[Depmix-commits] r342 - in trunk: . inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 11 16:49:13 CET 2010
Author: ingmarvisser
Date: 2010-02-11 16:49:13 +0100 (Thu, 11 Feb 2010)
New Revision: 342
Removed:
trunk/COPYING
trunk/DESCRIPTION
trunk/NAMESPACE
trunk/NEWS
trunk/R/
trunk/README
trunk/data/
trunk/inst/CITATION
trunk/inst/doc/
trunk/man/AIC.Rd
trunk/man/GLMresponse.Rd
trunk/man/balance.Rd
trunk/man/depmix-class.Rd
trunk/man/depmix-internal.Rd
trunk/man/depmix-methods.Rd
trunk/man/depmix.Rd
trunk/man/depmix.fit.Rd
trunk/man/depmix.fitted-class.Rd
trunk/man/depmix.sim-class.Rd
trunk/man/depmixS4-package.Rd
trunk/man/forwardbackward.Rd
trunk/man/llratio.Rd
trunk/man/makeDepmix.Rd
trunk/man/mix-class.Rd
trunk/man/mix.Rd
trunk/man/mix.fitted-class.Rd
trunk/man/mix.sim-class.Rd
trunk/man/posterior.Rd
trunk/man/response-class.Rd
trunk/man/response-classes.Rd
trunk/man/responses.Rd
trunk/man/simulate.Rd
trunk/man/speed.Rd
trunk/man/transInit.Rd
trunk/tests/
Log:
emptied trunk directory
Deleted: trunk/COPYING
===================================================================
--- trunk/COPYING 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/COPYING 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,340 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 2, June 1991
-
- Copyright (C) 1989, 1991 Free Software Foundation, Inc.
- 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
- Preamble
-
- The licenses for most software are designed to take away your
-freedom to share and change it. By contrast, the GNU General Public
-License is intended to guarantee your freedom to share and change free
-software--to make sure the software is free for all its users. This
-General Public License applies to most of the Free Software
-Foundation's software and to any other program whose authors commit to
-using it. (Some other Free Software Foundation software is covered by
-the GNU Library General Public License instead.) You can apply it to
-your programs, too.
-
- When we speak of free software, we are referring to freedom, not
-price. Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-this service if you wish), that you receive source code or can get it
-if you want it, that you can change the software or use pieces of it
-in new free programs; and that you know you can do these things.
-
- To protect your rights, we need to make restrictions that forbid
-anyone to deny you these rights or to ask you to surrender the rights.
-These restrictions translate to certain responsibilities for you if you
-distribute copies of the software, or if you modify it.
-
- For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must give the recipients all the rights that
-you have. You must make sure that they, too, receive or can get the
-source code. And you must show them these terms so they know their
-rights.
-
- We protect your rights with two steps: (1) copyright the software, and
-(2) offer you this license which gives you legal permission to copy,
-distribute and/or modify the software.
-
- Also, for each author's protection and ours, we want to make certain
-that everyone understands that there is no warranty for this free
-software. If the software is modified by someone else and passed on, we
-want its recipients to know that what they have is not the original, so
-that any problems introduced by others will not reflect on the original
-authors' reputations.
-
- Finally, any free program is threatened constantly by software
-patents. We wish to avoid the danger that redistributors of a free
-program will individually obtain patent licenses, in effect making the
-program proprietary. To prevent this, we have made it clear that any
-patent must be licensed for everyone's free use or not licensed at all.
-
- The precise terms and conditions for copying, distribution and
-modification follow.
-
- GNU GENERAL PUBLIC LICENSE
- TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
-
- 0. This License applies to any program or other work which contains
-a notice placed by the copyright holder saying it may be distributed
-under the terms of this General Public License. The "Program", below,
-refers to any such program or work, and a "work based on the Program"
-means either the Program or any derivative work under copyright law:
-that is to say, a work containing the Program or a portion of it,
-either verbatim or with modifications and/or translated into another
-language. (Hereinafter, translation is included without limitation in
-the term "modification".) Each licensee is addressed as "you".
-
-Activities other than copying, distribution and modification are not
-covered by this License; they are outside its scope. The act of
-running the Program is not restricted, and the output from the Program
-is covered only if its contents constitute a work based on the
-Program (independent of having been made by running the Program).
-Whether that is true depends on what the Program does.
