[r-cran-mcmcpack] 48/90: Imported Upstream version 1.0-7

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-cran-mcmcpack.

commit e94065b814f789cf505184f8ea0884212ab4dc2c
Author: Andreas Tille <tille at debian.org>
Date:   Fri Dec 16 08:07:17 2016 +0100

    Imported Upstream version 1.0-7
---
 DESCRIPTION             |  8 ++++----
 HISTORY                 |  6 ++++++
 NAMESPACE               | 11 ++++++++---
 R/MCMCbinaryChange.R    |  0
 R/SSVSquantregsummary.R |  2 +-
 R/distn.R               |  3 ++-
 man/invgamma.Rd         |  4 ++++
 src/MCMCquantreg.cc     |  3 +--
 8 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fc000d0..f37ee9a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MCMCpack
-Version: 1.0-6
-Date: 2009-5-11
+Version: 1.0-7
+Date: 2009-6-4
 Title: Markov chain Monte Carlo (MCMC) Package
 Author: Andrew D. Martin <admartin at wustl.edu>, Kevin M. Quinn
         <kevin_quinn at harvard.edu>, Jong Hee Park <jhp at uchicago.edu>
@@ -19,6 +19,6 @@ Description: This package contains functions to perform Bayesian
 License: GPL-2
 SystemRequirements: gcc (>= 4.0)
 URL: http://mcmcpack.wustl.edu
-Packaged: 2010-05-11 16:18:44 UTC; adm
+Packaged: 2010-06-04 16:41:34 UTC; adm
 Repository: CRAN
-Date/Publication: 2010-05-11 18:43:21
+Date/Publication: 2010-06-04 21:32:56
diff --git a/HISTORY b/HISTORY
index 5150247..a3d1560 100644
--- a/HISTORY
+++ b/HISTORY
@@ -3,6 +3,12 @@
 //
 
 
+1.0-6 to 1.0-7
+  * slight modifications to internals of rinvgamma to make parameterization 
+    more clear [thanks to Daniel Runcie and Richard Morey]
+  * fixed some NAMESPACE issues with SSVSquantreg and its methods [written by Craig
+    Reed]
+
 1.0-5 to 1.0-6
   * added SSVSquantreg [written by Craig Reed]
   * added functions to handle SSVSquantreg output [written by Craig Reed]
diff --git a/NAMESPACE b/NAMESPACE
index 6c4cddf..e2d1093 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -16,15 +16,12 @@ export(
        MCpoissongamma,
        MCnormalnormal,
        MCmultinomdirichlet,
-       MCMCbinaryChange,
        MCMCdynamicEI,
-       MCMCdynamicIRT1d,
        MCMCfactanal,
        MCMChierEI,
        MCMCirt1d,
        MCMCirtHier1d,
        MCMCirtKd,
-       MCMCirtKdHet,
        MCMCirtKdRob,
        MCMClogit,
        MCMCmetrop1R,
@@ -39,6 +36,7 @@ export(
        MCMCregress,
        MCMCSVDreg,
        MCMCtobit,
+       mptable,
        plotState,
        plotChangepoint,
        PostProbMod,
@@ -49,7 +47,9 @@ export(
        riwish,
        rnoncenhypergeom,
        rwish,
+       SSVSquantreg,
        tomogplot,
+       topmodels,
        vech,
        write.Scythe,
        xpnd
@@ -57,3 +57,8 @@ export(
 
 S3method(print, BayesFactor)
 S3method(summary, BayesFactor)
+S3method(plot, qrssvs)
+S3method(print, qrssvs)
+S3method(print, summary.qrssvs)
+S3method(summary, qrssvs)
+
diff --git a/R/MCMCbinaryChange.R b/R/MCMCbinaryChange.R
old mode 100755
new mode 100644
diff --git a/R/SSVSquantregsummary.R b/R/SSVSquantregsummary.R
index b9d227a..6b2e871 100644
--- a/R/SSVSquantregsummary.R
+++ b/R/SSVSquantregsummary.R
@@ -71,7 +71,7 @@ class(results)<-"summary.qrssvs"
 return(results)
 }
 
-print.summary.qrssvs<-function(x, digits=max(3, .Options$digits-3), ...){
+"print.summary.qrssvs"<-function(x, digits=max(3, .Options$digits-3), ...){
 attr(x, "class")<-"data.frame"
 cat("\nMarginal inclusion probability of each predictor:\n\n")
 print(x, digits=digits, ...)
diff --git a/R/distn.R b/R/distn.R
index 49e5ba8..6539524 100644
--- a/R/distn.R
+++ b/R/distn.R
@@ -218,10 +218,11 @@
 ##
 ## Kevin Rompala 5/6/2003
 ## fixed KQ 3/8/2005
+## shape and rate made explicit 5/25/2010 (KQ)
 
 "rinvgamma" <-
   function(n, shape, scale = 1) {
-    return(1 / rgamma(n, shape, scale=scale))
+    return(1 / rgamma(n=n, shape=shape, rate=scale))
   }
 
 ##
diff --git a/man/invgamma.Rd b/man/invgamma.Rd
index 466d53c..4ee1212 100644
--- a/man/invgamma.Rd
+++ b/man/invgamma.Rd
@@ -32,6 +32,10 @@ variance \eqn{\frac{b^2}{(a-1)^2(a-2)}}{(b^2)/((a-1)^2 (a-2))} (assuming
 \eqn{a>2}{a>2}).
 }
 
+\references{
+Andrew Gelman, John B. Carlin, Hal S. Stern, and Donald B. Rubin. 2004. \emph{Bayesian Data Analysis}. 2nd Edition. Boca Raton: Chapman & Hall. 
+}
+
 \examples{
 density <- dinvgamma(4.2, 1.1)
 draws <- rinvgamma(10, 3.2)
diff --git a/src/MCMCquantreg.cc b/src/MCMCquantreg.cc
index e1297be..1b75d3e 100644
--- a/src/MCMCquantreg.cc
+++ b/src/MCMCquantreg.cc
@@ -67,8 +67,7 @@ void MCMCquantreg_impl (rng<RNGTYPE>& stream, double tau, Matrix<>& Y,
    // define constants
    const unsigned int tot_iter = burnin + mcmc; //total iterations
    const unsigned int nstore = mcmc / thin; // number of draws to store
-   const unsigned int k = X.cols ();
-   const unsigned int n_obs = X.rows();
+   const unsigned int k = X.cols ();  
       
    // storage matrices
    Matrix<> betamatrix (k, nstore);

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