[Depmix-commits] r358 - trunk
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 23 00:04:46 CET 2010
Author: ingmarvisser
Date: 2010-02-23 00:04:46 +0100 (Tue, 23 Feb 2010)
New Revision: 358
Added:
trunk/baseI.RData
trunk/bugs.R
trunk/depmixNew-examples.R
trunk/depmixS4MultinomialIdentity.R
trunk/exgaus.R
trunk/exgausMIX.R
trunk/exgausOld.R
trunk/gamlssMXfits.R
trunk/rt.text
trunk/testmaartje.rda
Log:
Several test files, new code et cetera (to be processed)
Added: trunk/baseI.RData
===================================================================
(Binary files differ)
Property changes on: trunk/baseI.RData
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:mime-type
+ application/octet-stream
Added: trunk/bugs.R
===================================================================
--- trunk/bugs.R (rev 0)
+++ trunk/bugs.R 2010-02-22 23:04:46 UTC (rev 358)
@@ -0,0 +1,71 @@
+
+# Bug by Maartje
+
+library(depmixS4)
+
+setwd("~/Documents/projects/depmixProject/depmixNew/rforge/depmix/trunk/")
+
+load("testmaartje.rda")
+
+respstart <- c(rbind(rnorm(10,8,2),rep(0,10),runif(10,1,2),rnorm(10,8,2),rep(0,10),runif(10,1,2)))
+
+# respstart <- runif(30)
+
+mod1=depmix(list(i1~t,i2~t,i3~t,i4~t,i5~t,i6~t,i7~t,i8~t,i9~t,i10~t),
+ data=casematrix,nstates=2,ntimes=ntimes,
+ family=list(gaussian(),gaussian(),gaussian(),gaussian(),gaussian(),gaussian(),
+ gaussian(),gaussian(),gaussian(),gaussian()), respstart=respstart)
+
+ll <- logLik(mod1)
+
+fitmod1=fit(mod1)
+
+hist(posterior(fitmod1)[,2])
+
+
+
+# Bug by Rita Gaio
+
+library(depmixS4)
+library(Rdonlp2)
+library(nnet)
+
+
+mod.cov <- mix(list(sqrt(carnev)~1+CALORIES, sqrt(peixe)~1+CALORIES,
+ sqrt(vegetais)~1+CALORIES, sqrt(frutos)~1+CALORIES,
+ sqrt(armbat)~1+CALORIES, sqrt(sweet)~1+CALORIES,# 6 continuous variables
+ sumos2~1+CALORIES, alcool2.m ~1+CALORIES),
+ data=baseI,
+ nstates=4,
+ family=list(gaussian(), gaussian(), gaussian(),gaussian(), gaussian(), gaussian(),
+ multinomial(), multinomial()),
+ prior=~idade.c+CALORIES,
+ initdata=baseI
+) # end mod.cov
+getpars(mod.cov)
+print(mod.cov)
+
+ncont <- 6 Ê# nb continuous responses
+nbin <- 2 ÊÊ# nb binary responses
+nmixt <- 2 ÊÊ# nb of mixtures
+ncov1 <- 1 ÊÊÊ# nb covariates for densities WITHIN each cluster
+ncov2 <- 2 ÊÊÊ# nb covariates affecting the components/clusters
+value.cov=rep(0, nmixt*(1+ncov2)
+ÊÊÊÊÊÊÊÊÊÊÊ+ ncont*(1+ncov1+1) + nbin*2*(1+ncov1)
+ÊÊÊÊÊÊÊÊÊÊÊ+ ncont*(1+ncov1+1) + nbin*2*(1+ncov1),
+ÊÊÊÊÊÊÊÊÊÊÊ+ ncont*(1+ncov1+1) + nbin*2*(1+ncov1),
+ÊÊÊÊÊÊÊÊÊÊÊ+ ncont*(1+ncov1+1) + nbin*2*(1+ncov1) )
+
+
+## Choose value.cov with random values for the means and sample sd's for the sd's ...
+## deleted the vector I had since I slightly changed the model I had
+
+mod.cov2 <- setpars(mod.cov, value=value.cov)
+print(mod.cov2)
+
+fmod.cov2 <- fit(mod.cov2, method="donlp")
+## without method="donlp" we get Êiteration 0 logLik: -29803.8
+## Error in lm.wfit(x = object at x, y = object at y, w = w) :
+## Êmissing or negative weights not allowed
+
+## with method="donlp": runs forever...