-
- 1. You may copy and distribute verbatim copies of the Program's
-source code as you receive it, in any medium, provided that you
-conspicuously and appropriately publish on each copy an appropriate
-copyright notice and disclaimer of warranty; keep intact all the
-notices that refer to this License and to the absence of any warranty;
-and give any other recipients of the Program a copy of this License
-along with the Program.
-
-You may charge a fee for the physical act of transferring a copy, and
-you may at your option offer warranty protection in exchange for a fee.
-
- 2. You may modify your copy or copies of the Program or any portion
-of it, thus forming a work based on the Program, and copy and
-distribute such modifications or work under the terms of Section 1
-above, provided that you also meet all of these conditions:
-
- a) You must cause the modified files to carry prominent notices
- stating that you changed the files and the date of any change.
-
- b) You must cause any work that you distribute or publish, that in
- whole or in part contains or is derived from the Program or any
- part thereof, to be licensed as a whole at no charge to all third
- parties under the terms of this License.
-
- c) If the modified program normally reads commands interactively
- when run, you must cause it, when started running for such
- interactive use in the most ordinary way, to print or display an
- announcement including an appropriate copyright notice and a
- notice that there is no warranty (or else, saying that you provide
- a warranty) and that users may redistribute the program under
- these conditions, and telling the user how to view a copy of this
- License. (Exception: if the Program itself is interactive but
- does not normally print such an announcement, your work based on
- the Program is not required to print an announcement.)
-
-These requirements apply to the modified work as a whole. If
-identifiable sections of that work are not derived from the Program,
-and can be reasonably considered independent and separate works in
-themselves, then this License, and its terms, do not apply to those
-sections when you distribute them as separate works. But when you
-distribute the same sections as part of a whole which is a work based
-on the Program, the distribution of the whole must be on the terms of
-this License, whose permissions for other licensees extend to the
-entire whole, and thus to each and every part regardless of who wrote it.
-
-Thus, it is not the intent of this section to claim rights or contest
-your rights to work written entirely by you; rather, the intent is to
-exercise the right to control the distribution of derivative or
-collective works based on the Program.
-
-In addition, mere aggregation of another work not based on the Program
-with the Program (or with a work based on the Program) on a volume of
-a storage or distribution medium does not bring the other work under
-the scope of this License.
-
- 3. You may copy and distribute the Program (or a work based on it,
-under Section 2) in object code or executable form under the terms of
-Sections 1 and 2 above provided that you also do one of the following:
-
- a) Accompany it with the complete corresponding machine-readable
- source code, which must be distributed under the terms of Sections
- 1 and 2 above on a medium customarily used for software interchange; or,
-
- b) Accompany it with a written offer, valid for at least three
- years, to give any third party, for a charge no more than your
- cost of physically performing source distribution, a complete
- machine-readable copy of the corresponding source code, to be
- distributed under the terms of Sections 1 and 2 above on a medium
- customarily used for software interchange; or,
-
- c) Accompany it with the information you received as to the offer
- to distribute corresponding source code. (This alternative is
- allowed only for noncommercial distribution and only if you
- received the program in object code or executable form with such
- an offer, in accord with Subsection b above.)
-
-The source code for a work means the preferred form of the work for
-making modifications to it. For an executable work, complete source
-code means all the source code for all modules it contains, plus any
-associated interface definition files, plus the scripts used to
-control compilation and installation of the executable. However, as a
-special exception, the source code distributed need not include
-anything that is normally distributed (in either source or binary
-form) with the major components (compiler, kernel, and so on) of the
-operating system on which the executable runs, unless that component
-itself accompanies the executable.
-
-If distribution of executable or object code is made by offering
-access to copy from a designated place, then offering equivalent
-access to copy the source code from the same place counts as
-distribution of the source code, even though third parties are not
-compelled to copy the source along with the object code.
-
- 4. You may not copy, modify, sublicense, or distribute the Program
-except as expressly provided under this License. Any attempt
-otherwise to copy, modify, sublicense or distribute the Program is
-void, and will automatically terminate your rights under this License.
-However, parties who have received copies, or rights, from you under
-this License will not have their licenses terminated so long as such
-parties remain in full compliance.
-
- 5. You are not required to accept this License, since you have not
-signed it. However, nothing else grants you permission to modify or
-distribute the Program or its derivative works. These actions are
-prohibited by law if you do not accept this License. Therefore, by
-modifying or distributing the Program (or any work based on the
-Program), you indicate your acceptance of this License to do so, and
-all its terms and conditions for copying, distributing or modifying
-the Program or works based on it.
