[Depmix-commits] r461 - in pkg/depmixS4: data man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 15 14:33:00 CEST 2011
Author: ingmarvisser
Date: 2011-06-15 14:33:00 +0200 (Wed, 15 Jun 2011)
New Revision: 461
Modified:
pkg/depmixS4/data/speed.rda
pkg/depmixS4/man/depmix.Rd
pkg/depmixS4/man/depmix.fit.Rd
pkg/depmixS4/man/makeDepmix.Rd
pkg/depmixS4/man/responses.Rd
pkg/depmixS4/man/speed.Rd
pkg/depmixS4/tests/test1speed.R
pkg/depmixS4/tests/test1speed.Rout.save
pkg/depmixS4/tests/test2getsetpars.R
pkg/depmixS4/tests/test2getsetpars.Rout.save
Log:
Removed ntimes attribute from speed data (and adapted examples and tests accordingly), updated reference on speed data help page to Dutilh et al. (2011).
Modified: pkg/depmixS4/data/speed.rda
===================================================================
(Binary files differ)
Modified: pkg/depmixS4/man/depmix.Rd
===================================================================
--- pkg/depmixS4/man/depmix.Rd 2011-06-15 10:26:59 UTC (rev 460)
+++ pkg/depmixS4/man/depmix.Rd 2011-06-15 12:33:00 UTC (rev 461)
@@ -33,10 +33,10 @@
\arguments{
\item{response}{The response to be modeled; either a formula or a list
- of formulae in the multivariate case; this interfaces to the glm
- distributions. See 'Details'.}
+ of formulae (in the multivariate case); this interfaces to the glm
+ and other distributions. See 'Details'.}
- \item{data}{An optional data.frame to interpret the variables in
+ \item{data}{An optional \code{data.frame} to interpret the variables in
the response and transition arguments.}
\item{nstates}{The number of states of the model.}
@@ -67,8 +67,8 @@
\item{ntimes}{A vector specifying the lengths of individual, i.e.
independent, time series. If not specified, the responses are
assumed to form a single time series, i.e. \code{ntimes=nrow(data)}.
- If the \code{data} argument has an attribute ntimes, then this
- is used.}
+ If the \code{data} argument has an attribute \code{ntimes}, then this
+ is used. The first example in \code{\link{fit}} uses this argument.}
\item{...}{Not used currently.}
@@ -139,8 +139,7 @@
time-dependent or not; for internal use.}
\item{ntimes}{A vector containing the lengths of independent time
- series; if data is provided, sum(ntimes) must be equal to
- nrow(data).}
+ series.}
\item{nstates}{The number of states of the model.}
@@ -187,8 +186,10 @@
\examples{
# create a 2 state model with one continuous and one binary response
-data(speed)
-mod <- depmix(list(rt~1,corr~1),data=speed,nstates=2,family=list(gaussian(),multinomial()))
+# ntimes is used to specify the lengths of 3 separate series
+data(speed)
+mod <- depmix(list(rt~1,corr~1),data=speed,nstates=2,
+ family=list(gaussian(),multinomial("identity")),ntimes=c(168,134,137))
# print the model, formulae and parameter values
mod
Modified: pkg/depmixS4/man/depmix.fit.Rd
===================================================================
--- pkg/depmixS4/man/depmix.fit.Rd 2011-06-15 10:26:59 UTC (rev 460)
+++ pkg/depmixS4/man/depmix.fit.Rd 2011-06-15 12:33:00 UTC (rev 461)
@@ -164,6 +164,7 @@
# 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
Modified: pkg/depmixS4/man/makeDepmix.Rd
===================================================================
--- pkg/depmixS4/man/makeDepmix.Rd 2011-06-15 10:26:59 UTC (rev 460)
+++ pkg/depmixS4/man/makeDepmix.Rd 2011-06-15 12:33:00 UTC (rev 461)
@@ -287,7 +287,7 @@
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)
+mod <- makeDepmix(response=rModels,transition=transition,prior=inMod,ntimes=c(168,134,137),stat=FALSE)
fm3 <- fit(mod,emc=em.control(rand=FALSE))
summary(fm3)
Modified: pkg/depmixS4/man/responses.Rd
===================================================================
--- pkg/depmixS4/man/responses.Rd 2011-06-15 10:26:59 UTC (rev 460)
+++ pkg/depmixS4/man/responses.Rd 2011-06-15 12:33:00 UTC (rev 461)
@@ -109,8 +109,7 @@
# binomial response model
x <- rnorm(1000)
- library(boot)
- p <- inv.logit(x)
+ p <- plogis(x)
ss <- rbinom(1000,1,p)
mod <- GLMresponse(cbind(ss,1-ss)~x,family=binomial())
fit(mod)
Modified: pkg/depmixS4/man/speed.Rd
===================================================================
--- pkg/depmixS4/man/speed.Rd 2011-06-15 10:26:59 UTC (rev 460)
+++ pkg/depmixS4/man/speed.Rd 2011-06-15 12:33:00 UTC (rev 461)
@@ -17,7 +17,7 @@
pay-off for accurate responding, which is on a scale of zero to one.
