[r-cran-bayesm] 05/44: Import Upstream version 1.0-2
Andreas Tille
tille at debian.org
Thu Sep 7 11:16:20 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-bayesm.
commit 8fe582b9012dd1dfca7c1a0cba16ea46abf056a0
Author: Andreas Tille <tille at debian.org>
Date: Thu Sep 7 13:08:12 2017 +0200
Import Upstream version 1.0-2
---
DESCRIPTION | 6 +++---
R/rhierMnlRwMixture.R | 2 +-
R/rmnlIndepMetrop.R | 2 +-
man/breg.Rd | 5 ++++-
man/rbprobitGibbs.Rd | 4 +++-
man/rhierBinLogit.Rd | 7 ++-----
man/rhierLinearModel.Rd | 6 +-----
man/rhierMnlRwMixture.Rd | 12 +++++-------
man/rivGibbs.Rd | 4 +++-
man/rmnlIndepMetrop.Rd | 3 ++-
man/rmnpGibbs.Rd | 2 +-
man/rmultireg.Rd | 3 ++-
man/rmvpGibbs.Rd | 2 +-
man/rnmixGibbs.Rd | 9 ++++-----
man/rscaleUsage.Rd | 5 +++--
man/runireg.Rd | 2 +-
man/runiregGibbs.Rd | 2 +-
17 files changed, 38 insertions(+), 38 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 051ef4a..f232098 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: bayesm
-Version: 1.0-1
-Date: 2005-05-16
+Version: 1.0-2
+Date: 2005-05-25
Title:Bayesian Inference for Marketing/Micro-econometrics
Author: Peter Rossi <peter.rossi at ChicagoGsb.edu>,
Rob McCulloch <robert.mcculloch at ChicagoGsb.edu>.
@@ -25,4 +25,4 @@ Description: bayesm covers many important models used
Marketing by Allenby, McCulloch and Rossi.
License: GPL (version 2 or later)
URL: http://gsbwww.uchicago.edu/fac/peter.rossi/research/bsm.html
-Packaged: Wed May 18 17:24:34 2005; per
+Packaged: Wed May 25 09:59:25 2005; per
diff --git a/R/rhierMnlRwMixture.R b/R/rhierMnlRwMixture.R
index 275be01..8b90465 100755
--- a/R/rhierMnlRwMixture.R
+++ b/R/rhierMnlRwMixture.R
@@ -184,7 +184,7 @@ compdraw=NULL
llmnlFract=
function(beta,y,X,betapooled,rootH,w){
z=as.vector(rootH%*%(beta-betapooled))
-llmnl(y,X,beta)+w*(-5.*(z%*%z))
+llmnl(y,X,beta)+w*(-.5*(z%*%z))
}
mnlRwMetropOnce=
diff --git a/R/rmnlIndepMetrop.R b/R/rmnlIndepMetrop.R
index 64a984a..313c978 100755
--- a/R/rmnlIndepMetrop.R
+++ b/R/rmnlIndepMetrop.R
@@ -39,7 +39,7 @@ if(missing(Data)) {pandterm("Requires Data argument -- list of p, y, X")}
if(is.null(Data$y)) {pandterm("Requires Data element y")}
y=Data$y
if(is.null(Data$p)) {pandterm("Requires Data element p")}
- m=Data$m
+ p=Data$p
nvar=ncol(X)
nobs=length(y)
#
diff --git a/man/breg.Rd b/man/breg.Rd
index 9fbebf0..793951f 100755
--- a/man/breg.Rd
+++ b/man/breg.Rd
@@ -45,6 +45,10 @@ breg(y, X, betabar, A)
}
\examples{
+##
+
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=1000} else {R=10}
+
## simulate data
set.seed(66)
n=100
@@ -55,7 +59,6 @@ y=X\%*\%beta+rnorm(n)
A=diag(c(.05,.05)); betabar=c(0,0)
##
## make draws from posterior
-R=1000
betadraw=matrix(double(R*2),ncol=2)
for (rep in 1:R) {betadraw[rep,]=breg(y,X,betabar,A)}
##
diff --git a/man/rbprobitGibbs.Rd b/man/rbprobitGibbs.Rd
index 1735cae..34f2cae 100755
--- a/man/rbprobitGibbs.Rd
+++ b/man/rbprobitGibbs.Rd
@@ -54,6 +54,8 @@ rbprobitGibbs(Data, Prior, Mcmc)
