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Revision 679 - Directory Listing
Modified Thu Mar 14 11:20:05 2019 UTC (2 months, 1 week ago) by ingmarvisser
=doc update in comments in fit function

Revision 678 - Directory Listing
Modified Thu Feb 28 14:14:58 2019 UTC (2 months, 3 weeks ago) by ingmarvisser
=Added function 'stationary' to export and added help file for it

Revision 677 - Directory Listing
Modified Sat Dec 8 14:38:37 2018 UTC (5 months, 1 week ago) by ingmarvisser
=removed NPSOL support and added registration of native routines

Revision 676 - Directory Listing
Modified Wed Nov 14 16:15:17 2018 UTC (6 months ago) by ingmarvisser
=added documentation for vcov and friends

Revision 675 - Directory Listing
Modified Wed Nov 14 11:33:25 2018 UTC (6 months, 1 week ago) by ingmarvisser
=added files/functions standardError.R, confint.R and format.perc.R function

Revision 674 - Directory Listing
Modified Fri Oct 19 15:25:03 2018 UTC (7 months ago) by ingmarvisser
=added vcov function, moved lincon code from hessian to vcov

Revision 673 - Directory Listing
Modified Wed Oct 17 15:50:42 2018 UTC (7 months ago) by ingmarvisser
=finished hessian function, now includes checks for boundary parameters

Revision 672 - Directory Listing
Modified Wed Oct 17 14:12:03 2018 UTC (7 months ago) by ingmarvisser
=changed default for verbose in fit function to FALSE

Revision 671 - Directory Listing
Modified Wed Oct 17 10:42:07 2018 UTC (7 months ago) by ingmarvisser
=changed filename from fdHessHmm.R to hessian.R

Revision 670 - Directory Listing
Modified Wed Oct 17 09:53:34 2018 UTC (7 months ago) by ingmarvisser
=changed filename from hess2cov.R to hessian2vcov.R

Revision 669 - Directory Listing
Modified Thu Sep 20 12:59:46 2018 UTC (8 months ago) by ingmarvisser
=added fdHessHmm.R

Revision 668 - Directory Listing
Modified Tue Sep 11 15:03:34 2018 UTC (8 months, 1 week ago) by maarten
Fixed issue with MVNnorm using unbiased rather than ML estimate of covariance; message provides a little more information when likelihood increases during EM iteration

Revision 667 - Directory Listing
Modified Fri Aug 24 12:30:29 2018 UTC (8 months, 4 weeks ago) by ingmarvisser
=added reference (+DOI) to JSS paper in Description file

Revision 666 - Directory Listing
Modified Fri Aug 24 08:01:14 2018 UTC (8 months, 4 weeks ago) by ingmarvisser
=added revision nr to description

Revision 665 - Directory Listing
Modified Fri Aug 24 07:57:35 2018 UTC (8 months, 4 weeks ago) by ingmarvisser
=added depmixS4_init.c

Revision 664 - Directory Listing
Modified Fri Aug 24 07:54:16 2018 UTC (8 months, 4 weeks ago) by ingmarvisser
=renamed the C-version of forwardbackward to forwardbackwardC

Revision 663 - Directory Listing
Modified Fri Aug 24 07:31:47 2018 UTC (8 months, 4 weeks ago) by ingmarvisser
=added useDynlib to Namespace

Revision 662 - Directory Listing
Modified Thu Aug 23 14:46:45 2018 UTC (8 months, 4 weeks ago) by ingmarvisser
=changed loading of compiled code

Revision 661 - Directory Listing
Modified Thu Aug 23 12:38:20 2018 UTC (8 months, 4 weeks ago) by maarten
additions to news file

Revision 660 - Directory Listing
Modified Thu Aug 23 12:37:34 2018 UTC (8 months, 4 weeks ago) by maarten
additions to news file

Revision 659 - Directory Listing
Modified Thu Aug 23 11:56:10 2018 UTC (8 months, 4 weeks ago) by maarten
allow missing covariates in responseGLM as long as the DV is missing too

Revision 658 - Directory Listing
Modified Wed Jul 25 16:11:37 2018 UTC (9 months, 3 weeks ago) by maarten
EM returns object as fitted (with warning) if likelihood decreases

Revision 657 - Directory Listing
Modified Wed Jul 25 15:53:33 2018 UTC (9 months, 3 weeks ago) by maarten
EM returns object as fitted (with warning) if likelihood decreases

Revision 656 - Directory Listing
Modified Wed Jul 25 15:13:08 2018 UTC (9 months, 3 weeks ago) by ingmarvisser
=changed version nr to 1.3-5; changed NEWS file accordingly

