diff -Nru r-cran-bayesm-2.2-4/DESCRIPTION r-cran-bayesm-2.2-5/DESCRIPTION --- r-cran-bayesm-2.2-4/DESCRIPTION 2011-02-27 18:04:44.000000000 +0000 +++ r-cran-bayesm-2.2-5/DESCRIPTION 2012-05-16 07:49:34.000000000 +0000 @@ -1,12 +1,12 @@ Package: bayesm -Version: 2.2-4 -Date: 2011-02-25 +Version: 2.2-5 +Date: 2012-05-15 Title: Bayesian Inference for Marketing/Micro-econometrics Author: Peter Rossi . Maintainer: Peter Rossi -Depends: R (>= 2.12.1) +Depends: R (>= 2.10) Description: bayesm covers many important models used in marketing and - micro-econometrics applications. The package includes: Bayes + micro-econometrics applications. The package includes: Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP), @@ -22,11 +22,11 @@ choice-based conjoint data, Bayesian treatment of linear instrumental variables models, and Analysis of Multivariate Ordinal survey data with scale usage heterogeneity (as in Rossi - et al, JASA (01)). For further reference, consult our book, + et al, JASA (01)). For further reference, consult our book, Bayesian Statistics and Marketing by Rossi, Allenby and McCulloch. License: GPL (>= 2) URL: http://www.perossi.org/home/bsm-1 -Packaged: 2011-02-26 20:38:56 UTC; perossichi +Packaged: 2012-05-15 22:08:17 UTC; perossichi Repository: CRAN -Date/Publication: 2011-02-27 18:04:44 +Date/Publication: 2012-05-16 07:49:34 diff -Nru r-cran-bayesm-2.2-4/MD5 r-cran-bayesm-2.2-5/MD5 --- r-cran-bayesm-2.2-4/MD5 1970-01-01 00:00:00.000000000 +0000 +++ r-cran-bayesm-2.2-5/MD5 2012-05-16 07:49:35.000000000 +0000 @@ -0,0 +1,141 @@ +25ab0816dcfccb2b5c1148c87e1f715a *DESCRIPTION +104c849c818b9997da00644d0a85a400 *NAMESPACE +401e4f6588cb831c2f8b4f35ba2bc1af *R/breg.R +33cab325b0b50726929a8392e9c909e0 *R/cgetC.R +027f3ae5fd398edd39b46aa12531609f *R/clusterMix.R +0207b70adcd95129ba38b6177b235d51 *R/condMom.R +5791169a4fdf78dc93bfaebfa1bcfd46 *R/createX.R +f0ab1f89e4c7b93a3abf2969c94b4b19 *R/eMixMargDen.R +a6774f78661955079a5fae59bb3be712 *R/fsh.R +0a73563b2dd400bf166539d86416eeec *R/ghkvec.R +dc005ba67612e70f9786831cd706c71c *R/llmnl.R +e37549412e0e9dbac1d400e99c28f82a 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r-cran-bayesm-2.2-5/R/plot.bayesm.hcoef.R 2012-05-14 22:17:14.000000000 +0000 @@ -1,4 +1,4 @@ -plot.bayesm.hcoef=function(x,burnin=trunc(.1*R),...){ +plot.bayesm.hcoef=function(x,names,burnin=trunc(.1*R),...){ # # S3 method to plot arrays of draws of coefs in hier models # 3 dimensional arrays: unit x var x draw @@ -18,6 +18,7 @@ # # plot posterior distributions of nvar coef for 30 rand units # + if(missing(names)) {names=as.character(1:nvar)} rsam=sort(sample(c(1:nunits),30)) # randomly sample 30 cross-sectional units par(mfrow=c(1,1)) par(las=3) # horizontal labeling @@ -26,7 +27,7 @@ colnames(ext)=as.character(rsam) out=boxplot(ext,plot=FALSE,...) out$stats=apply(ext,2,quantile,probs=c(0,.05,.95,1)) - bxp(out,xlab="Cross-sectional Unit",main=paste("Coefficients on Var ",var,sep=""),boxfill="magenta",...) + bxp(out,xlab="Cross-sectional Unit",main=paste("Coefficients on Var ",names[var],sep=""),boxfill="magenta",...) if(var==1) par(ask=dev.interactive()) } # @@ -37,7 +38,7 @@ for(i