[Depmix-commits] r493 - in pkg/depmix: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 22 11:26:36 CEST 2011
Author: ingmarvisser
Date: 2011-09-22 11:26:35 +0200 (Thu, 22 Sep 2011)
New Revision: 493
Removed:
pkg/depmix/COPYING
Modified:
pkg/depmix/CHANGES
pkg/depmix/DESCRIPTION
pkg/depmix/NAMESPACE
pkg/depmix/R/depmix.R
pkg/depmix/man/fitdmm.Rd
Log:
Added a NAMESPACE file (required starting with R version 2.14.0).
Fixed a bug in bootstrap which was using a $ to access a field of
an S3 object, and added an example of using bootstrap to the ?fitdmm
help page.
Modified: pkg/depmix/CHANGES
===================================================================
--- pkg/depmix/CHANGES 2011-09-20 14:47:56 UTC (rev 492)
+++ pkg/depmix/CHANGES 2011-09-22 09:26:35 UTC (rev 493)
@@ -1,58 +1,62 @@
-Changes from 0.9.0 to 0.9.1
-
-1) Added case replicate-weights to save computational load in fitting
-latent class models on categorical data. Markovdata now has an extra
-argument which can be used to provide the number of replicates for each
-case.
-
-2) Updated references and added a vignette called depmix-intro.
-
-Changes from 0.9.1 to 0.9.2
-
-No changes except the addition that the package is now ORPHANED; this is
-an automatic change in the CRAN repositories because warnings occur.
-
-
-Changes from 0.9.2 to 0.9.3
-
-1) Optimization is now done using the Rdonlp2 package by Tamura (optional
-support for NPSOL also still exists); the major advantage of this is that
-donlp2 handles general linear constraints without problems.
-
-2) Options for optimization with nlm and optim are removed as they were
-functioning suboptimal in some cases and have become unnessary.
-
-
-Changes from 0.9.3 to 0.9.4
-
-1) Minor changes in C++ headers to make them compatible with new g++ versions.
+Changes from 0.9.8 to 0.9.9
-Changes from 0.9.4 to 0.9.5
+1) Fixed a bug which led to an error when specifying multigroup models
+in which one or more groups had a 1-state model (fixed by adding a
+drop=FALSE in function mgdmm).
-1) Minor changes; fixed some documentation and warning issues.
+2) Added a NAMESPACE file (required starting with R version 2.14.0).
-Changes from 0.9.5 to 0.9.6
+3) Fixed a bug in bootstrap which was using a $ to access a field of
+an S3 object, and added an example of using bootstrap to the ?fitdmm
+help page.
-1) Minor changes to make depmix compatible with R 2.9.1
+Changes from 0.9.7 to 0.9.8
-2) NPSOL support now works with an options file (see the NPSOL manual
-for details on how to structure that file), which should live in your
-working directory.
+1) Minor changes in C++ code to conform to compiler standards (producing
+an error on SUN systems).
Changes from 0.9.6 to 0.9.7
1) Minor changes in documentation that produced warnings in R CMD CHECK
as of version R 2.10.0
+
+Changes from 0.9.5 to 0.9.6
-Changes from 0.9.7 to 0.9.8
+1) Minor changes to make depmix compatible with R 2.9.1
-1) Minor changes in C++ code to conform to compiler standards (producing
-an error on SUN systems).
+2) NPSOL support now works with an options file (see the NPSOL manual
+for details on how to structure that file), which should live in your
+working directory.
+
+Changes from 0.9.4 to 0.9.5
-Changes from 0.9.8 to 0.9.9
+1) Minor changes; fixed some documentation and warning issues.
-1) Fixed a bug which led to an error when specifying multigroup models
-in which one or more groups had a 1-state model (fixed by adding a
-drop=FALSE in function mgdmm).
+Changes from 0.9.3 to 0.9.4
+
+1) Minor changes in C++ headers to make them compatible with new g++ versions.
+Changes from 0.9.2 to 0.9.3
+
+1) Optimization is now done using the Rdonlp2 package by Tamura (optional
+support for NPSOL also still exists); the major advantage of this is that
+donlp2 handles general linear constraints without problems.
+
+2) Options for optimization with nlm and optim are removed as they were
+functioning suboptimal in some cases and have become unnessary.
+
+Changes from 0.9.1 to 0.9.2
+
+No changes except the addition that the package is now ORPHANED; this is
+an automatic change in the CRAN repositories because warnings occur.
+
+Changes from 0.9.0 to 0.9.1
+
+1) Added case replicate-weights to save computational load in fitting
+latent class models on categorical data. Markovdata now has an extra
+argument which can be used to provide the number of replicates for each
+case.
+
+2) Updated references and added a vignette called depmix-intro.
