Dependency Modeling Toolkit

Probabilistic dependency modeling toolkit.


CHANGES IN VERSION 0.8.09 (2012-05-25)

o added treatment of one-dimensional data in pfa

CHANGES IN VERSION 0.8.08 (2012-05-24)


o changed argument log -> logarithm in determinant function

CHANGES IN VERSION 0.8.07 (2011-10-14)

o removed compiler and methods from dependencies o packageStartupMessage in firstlib.R

CHANGES IN VERSION 0.8.06 (2011-07-27)

o added compiler package to dependencies o option for exponential prior on W added in pfa

CHANGES IN VERSION 0.8.05 (2011-07-15)

o optimize.parameters.R sometimes got stuck due to very mild convergence criterion bug. Now corrected.

CHANGES IN VERSION 0.8.04 (2011-07-11)

o added pfa.log.likelihood

CHANGES IN VERSION 0.8.03 (2011-04-13)

o plotVar fixed (screen removed)

CHANGES IN VERSION 0.8.01 (2011-03-28)

o bug with matched = TRUE, Nm.Wx.Wy.sigma = 0, with diagonal covariances and identical isotropic covariances; in W.simcca.EM function the W$total name was missing, causing failure. Corrected.

CHANGES IN VERSION 0.7.07 (2011-02-25)

o package was accepted to CRAN and passed all tests; added links to vignette and website o tests/ directory removed, too time-consuming.

CHANGES IN VERSION 0.7.04 (2011-02-21)

o covLimit parameter name was changed into epsilon

o convergence is now checked across multiple consecutive steps to improve stability of the results: the par.change option was removed, and convergence.steps option added in fit.dependency.model/optimize.parameters

o added intercept calculation in


o marginalCovariances definition was missing in some optimize.parameters calls in fit.dependency.model.R; corrected.

CHANGES IN VERSION 0.7.01 (2011-02-13)

o updated vignette and man pages. ready for initial submission to CRAN.

CHANGES IN VERSION 0.4.20 (2011-02-13)

o added tests/depmod.simcca.R for case Wx = Wy; W free still some unoptimal convergence with full covariances

CHANGES IN VERSIOn 0.4.19 (2011-02-13)

o added tests/depmod.R for case Wx != Wy; W free still some unoptimal convergence with full covariances

CHANGES IN VERSIOn 0.4.18 (2011-02-13)

o added marginalCovariances isotropic, identical isotropic, diagonal in fit.dependency.model and tests/psimcca.nnW.R. Still needs simple speedups and more robustness but tests are ok.

CHANGES IN VERSIOn 0.4.17 (2011-02-13)

o added tests/pcca.nnW.R for case Wx != Wy; W>=0

CHANGES IN VERSIOn 0.4.15 (2011-02-12)

o added tests/psimcca.nnW.R for case Wx = Wy; W>=0 o tidied up the code; combined some files in R directory o added toy data generation function generate.toydata

CHANGES IN VERSIOn 0.4.09 (2011-02-02)

o in calculate.ppca removed X field from W output in Y = NULL i.e. one data case (now only W$total available)

CHANGES IN VERSIOn 0.4.08 (2011-01-25)

o The latent variable is calculated as dependency model is calculated. getZ method is used to retrieve the latent variable

o All a priori information is given as priors argument to fit.dependency.model. H is changed to priors$Nm.wxwy.mean and sigmas to priors$Nm.wxwy.sigma.

CHANGES IN VERSION 0.4.07 (2011-01-17)

o W.effects and z.effects removed from the package

CHANGES IN VERSION 0.4.06 (2011-01-17)

o ppca method works with non-mathced data

CHANGES IN VERSION 0.4.05 (2011-01-17)

o pfa method works with non-mathced data

CHANGES IN VERSION 0.4.04 (2011-01-14)

o 'title' argument added to plot.DependencyModel

CHANGES IN VERSION 0.4.02 (2011-01-13)

o first functional version

CHANGES IN VERSION 0.3.2 (2010-06-09)

SIGNIFICANT USER-VISIBLE CHANGES o combined pint and drCCA modules into a single package

DOCUMENTATION o collected all modules (pint, drCCA, MultiWayCCA) into a single vignette

Reference manual

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0.8.20 by Leo Lahti, 8 years ago

Browse source code at

Authors: Leo Lahti and Olli-Pekka Huovilainen

Documentation:   PDF Manual  

BSD_2_clause + file LICENSE license

Imports Matrix

Depends on methods, mvtnorm, MASS

See at CRAN