in 1:nunits) pmeans[i,]=apply(X[i,,(burnin+1):R],1,mean) names=as.character(1:nvar) attributes(pmeans)$class="bayesm.mat" - for(i in 1:nvar) names[i]=paste("Posterior Means of Coef ",i,sep="") + for(i in 1:nvar) names[i]=paste("Posterior Means of Coef ",names[var],sep="") plot(pmeans,names,TRACEPLOT=FALSE,INT=FALSE,DEN=FALSE,CHECK_NDRAWS=FALSE,...) invisible() } diff -Nru r-cran-bayesm-2.2-4/R/plot.bayesm.nmix.R r-cran-bayesm-2.2-5/R/plot.bayesm.nmix.R --- r-cran-bayesm-2.2-4/R/plot.bayesm.nmix.R 2008-03-04 20:11:48.000000000 +0000 +++ r-cran-bayesm-2.2-5/R/plot.bayesm.nmix.R 2012-05-14 18:45:40.000000000 +0000 @@ -26,14 +26,16 @@ if(!missing(Data)){ if(!is.matrix(Data)) stop("Data argument must be a matrix \n") if(ncol(Data)!= datad) stop("Data matrix is of wrong dimension \n") - } + } + if(mode(bi.sel) != "list") stop("bi.sel must be as list, e.g. bi.sel=list(c(1,2),c(3,4)) \n") if(missing(Grid)){ Grid=matrix(0,nrow=ngrid,ncol=datad) if(!missing(Data)) {for(i in 1:datad) Grid[,i]=c(seq(from=range(Data[,i])[1],to=range(Data[,i])[2],length=ngrid))} else - {out=momMix(probdraw[ind,,drop=FALSE],compdraw[ind]) + { + out=momMix(probdraw[ind,,drop=FALSE],compdraw[ind]) mu=out$mu sd=out$sd for(i in 1:datad ) Grid[,i]=c(seq(from=(mu[i]-nstd*sd[i]), diff -Nru r-cran-bayesm-2.2-4/R/rhierNegbinRw.R r-cran-bayesm-2.2-5/R/rhierNegbinRw.R --- r-cran-bayesm-2.2-4/R/rhierNegbinRw.R 2008-03-07 16:45:43.000000000 +0000 +++ r-cran-bayesm-2.2-5/R/rhierNegbinRw.R 2012-05-15 22:00:41.000000000 +0000 @@ -55,7 +55,7 @@ mean=exp(X%*%beta) prob=alpha/(alpha+mean) prob=ifelse(prob<1.0e-100,1.0e-100,prob) - out=.Internal(dnbinom(y,alpha,prob,TRUE)) + out=dnbinom(y,size=alpha,prob=prob,log=TRUE) return(sum(out)) } diff -Nru r-cran-bayesm-2.2-4/R/rivDP.R r-cran-bayesm-2.2-5/R/rivDP.R --- r-cran-bayesm-2.2-4/R/rivDP.R 2010-08-26 15:48:32.000000000 +0000 +++ r-cran-bayesm-2.2-5/R/rivDP.R 2012-05-14 18:41:36.000000000 +0000 @@ -8,6 +8,7 @@ # added automatic scaling 2/06 # removed reqfun 7/07 -- now functions are in rthetaDP # fixed initialization of theta 3/09 +# fixed error in assigning user defined prior parms # # purpose: # draw from posterior for linear I.V. model with DP process for errors @@ -108,7 +109,7 @@ else { if(is.null(Prior$md)) md=c(rep(0,dimd)) else md=Prior$md - if(is.null(Prior$Ad)) Ad=diag(0.01,dimd) else md=Prior$Ad + if(is.null(Prior$Ad)) Ad=diag(0.01,dimd) else Ad=Prior$Ad if(isgamma) dimbg=1+dimg else dimbg=1 if(is.null(Prior$mbg)) mbg=c(rep(0,dimbg)) else md=Prior$mbg if(is.null(Prior$Abg)) Abg=diag(0.01,dimbg) else md=Prior$Abg diff -Nru r-cran-bayesm-2.2-4/R/rnegbinRw.R r-cran-bayesm-2.2-5/R/rnegbinRw.R --- r-cran-bayesm-2.2-4/R/rnegbinRw.R 2008-03-06 22:59:43.000000000 +0000 +++ r-cran-bayesm-2.2-5/R/rnegbinRw.R 2012-05-15 22:00:16.000000000 +0000 @@ -44,7 +44,7 @@ mean=exp(X%*%beta) prob=alpha/(alpha+mean) prob=ifelse(prob<1.0e-100,1.0e-100,prob) - out=.Internal(dnbinom(y,alpha,prob,TRUE)) + out=dnbinom(y,size=alpha,prob=prob,log=TRUE) return(sum(out)) } diff -Nru r-cran-bayesm-2.2-4/R/summary.bayesm.mat.R r-cran-bayesm-2.2-5/R/summary.bayesm.mat.R --- r-cran-bayesm-2.2-4/R/summary.bayesm.mat.R 2007-03-22 