Revision 655 - Directory Listing
Modified Wed Jul 25 13:02:52 2018 UTC (9 months, 3 weeks ago) by ingmarvisser
=upped version nr to 1.4-0; changed NEWS file accordingly; added doc for makeMix

Revision 654 - Directory Listing
Modified Thu Mar 30 11:54:19 2017 UTC (2 years, 1 month ago) by ingmarvisser
=upped version nr to 1.3-4 for bug fix release

Revision 653 - Directory Listing
Modified Thu Mar 30 10:24:40 2017 UTC (2 years, 1 month ago) by maarten
fixed problem with missing values in glm.fit

Revision 652 - Directory Listing
Modified Fri Feb 12 08:12:29 2016 UTC (3 years, 3 months ago) by ingmarvisser
=changed name info in citation file

Revision 651 - Directory Listing
Modified Fri Feb 12 07:50:29 2016 UTC (3 years, 3 months ago) by ingmarvisser
=test stuff from development version

Revision 650 - Directory Listing
Modified Fri Feb 12 07:50:14 2016 UTC (3 years, 3 months ago) by ingmarvisser
=test stuff from development version

Revision 649 - Directory Listing
Modified Wed Feb 10 17:25:34 2016 UTC (3 years, 3 months ago) by ingmarvisser
=added posterior state sequence example for new data

Revision 648 - Directory Listing
Modified Wed Feb 10 17:04:00 2016 UTC (3 years, 3 months ago) by ingmarvisser
=docementation updates

Revision 647 - Directory Listing
Modified Wed Feb 10 16:18:11 2016 UTC (3 years, 3 months ago) by ingmarvisser
=updated NEWS and DESCRIPTION files

Revision 646 - Directory Listing
Modified Wed Feb 10 16:10:33 2016 UTC (3 years, 3 months ago) by ingmarvisser
=added support for fitting inequality constraints with solnp optimization

Revision 645 - Directory Listing
Modified Wed Feb 10 11:38:13 2016 UTC (3 years, 3 months ago) by ingmarvisser
=C-header changes

Revision 644 - Directory Listing
Modified Wed Feb 10 11:22:47 2016 UTC (3 years, 3 months ago) by ingmarvisser
=C-header changes

Revision 643 - Directory Listing
Modified Sun Dec 21 21:21:50 2014 UTC (4 years, 5 months ago) by ingmarvisser
Added Additional_repositories field to Description file so that Rdonlp2 can be installed from that repository.

Revision 642 - Directory Listing
Modified Mon Nov 3 15:41:37 2014 UTC (4 years, 6 months ago) by ingmarvisser
Remove cusp package -> moved to its own project

Revision 641 - Directory Listing
Modified Thu Oct 9 14:44:58 2014 UTC (4 years, 7 months ago) by ingmarvisser
Added function hess2cov that computes the corrected hessian given an (approximate) hessian subject to linear equality constraints; the constraint matrix is passed as argument next the hessian.

Revision 640 - Directory Listing
Modified Mon Sep 29 19:05:02 2014 UTC (4 years, 7 months ago) by ingmarvisser
Removed redundant files

Revision 639 - Directory Listing
Modified Mon Sep 29 19:04:33 2014 UTC (4 years, 7 months ago) by ingmarvisser
Added modifications to NEWS

Revision 638 - Directory Listing
Modified Mon Sep 29 18:58:31 2014 UTC (4 years, 7 months ago) by ingmarvisser
Minor stuff ...

Revision 637 - Directory Listing
Modified Mon Sep 29 12:59:44 2014 UTC (4 years, 7 months ago) by ingmarvisser
Cusp package added

Revision 636 - Directory Listing
Modified Thu Sep 25 11:40:51 2014 UTC (4 years, 7 months ago) by maarten
removed extra white line between prior and transition model in summary.depmix

Revision 635 - Directory Listing
Modified Tue Aug 26 11:07:30 2014 UTC (4 years, 8 months ago) by ingmarvisser
1) improved error message when optimization method is wrongly specified in fit function
2) fixed a bug in the summary method for fitted models (in some cases parameters of the prior model were printed in the transition matrix; thanks to Verena Schmittmann for catching this bug)

Revision 633 - Directory Listing
Modified Thu May 22 11:07:54 2014 UTC (5 years ago) by ingmarvisser
Updated version nr

Revision 632 - Directory Listing
Modified Thu May 22 11:07:13 2014 UTC (5 years ago) by ingmarvisser
Fixed documentation bug

Revision 631 - Directory Listing
Modified Tue May 13 08:24:51 2014 UTC (5 years ago) by ingmarvisser
Fixed names for GLMresponse models.