-
- 6. Each time you redistribute the Program (or any work based on the
-Program), the recipient automatically receives a license from the
-original licensor to copy, distribute or modify the Program subject to
-these terms and conditions. You may not impose any further
-restrictions on the recipients' exercise of the rights granted herein.
-You are not responsible for enforcing compliance by third parties to
-this License.
-
- 7. If, as a consequence of a court judgment or allegation of patent
-infringement or for any other reason (not limited to patent issues),
-conditions are imposed on you (whether by court order, agreement or
-otherwise) that contradict the conditions of this License, they do not
-excuse you from the conditions of this License. If you cannot
-distribute so as to satisfy simultaneously your obligations under this
-License and any other pertinent obligations, then as a consequence you
-may not distribute the Program at all. For example, if a patent
-license would not permit royalty-free redistribution of the Program by
-all those who receive copies directly or indirectly through you, then
-the only way you could satisfy both it and this License would be to
-refrain entirely from distribution of the Program.
-
-If any portion of this section is held invalid or unenforceable under
-any particular circumstance, the balance of the section is intended to
-apply and the section as a whole is intended to apply in other
-circumstances.
-
-It is not the purpose of this section to induce you to infringe any
-patents or other property right claims or to contest validity of any
-such claims; this section has the sole purpose of protecting the
-integrity of the free software distribution system, which is
-implemented by public license practices. Many people have made
-generous contributions to the wide range of software distributed
-through that system in reliance on consistent application of that
-system; it is up to the author/donor to decide if he or she is willing
-to distribute software through any other system and a licensee cannot
-impose that choice.
-
-This section is intended to make thoroughly clear what is believed to
-be a consequence of the rest of this License.
-
- 8. If the distribution and/or use of the Program is restricted in
-certain countries either by patents or by copyrighted interfaces, the
-original copyright holder who places the Program under this License
-may add an explicit geographical distribution limitation excluding
-those countries, so that distribution is permitted only in or among
-countries not thus excluded. In such case, this License incorporates
-the limitation as if written in the body of this License.
-
- 9. The Free Software Foundation may publish revised and/or new versions
-of the General Public License from time to time. Such new versions will
-be similar in spirit to the present version, but may differ in detail to
-address new problems or concerns.
-
-Each version is given a distinguishing version number. If the Program
-specifies a version number of this License which applies to it and "any
-later version", you have the option of following the terms and conditions
-either of that version or of any later version published by the Free
-Software Foundation. If the Program does not specify a version number of
-this License, you may choose any version ever published by the Free Software
-Foundation.
-
- 10. If you wish to incorporate parts of the Program into other free
-programs whose distribution conditions are different, write to the author
-to ask for permission. For software which is copyrighted by the Free
-Software Foundation, write to the Free Software Foundation; we sometimes
-make exceptions for this. Our decision will be guided by the two goals
-of preserving the free status of all derivatives of our free software and
-of promoting the sharing and reuse of software generally.
-
- NO WARRANTY
-
- 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
-FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
-OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
-PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
-OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
-TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
-PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
-REPAIR OR CORRECTION.
-
- 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
-REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
-INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
-OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
-TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
-YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
-PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGES.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-convey the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
- <one line to give the program's name and a brief idea of what it does.>
- Copyright (C) <year> <name of author>
-
- This program is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-
-
-Also add information on how to contact you by electronic and paper mail.
-
-If the program is interactive, make it output a short notice like this
-when it starts in an interactive mode:
-
- Gnomovision version 69, Copyright (C) year name of author
- Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, the commands you use may
-be called something other than `show w' and `show c'; they could even be
-mouse-clicks or menu items--whatever suits your program.
-
-You should also get your employer (if you work as a programmer) or your
-school, if any, to sign a "copyright disclaimer" for the program, if
-necessary. Here is a sample; alter the names:
-
- Yoyodyne, Inc., hereby disclaims all copyright interest in the program
- `Gnomovision' (which makes passes at compilers) written by James Hacker.
-
- <signature of Ty Coon>, 1 April 1989
- Ty Coon, President of Vice
-
-This General Public License does not permit incorporating your program into
-proprietary programs. If your program is a subroutine library, you may
-consider it more useful to permit linking proprietary applications with the
-library. If this is what you want to do, use the GNU Library General
-Public License instead of this License.