20:15:36.000000000 +0000 +++ r-cran-bayesm-2.2-5/R/summary.bayesm.mat.R 2012-05-15 20:42:59.000000000 +0000 @@ -43,6 +43,6 @@ cat("\nQuantiles \n") print(t(qmat),digits=2)} if(TRAILER) cat(paste(" based on ",nrow(X)," valid draws (burn-in=",burnin,") \n",sep="")) - invisible() + invisible(t(mat)) } Binary files /tmp/UWy6fl5oMC/r-cran-bayesm-2.2-4/data/Scotch.rda and /tmp/a8JXy8tpav/r-cran-bayesm-2.2-5/data/Scotch.rda differ Binary files /tmp/UWy6fl5oMC/r-cran-bayesm-2.2-4/data/bank.rda and /tmp/a8JXy8tpav/r-cran-bayesm-2.2-5/data/bank.rda differ Binary files /tmp/UWy6fl5oMC/r-cran-bayesm-2.2-4/data/cheese.rda and /tmp/a8JXy8tpav/r-cran-bayesm-2.2-5/data/cheese.rda differ Binary files /tmp/UWy6fl5oMC/r-cran-bayesm-2.2-4/data/customerSat.rda and /tmp/a8JXy8tpav/r-cran-bayesm-2.2-5/data/customerSat.rda differ diff -Nru r-cran-bayesm-2.2-4/data/datalist r-cran-bayesm-2.2-5/data/datalist --- r-cran-bayesm-2.2-4/data/datalist 1970-01-01 00:00:00.000000000 +0000 +++ r-cran-bayesm-2.2-5/data/datalist 2012-05-15 22:08:17.000000000 +0000 @@ -0,0 +1,8 @@ +Scotch +bank +cheese +customerSat +detailing +margarine +orangeJuice +tuna Binary files /tmp/UWy6fl5oMC/r-cran-bayesm-2.2-4/data/detailing.rda and /tmp/a8JXy8tpav/r-cran-bayesm-2.2-5/data/detailing.rda differ Binary files /tmp/UWy6fl5oMC/r-cran-bayesm-2.2-4/data/margarine.rda and /tmp/a8JXy8tpav/r-cran-bayesm-2.2-5/data/margarine.rda differ Binary files /tmp/UWy6fl5oMC/r-cran-bayesm-2.2-4/data/orangeJuice.rda and /tmp/a8JXy8tpav/r-cran-bayesm-2.2-5/data/orangeJuice.rda differ Binary files /tmp/UWy6fl5oMC/r-cran-bayesm-2.2-4/data/tuna.rda and /tmp/a8JXy8tpav/r-cran-bayesm-2.2-5/data/tuna.rda differ diff -Nru r-cran-bayesm-2.2-4/debian/changelog r-cran-bayesm-2.2-5/debian/changelog --- r-cran-bayesm-2.2-4/debian/changelog 2011-02-28 01:11:35.000000000 +0000 +++ r-cran-bayesm-2.2-5/debian/changelog 2013-04-01 00:16:45.000000000 +0000 @@ -1,3 +1,10 @@ +r-cran-bayesm (2.2-5-1) unstable; urgency=low + + * New upstream release. + * Rebuild for R 3.0.0. + + -- Chris Lawrence Sun, 31 Mar 2013 20:16:20 -0400 + r-cran-bayesm (2.2-4-1) unstable; urgency=low * New upstream release. diff -Nru r-cran-bayesm-2.2-4/debian/compat r-cran-bayesm-2.2-5/debian/compat --- r-cran-bayesm-2.2-4/debian/compat 2011-01-15 17:31:43.000000000 +0000 +++ r-cran-bayesm-2.2-5/debian/compat 2013-04-01 00:17:07.000000000 +0000 @@ -1 +1 @@ -7 +9 diff -Nru r-cran-bayesm-2.2-4/debian/control r-cran-bayesm-2.2-5/debian/control --- r-cran-bayesm-2.2-4/debian/control 2011-01-15 17:32:09.000000000 +0000 +++ r-cran-bayesm-2.2-5/debian/control 2013-04-01 00:20:02.000000000 +0000 @@ -2,13 +2,13 @@ Section: gnu-r Priority: optional Maintainer: Chris Lawrence -Build-Depends: debhelper (>> 7), r-base-dev (>> 2.5.1), cdbs -Standards-Version: 3.9.1 +Build-Depends: debhelper (>> 9), r-base-dev (>= 3.0), cdbs, dpkg-dev (>= 1.16.1~) +Standards-Version: 3.9.3 Homepage: http://www.perossi.org/home/bsm-1 Package: r-cran-bayesm Architecture: any -Depends: r-base-core (>> 2.5.1), ${shlibs:Depends}, ${misc:Depends} +Depends: ${R:Depends}, ${shlibs:Depends}, ${misc:Depends} Description: GNU R package for Bayesian