  -- print statements
-  -- multiply_lower_tri_self_transpose function
-  -- vectorized several probability functions (see the manual)
-Manual Additions:
-  -- programming guide: IRT models 
-  -- new appendix: style guide
-  -- new appendix: migrating from Stan
-  -- new index: function and distribution index
-
 v 1.0.3 Release Notes (25 Oct 2012)
 ======================================================================
 Stan Bug Fixes:
@@ -97,3 +119,40 @@ RStan New Features:
  -- turn off refresh if value <= 0
 
 
+V 1.0.2 Release Notes (28 Sep 2012)
+----------------------------------------------------------------------
+Bug Fixes:
+  -- check ranges for LHS of assignment to prevent seg faults
+  -- added matrix size and shape tests to avoid seg faults
+  -- changed matrix to throw domain_error rather than illegal_argument
+  -- removed template variable names from distribution error msgs
+  -- indexing fixed for arrays of matrix/vector/row_vector
+  -- fixed sd() and variance() to return 0.0 for sequences of size 1
+  -- fixed void return type in auto_covariance
+  -- patch truncation to return -inf for variates out of range
+  -- upgraded BUGS ring model to use constraints plus tan2()
+New Features:
+  -- print statements
+  -- multiply_lower_tri_self_transpose function
+  -- vectorized several probability functions (see the manual)
+Manual Additions:
+  -- programming guide: IRT models 
+  -- new appendix: style guide
+  -- new appendix: migrating from Stan
+  -- new index: function and distribution index
+
+
+v1.0.1
+----------------------------------------------------------------------
+Patch release.
+
+
+v1.0.0
+----------------------------------------------------------------------
+First release.
+
+
+
+
+
+

TO-DO.txt

@@ -11,35 +11,6 @@ The to-do list is organized into the following sections:
 * Testing                       * Release Mgmt
 * Command-Line                  * ModelsC++ API
 
-v1.1.0
-======================================================================
--- New Features
-   * Conditiaonl (if-then-else) statements
-   * While statements
--- New Functions
-   * generalized multiply_lower_tri_self_transpose() to non-square
-     matrices
-   * special functions: log_inv_logit(), log1m_inv_logit()
-   * matrix special functions: cumulative_sum()
-   * probability functions: poisson_log_log() for log-rate 
-     parameterized Poisson
-   * matrix functions: block(), diag_pre_multiply(), diag_post_multiply()
-   * comparison operators (<, >, <=, >=, ==, !=)
-   * boolean operators (!, ||, &&)
--- Bug Fixes
-   * fixed bug introduced in 1.0.3 that hid line and column number
-     bug reporting
-   * added checks that data dimensions match as well as sizes
-   * removed non-symmetric versions of eigenvalues() and eigenvectors()
-   * testing identifiers are not reserved words in C++/Stan
-   * trapping/reporting locations of errors in data and init reads
--- Code Improvements
-   * templated out matrix libs to reduce code duplication
-   * vectorized auto-dif for tcrossprod() and crossprod()
--- Libraries Updated
-   * Eigen version 3.1.1 replaced with version 3.1.2
-   * Boost version 1.51.0 replaced with version 1.52.0
-
 PRIORITIES?
 ======================================================================
 + (name): actively assigned

src/docs/stan-reference/title.tex

@@ -30,7 +30,7 @@
 \small
 \Stan Development Team. 2012.  
 {\it \Stan Modeling Language: User's Guide and Reference Manual}. Version
-1.0.3
+1.1.0
 \vspace*{20pt}
 \mbox{ }
 \\

src/stan/version.hpp

@@ -9,10 +9,10 @@ namespace stan {
   const std::string MAJOR_VERSION = "1";
 
   /** Minor version number for Stan package. */
-  const std::string MINOR_VERSION = "0";
+  const std::string MINOR_VERSION = "1";
 
   /** Patch version for Stan package. */
-  const std::string PATCH_VERSION = "3";
+  const std::string PATCH_VERSION = "0";
 
 }
 

web/mc-stan.org/index.html

@@ -9,9 +9,9 @@
       content="application/xhtml+xml; charset=utf-8"/>
 <meta http-equiv="Content-Language"
       content="en"/>
-<meta name="description" content="Stan, C++ and R, package/library, Bayesian posterior/predictive
-inference, NUTS adaptive MCMC HMC sampling, automatic differentiation,
-Gelman"/>
+<meta name="description" content="Stan modeling language and C++ library for Bayesian inference.
+NUTS adaptive HMC (MCMC) sampling, automatic differentiation,
+R, shell interfaces.  Gelman." />
 <link href="stan.css"
       type="text/css"
       rel="stylesheet"
@@ -59,24 +59,25 @@ <h2>Getting Started</h2>
 <h2>Manual / Examples</h2>
 <ul>
   <li><a
-  href="http://stan.googlecode.com/files/stan-reference-1.0.3.pdf">Modeling
-  Language User's Guide and Reference Manual</a></li>
+  href="http://stan.googlecode.com/files/stan-reference-1.0.3.pdf">
+  User's Guide and Reference Manual</a></li>
   <li><a
   href="http://code.google.com/p/stan/source/browse/#git%2Fsrc%2Fmodels%2Fbugs_examples">BUGS Examples</a></li>
 </ul>
 
 
 <h2>Download Latest Releases</h2>
+
 <p>Stan is freedom-respecting, open-source software. </p>
 
 <ul>
   <li><a
-  href="http://code.google.com/p/stan/downloads/detail?name=stan-src-1.0.3.tgz">Stan
-  1.0.3</a> &nbsp;
-  <small>(25 Oct 2012; new BSD license)</small> </li>
+  href="http://code.google.com/p/stan/downloads/detail?name=stan-src-1.1.0.tgz">Stan
+  1.1.0</a> &nbsp;
+  <small>(17 Dec 2012; new BSD license)</small> </li>
   <li><a
   href="http://code.google.com/p/stan/wiki/RStanGettingStarted#How_to_Install_RStan">RStan
-  1.0.3</a> &nbsp; <small>(25 Oct 2012; GPLv3 license)</small></li>
+  1.1.0</a> &nbsp; <small>(17 Dec 2012; GPLv3 license)</small></li>
 </ul>
 
 <h2>Contact</h2>