Deleted: trunk/DESCRIPTION
===================================================================
--- trunk/DESCRIPTION 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/DESCRIPTION 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,12 +0,0 @@
-Package: depmixS4
-Version: 0.3-0
-Date: 2010-01-19
-Title: Dependent Mixture Models
-Author: Ingmar Visser <i.visser at uva.nl>, Maarten Speekenbrink <m.speekenbrink at ucl.ac.uk>
-Maintainer: Ingmar Visser <i.visser at uva.nl>
-Depends: R (>= 2.9.1), stats, nnet, methods, MASS, MCMCpack
-Suggests: Rdonlp2
-Description: Fit latent (hidden) Markov models on mixed categorical and continuous (timeseries)
- data, otherwise known as dependent mixture models
-License: GPL (>=2)
-URL: http://depmix.r-forge.r-project.org/
Deleted: trunk/NAMESPACE
===================================================================
--- trunk/NAMESPACE 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/NAMESPACE 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,58 +0,0 @@
-import(methods)
-
-importFrom(stats, predict, simulate, AIC, logLik)
-
-export(
- makeDepmix,
- makeMix,
- lystig,
- fb,
- forwardbackward,
- MVNresponse,
- llratio,
- multinomial,
- em,
- viterbi,
- mlogit
-)
-
-exportClasses(
- depmix,
- depmix.sim,
- mix,
- mix.sim,
- depmix.fitted,
- mix.fitted,
- response,
- GLMresponse,
- MVNresponse,
- transInit
-)
-
-exportMethods(
- AIC,
- BIC,
- fit,
- npar,
- freepars,
- nlin,
- getdf,
- nobs,
- nresp,
- ntimes,
- nstates,
- depmix,
- mix,
- posterior,
- GLMresponse,
- MVNresponse,
- transInit,
- setpars,
- getpars,
- logLik,
- predict,
- dens,
- show,
- simulate,
- summary
-)
Deleted: trunk/NEWS
===================================================================
--- trunk/NEWS 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/NEWS 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,81 +0,0 @@
-
-Changes in depmixS4 version 0.3-0
-
- o added multinomial response function with identity link (no covariates
- allowed in such a model); useful when (many) boundary values occur;
- currently no constraints are used for such models, and hence only EM
- can be used for optimization, or alternatively, if and when Rdonlp2
- is used, sum constraints need to be added when fitting the model.
- See ?GLMresponse for details.
-
- o added an example of how to specify a model with multivariate normal
- responses (and fixed a bug in MVNresponse that prevented such models
- from being specified in the first place). See ?makeDepmix for an
- example.
-
-Changes in depmixS4 version 0.2-2
-
- o fixed a warning produced when specifying conrows.upper and .lower in the
- the fit function
-
- o added error message in case the initial log likelihood is infeasible
-
- o fixed a bug in the fit function for multinomial response models with
- covariates (thanks to Gilles Dutilh for spotting this)
-
-Changes in depmixS4 version 0.2-1
-
- o fixed a bug in the Viterbi algorithm used to compute posterior states
- (this bug was introduced in version 0.2-0)
-
- o restructured test files somewhat
-
- o fixed a bug in the use of the conrows argument in the fit function (a
- missing drop=FALSE statement)
-
- o updated help files for mix classes
-
- o fixed a bug in setting the starting values of regression coefficients in
- prior and transInit models with covariates (thanks to Verena Schmittmann
- for reporting this)
-
- o added newx argument to predict function of transInit objects, to be used
- for predicting probabilities depending on covariates (useful in eg plotting
- transition probabilities as function of a covariate)
-
- o added example of the use of conrows argument in fitting functions and other
- minor updates in documentation
-
-Changes in depmixS4 version 0.2-0
-
- o restructured R and Rd (help) files; added depmixS4 help with a short
- overview of the package and links to appropriate help files
-
- o added function 'simulate' to generate new data from a (fitted) model
-
- o added function 'forwardbackward' to access the forward and backward
- variables as well as the smoothed transition and state variables
-
- o added new glm distributions: gamma, poisson
-
- o added multivariate normal distribution
-
- o freepars now works correctly on both depmix and depmix.fitted objects
-
- o added function 'nlin' to compute the number of linear constraints in
- a fitted model object
-
- o added mix class for mixture and latent class models; the depmix class
- extends this mix class and adds a transition model to it
-
- o added help file for makeDepmix to provide full control in specifying
- models
-
- o minor changes to make depmixS4 compatible with R 2.7.1
-
-
-Changes in depmixS4 version 0.1-1
-
- o adjusted for R 2.7.0
-
-First version released on CRAN: 0.1-0
Deleted: trunk/README
===================================================================
--- trunk/README 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/README 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,17 +0,0 @@
-
-depmixS4 provides a framework for specifying and fitting hidden Markov models. Currently, it interfaces the glm functions to specify the state dependent measurement models. There is also a multinomial() family function that provides functionality for multinomial logistic responses with covariates. The transition matrix and the initial state probabilities are also modeled as multinomial logistics with the possibility of including covariates. Optimization is by default done by the EM algorithm. When linear constraints are included, Rdonlp2 is used for optimization (see details below). New response distributions can be added by extending the response-class and writing appropriate methods for it (dens, and getpars and setpars). depmixS4 also fits latent class and mixture models.