inference The bayesm package covers many important models used in marketing and micro-econometrics applications. The package includes: diff -Nru r-cran-bayesm-2.2-4/debian/rules r-cran-bayesm-2.2-5/debian/rules --- r-cran-bayesm-2.2-4/debian/rules 2011-01-15 17:27:58.000000000 +0000 +++ r-cran-bayesm-2.2-5/debian/rules 2013-04-01 00:21:44.000000000 +0000 @@ -3,24 +3,12 @@ # debian/rules file for the Debian/GNU Linux r-cran-car package # Copyright 2003 by Dirk Eddelbuettel -include /usr/share/cdbs/1/rules/debhelper.mk -include /usr/share/cdbs/1/class/langcore.mk +DPKG_EXPORT_BUILDFLAGS = 1 +include /usr/share/dpkg/buildflags.mk -## We need the CRAN (upstream) name -cranName := $(shell grep Package: DESCRIPTION | cut -f2 -d" ") -## and we need to build a Debian Policy-conformant lower-case package name -cranNameLC := $(shell echo $(cranName) | tr "[A-Z]" "[a-z]" | tr "." "-" ) -## which we can use to build the package directory -package := r-cran-$(cranNameLC) -## which we use for the to-be-installed-in directory -debRlib := $(CURDIR)/debian/$(package)/usr/lib/R/site-library +include /usr/share/R/debian/r-cran.mk -common-install-indep:: R_any_arch common-install-arch:: R_any_arch - -R_any_arch: - dh_installdirs usr/lib/R/site-library - R CMD INSTALL --clean -l $(debRlib) . rm -vf $(debRlib)/R.css $(debRlib)/$(cranName)/COPYING mkdir -p debian/r-cran-bayesm/usr/share/doc/r-cran-bayesm/ (cd debian/r-cran-bayesm/usr/share/doc/r-cran-bayesm/; ln -s ../../../lib/R/site-library/bayesm/doc/Some_Useful_R_Pointers.pdf ../../../lib/R/site-library/bayesm/doc/Tips_On_Using_bayesm.pdf .) Binary files /tmp/UWy6fl5oMC/r-cran-bayesm-2.2-4/inst/doc/bayesm-manual.pdf and /tmp/a8JXy8tpav/r-cran-bayesm-2.2-5/inst/doc/bayesm-manual.pdf differ diff -Nru r-cran-bayesm-2.2-4/man/condMom.Rd r-cran-bayesm-2.2-5/man/condMom.Rd --- r-cran-bayesm-2.2-4/man/condMom.Rd 2010-08-10 21:30:46.000000000 +0000 +++ r-cran-bayesm-2.2-5/man/condMom.Rd 2011-05-23 22:56:39.000000000 +0000 @@ -14,7 +14,7 @@ \arguments{ \item{x}{ vector of values to condition on - ith element not used } \item{mu}{ length(x) mean vector } - \item{sigi}{ length(x)-dim covariance matrix } + \item{sigi}{ length(x) dim inverse of covariance matrix } \item{i}{ conditional distribution of ith element } } \details{ diff -Nru r-cran-bayesm-2.2-4/man/createX.Rd r-cran-bayesm-2.2-5/man/createX.Rd --- r-cran-bayesm-2.2-4/man/createX.Rd 2010-08-10 21:31:30.000000000 +0000 +++ r-cran-bayesm-2.2-5/man/createX.Rd 2011-05-23 22:58:51.000000000 +0000 @@ -36,7 +36,9 @@ by Rossi, Allenby and McCulloch. \cr \url{http://www.perossi.org/home/bsm-1} } - +\note{ + \code{\link{rmnpGibbs}} assumes that the base alternative is the default. +} \author{ Peter Rossi, Anderson School, UCLA, \email{perossichi@gmail.com}. } diff -Nru r-cran-bayesm-2.2-4/man/eMixMargDen.Rd r-cran-bayesm-2.2-5/man/eMixMargDen.Rd --- r-cran-bayesm-2.2-4/man/eMixMargDen.Rd 2010-08-11 19:23:59.000000000 +0000 +++ r-cran-bayesm-2.2-5/man/eMixMargDen.Rd 2012-05-15 00:02:44.000000000 +0000 @@ -17,7 +17,7 @@ } \arguments{ - \item{grid}{ array of grid points, grid[,i] are ordinates for ith component } + \item{grid}{ array of