[r-cran-mnp] 40/51: Import Upstream version 2.5-6

[Andreas Tille]

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

commit a37291f49d32a61a84be10d125f6648d98d84e4e
Author: Andreas Tille <tille at debian.org>
Date:   Fri Sep 8 15:54:59 2017 +0200

    Import Upstream version 2.5-6
---
 DESCRIPTION     |  8 ++++----
 R/ymatrix.mnp.R | 11 +++++------
 man/mnp.Rd      |  2 +-
 src/MNP.c       |  6 ++++--
 4 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 93691f7..09f5cfa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MNP
-Version: 2.5-5
-Date: 2007-08-01
+Version: 2.5-6
+Date: 2008-03-24
 Title: R Package for Fitting the Multinomial Probit Model
 Author: Kosuke Imai <kimai at princeton.edu>, 
         David A. van Dyk <dvd at uci.edu>. 
@@ -25,6 +25,6 @@ Description: MNP is a publicly available R package that fits the Bayesian
   Vol. 14, No. 3 (May), pp. 1-32.
 LazyLoad: yes
 LazyData: yes
-License: GPL (version 2 or later)
+License: GPL (>= 2)
 URL: http://imai.princeton.edu/research/MNP.html
-Packaged: Wed Aug  1 20:15:11 2007; kimai
+Packaged: Mon Mar 24 23:57:37 2008; kimai
diff --git a/R/ymatrix.mnp.R b/R/ymatrix.mnp.R
index 7c1e2f2..9d46a55 100644
--- a/R/ymatrix.mnp.R
+++ b/R/ymatrix.mnp.R
@@ -10,17 +10,16 @@ ymatrix.mnp <- function(data, base=NULL, extra=FALSE, verbose=verbose) {
     if(!is.null(base))
       stop("Error: The last column of the response matrix must be the base category.\n No need to specify `base.'") 
     base <- lev[p]
-  }
-  else { # standard Multinomial Probit model        
+  } else { # standard Multinomial Probit model        
     Y <- as.factor(Y)
     lev <- levels(Y)
     if (!is.null(base))
       if (base %in% lev) {
-        lev <- c(base, lev[-pmatch(base, lev)])
-        levels(Y) <- lev
+        Y <- relevel(Y, ref = base)
+        lev <- levels(Y)
+      } else {
+        stop(paste("Error: `base' does not exist in the response variable."))
       }
-      else
-        stop(paste("Error: `base' does not exist in the response variable.")) 
     base <- lev[1]
     counts <- table(Y)
     if (any(counts == 0)) {
diff --git a/man/mnp.Rd b/man/mnp.Rd
index 5240a3e..82dacca 100644
--- a/man/mnp.Rd
+++ b/man/mnp.Rd
@@ -200,9 +200,9 @@ pre2 <- predict(res2, newdata = japan[10,], type = "prob", n.draws = 100,
   \item{p.scale}{The prior scale matrix for the covariance matrix.}
   \item{burnin}{The number of initial burnin draws.}
   \item{thin}{The thinning interval.}
-  }
 }
 
+
 \references{
   Imai, Kosuke and David A. van Dyk. (2005a) \dQuote{A Bayesian Analysis
     of the Multinomial Probit Model Using the Marginal Data
diff --git a/src/MNP.c b/src/MNP.c
index 9280caf..6928776 100644
--- a/src/MNP.c
+++ b/src/MNP.c
@@ -112,8 +112,10 @@ void cMNPgibbs(int *piNDim, int *piNCov, int *piNSamp, int *piNGen,
   itemp = 0;
   for (k = 0; k < n_cov; k++) 
     for (j = 0; j < n_dim; j++) 
-      for (i = 0; i < n_samp; i++) X[i*n_dim+j][k] = pdX[itemp++];
-
+      for (i = 0; i < n_samp; i++) 
+	X[i*n_dim+j][k] = pdX[itemp++];
+      
+  /* PdoubleMatrix(X, n_dim*3, n_cov); */
   itemp = 0;
   for (k = 0; k < n_cov; k++) 
     for (j = 0; j < n_cov; j++)	A0[j][k] = pdA0[itemp++];

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