[Depmix-commits] r359 - /

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

Author: ingmarvisser
Date: 2010-02-23 00:05:48 +0100 (Tue, 23 Feb 2010)
New Revision: 359

Removed:
   README
   todo
Log:
Removed unneccesary files

Deleted: README
===================================================================
--- README	2010-02-22 23:04:46 UTC (rev 358)
+++ README	2010-02-22 23:05:48 UTC (rev 359)
@@ -1,49 +0,0 @@
-			R-Forge SVN README
-
-
-(See "http://download.r-forge.r-project.org/manuals/R-Forge_Manual.pdf"
-       for detailed information on registering a new project.
-
-1. Introduction
------------------------------------------------------------------------
-R is free software distributed under a GNU-style copyleft. R-Forge is
-a service for R users and package developers providing certain tools
-for collaborative source code management.
-
-2. The directory you're in
------------------------------------------------------------------------
-This is the repository of your project. It contains two important
-pre-defined directories namely 'www' and 'pkg'. They must not be
-deleted otherwise R-Forge's core functionality will not be available
-(daily check and build of your package or project websites).
-These two directories are standardized and therefore are going to be
-described in this README. The rest of your repository can be used as
-you like.
-
-3. 'pkg' directory
------------------------------------------------------------------------
-Typically this directory contains the R package with the usual
-DESCRIPTION and R/, man/, data/ directories etc (see 'Writing R 
-Extension' for more details). In the future it will also be possible to
-have multiple packages managed by a control file, however currently
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-.zip). It should be possible to install the package via
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-5. Help
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Deleted: todo
===================================================================
--- todo	2010-02-22 23:04:46 UTC (rev 358)
+++ todo	2010-02-22 23:05:48 UTC (rev 359)
@@ -1,73 +0,0 @@
-
-TODO list for paper
-
-1) do extensive testing:
-	- generate data for response models and parameter recovery (mostly
-	done in the test files)
-	- similarly for actual markov models and mixture models
-
-2) add example of adding new response model to JSS paper: exgaus models
-for speed data
-
-3) write the paper
-
-4) balance data set refs toevoegen en toestemming vragen aan Brenda, data set 
-reduceren dmv random subset
-
-5) Tests: 
-	- make output files for test files
-
-6) Bugs: 
-	- check error sent by Rita Gaio
-	- check error by Maartje
-
-
-
-
-TODO Medium term
-
-1) Discrimination learning example, need covariates with these data!
-
-2) BB or other optimization routines??
-
-3) Speed issues: 
-	- add gradients
-	- run Rprofile tests to determine speed limits
-	- possibly move lystig and forward/backward to C routines
-
-4) Get Hessian for standard errors (computed by e.g. Louis' method)
-
-5) check models with boundary values in the transition and initial
-state probabilities (possibly work on identity link for multinomial
-models, but this involves also adding parstruct or something like it
-to the response models to incorporate linear constraints within those
-parameter vectors)
-
-
-TODO long term 
-
-Design issues
-
-1) Multi group possibilities: use group factor in call to depmix??
-
-2) Missing data options?
-
-3) Mixture of depmix models?
-
-
-Other capabilities
-
-1) Look at log and exp of matrices to have continuous time observations
-(also see mlm, see Bockenholt 2005
-
-2) Look at HMISC for mapply -> multivariate apply for mv densities
-
-3) Look at package ks for mv normal mixture densities
-
-4) Check glmc pack for constrained glm models
-
-5) stochmod pack for stochastic models
-
-6) use relevel function to recode factors into different base categories
-
-