[Depmix-commits] r332 - trunk/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 29 15:15:29 CET 2010
Author: ingmarvisser
Date: 2010-01-29 15:15:29 +0100 (Fri, 29 Jan 2010)
New Revision: 332
Modified:
trunk/man/balance.Rd
trunk/man/depmix-internal.Rd
trunk/man/depmix-methods.Rd
trunk/man/depmix.Rd
trunk/man/makeDepmix.Rd
trunk/man/mix.Rd
trunk/man/response-class.Rd
trunk/man/response-classes.Rd
trunk/man/responses.Rd
trunk/man/speed.Rd
Log:
Help file updates: links, refs, structure et cetera.
Modified: trunk/man/balance.Rd
===================================================================
--- trunk/man/balance.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/balance.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -6,35 +6,39 @@
\title{Balance Scale Data}
-\description{Balance scale data of four distance items from 779 subjects;
-participants' ages are included.}
+\description{Balance scale data of four distance items from 779 participants;
+participants ages are included.}
\usage{data(balance)}
\format{
- A data frame with 779 observations on the following variables.
-
- \describe{
- \item{\code{sex}}{Participants' sex.}
- \item{\code{agedays}}{Age in days.}
- \item{\code{age}}{Age in years.}
- \item{\code{t1}}{Trichotomously scored distance item.}
- \item{\code{t2}}{Trichotomously scored distance item.}
- \item{\code{t3}}{Trichotomously scored distance item.}
- \item{\code{t4}}{Trichotomously scored distance item.}
- \item{\code{d1}}{Dichotomously scored distance item.}
- \item{\code{d2}}{Dichotomously scored distance item.}
- \item{\code{d3}}{Dichotomously scored distance item.}
- \item{\code{d4}}{Dichotomously scored distance item.}
- }
+ A data frame with 779 observations on the following variables. The full
+ dataset is described and analyzed extensively in
+ Jansen & Van der Maas (2002). The trichotomous data are left, balance, right.
+ The dichotomous version of the data is scored correct, incorrect.
+
+ \describe{
+ \item{\code{sex}}{Participants sex.}
+ \item{\code{agedays}}{Age in days.}
+ \item{\code{age}}{Age in years.}
+ \item{\code{t1}}{Trichotomously scored distance item.}
+ \item{\code{t2}}{Trichotomously scored distance item.}
+ \item{\code{t3}}{Trichotomously scored distance item.}
+ \item{\code{t4}}{Trichotomously scored distance item.}
+ \item{\code{d1}}{Dichotomously scored distance item.}
+ \item{\code{d2}}{Dichotomously scored distance item.}
+ \item{\code{d3}}{Dichotomously scored distance item.}
+ \item{\code{d4}}{Dichotomously scored distance item.}
+ }
+
}
\source{
- Brenda Jansen (2001),\emph{Development of reasoning on the balance
- scale task: Psychometric assessment of cognitive strategies}. PhD
- thesis, University of Amsterdam, Department of Psychology.
+ Brenda Jansen & Han van der Maas (2002). The development of
+ children's rule use on the balance scale task. \emph{Journal
+ of experimental Child Psychology, 81}, p. 383-416.