Revision 630 - Directory Listing
Modified Wed Apr 2 12:09:29 2014 UTC (5 years, 1 month ago) by maarten
updated news file

Revision 629 - Directory Listing
Modified Wed Apr 2 11:44:44 2014 UTC (5 years, 1 month ago) by ingmarvisser
Added change to getpars to NEWS file

Revision 628 - Directory Listing
Modified Wed Apr 2 11:32:06 2014 UTC (5 years, 1 month ago) by maarten
- added names to getpars for mlogit model

Revision 627 - Directory Listing
Modified Wed Apr 2 10:58:55 2014 UTC (5 years, 1 month ago) by ingmarvisser
Added factor names to summary of multinomial("identity") models such that parameter interpretation is now easier

Revision 626 - Directory Listing
Modified Wed Apr 2 07:38:17 2014 UTC (5 years, 1 month ago) by ingmarvisser
Reduced runtime of examples in fitdmm to comply with CRAN policy

Revision 625 - Directory Listing
Modified Tue Apr 1 11:37:23 2014 UTC (5 years, 1 month ago) by ingmarvisser
Minor update in depmix to include availability of Rdonlp2 in the DESCIPTION file

Revision 624 - Directory Listing
Modified Thu Mar 27 23:14:42 2014 UTC (5 years, 1 month ago) by maarten
solves  some problems in classification EM when a state/component does not have any assignments (keeps parameters the same as on the previous iteration)

Revision 623 - Directory Listing
Modified Wed Mar 26 18:28:09 2014 UTC (5 years, 1 month ago) by maarten
- fixed bug in hard classification with mix models

Revision 622 - Directory Listing
Modified Tue Feb 25 08:40:06 2014 UTC (5 years, 2 months ago) by ingmarvisser
Changes to fulfill requirements in R 3.1.0

Revision 621 - Directory Listing
Modified Thu Feb 20 12:23:36 2014 UTC (5 years, 3 months ago) by ingmarvisser
removed unused variables

Revision 620 - Directory Listing
Modified Thu Feb 20 08:30:36 2014 UTC (5 years, 3 months ago) by ingmarvisser
Resolved issues with global variables and (C/C++) memory issues

Revision 619 - Directory Listing
Modified Wed Feb 5 21:29:21 2014 UTC (5 years, 3 months ago) by maarten
- fixed bug in classification = "hard" option; now uses proper classification likelihood criterion to determine convergence
- speed improvement in emviterbi help function in em 

Revision 616 - Directory Listing
Modified Tue Feb 4 11:11:47 2014 UTC (5 years, 3 months ago) by ingmarvisser
Minor changes to conform to upcoming changes in R 3.1.0

Revision 615 - Directory Listing
Modified Mon Feb 3 22:02:05 2014 UTC (5 years, 3 months ago) by ingmarvisser
Fixed partially matched argument to check.attributes on ?responses, fixed a reference error in the vignette, upped version nr to 1.3-2

Revision 614 - Directory Listing
Modified Wed Dec 11 10:33:02 2013 UTC (5 years, 5 months ago) by ingmarvisser
Fixed a typo ...

Revision 611 - Directory Listing
Modified Wed Dec 11 10:24:33 2013 UTC (5 years, 5 months ago) by ingmarvisser
Bug fix in passing boundary values of general linear inequality constraints to the optimization routines, arguments conrows.upper and conrows.lower in the fit function. Values were only passed when all of them were different from zero; in other cases, all values were set to zero. The default argument values are now set to NULL; zeroes are then the default value and if not null, those values are passed.

Revision 610 - Directory Listing
Modified Wed Nov 27 10:36:52 2013 UTC (5 years, 5 months ago) by ingmarvisser
Added a more appropriate reference in the vignette about likelihood ratio testing in standard cases for parameter testing, Giudici et al 2000

Revision 609 - Directory Listing
Modified Wed Nov 20 18:37:53 2013 UTC (5 years, 6 months ago) by ingmarvisser
Changed warning message concerning missing data as it was potentially ambiguous

Revision 608 - Directory Listing
Modified Wed Nov 6 12:31:09 2013 UTC (5 years, 6 months ago) by ingmarvisser
Added a conditional to set the log likelihood of a model to a value just above the starting value (ie the values before iterations start) when the logl functions returns Infinite (which may sometimes occur when parameters are set outside their boundaries).

Revision 604 - Directory Listing
Modified Wed Sep 18 13:24:36 2013 UTC (5 years, 8 months ago) by ingmarvisser
...