+
Deleted: pkg/depmix/COPYING
===================================================================
--- pkg/depmix/COPYING 2011-09-20 14:47:56 UTC (rev 492)
+++ pkg/depmix/COPYING 2011-09-22 09:26:35 UTC (rev 493)
@@ -1,340 +0,0 @@
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Modified: pkg/depmix/DESCRIPTION
===================================================================
--- pkg/depmix/DESCRIPTION 2011-09-20 14:47:56 UTC (rev 492)
+++ pkg/depmix/DESCRIPTION 2011-09-22 09:26:35 UTC (rev 493)
@@ -1,10 +1,10 @@
Package: depmix
Version: 0.9.9
-Date: 2011-09-16
+Date: 2011-09-22
Title: Dependent Mixture Models
Author: Ingmar Visser <i.visser at uva.nl>
Maintainer: Ingmar Visser <i.visser at uva.nl>
-Depends: R (>= 2.12.1), MASS
+Depends: R (>= 2.13.1), MASS
Suggests: Rdonlp2
Description: Fit (multigroup) mixtures of latent Markov models on mixed categorical and continuous (timeseries) data
-License: GPL
\ No newline at end of file
+License: GPL-3
\ No newline at end of file
Modified: pkg/depmix/NAMESPACE
===================================================================
--- pkg/depmix/NAMESPACE 2011-09-20 14:47:56 UTC (rev 492)
+++ pkg/depmix/NAMESPACE 2011-09-22 09:26:35 UTC (rev 493)
@@ -1,9 +1,8 @@
useDynLib(depmix)
-# import(methods)
-
export(dmm,mgdmm,fitdmm,mixdmm,loglike,oneliner,bootstrap,posterior,
- generate,lca)
+ generate,lca,ntimes,itemtypes,dname,replicates,ncov,inames,
+ nitems,ind,markovdata)
S3method(summary,dmm)
S3method(summary,mgd)
Modified: pkg/depmix/R/depmix.R
===================================================================
--- pkg/depmix/R/depmix.R 2011-09-20 14:47:56 UTC (rev 492)
+++ pkg/depmix/R/depmix.R 2011-09-22 09:26:35 UTC (rev 493)
@@ -419,7 +419,7 @@
REPORT=10
if(printlevel>1 && printlevel<5) REPORT=5
if(printlevel>4) REPORT=1
- if(printlevel==0) REPORT=0
+ if(printlevel==0) trace=0
control=list(fnscale=fnscale,trace=trace,factr=factr,maxit=maxit,REPORT=REPORT)
oldObjf=initLogl
@@ -566,7 +566,7 @@
## compute posteriors
if(poster) {
- cat("Computing posteriors \n")
+ if(printlevel>0) cat("Computing posteriors \n")
x<-system.time(pp<-posterior(dat=dat,dmm=mod,tdcov,printlevel))
z$timeUsed=z$timeUsed+x[3]
}
@@ -601,6 +601,8 @@
loglike <- function(dat,dmm,tdcov=0,grad=FALSE,hess=FALSE,set=TRUE,grInd=0,sca=1.0,printlevel=1) {
+ if(class(dmm)[1]=="fit") dmm <- dmm$mod
+
if(set) {
xgmod=checkSetRecode(dat,dmm,tdcov,printlevel)
} else {
@@ -675,6 +677,8 @@
# compute posterior probabilities
posterior <- function(dat,dmm,tdcov=0,printlevel=1) {
+ if(class(dmm)[1]=="fit") dmm <- dmm$mod
+
xgmod=checkSetRecode(dat,dmm,tdcov,printlevel)
if(xgmod$ng==1) dat=list(dat)
@@ -714,6 +718,9 @@
}
computeSes <- function(dat,dmm) {
+
+ if(class(dmm)[1]=="fit") dmm <- dmm$mod
+
cat("Computing standard errors \n")
mod=dmm
eps=1e-8
@@ -792,9 +799,9 @@
PACKAGE="depmix")
}
for(i in 1:samples) {
- gen=generate(dmm=mod, nt=dat$ntimes)
+ gen=generate(dmm=mod, nt=ntimes(dat))
ll=loglike(dat=gen,dmm=mod,print=0)$logl
- fit=fitdmm(dat=gen,dmm=mod,print=0,ses=0,postst=0)
+ fit=fitdmm(dat=gen,dmm=mod,print=0,ses=0,postst=0,poster=FALSE)
bootpars[i,]=fit$mod$pars
ll=fit$loglike
gof[i,]=c(ll,fit$aic,fit$bic)
Modified: pkg/depmix/man/fitdmm.Rd
===================================================================
--- pkg/depmix/man/fitdmm.Rd 2011-09-20 14:47:56 UTC (rev 492)
+++ pkg/depmix/man/fitdmm.Rd 2011-09-22 09:26:35 UTC (rev 493)
@@ -225,8 +225,12 @@
data(speed)
mod <- dmm(nsta=2,itemt=c(1,2)) # gaussian and binary items
+ll <- loglike(speed,mod)
fit1 <- fitdmm(dat=speed,dmm=mod)
summary(fit1)
+ll <- loglike(speed,fit1)
+pst <- posterior(dat=speed,dmm=fit1)
+bs <- bootstrap(fit1,speed,samples=10)
# add some constraints using conpat
conpat=rep(1,15)
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