}
Modified: trunk/man/depmix-internal.Rd
===================================================================
--- trunk/man/depmix-internal.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/depmix-internal.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -36,6 +36,7 @@
\alias{fit,GLMresponse-method}
\alias{fit,BINOMresponse-method}
\alias{fit,NORMresponse-method}
+
\alias{fit,MULTINOMresponse-method}
\alias{fit,MVNresponse-method}
\alias{fit,transInit-method}
@@ -45,8 +46,10 @@
\alias{predict,GLMresponse-method}
\alias{predict,BINOMresponse-method}
\alias{predict,NORMresponse-method}
+
\alias{predict,MULTINOMresponse-method}
\alias{predict,transInit-method}
+\alias{predict,MVNresponse-method}
\alias{getpars,GLMresponse-method}
\alias{setpars,GLMresponse-method}
@@ -56,6 +59,9 @@
\alias{npar,response-method}
+\alias{MVNresponse,formula-method}
+
+
\title{DepmixS4 internal functions}
\description{
Modified: trunk/man/depmix-methods.Rd
===================================================================
--- trunk/man/depmix-methods.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/depmix-methods.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -74,8 +74,7 @@
through the \code{\link{forwardbackward}} function.}
\item{which}{The default "pars" returns a vector of all parameters of a
-
- \code{depmix} object; the alternative value "fixed" return a logical
+ \code{depmix} object; the alternative value "fixed" returns a logical
vector of the same length indicating which parameters are fixed. The
setpars functions sets parameters (or the logical fixed vector) to new
values; \code{setpars} also recomputes the dens, trans and init slots of
@@ -95,7 +94,7 @@
\item{npar}{returns the number of paramters of a model.}
- \item{freepars}{returns the number of non-fixed parameters.}
+ \item{freepars}{returns the number of non-redundant parameters.}
\item{setpars}{returns a \code{(dep-)mix} object with new parameter values.}
Modified: trunk/man/depmix.Rd
===================================================================
--- trunk/man/depmix.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/depmix.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -26,7 +26,7 @@
depmix(response, data=NULL, nstates, transition=~1, family=gaussian(),
prior=~1, initdata=NULL, respstart=NULL, trstart=NULL, instart=NULL,
- ntimes=NULL,...)
+ ntimes=NULL,...)
}
@@ -45,14 +45,15 @@
transitions. See 'Details'.}
\item{family}{A family argument for the response. This must be a list
- of family's if the response is multivariate.}
+ of \code{family}'s if the response is multivariate.}
\item{prior}{A one-sided formula specifying the density for the prior
or initial state probabilities.}
\item{initdata}{An optional data.frame to interpret the variables
- occuring in prior. The number of rows of this data.frame must be
- equal to the number of cases being modeled. See 'Details'.}
+ occuring in \code{prior}. The number of rows of this data.frame
+ must be equal to the number of cases being modeled,
+ \code{length(ntimes)}. See 'Details'.}
\item{respstart}{Starting values for the parameters of the response
models.}
@@ -63,10 +64,11 @@
\item{instart}{Starting values for the parameters of the prior or
initial state probability model.}
- \item{ntimes}{A vector specifying the lengths of individual, ie
+ \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. If the data argument has an
- attribute ntimes, then this is used.}
+ 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.}
\item{...}{Not used currently.}
@@ -78,21 +80,31 @@
which needs to be fitted using \code{\link{fit}} to optimize the
parameters.
- The response model(s) are by default created by call(s) to
- \code{\link{GLMresponse}} providing the response formula and the
- family specifying the error distribution. If response is a list of
- formulae, the \code{response}'s are assumed to be independent
- conditional on the latent state.
+ The response model(s) are by default created by call(s) to
+ \code{GLMresponse} using the \code{formula} and the \code{family}
+ arguments, the latter specifying the error distribution. See
+ \code{\link{GLMresponse}} for possible values of the \code{family}
+ argument for \code{glm}-type responses (ie a subset of the \code{glm}
+ family options, and the multinomial). Alternative response
+ distributions are specified by using the \code{\link{makeDepmix}}
+ function. Its help page has examples of specifying a model with a
+ multivariate normal response, as well as an example of adding a
+ user-defined response model, in this case for the ex-gauss
+ distribution.
+ If \code{response} is a list of formulae, the \code{response}'s are
+ assumed to be independent conditional on the latent state.
+
The transitions are modeled as a multinomial logistic model for each
- state. Hence, the transition matrix can be modeled as time-dependent,
- depending on predictors. The prior density is also modeled as a
- multinomial logistic. Both of these models are created by calls to
+ state. Hence, the transition matrix can be modeled using time-varying
+ covariates. The prior density is also modeled as a multinomial
+ logistic. Both of these models are created by calls to
\code{\link{transInit}}.
- Starting values may be provided by the respective arguments. The order
- in which parameters must be provided can be easily studied by using the
- \code{\link{setpars}} and \code{\link{getpars}} functions.
