[Depmix-commits] r581 - pkg/depmixS4/tests

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

Author: ingmarvisser
Date: 2013-09-03 22:11:07 +0200 (Tue, 03 Sep 2013)
New Revision: 581

Modified:
   pkg/depmixS4/tests/test1speed.R
   pkg/depmixS4/tests/test1speed.Rout.save
Log:
Added test for EM optimized logLikelihood of speed data model (so we can safely change around the EM function to optimize it for speed)

Modified: pkg/depmixS4/tests/test1speed.R
===================================================================
--- pkg/depmixS4/tests/test1speed.R	2013-09-03 20:10:02 UTC (rev 580)
+++ pkg/depmixS4/tests/test1speed.R	2013-09-03 20:11:07 UTC (rev 581)
@@ -98,7 +98,7 @@
 cat("Test 3: ", all.equal(c(dev),acc$deviance),"(same but now with covariate) \n")
 
 # 
-# 2-state model with covariate
+# TEST 4: 2-state model with covariate
 # 
 
 trstart=c(0.896,0.104,0.084,0.916)
@@ -112,3 +112,24 @@
 cat("Test 4: ll is now larger than speedll, ie ll is better due to introduction of a covariate \n")
 cat("Test 4: ", ll,"\t", logl, "\n")
 cat("Test 4: ", ll > logl, "\n")
+
+
+#
+# TEST 5: use em to optimize the model
+# 
+
+data(speed)
+
+# 2-state model on rt and corr from speed data set 
+# with Pacc as covariate on the transition matrix
+# ntimes is used to specify the lengths of 3 separate series
+mod1 <- depmix(list(rt~1,corr~1),data=speed,transition=~Pacc,nstates=2,
+	family=list(gaussian(),multinomial("identity")),ntimes=c(168,134,137))
+# fit the model
+set.seed(3)
+fmod1 <- fit(mod1, verbose=FALSE)
+
+llEM <- logLik(fmod1)
+lltest <- -248.972219
+
+cat("Test 5: ", all.equal(c(lltest),c(llEM),check.att=FALSE), "(loglike EM optimized model for speed data) \n")

Modified: pkg/depmixS4/tests/test1speed.Rout.save
===================================================================
--- pkg/depmixS4/tests/test1speed.Rout.save	2013-09-03 20:10:02 UTC (rev 580)
+++ pkg/depmixS4/tests/test1speed.Rout.save	2013-09-03 20:11:07 UTC (rev 581)
@@ -1,7 +1,7 @@
 
-R version 2.7.1 (2008-06-23)
-Copyright (C) 2008 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.1 (2013-05-16) -- "Good Sport"
+Copyright (C) 2013 The R Foundation for Statistical Computing
+Platform: x86_64-apple-darwin10.8.0 (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -121,7 +121,7 @@
 Test 3:  TRUE (same but now with covariate) 
 > 
 > # 
-> # 2-state model with covariate
+> # TEST 4: 2-state model with covariate
 > # 
 > 
 > trstart=c(0.896,0.104,0.084,0.916)
@@ -139,3 +139,26 @@
 > cat("Test 4: ", ll > logl, "\n")
 Test 4:  TRUE 
 > 
+> 
+> #
+> # TEST 5: use em to optimize the model
+> # 
+> 
+> data(speed)
+> 
+> # 2-state model on rt and corr from speed data set 
+> # with Pacc as covariate on the transition matrix
+> # ntimes is used to specify the lengths of 3 separate series
+> mod1 <- depmix(list(rt~1,corr~1),data=speed,transition=~Pacc,nstates=2,
++ 	family=list(gaussian(),multinomial("identity")),ntimes=c(168,134,137))
+> # fit the model
+> set.seed(3)
+> fmod1 <- fit(mod1, verbose=FALSE)
+iteration 26 logLik: -248.9722 
+> 
+> llEM <- logLik(fmod1)
+> lltest <- -248.972219
+> 
+> cat("Test 5: ", all.equal(c(lltest),c(llEM),check.att=FALSE), "(loglike EM optimized model for speed data) \n")
+Test 5:  TRUE (loglike EM optimized model for speed data) 
+>