##
## rbprobitGibbs example
##
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10}
+
set.seed(66)
simbprobit=
function(X,beta) {
@@ -69,7 +71,7 @@ nvar=ncol(X)
simout=simbprobit(X,beta)
Data=list(X=simout$X,y=simout$y)
-Mcmc=list(R=2000,keep=1)
+Mcmc=list(R=R,keep=1)
out=rbprobitGibbs(Data=Data,Mcmc=Mcmc)
diff --git a/man/rhierBinLogit.Rd b/man/rhierBinLogit.Rd
index df47ec9..4c2fe40 100755
--- a/man/rhierBinLogit.Rd
+++ b/man/rhierBinLogit.Rd
@@ -73,8 +73,7 @@ rhierBinLogit(Data, Prior, Mcmc)
}
\examples{
##
-if(nchar(Sys.getenv("LONG_TEST")) != 0)
-{
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=10000} else {R=10}
set.seed(66)
nvar=5 ## number of coefficients
@@ -103,7 +102,7 @@ for (i in 1:nlgt)
}
Data=list(Dat=lgtdata,Demo=Z)
-out=rhierBinLogit(Data=list(lgtdata=lgtdata,Z=Z),Mcmc=list(R=5000))
+out=rhierBinLogit(Data=list(lgtdata=lgtdata,Z=Z),Mcmc=list(R=R))
cat(" Deltadraws ",fill=TRUE)
mat=apply(out$Deltadraw,2,quantile,probs=c(.01,.05,.5,.95,.99))
@@ -126,8 +125,6 @@ abline(h=.5)
}
}
-
-}
\seealso{ \code{\link{rhierMnlRwMixture}} }
\keyword{ models}
diff --git a/man/rhierLinearModel.Rd b/man/rhierLinearModel.Rd
index 54b54c0..fbbc82f 100755
--- a/man/rhierLinearModel.Rd
+++ b/man/rhierLinearModel.Rd
@@ -65,8 +65,7 @@ rhierLinearModel(Data, Prior, Mcmc)
}
\examples{
##
-if(nchar(Sys.getenv("LONG_TEST")) != 0) # set env var LONG_TEST to run
-{
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10}
nreg=100; nobs=100; nvar=3
Vbeta=matrix(c(1,.5,0,.5,2,.7,0,.7,1),ncol=3)
@@ -89,7 +88,6 @@ V=nu*diag(c(rep(1,nvar)))
A=diag(c(rep(.01,nz)),ncol=nz)
Deltabar=matrix(c(rep(0,nz*nvar)),nrow=nz)
-R=2000
Data=list(regdata=regdata,Z=Z)
Prior=list(Deltabar=Deltabar,A=A,nu.e=nu.e,ssq=ssq,nu=nu,V=V)
@@ -104,6 +102,4 @@ mat=apply(out$Vbetadraw,2,quantile,probs=c(.01,.05,.5,.95,.99))
mat=rbind(as.vector(Vbeta),mat); rownames(mat)[1]="Vbeta"; print(mat)
}
-
-}
\keyword{ regression }
diff --git a/man/rhierMnlRwMixture.Rd b/man/rhierMnlRwMixture.Rd
index bd13ad4..80310e1 100755
--- a/man/rhierMnlRwMixture.Rd
+++ b/man/rhierMnlRwMixture.Rd
@@ -93,8 +93,7 @@ rhierMnlRwMixture(Data, Prior, Mcmc)
\seealso{ \code{\link{rmnlIndepMetrop}} }
\examples{
##
-if(nchar(Sys.getenv("LONG_TEST")) != 0) # set env var LONG_TEST to run
-{
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=10000} else {R=10}
set.seed(66)
p=3 # num of choice alterns
@@ -142,7 +141,6 @@ deltabar=rep(0,ncoef*nz)
Amu=matrix(.01,ncol=1)
a=rep(5,ncoef)
-R=20000
keep=5
c=2
s=2.93/sqrt(ncoef)
@@ -151,7 +149,8 @@ Prior1=list(ncomp=ncomp,nu=nu,V=V,Amu=Amu,mubar=mubar,a=a,Ad=Ad,deltabar=deltaba
Mcmc1=list(s=s,c=c,R=R,keep=keep)
out=rhierMnlRwMixture(Data=Data1,Prior=Prior1,Mcmc=Mcmc1)
-begin=1000/keep; end=R/keep
+if(R < 1000) {begin=1} else {begin=1000/keep}
+end=R/keep
cat(" Deltadraws ",fill=TRUE)
mat=apply(out$Deltadraw[begin:end,],2,quantile,probs=c(.01,.05,.5,.95,.99))
mat=rbind(as.vector(Delta),mat); rownames(mat)[1]="delta"; print(mat)
