[Depmix-commits] r54 - / trunk

[noreply at r-forge.r-project.org]

Author: ingmarvisser
Date: 2008-03-06 16:44:05 +0100 (Thu, 06 Mar 2008)
New Revision: 54

Modified:
   todo
   trunk/depmix-test2.R
   trunk/depmix-test3EM2.R
   trunk/fb.R
   trunk/hmModel.R
Log:
Minor changes

Modified: todo
===================================================================
--- todo	2008-03-06 15:15:41 UTC (rev 53)
+++ todo	2008-03-06 15:44:05 UTC (rev 54)
@@ -9,11 +9,9 @@
 	3) depmix.fit.Rd: help on fitting models: Ingmar
 		Other methods for depmix.fitted objects include:
 		a) posterior: get posterior state sequence: we still need the code for this!
-		
 		b) logLik: done!!!
 		c) AIC, BIC: done!!!
-		d) getpars, setpars
-		
+		d) getpars, setpars: done!!!!
 		e) llratio: done!!!!!
 		
 	4) responses.Rd: detailed description on constructing response models
@@ -32,9 +30,10 @@
 - viterbi algorithm to get posterior probabilities as part of depmix.fitted
 
 
-- general documentation: depmix-introduction needs updating
+- general documentation: depmix-introduction.pdf needs updating
 
 
+- generate initial values?!?!?
 
 
 

Modified: trunk/depmix-test2.R
===================================================================
--- trunk/depmix-test2.R	2008-03-06 15:15:41 UTC (rev 53)
+++ trunk/depmix-test2.R	2008-03-06 15:44:05 UTC (rev 54)
@@ -16,7 +16,7 @@
 # Test optimization using Rdonlp2
 # 
 
-setwd("/Users/ivisser/Documents/projects/depmixProject/depmixNew/code/depmix/trunk/")
+setwd("/Users/ivisser/Documents/projects/depmixProject/depmixNew/rforge/depmix/trunk/")
 
 source("depmixS4.r")
 source("classes.r")
@@ -26,23 +26,27 @@
 source("lystig.R")
 source("fb.R")
 
-load("speed.Rda")
+load("data/speed.Rda")
 
 rModels <- list(
   list(
-	rModel(formula=rt~1,data=speed,family=gaussian(),pstart=c(5.52,.2)),
+	rModel(formula=rt~1,data=speed,family=gaussian()),#,pstart=c(5.52,.2)
 	rModel(formula=corr~1,data=speed,family=multinomial())),
   list(
-	rModel(formula=rt~1,data=speed,family=gaussian(),pstart=c(6.39,.24)),
-	rModel(formula=corr~1,data=speed,family=multinomial(),pstart=c(.098,.902)))
+	rModel(formula=rt~1,data=speed,family=gaussian()),#,pstart=c(6.39,.24)
+	rModel(formula=corr~1,data=speed,family=multinomial()))#,pstart=c(.098,.902)
 )
 
-instart=c(0.45,.55)
-trstart=c(0.896,0.104,0.084,0.916)
-trstart=c(trstart[1:2],0,0.01,trstart[3:4],0,0)
+instart=c(0.5,.5)
+trstart1=c(0.896,0.104,0.084,0.916)
+trstart2=c(trstart[1:2],0,0.01,trstart[3:4],0,0)
 
-mod <- depmix(rModels=rModels,data=speed,transition=~Pacc,trstart=trstart,instart=instart)
+mod <- depmix(rModels=rModels,data=speed,transition=~1,trstart=trstart1,instart=instart)
 
+logLik(mod)
+
+fmod <- em(mod,ver=T)
+
 # fit the model
 mod1 <- fit(mod)
 ll <- logLik(mod1)
Modified: trunk/depmix-test3EM2.R
===================================================================
--- trunk/depmix-test3EM2.R	2008-03-06 15:15:41 UTC (rev 53)
+++ trunk/depmix-test3EM2.R	2008-03-06 15:44:05 UTC (rev 54)
@@ -18,19 +18,21 @@
 
 rModels <- list(
   list(
-	rModel(formula=rt~1,data=speed,family=gaussian(),pstart=c(5.5,.2))),
+	rModel(formula=rt~1,data=speed,family=gaussian())),#,pstart=c(5.5,.2)
   list(
-	rModel(formula=rt~1,data=speed,family=gaussian(),pstart=c(6.3,.2)))
+	rModel(formula=rt~1,data=speed,family=gaussian()))#,pstart=c(6.3,.2)
 )
 
-trstart=c(0.8,0.2,0.1,0.9)
+trstart=runif(4)
 instart=c(0,1)
 
-
 mod <- depmix(rModels=rModels,data=speed,transition=~1,trstart=trstart,instart=instart)
 
 logLik(mod)
 source("EM.R")
+
+mod
+
 fmod <- em(mod,verbose=T)
 
 # 

Modified: trunk/fb.R
===================================================================
--- trunk/fb.R	2008-03-06 15:15:41 UTC (rev 53)
+++ trunk/fb.R	2008-03-06 15:44:05 UTC (rev 54)
@@ -19,7 +19,6 @@
 	nt <- nrow(B)	
 	ns <- ncol(init)
 	
-	
 	alpha <- matrix(ncol=ns,nrow=nt)
 	beta <- matrix(ncol=ns,nrow=nt)
 	sca <- vector(length=nt)
Modified: trunk/hmModel.R
===================================================================
--- trunk/hmModel.R	2008-03-06 15:15:41 UTC (rev 53)
+++ trunk/hmModel.R	2008-03-06 15:44:05 UTC (rev 54)
@@ -60,7 +60,7 @@
 	
 	# make appropriate array for observation densities
 	dens <- array(,c(nt,nresp,nstates))
-	
+		
 	# compute observation and transition densities
 	for(i in 1:nstates) {
 		for(j in 1:nresp) {