\ No newline at end of file
Property changes on: trunk/bugs.R
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:eol-style
+ native
Added: trunk/depmixNew-examples.R
===================================================================
--- trunk/depmixNew-examples.R (rev 0)
+++ trunk/depmixNew-examples.R 2010-02-22 23:04:46 UTC (rev 358)
@@ -0,0 +1,79 @@
+
+#
+# Started by Ingmar Visser may 4, 2009
+#
+
+#
+# add response model for exgaus responses
+#
+
+setwd("~/Documents/projects/depmixProject/depmixNew/rforge/depmix/trunk/")
+
+library(depmixS4)
+library(gamlss)
+library(gamlss.dist)
+
+data(speed)
+rt <- speed$rt
+
+source("exgaus.R")
+
+#
+# test basic exgaus function: this should reproduce the gamlss output
+#
+
+mod <- exgaus(rt,pstart=c(5,.1,.1))
+fm <- fit(mod)
+mod1 <- gamlss(rt~1,family=exGAUS(),control=gamlss.control(n.cyc=100),
+ mu.st=4.5,sigma.st=0.1,nu.st=0.7)
+
+fm
+mod1
+
+#
+# test the weighted version of this
+#
+
+w=runif(439)
+fm <- fit(mod,w)
+mod1 <- gamlss(rt~1,family=exGAUS(),control=gamlss.control(n.cyc=100),
+ mu.st=4.5,sigma.st=0.1,nu.st=0.7,weights=w)
+
+fm
+mod1
+
+
+
+#
+# test a hidden Markov model with exgaus responses
+#
+
+rModels <- list(
+ list(
+ exgaus(rt,pstart=c(5,.1,.1)),
+ GLMresponse(formula=corr~1,data=speed,family=multinomial(),pstart=c(0.5,0.5))
+ ),
+ list(
+ exgaus(rt,pstart=c(6,.1,.1)),
+ GLMresponse(formula=corr~1,data=speed,family=multinomial(),pstart=c(.1,.9))
+ )
+)
+
+trstart=c(0.9,0.1,0.1,0.9)
+
+transition <- list()
+transition[[1]] <- transInit(~Pacc,nstates=2,data=speed,pstart=c(trstart[1:2],0,0))
+transition[[2]] <- transInit(~Pacc,nstates=2,data=speed,pstart=c(trstart[3:4],0,0))
+
+instart=c(0.5,0.5)
+inMod <- transInit(~1,ns=2,ps=instart,data=data.frame(rep(1,3)))
+
+mod <- makeDepmix(response=rModels,transition=transition,prior=inMod,ntimes=attr(speed,"ntimes"),stat=FALSE)
+
+logLik(mod)
+
+fm1 <- fit(mod)
+fm2 <- fit(mod,meth="donlp")
+
+summary(fm1)
+summary(fm2)
\ No newline at end of file
Property changes on: trunk/depmixNew-examples.R
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:eol-style
+ native
Added: trunk/depmixS4MultinomialIdentity.R
===================================================================
--- trunk/depmixS4MultinomialIdentity.R (rev 0)
+++ trunk/depmixS4MultinomialIdentity.R 2010-02-22 23:04:46 UTC (rev 358)
@@ -0,0 +1,470 @@
+setwd("C:\\cverena\\projects\\OP49add\\analyse\\depmixS4")
+library(depmixS4)
+#source("fix_transinit_bug_source.R")
+#source("fix_constraint_bug_source.R")
+
+################################
+# data
+###################################
+data=list(N = 302, lengths = c(13, 49, 12, 18, 16, 24, 11, 13, 13,
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+1, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1,
+0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1,
+0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1,
+0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 1,
+1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 1,
+0, 0, 1, 0, 0, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 0,
+1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0,
+0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0,
+0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0,
+1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0,
+0, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1,
+0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0,