@@ -191,8 +190,8 @@ plot(out$Deltadraw[,3])
abline(h=Delta[3,1])
plot(out$Deltadraw[,6])
abline(h=Delta[3,2])
-begin=100
-end=1000
+begin=1000/keep
+end=R/keep
ngrid=50
grid=matrix(0,ngrid,ncoef)
rgm=matrix(c(-3,-7,-10,3,1,0),ncol=2)
@@ -208,5 +207,4 @@ for(i in 1:ncoef)
}
}
-}
\keyword{ models }
diff --git a/man/rivGibbs.Rd b/man/rivGibbs.Rd
index 4f85d57..133dc34 100755
--- a/man/rivGibbs.Rd
+++ b/man/rivGibbs.Rd
@@ -54,6 +54,8 @@ rivGibbs(Data, Prior, Mcmc)
}
\examples{
##
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10}
+
set.seed(66)
simIV = function(delta,beta,Sigma,n,z,w,gamma) {
eps = matrix(rnorm(2*n),ncol=2) \%*\% chol(Sigma)
@@ -69,7 +71,7 @@ simiv = simIV(delta,beta,Sigma,n,z,w,gamma)
Mcmc=list(); Prior=list(); Data = list()
Data$z = z; Data$w=w; Data$x=simiv$x; Data$y=simiv$y
-Mcmc$R = 5000
+Mcmc$R = R
Mcmc$keep=1
out=rivGibbs(Data=Data,Prior=Prior,Mcmc=Mcmc)
diff --git a/man/rmnlIndepMetrop.Rd b/man/rmnlIndepMetrop.Rd
index d79ba6f..6a47880 100755
--- a/man/rmnlIndepMetrop.Rd
+++ b/man/rmnlIndepMetrop.Rd
@@ -43,12 +43,13 @@ rmnlIndepMetrop(Data, Prior, Mcmc)
\examples{
##
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10}
+
set.seed(66)
n=200; p=3; beta=c(1,-1,1.5,.5)
simout=simmnl(p,n,beta)
A=diag(c(rep(.01,length(beta)))); betabar=rep(0,length(beta))
-R=2000
Data=list(y=simout$y,X=simout$X,p=p); Mcmc=list(R=R,keep=1) ; Prior=list(A=A,betabar=betabar)
out=rmnlIndepMetrop(Data=Data,Prior=Prior,Mcmc=Mcmc)
cat(" Betadraws ",fill=TRUE)
diff --git a/man/rmnpGibbs.Rd b/man/rmnpGibbs.Rd
index 940a8c5..d4f14f4 100755
--- a/man/rmnpGibbs.Rd
+++ b/man/rmnpGibbs.Rd
@@ -71,6 +71,7 @@ rmnpGibbs(Data, Prior, Mcmc)
\seealso{ \code{\link{rmvpGibbs}} }
\examples{
##
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10}
set.seed(66)
p=3
@@ -84,7 +85,6 @@ for(i in 2:n) { xadd=rbind(xadd,I2)}
X=cbind(xadd,x1,x2)
simout=simmnp(X,p,500,beta,Sigma)
-R=2000
Data=list(p=p,y=simout$y,X=simout$X)
Mcmc=list(R=R,keep=1)
diff --git a/man/rmultireg.Rd b/man/rmultireg.Rd
index cb62ec5..0404947 100755
--- a/man/rmultireg.Rd
+++ b/man/rmultireg.Rd
@@ -51,6 +51,8 @@ rmultireg(Y, X, Bbar, A, nu, V)
\seealso{ \code{\link{rmultiregfp}},\code{\link{init.rmultiregfp}}}
\examples{
##
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10}
+
set.seed(66)
n=200
m=2
@@ -64,7 +66,6 @@ betabar=rep(0,k*m);Bbar=matrix(betabar,ncol=m)
A=diag(rep(.01,k))
nu=3; V=nu*diag(m)
-R=1000
betadraw=matrix(double(R*k*m),ncol=k*m)
Sigmadraw=matrix(double(R*m*m),ncol=m*m)
for (rep in 1:R)
diff --git a/man/rmvpGibbs.Rd b/man/rmvpGibbs.Rd
index b8ecebe..ceddebd 100755
--- a/man/rmvpGibbs.Rd
+++ b/man/rmvpGibbs.Rd
@@ -71,6 +71,7 @@ rmvpGibbs(Data, Prior, Mcmc)
\seealso{ \code{\link{rmnpGibbs}} }
\examples{
##
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10}
set.seed(66)
p=3
@@ -83,7 +84,6 @@ for(i in 2:n) { xadd=rbind(xadd,I2)}; X=xadd
simout=simmvp(X,p,500,beta,Sigma)
Data=list(p=p,y=simout$y,X=simout$X)