+ Starting values the initial, transition, and response models may be
+ provided by their respective arguments. The order in which parameters
+ must be provided can be easily studied by using the
+ \code{\link{setpars}} and \code{\link{getpars}} functions.
Linear constraints on parameters can be provided as argument to the
\code{\link{fit}} function.
@@ -148,12 +160,14 @@
\seealso{
- \code{\link{fit}}, \code{\link{transInit}}, \code{\link{response}},
+ \code{\link{fit}}, \code{\link{transInit}}, \code{\link{GLMresponse}},
\code{\link{depmix-methods}} for accessor functions to \code{depmix}
objects.
- For full control check the \code{\link{makeDepmix}} help page and its
- example section for the possibility to add new response distributions.
+ For full control see the \code{\link{makeDepmix}} help page and its
+ example section for the possibility to add user-defined response
+ distributions.
+
}
\references{
Modified: trunk/man/makeDepmix.Rd
===================================================================
--- trunk/man/makeDepmix.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/makeDepmix.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -27,13 +27,12 @@
\arguments{
- \item{response}{A two-dimensional list of response models. See
- 'Details'.}
+ \item{response}{A two-dimensional list of response models. See
+ 'Details'.}
- \item{transition}{A list of transition models, each created by a call
- to \code{\link{transInit}} on for possibilities of specifying such
- models. The lenght of this list should be the nubmer of states of the
- model.}
+ \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.}
\item{prior}{The initial state probabilities model; created through a
call to \code{\link{transInit}}.}
@@ -52,22 +51,22 @@
\details{
- The function \code{makeDepmix} creates an S4 object of class \code{depmix},
- which needs to be fitted using \code{\link{fit}} to optimize the
- parameters. This function is provided to have full control, eg by
- specifying one's own response models with distributions that are not
- provided.
+ The function \code{makeDepmix} creates an S4 object of class
+ \code{depmix}, which needs to be fitted using \code{\link{fit}} to
+ optimize the parameters. This function is provided to have full
+ control, eg by specifying one's own response models with distributions
+ that are not provided.
The response model(s) should be created by call(s) to
- \code{\link{response}} or one's own created response models that should
- extend the response class and have the following methods: dens, predict
- and optionally fit. The fit function should have an argument w,
- providing the weights. If the fit function is not provided,
+ \code{\link{GLMresponse}}, \code{MVNresponse} (see example below) or
+ user-defined response models (see example below) that should extend the
+ \code{\link{response-class}} and have the following methods: dens,
+ predict and optionally fit. The fit function should have an argument
+ w, providing the weights. If the fit function is not provided,
optimization should be done by using Rdonlp (use method="donlp" in
- calling fit on the depmix model, this is currently not done
- automatically). The first index of response models runs over the
- states of the model, and the seconde index over the responses to be
- modeled.
+ calling fit on the depmix model, note that this is \emph{not} the default).
+ The first index of response models runs over the states of the model,
+ and the second index over the responses to be modeled.
}
@@ -82,7 +81,7 @@
\seealso{
- \code{\link{fit}}, \code{\link{transInit}}, \code{\link{response}},
+ \code{\link{fit}}, \code{\link{transInit}}, \code{\link{GLMresponse}},
\code{\link{depmix-methods}} for accessor functions to \code{depmix}
objects.
Modified: trunk/man/mix.Rd
===================================================================
--- trunk/man/mix.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/mix.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -65,17 +65,27 @@
which needs to be fitted using \code{\link{fit}} to optimize the
parameters.
- The response model(s) are created by call(s) to \code{\link{response}}
- providing the response formula and the family specifying the error
- distribution. If response is a list of formulae, the \code{response}'s
- are assumed to be independent conditional on the latent class.