+0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1,
+1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0,
+0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0,
+0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1, 1,
+0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1,
+1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+0, 0, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 1,
+1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 1, 0,
+0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0,
+1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1,
+0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0,
+0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1,
+1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1,
+0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1,
+0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0, 1,
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 1, 0,
+0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1,
+1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1,
+0, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1,
+0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 1,
+1, 1, 1, 1, 1, 1, 1, 1), age = c(14.69, 13.44, 13.58, 12.8, 13.3,
+13.7, 14.57, 13.33, 13.04, 13.48, 12.68, 14.07, 14.07, 14.14,
+12.71, 12.81, 12.73, 14.61, 12.78, 13.36, 12.61, 13.37, 13.21,
+13.39, 14.09, 14.53, 14.99, 13.95, 14.08, 14.2, 13.64, 14.29,
+13.72, 14.29, 14.35, 14.61, 14.67, 14.35, 13.55, 14.65, 13.93,
+13.7, 14.51, 14.93, 14.48, 13.79, 13.91, 13.75, 14.78, 14.61,
+13.96, 14.44, 13.72, 13.84, 14.37, 13.71, 14.85, 14.35, 14.61,
+13.91, 14.12, 13.9, 14.54, 13.72, 13.52, 12.68, 11.85, 13.48,
+12.84, 13.05, 12.88, 12.6, 13.07, 13.06, 13.33, 13.59, 13.6,
+13.64, 13.21, 13.05, 12.8, 13.53, 12.34, 11.63, 12.69, 11.33,
+11.13, 9.78, 11.64, 12.96, 11.65, 11.59, 12.28, 11.99, 6.66,
+7.62, 7.25, 6.83, 6.73, 8.01, 6.59, 7.48, 7.54, 6.98, 7.08, 7.06,
+7.04, 7.18, 7.44, 10.55, 10.22, 10.76, 10.39, 11.5, 10.6, 10.28,
+10.93, 9.65, 9.39, 9.54, 9.39, 10.19, 10.82, 9.95, 10.91, 8.47,
+8.39, 8.97, 7.72, 7.81, 7.01, 8.93, 7.89, 8.76, 8.27, 8.11, 8.8,
+7.76, 7.76, 7.73, 7.94, 6.84, 9.1, 7.86, 7.73, 9.01, 9.33, 9.32,
+9.23, 9.04, 9.8, 9.73, 9.47, 9.02, 9.98, 10.28, 10.39, 8.92,
+4.86, 4.85, 4.5, 4.25, 4.51, 4.97, 5.28, 5.06, 5.22, 5.43, 5.99,
+5.42, 5.21, 5.13, 6.15, 5.78, 5.44, 5.14, 5.07, 4.95, 5.67, 4.2,
+4.2, 4.21, 4.24, 5.06, 4.38, 4.83, 5.78, 7, 6.84, 6.73, 7.08,
+7.48, 6.72, 6.5, 6.56, 6.42, 7.2, 6.72, 6.38, 6.58, 6.89, 6.73,
+7.23, 6.54, 6.34, 6.27, 6.92, 6.65, 7.04, 6.79, 6.45, 10.13,
+10.18, 11.01, 10.74, 9.49, 9.32, 9.78, 9.76, 9.85, 9.83, 9.83,
+10.04, 10.04, 10.65, 10.75, 10.9, 10.37, 11.94, 8.01, 8.38, 8.35,
+8.18, 8.41, 8.67, 8.12, 9.15, 10.75, 12.13, 8.72, 8.18, 8.19,
+8.88, 8.86, 8.31, 8.46, 8.53, 5.59, 5.57, 5.13, 10.99, 12.45,
+11.26, 12.47, 12.32, 12.45, 12.32, 12.18, 12.06, 12.18, 12.59,
+11.83, 11.41, 11.79, 11.71, 11.42, 11.61, 11.49, 11.13, 12, 11.37,
+4.21, 4.14, 11.58, 4.3, 5.1, 4.92, 4.54, 4.35, 4.4, 4.27, 5.19,
+4.38, 4.4, 4.38, 5.32, 5.12, 4.58, 4.47, 4.61, 4.2, 4.89, 4.56,
+4.9, 4.3, 4.18, 5.88, 5.34, 5.8, 5.25, 5.74, 5.56))
+
+
+ndat<-data$acc
+N=data$N
+lengths=data$lengths
+age=data$age
+# nine state model = mixture of all-or-none , ci, and guessing model
+# covariate age on the initial probabilities
+nn<-.000000000001
+rModels <- list(
+ list(GLMresponse(formula=ndat~1,family=multinomial(),pstart=c(nn,1),fixed=c(T,T))), #init AN
