[Depmix-commits] r648 - pkg/depmixS4/man

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

Author: ingmarvisser
Date: 2016-02-10 18:04:00 +0100 (Wed, 10 Feb 2016)
New Revision: 648

Modified:
   pkg/depmixS4/man/depmix-methods.Rd
   pkg/depmixS4/man/depmix.fit.Rd
   pkg/depmixS4/man/forwardbackward.Rd
   pkg/depmixS4/man/llratio.Rd
   pkg/depmixS4/man/makeDepmix.Rd
   pkg/depmixS4/man/posterior.Rd
Log:
=docementation updates

Modified: pkg/depmixS4/man/depmix-methods.Rd
===================================================================
--- pkg/depmixS4/man/depmix-methods.Rd	2016-02-10 16:18:11 UTC (rev 647)
+++ pkg/depmixS4/man/depmix-methods.Rd	2016-02-10 17:04:00 UTC (rev 648)
@@ -128,7 +128,7 @@
 	
 	\item{nobs}{returns the number of observations (used in computing the BIC).}
 
-	\item{npar}{returns the number of paramters of a model.}
+	\item{npar}{returns the number of paramaters of a model.}
 
 	\item{freepars}{returns the number of non-redundant parameters.}
 

Modified: pkg/depmixS4/man/depmix.fit.Rd
===================================================================
--- pkg/depmixS4/man/depmix.fit.Rd	2016-02-10 16:18:11 UTC (rev 647)
+++ pkg/depmixS4/man/depmix.fit.Rd	2016-02-10 17:04:00 UTC (rev 648)
@@ -186,6 +186,9 @@
 # to see the parameters
 summary(fmod1)
 
+# to see the posterior state sequence and associated delta probabilties
+pst <- posterior(fmod1)
+
 # same model, now with missing data
 \dontrun{
 speed[2,1] <- NA

Modified: pkg/depmixS4/man/forwardbackward.Rd
===================================================================
--- pkg/depmixS4/man/forwardbackward.Rd	2016-02-10 16:18:11 UTC (rev 647)
+++ pkg/depmixS4/man/forwardbackward.Rd	2016-02-10 17:04:00 UTC (rev 648)
@@ -50,7 +50,7 @@
 	
 	\item{sca}{The scale factors (called lambda in Rabiner, 1989).}
 	
-	\item{logLike}{The log likelihood (computed as \code{sum(log(sca))}.}
+	\item{logLike}{The log likelihood (computed as \code{-sum(log(sca))}.}
 	
 	If return.all=FALSE, only gamma, xi and the log likelihood are returned.
 }
@@ -66,7 +66,18 @@
 \author{ Maarten Speekenbrink & Ingmar Visser }
 
 \examples{
-	# add some later
+
+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))
+
+fb <- forwardbackward(mod1)
+all.equal(-sum(log(fb$sca)),fb$logLike)
+
 }
 
 \keyword{ methods }

Modified: pkg/depmixS4/man/llratio.Rd
===================================================================
--- pkg/depmixS4/man/llratio.Rd	2016-02-10 16:18:11 UTC (rev 647)
+++ pkg/depmixS4/man/llratio.Rd	2016-02-10 17:04:00 UTC (rev 648)
@@ -44,6 +44,10 @@
 	
 }
 
+\details{
+	See the \code{\link{fit}} help page for an example. 
+}
+
 \author{Ingmar Visser}
 
 \keyword{methods}
\ No newline at end of file

Modified: pkg/depmixS4/man/makeDepmix.Rd
===================================================================
--- pkg/depmixS4/man/makeDepmix.Rd	2016-02-10 16:18:11 UTC (rev 647)
+++ pkg/depmixS4/man/makeDepmix.Rd	2016-02-10 17:04:00 UTC (rev 648)
@@ -32,7 +32,7 @@
 	
 	\item{transition}{A list of transition models, each created by a
 		call to \code{\link{transInit}}.  The lenght of this list should be
-		the nubmer of states of the model.}
+		the number of states of the model.}
 	
 	\item{prior}{The initial state probabilities model; created through a
 	call to \code{\link{transInit}}.}

Modified: pkg/depmixS4/man/posterior.Rd
===================================================================
--- pkg/depmixS4/man/posterior.Rd	2016-02-10 16:18:11 UTC (rev 647)
+++ pkg/depmixS4/man/posterior.Rd	2016-02-10 17:04:00 UTC (rev 648)
@@ -43,8 +43,8 @@
 
 \author{ Ingmar Visser }
 
-\examples{
-	# add some later
+\details{
+	See the \code{\link{fit}} help page for an example. 
 }
 
 \keyword{ methods }