-R=2000
Mcmc=list(R=R,keep=1)
out=rmvpGibbs(Data=Data,Mcmc=Mcmc)
diff --git a/man/rnmixGibbs.Rd b/man/rnmixGibbs.Rd
index 0f08d0b..d6375c5 100755
--- a/man/rnmixGibbs.Rd
+++ b/man/rnmixGibbs.Rd
@@ -74,8 +74,7 @@ rnmixGibbs(Data, Prior, Mcmc)
\seealso{ \code{\link{rmixture}}, \code{\link{rmixGibbs}} ,\code{\link{eMixMargDen}}, \code{\link{momMix}}}
\examples{
##
-if(nchar(Sys.getenv("LONG_TEST")) != 0) # set env var LONG_TEST to run
-{
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10}
set.seed(66)
dim=5; k=3 # dimension of simulated data and number of "true" components
@@ -92,11 +91,12 @@ dm = rmixture(nobs,pvec,comps)
Data=list(y=dm$x)
ncomp=9
Prior=list(ncomp=ncomp,a=c(rep(1,ncomp)))
-Mcmc=list(R=2000,keep=1)
+Mcmc=list(R=R,keep=1)
out=rnmixGibbs(Data=Data,Prior=Prior,Mcmc=Mcmc)
tmom=momMix(matrix(pvec,nrow=1),list(comps))
-pmom=momMix(out$probdraw[500:2000,],out$compdraw[500:2000])
+if(R < 1000) {begin=1} else {begin=500}
+pmom=momMix(out$probdraw[begin:R,],out$compdraw[begin:R])
mat=rbind(tmom$mu,pmom$mu)
rownames(mat)=c("true","post expect")
cat(" mu and posterior expectation of mu",fill=TRUE)
@@ -111,5 +111,4 @@ cat(" corr and posterior expectation of corr",fill=TRUE)
print(t(mat))
}
-}
\keyword{ multivariate }
diff --git a/man/rscaleUsage.Rd b/man/rscaleUsage.Rd
index 16ea665..8abf18f 100755
--- a/man/rscaleUsage.Rd
+++ b/man/rscaleUsage.Rd
@@ -67,12 +67,13 @@ rscaleUsage(Data,Prior, Mcmc)
\examples{
##
-if(nchar(Sys.getenv("LONG_TEST")) != 0)
+if(nchar(Sys.getenv("LONG_TEST")) != 0)
{
data(customerSat)
surveydat = list(k=10,x=as.matrix(customerSat))
-mcmc = list(R=1000)
+R=1000
+mcmc = list(R=R)
set.seed(66)
out=rscaleUsage(Data=surveydat,Mcmc=mcmc)
diff --git a/man/runireg.Rd b/man/runireg.Rd
index 16c5889..a095458 100755
--- a/man/runireg.Rd
+++ b/man/runireg.Rd
@@ -46,6 +46,7 @@ runireg(y, X, betabar, A, nu, ssq)
\seealso{ \code{\link{runiregGibbs}} }
\examples{
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=1000} else {R=10}
set.seed(66)
n=100
X=cbind(rep(1,n),runif(n)); beta=c(1,2); sigsq=.25
@@ -54,7 +55,6 @@ y=X\%*\%beta+rnorm(n,sd=sqrt(sigsq))
A=diag(c(.05,.05)); betabar=c(0,0)
nu=3; ssq=1.0
-R=1000
betadraw=matrix(double(R*2),ncol=2)
sigsqdraw=double(R)
for (rep in 1:R)
diff --git a/man/runiregGibbs.Rd b/man/runiregGibbs.Rd
index c05b03f..bbd641e 100755
--- a/man/runiregGibbs.Rd
+++ b/man/runiregGibbs.Rd
@@ -49,6 +49,7 @@ runiregGibbs(Data, Prior, Mcmc)
\seealso{ \code{\link{runireg}} }
\examples{
+if(nchar(Sys.getenv("LONG_TEST")) != 0) {R=2000} else {R=10}
set.seed(66)
n=100
X=cbind(rep(1,n),runif(n)); beta=c(1,2); sigsq=.25
@@ -57,7 +58,6 @@ y=X\%*\%beta+rnorm(n,sd=sqrt(sigsq))
A=diag(c(.05,.05)); betabar=c(0,0)
nu=3; ssq=1.0
-R=1000
Data=list(y=y,X=X); Mcmc=list(R=R,keep=1) ; Prior=list(A=A,betabar=betabar,nu=nu,ssq=ssq)
out=runiregGibbs(Data=Data,Prior=Prior,Mcmc=Mcmc)
cat(" Betadraws ",fill=TRUE)
--
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