The value of Pacc was varied during the experiment to induce the
switching. This data set is a from participant A in experiment
- 1a from Dutilh et al (2010).
+ 1a from Dutilh et al (2011).
}
@@ -26,7 +26,7 @@
\format{
A data frame with 439 observations on the following 3 variables.
\describe{
- \item{\code{rt}}{a numeric vector of response times}
+ \item{\code{rt}}{a numeric vector of response times (log ms)}
\item{\code{corr}}{a numeric vector of accuracy scores (0/1)}
\item{\code{Pacc}}{a numeric vector of the pay-off for accuracy}
}
@@ -34,12 +34,12 @@
\source{
- Gilles Dutilh, Ingmar Visser, Eric-Jan Wagenmakers, & Han L. J. van der Maas.
- A Phase Transition Model for the Speed-Accuracy Trade-Off in
- Response Time Experiments. \emph{2010, submitted for publication.}
-
- Please contact g.dutilh at uva.nl for preprints and more information.
+ Gilles Dutilh, Eric-Jan Wagenmakers, Ingmar Visser, & Han L. J. van der Maas (2011).
+ A phase transition model for the speed-accuracy trade-off in response time experiments.
+ \emph{Cognitive Science}, 35:211-250.
+ Corresponding author: g.dutilh at uva.nl
+
}
\examples{
Modified: pkg/depmixS4/tests/test1speed.R
===================================================================
--- pkg/depmixS4/tests/test1speed.R 2011-06-15 10:26:59 UTC (rev 460)
+++ pkg/depmixS4/tests/test1speed.R 2011-06-15 12:33:00 UTC (rev 461)
@@ -28,7 +28,7 @@
instart=c(0,1)
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"))
+mod <- makeDepmix(response=rModels,transition=transition,prior=inMod,ntimes=c(168,134,137))
ll <- logLik(mod)
ll.fb <- logLik(mod,method="fb")
@@ -47,7 +47,7 @@
resp <- c(5.52,0.202,0.472,0.528,6.39,0.24,0.098,0.902)
trstart=c(0.899,0.101,0.084,0.916)
instart=c(0,1)
-mod <- depmix(list(rt~1,corr~1),data=speed,nstates=2,family=list(gaussian(),multinomial()),respstart=resp,trstart=trstart,instart=instart,prob=T)
+mod <- depmix(list(rt~1,corr~1),data=speed,nstates=2,family=list(gaussian(),multinomial()),respstart=resp,trstart=trstart,instart=instart,prob=T,ntimes=c(168,134,137))
ll2 <- logLik(mod)
@@ -68,7 +68,7 @@
p1 <- invlogit(coef(acc)[1])
p0 <- 1-p1
-mod <- depmix(corr~1,data=speed,nst=1,family=multinomial(),trstart=1,instart=c(1),respstart=c(p0,p1))
+mod <- depmix(corr~1,data=speed,nst=1,family=multinomial(),trstart=1,instart=c(1),respstart=c(p0,p1),ntimes=c(168,134,137))
ll <- logLik(mod)
@@ -90,7 +90,7 @@
pstart=c(p0,p1,0,coef(acc)[2])
-mod <- depmix(corr~Pacc,data=speed,family=multinomial(),trstart=1,instart=1,respst=pstart,nstate=1)
+mod <- depmix(corr~Pacc,data=speed,family=multinomial(),trstart=1,instart=1,respst=pstart,nstate=1,ntimes=c(168,134,137))
ll <- logLik(mod)
dev <- -2*ll
@@ -106,7 +106,7 @@
instart=c(0,1)
resp <- c(5.52,0.202,0.472,0.528,6.39,0.24,0.098,0.902)
-mod <- depmix(list(rt~1,corr~1),data=speed,family=list(gaussian(),multinomial()),transition=~Pacc,trstart=trstart,instart=instart,respst=resp,nst=2)
+mod <- depmix(list(rt~1,corr~1),data=speed,family=list(gaussian(),multinomial()),transition=~Pacc,trstart=trstart,instart=instart,respst=resp,nst=2,ntimes=c(168,134,137))
ll <- logLik(mod)
cat("Test 4: ll is now larger than speedll, ie ll is better due to introduction of a covariate \n")
Modified: pkg/depmixS4/tests/test1speed.Rout.save
===================================================================
--- pkg/depmixS4/tests/test1speed.Rout.save 2011-06-15 10:26:59 UTC (rev 460)
+++ pkg/depmixS4/tests/test1speed.Rout.save 2011-06-15 12:33:00 UTC (rev 461)