-
-The latest development version of depmix can be found at:
-https://r-forge.r-project.org/projects/depmix/
-
-
-DIFFERENCES BETWEEN DEPMIXS4 AND DEPMIX
-
-depmixS4 is a completely new implementation of the depmix package using S4 classes. Model specification now uses formulae and family objects, familiar from the lm and glm functions. Moreover, the transition matrix and the initial state probabilities (as well as multinomial responses) are now modeled by default as multinomial logistics with a baseline. Specification of linear constraints uses the same mechanism as was used in depmix, with the only difference that constraints are passed as arguments to the fit function rather than the model specification function. See the help files for further details.
-
-
-USING RDONLP2
-
-Optimization of models with (general) linear (in-)equality constraints can be done using the Rdonlp2 package, written Ryuichi Tamura(ry.tamura @ gmail.com), which is available from: http://arumat.net/Rdonlp2/
-
-Optimization with Rdonlp2 is automatically selected when constraints are specified in the fit function.
Deleted: trunk/inst/CITATION
===================================================================
--- trunk/inst/CITATION 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/inst/CITATION 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,15 +0,0 @@
-citHeader("To cite package depmix in publications, use the following:")
-
-citEntry(entry="Article",
- title = "{depmixS4}: An R-package for fitting mixture models on mixed
- multivariate data with Markov dependencies",
- author = personList(person(first="Ingmar", last="Visser"),
- person(first="Maarten", last="Speekenbrink")),
- journal = "R-package manual",
- year = "2009",
- url = "http://cran.r-project.org",
- textVersion = paste("Ingmar Visser & Maarten Speekenbrink (2009). DepmixS4:
- An R-package for fitting mixture models on mixed multivariate data with Markov
- dependencies. R-package manual and introduction into Dependent
- Mixture models")
-)
Deleted: trunk/man/AIC.Rd
===================================================================
--- trunk/man/AIC.Rd 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/man/AIC.Rd 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,48 +0,0 @@
-\name{AIC}
-
-\alias{AIC}
-\alias{AIC,depmix-method}
-\alias{AIC,mix-method}
-
-\alias{BIC}
-\alias{BIC,depmix-method}
-\alias{BIC,mix-method}
-
-\title{Compute AIC and BIC for (dep-)mix objects}
-
-\description{
- Compute AIC and BIC for \code{depmix} and \code{mix} objects.
-}
-
-\usage{
- AIC(object, ..., k = 2)
- BIC(object, ...)
-}
-
-\arguments{
- \item{object}{A \code{depmix} or \code{mix} model.}
- \item{\dots}{Not used currently.}
- \item{k}{The penalty factor which defaults to 2.}
-}
-
-\value{
- The value of the AIC or BIC respectively.
-}
-
-\details{
- The \code{n} that is used in the BIC is \code{sum(ntimes(object))}, where
- object is the model under consideration.
-}
-
-\references{
- H. Akaike. Information theory and an extension of the maximum likelihood
- principle. In B. N. Petrov and F. Csaki, editors, Second International
- Symposium on Information Theory, p. 267-281. Budapest: Academiai Kiado, 1973.
-
- G. Schwarz. Estimating the dimension of a model. Annals of Statistics,
- volume 6, p. 4761-464, 1978.
-}
-
-\author{Ingmar Visser}
-
-\keyword{htest}
Deleted: trunk/man/GLMresponse.Rd
===================================================================
--- trunk/man/GLMresponse.Rd 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/man/GLMresponse.Rd 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,90 +0,0 @@
-\name{GLMresponse}
-
-\docType{method}
-
-\alias{GLMresponse}
-\alias{GLMresponse,formula-method}
-
-\alias{getdf}
-\alias{getdf,response-method}
-
-\alias{show,GLMresponse-method}
-
-\title{Methods for creating depmix response models}
-
-\description{
-
- Create \code{GLMresponse} objects for \code{\link{depmix}} models using
- formulae and family objects.