+ list(GLMresponse(formula=ndat~1,family=multinomial(),pstart=c(nn,1),fixed=c(T,T))), #init CI
+ list(GLMresponse(formula=ndat~1,family=multinomial(),pstart=c(nn,1),fixed=c(T,T))), #init G
+ list(GLMresponse(formula=ndat~1,family=multinomial(),pstart=c(0.05,0.95),fixed=c(T,F))), #AN L
+ list(GLMresponse(formula=ndat~1,family=multinomial(),pstart=c(0.5,0.5),fixed=c(T,F))), #AN g
+ list(GLMresponse(formula=ndat~1,family=multinomial(),pstart=c(.05,.95),fixed=c(T,F))), #CI L
+ list(GLMresponse(formula=ndat~1,family=multinomial(),pstart=c(nn,1),fixed=c(T,T))), #CI C
+ list(GLMresponse(formula=ndat~1,family=multinomial(),pstart=c(1,nn),fixed=c(T,T))), #CI E
+ list(GLMresponse(formula=ndat~1,family=multinomial(),pstart=c(0.5,0.5),fixed=c(T,T))) # G
+)
+trstart=c(
+rep(nn,4),1,rep(nn,4),
+rep(nn,5),.02,1-.5-.02,.5,nn,
+rep(nn,8),1,
+rep(nn,3),1,rep(nn,5),
+rep(nn,3),.04,1-.04,rep(nn,4),
+rep(nn,5),1,rep(nn,3),
+rep(nn,5),nn,3/8,5/8,nn,
+rep(nn,5),.4,(1-.4)*3/8,(1-.4)*5/8,nn,
+rep(nn,8),1)
+trfix<-c(
+rep(T,4),T,rep(T,4),
+rep(T,5),F,F,F,T,
+rep(T,9),
+rep(T,3),T,rep(T,5),
+rep(T,3),F,F,rep(T,4),
+rep(T,5),T,rep(T,3),
+rep(T,5),T,T,T,T,
+rep(T,5),F,F,F,T,
+rep(T,8),T)
+
+nstates=9
+transition <- list()
+for (i in 0:(nstates-1)){
+tmp<-trfix[i*9+(1:9)]
+if (all(tmp)) {base=1
+}else {base=min(which(trfix[i*9+(1:9)]==F));tmp[min(which(trfix[i*9+(1:9)]==F))]<-T;}
+transition[[i+1]] <- transInit(~1,nstates=9,data=data.frame(1),pstart=c(trstart[i*9+(1:9)]),family=multinomial(base=base),fixed=tmp)
+}
+# hoe kan ik de constraint in de transitiematrix specificeren? de 8ste KANS in rij 2 moet gelijk aan .5 zijn
+#tmp<-c(rep(T,5),F,F,T,T,)
+#transition[[2]] <- transInit(~1,nstates=9,data=data.frame(1),pstart=c(trstart[1*9+(1:9)]),family=multinomial(base=8),fixed=tmp)
+
+instart=c(.5,.4,.1,rep(nn,9-3),rep(0,9))
+infix=c(T,F,F,rep(T,9-3),rep(T,9))
+inCov <- transInit(~age,ns=nstates,ps=instart,data=data.frame(age=age),fixed=infix,family=multinomial(base=1))
+inmod <- transInit(~1,ns=nstates,ps=instart[1:nstates],data=data.frame(rep(1,length(lengths))),fixed=infix[1:nstates])
+
+modcov <- makeDepmix(response=rModels,transition=transition,prior=inCov,ntimes=lengths)
+#param<-getpars(modcov)
+#param[which(param < -12)]<- -20
+#modcov<- setpars(modcov,param)
+mod <- makeDepmix(response=rModels,transition=transition,prior=inmod,ntimes=lengths)
+param<-getpars(mod)
+#parnr<-1:length(param)
+#mod<- setpars(mod,parnr)
+#mod
+#param[which(param < -12)]<- -20
+#mod<- setpars(mod,param)
+#mod
+logLik(mod)
+logLik(modcov)
+# constraint met cov op inits
+constr<-matrix(rep(0,117),1,117)
+constr[1,c(88,89)]<-c(1,-1)
+#constr[2,c(33,34)]<-c(1,1)
+conrows.upper=conrows.lower= c(-log(5/3))#,0)
+# constraint zonder cov op inits
+constrz<-matrix(rep(0,108),1,108)
+constrz[1,c(79,80)]<-c(1,-1)
+#constrz[2,c(33,34)-9]<-c(1,1)
+
+fitage<-fit(modcov)
+fitageconstr<-fit(modcov, conrows=constr,conrows.upper=conrows.upper, conrows.lower=conrows.lower)
+
+fitfree<-fit(mod)
+fitconstr<-fit(mod, conrows=constrz,conrows.upper=conrows.upper, conrows.lower=conrows.lower)
+
+save(list = ls(all=TRUE), file = "depmix_covage_bestfit_1.RData")
Property changes on: trunk/depmixS4MultinomialIdentity.R
___________________________________________________________________
Name: svn:executable
+ *
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/depmix -r 358
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