@@ -47,7 +47,7 @@
> instart=c(0,1)
> 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"))
+> mod <- makeDepmix(response=rModels,transition=transition,prior=inMod,ntimes=c(168,134,137))
>
> ll <- logLik(mod)
> ll.fb <- logLik(mod,method="fb")
@@ -67,7 +67,7 @@
> resp <- c(5.52,0.202,0.472,0.528,6.39,0.24,0.098,0.902)
> trstart=c(0.899,0.101,0.084,0.916)
> instart=c(0,1)
-> mod <- depmix(list(rt~1,corr~1),data=speed,nstates=2,family=list(gaussian(),multinomial()),respstart=resp,trstart=trstart,instart=instart,prob=T)
+> mod <- depmix(list(rt~1,corr~1),data=speed,nstates=2,family=list(gaussian(),multinomial()),respstart=resp,trstart=trstart,instart=instart,prob=T,ntimes=c(168,134,137))
>
> ll2 <- logLik(mod)
>
@@ -89,7 +89,7 @@
> p1 <- invlogit(coef(acc)[1])
> p0 <- 1-p1
>
-> mod <- depmix(corr~1,data=speed,nst=1,family=multinomial(),trstart=1,instart=c(1),respstart=c(p0,p1))
+> mod <- depmix(corr~1,data=speed,nst=1,family=multinomial(),trstart=1,instart=c(1),respstart=c(p0,p1),ntimes=c(168,134,137))
>
> ll <- logLik(mod)
>
@@ -112,7 +112,7 @@
>
> pstart=c(p0,p1,0,coef(acc)[2])
>
-> mod <- depmix(corr~Pacc,data=speed,family=multinomial(),trstart=1,instart=1,respst=pstart,nstate=1)
+> mod <- depmix(corr~Pacc,data=speed,family=multinomial(),trstart=1,instart=1,respst=pstart,nstate=1,ntimes=c(168,134,137))
>
> ll <- logLik(mod)
> dev <- -2*ll
@@ -129,7 +129,7 @@
> instart=c(0,1)
> resp <- c(5.52,0.202,0.472,0.528,6.39,0.24,0.098,0.902)
>
-> mod <- depmix(list(rt~1,corr~1),data=speed,family=list(gaussian(),multinomial()),transition=~Pacc,trstart=trstart,instart=instart,respst=resp,nst=2)
+> mod <- depmix(list(rt~1,corr~1),data=speed,family=list(gaussian(),multinomial()),transition=~Pacc,trstart=trstart,instart=instart,respst=resp,nst=2,ntimes=c(168,134,137))
> ll <- logLik(mod)
>
> cat("Test 4: ll is now larger than speedll, ie ll is better due to introduction of a covariate \n")
Modified: pkg/depmixS4/tests/test2getsetpars.R
===================================================================
--- pkg/depmixS4/tests/test2getsetpars.R 2011-06-15 10:26:59 UTC (rev 460)
+++ pkg/depmixS4/tests/test2getsetpars.R 2011-06-15 12:33:00 UTC (rev 461)
@@ -11,7 +11,7 @@
instart=c(0,1)
resp <- c(5.52,0.202,0.472,0.528,6.39,0.24,0.098,0.902)
-mod <- depmix(list(rt~1,corr~1),data=speed,family=list(gaussian(),multinomial()),transition=~Pacc,trstart=trstart,instart=instart,respst=resp,nst=2)
+mod <- depmix(list(rt~1,corr~1),data=speed,family=list(gaussian(),multinomial()),transition=~Pacc,trstart=trstart,instart=instart,respst=resp,nst=2,ntimes=c(168,134,137))
mod1 <- setpars(mod,getpars(mod))
Modified: pkg/depmixS4/tests/test2getsetpars.Rout.save
===================================================================
--- pkg/depmixS4/tests/test2getsetpars.Rout.save 2011-06-15 10:26:59 UTC (rev 460)
+++ pkg/depmixS4/tests/test2getsetpars.Rout.save 2011-06-15 12:33:00 UTC (rev 461)
@@ -30,7 +30,7 @@
> instart=c(0,1)
> resp <- c(5.52,0.202,0.472,0.528,6.39,0.24,0.098,0.902)
>
-> mod <- depmix(list(rt~1,corr~1),data=speed,family=list(gaussian(),multinomial()),transition=~Pacc,trstart=trstart,instart=instart,respst=resp,nst=2)
+> mod <- depmix(list(rt~1,corr~1),data=speed,family=list(gaussian(),multinomial()),transition=~Pacc,trstart=trstart,instart=instart,respst=resp,nst=2,ntimes=c(168,134,137))
>
> mod1 <- setpars(mod,getpars(mod))
>
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