grid points, grid[,i] are ordinates for ith dimension of the density } \item{probdraw}{ array - each row of which contains a draw of probabilities of mixture comp } \item{compdraw}{ list of lists of draws of mixture comp moments } } diff -Nru r-cran-bayesm-2.2-4/man/plot.bayesm.hcoef.Rd r-cran-bayesm-2.2-5/man/plot.bayesm.hcoef.Rd --- r-cran-bayesm-2.2-4/man/plot.bayesm.hcoef.Rd 2010-08-10 21:51:56.000000000 +0000 +++ r-cran-bayesm-2.2-5/man/plot.bayesm.hcoef.Rd 2012-05-15 21:26:08.000000000 +0000 @@ -10,10 +10,11 @@ Arrays are of class bayesm.hcoef with dimensions: cross-sectional unit x coef x MCMC draw. } \usage{ -\method{plot}{bayesm.hcoef}(x,burnin,...) +\method{plot}{bayesm.hcoef}(x,names,burnin,...) } \arguments{ \item{x}{ An object of S3 class, bayesm.hcoef } + \item{names}{ a list of names for the variables in the hierarchical model} \item{burnin}{ no draws to burnin, def: .1*R } \item{...}{ standard graphics parameters } } diff -Nru r-cran-bayesm-2.2-4/man/rhierMnlRwMixture.Rd r-cran-bayesm-2.2-5/man/rhierMnlRwMixture.Rd --- r-cran-bayesm-2.2-4/man/rhierMnlRwMixture.Rd 2010-08-10 22:01:23.000000000 +0000 +++ r-cran-bayesm-2.2-5/man/rhierMnlRwMixture.Rd 2012-04-25 00:24:07.000000000 +0000 @@ -43,7 +43,7 @@ \item{\code{p}}{ p is number of choice alternatives} \item{\code{lgtdata}}{list of lists with each cross-section unit MNL data} \item{\code{lgtdata[[i]]$y}}{ \eqn{n_i} vector of multinomial outcomes (1,\ldots,m)} - \item{\code{lgtdata[[i]]$X}}{ \eqn{n_i} by nvar design matrix for ith unit} + \item{\code{lgtdata[[i]]$X}}{ \eqn{n_i}*p by nvar design matrix for ith unit} \item{\code{a}}{vector of length ncomp of Dirichlet prior parms (def: rep(5,ncomp))} \item{\code{deltabar}}{nz*nvar vector of prior means (def: 0)} \item{\code{Ad}}{ prior prec matrix for vec(D) (def: .01I)} diff -Nru r-cran-bayesm-2.2-4/man/summary.bayesm.mat.Rd r-cran-bayesm-2.2-5/man/summary.bayesm.mat.Rd --- r-cran-bayesm-2.2-4/man/summary.bayesm.mat.Rd 2010-08-10 22:16:39.000000000 +0000 +++ r-cran-bayesm-2.2-5/man/summary.bayesm.mat.Rd 2012-05-15 20:47:41.000000000 +0000 @@ -25,6 +25,9 @@ \cr \code{summary.bayesm.mat} is also exported for direct use as a standard function, as in \code{summary.bayesm.mat(matrix)}. + \cr + \code{summary.bayesm.mat(matrix)} returns (invisibly) the array of the various summary statistics for further use. To + assess this array use\code{stats=summary(Drawmat)}. } \author{ Peter Rossi, Anderson School, UCLA, \email{perossichi@gmail.com}. diff -Nru r-cran-bayesm-2.2-4/src/bayesmcpp.cpp r-cran-bayesm-2.2-5/src/bayesmcpp.cpp --- r-cran-bayesm-2.2-4/src/bayesmcpp.cpp 2011-02-26 20:38:56.000000000 +0000 +++ r-cran-bayesm-2.2-5/src/bayesmcpp.cpp 2012-05-15 22:08:17.000000000 +0000 @@ -1,4 +1,5 @@ // R.McCulloch, 12/04 code for scale usage R function (rScaleUsage) +// changed to R error function, P. Rossi 05/12 #include #include @@ -30,7 +31,7 @@ //get a and b double det = bq*bq - 4*aq*cq; - if(det<0) std::cout << "error: no solution for c's given e and m1, m2" << std::endl; + if(det<0) error("no solution for c's given e and m1, m2 \n"); double b=(-bq+sqrt(det))/(2.0*aq); double a=(m1-b*s1-e*s2)/s0;