-
-}
-
-\usage{
-
- GLMresponse(formula, data=NULL, family=gaussian(), pstart=NULL,
- fixed=NULL, prob=TRUE, ...)
-
- \S4method{getdf}{response}(object)
-}
-
-\arguments{
- \item{formula}{A model \code{\link{formula}}.}
- \item{data}{An optional data.frame to interpret the variables from the
- formula argument in.}
- \item{family}{A family object; }
- \item{pstart}{Starting values for the coefficients and other
- parameters, e.g. the standard deviation for the gaussian() family.}
- \item{fixed}{Logical vector indicating which paramters are to be fixed.}
- \item{prob}{Logical indicating whether the starting values for
- multinomial() family models are probabilities or logistic
- parameters (see details).}
- \item{object}{Object of class response.}
- \item{...}{Not used currently.}
-}
-
-\details{
-
- \code{GLMresponse} is the default driver for specifying response
- distributions of \code{depmix} models. It uses the familiar formula
- interface from \code{\link{glm}} to specify how responses depend on
- covariates/predictors.
-
- Currently available options for the family argument are
- \code{binomial}, \code{gaussian}, \code{poisson}, \code{Gamma}, and
- \code{multinomial}. Except for the latter option, the
- \code{GLMresponse} model is an interface to the \code{glm} functions of
- which the functionality is used: predict, fit and density functions.
-
- The \code{multinomial} model takes as link functions \code{mlogit}, the
- default, and then uses functionality from the \code{nnet} package to
- fit multinomial logistic models; it also takes \code{identity} as a
- link function. The latter is typically faster and is hence preferred
- when no covariates are present. Note that the sum constraint inherent
- in such a model is automatically respected in the EM algorithm, but
- must be supplied by the user in case of using Rdonlp optimization.
-
- See the \code{\link{responses}} help page for examples.
-
-}
-
-\value{
-
- \code{GLMresponse} returns an object of class \code{GLMresponse} which
- extends the \code{\link{response-class}}.
-
- \code{getdf} returns the number of free parameters of a
- \code{response} model.
-
-}
-
-\seealso{
-
- \code{\link{makeDepmix}} has an example of specifying a model with a
- multivariate normal response and an example of how to add a user-defined
- response model, in particular an ex-gauss distribution used for the
- \code{speed} data.
-}
-
-\author{Ingmar Visser & Maarten Speekenbrink}
-
-\keyword{methods}
Deleted: trunk/man/balance.Rd
===================================================================
--- trunk/man/balance.Rd 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/man/balance.Rd 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,49 +0,0 @@
-\name{balance}
-
-\docType{data}
-
-\alias{balance}
-
-\title{Balance Scale Data}
-
-\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. 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 & 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.
-
-}
-
-\examples{
-data(balance)
-}
-
-\keyword{datasets}
Deleted: trunk/man/depmix-class.Rd
===================================================================
--- trunk/man/depmix-class.Rd 2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/man/depmix-class.Rd 2010-02-11 15:49:13 UTC (rev 342)
@@ -1,73 +0,0 @@
-\name{depmix-class}
-
-\docType{class}
-
-\alias{depmix-class}
-
-\alias{nresp}
-\alias{nresp,depmix-method}
-
-\alias{ntimes}
-\alias{ntimes,depmix-method}
-
-\alias{nstates}
-\alias{nstates,depmix-method}
-
-
-\title{Class "depmix"}
-
-\description{A \code{\link{depmix}} model.}
-
-\section{Slots}{
-
- \describe{
-
- \item{\code{response}:}{List of list of \code{response} objects.}
-
- \item{\code{transition}}{List of \code{\link{transInit}} objects.}
-
- \item{\code{prior}:}{\code{\link{transInit}} object.}
-
- \item{\code{dens}:}{Array of dimension sum(ntimes)*nresp*nstates
- providing the densities of the observed responses for each state.}
-
- \item{\code{trDens}:}{Array of dimension \code{sum(ntimes)}*nstates
- providing the probability of a state transition depending on the
- predictors.}
-
- \item{\code{init}:}{Array of dimension \code{length(ntimes)}*nstates with
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/depmix -r 342
More information about the depmix-commits
mailing list