+ The response model(s) are by default created by call(s) to
+ \code{GLMresponse} using the \code{formula} and the \code{family}
+ arguments, the latter specifying the error distribution. See
+ \code{\link{GLMresponse}} for possible values of the \code{family}
+ argument for \code{glm}-type responses (ie a subset of the \code{glm}
+ family options, and the multinomial). Alternative response
+ distributions are specified by using the \code{\link{makeDepmix}}
+ function. Its help page has examples of specifying a model with a
+ multivariate normal response, as well as an example of adding a
+ user-defined response model, in this case for the ex-gauss
+ distribution.
+ If \code{response} is a list of formulae, the \code{response}'s are
+ assumed to be independent conditional on the latent state.
+
The prior density is modeled as a multinomial logistic. This model is
created by a call to \code{\link{transInit}}.
Starting values may be provided by the respective arguments. The order
in which parameters must be provided can be easily studied by using the
- \code{\link{setpars}} function.
+ \code{\link{setpars}} and \code{\link{getpars}} functions.
Linear constraints on parameters can be provided as argument to the
\code{\link{fit}} function.
@@ -118,7 +128,7 @@
\seealso{
- \code{\link{fit}}, \code{\link{transInit}}, \code{\link{response}},
+ \code{\link{fit}}, \code{\link{transInit}}, \code{\link{GLMresponse}},
\code{\link{depmix-methods}} for accessor functions to \code{depmix}
objects.
Modified: trunk/man/response-class.Rd
===================================================================
--- trunk/man/response-class.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/response-class.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -8,7 +8,7 @@
\description{
-A generic \code{\link{response}} model for \code{\link{depmix}} models.
+A generic \code{response} model for \code{\link{depmix}} models.
}
Modified: trunk/man/response-classes.Rd
===================================================================
--- trunk/man/response-classes.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/response-classes.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -24,7 +24,7 @@
\item{\code{formula}:}{A formula that specifies the model.}
\item{\code{family}:}{A family object specifying the link
- function. See the \code{\link{response}} help page for
+ function. See the \code{\link{GLMresponse}} help page for
possible options.}
}
Modified: trunk/man/responses.Rd
===================================================================
--- trunk/man/responses.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/responses.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -148,7 +148,6 @@
fm <- fit(mod)
cat("Test gaussian fit: ", all.equal(getpars(fm),c(mean(y),sd(y)),check=FALSE))
-
# poisson response model
x <- abs(rnorm(1000,2))
res <- rpois(1000,x)
Modified: trunk/man/speed.Rd
===================================================================
--- trunk/man/speed.Rd 2010-01-29 14:14:48 UTC (rev 331)
+++ trunk/man/speed.Rd 2010-01-29 14:15:29 UTC (rev 332)
@@ -8,16 +8,16 @@
\description{
- This data set is a bivariate series of reaction times and accuracy
- scores of a single subject switching between slow and accurate
+ This data set is a bivariate series of response times and accuracy
+ scores of a single participant switching between slow/accurate
responding and fast guessing on a lexical decision task. The slow and
accurate responding, and the fast guessing can be modelled using two
states, with a switching regime between them. The dataset further
contains a third variable called Pacc, representing the relative
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 a single subject from experiment 2
- in \cite{Van der Maas et al, 2005}.
+ switching. This data set is a from participant X in experiment
+ Y from Dutilh et al submitted).
}
@@ -26,18 +26,20 @@
\format{
A data frame with 439 observations on the following 3 variables.
\describe{
- \item{\code{rt}}{a numeric vector}
- \item{\code{corr}}{a numeric vector}
- \item{\code{Pacc}}{a numeric vector}
+ \item{\code{rt}}{a numeric vector of response times}
+ \item{\code{corr}}{a numeric vector of accuracy (0/1)}
+ \item{\code{Pacc}}{a numeric vector of the pay-off for accuracy}
}
}
\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{submitted for publication.}
- Han L. J. Van der Maas, Conor V. Dolan and Peter C. M. Molenaar (2007),
- Phase Transitions in the Trade-Off between Speed and Accuracy in Choice
- Reaction Time Tasks. \emph{Manuscript in preparation}.
-
+ Please contact g.dutilh at uva.nl for preprints and more information.
+
}
\examples{
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