Revision 603 - Directory Listing
Modified Wed Sep 18 11:35:33 2013 UTC (5 years, 8 months ago) by ingmarvisser
Added NEWS item about faster EM code provided by Robert McGehee

Revision 602 - Directory Listing
Modified Wed Sep 18 11:34:36 2013 UTC (5 years, 8 months ago) by ingmarvisser
Reduced run time of examples to less than 5 seconds each

Revision 601 - Directory Listing
Modified Tue Sep 17 12:18:33 2013 UTC (5 years, 8 months ago) by ingmarvisser
Reduced time of examples running by using dontrun on the ?depmix help page

Revision 600 - Directory Listing
Modified Tue Sep 17 09:58:56 2013 UTC (5 years, 8 months ago) by maarten
- added names for posterior state columns in "posterior"
- added reference to classification likelihood in ?em.control
- moved classification likelihood example from ?depmix to ?em.control 

Revision 596 - Directory Listing
Modified Tue Sep 17 07:55:38 2013 UTC (5 years, 8 months ago) by ingmarvisser
Changed version nr and date in several places.

Revision 595 - Directory Listing
Modified Tue Sep 17 07:45:50 2013 UTC (5 years, 8 months ago) by ingmarvisser
Set the right date, moved stats, stats4 and methods from Depends to Imports field, following the R-exts guide

Revision 594 - Directory Listing
Modified Tue Sep 17 07:41:48 2013 UTC (5 years, 8 months ago) by ingmarvisser
Added MASS, nnet and Rsolnp to import statement

Revision 593 - Directory Listing
Modified Tue Sep 17 07:41:15 2013 UTC (5 years, 8 months ago) by ingmarvisser
fixed lines that were too loooonggg (wider than 100 characters)

Revision 592 - Directory Listing
Modified Tue Sep 17 07:29:14 2013 UTC (5 years, 8 months ago) by ingmarvisser
Moved vignette to vignettes directory.

Revision 591 - Directory Listing
Modified Tue Sep 17 07:28:08 2013 UTC (5 years, 8 months ago) by ingmarvisser
Reduced line lengths to 100 characters.

Revision 590 - Directory Listing
Modified Fri Sep 13 15:05:47 2013 UTC (5 years, 8 months ago) by ingmarvisser
Added sp500 data set (instead of generating it on the fly as was previously the case in the example on ?depmix); as a result the Suggested package TTR is no longer needed.

Revision 589 - Directory Listing
Modified Fri Sep 13 14:25:31 2013 UTC (5 years, 8 months ago) by ingmarvisser
Replaced stationary with homogenous as class slot in depmix models and as argument in function makeDepmix. In the latter the stationary argument is retained with default value NULL and a warning is given when it is used.

Revision 588 - Directory Listing
Modified Thu Sep 12 09:36:21 2013 UTC (5 years, 8 months ago) by ingmarvisser
Set solnp control parameters to defaults used that package.

Revision 587 - Directory Listing
Modified Thu Sep 12 09:29:50 2013 UTC (5 years, 8 months ago) by ingmarvisser
Added cautionary note on use of donlpcntrl

Revision 586 - Directory Listing
Modified Wed Sep 11 18:57:08 2013 UTC (5 years, 8 months ago) by ingmarvisser
Added an example of using argument donlpcntrl

Revision 585 - Directory Listing
Modified Wed Sep 11 18:38:32 2013 UTC (5 years, 8 months ago) by ingmarvisser
Minor changes in argument donlpcntrl

Revision 584 - Directory Listing
Modified Wed Sep 4 09:21:17 2013 UTC (5 years, 8 months ago) by maarten
- To increase speed with large objects, in em.mix and em.depmix, we now make local copies of slots, update these, and finally assign them back to the object, rather than repeatedly changing the slots in the object itself. 

Revision 583 - Directory Listing
Modified Tue Sep 3 21:10:22 2013 UTC (5 years, 8 months ago) by ingmarvisser
Fixed bug in vignette

Revision 582 - Directory Listing
Modified Tue Sep 3 20:42:31 2013 UTC (5 years, 8 months ago) by ingmarvisser
Added warning about classification likelihood to the NEWS file

Revision 581 - Directory Listing
Modified Tue Sep 3 20:11:07 2013 UTC (5 years, 8 months ago) by ingmarvisser
Added test for EM optimized logLikelihood of speed data model (so we can safely change around the EM function to optimize it for speed)

Revision 580 - Directory Listing
Modified Tue Sep 3 20:10:02 2013 UTC (5 years, 8 months ago) by ingmarvisser
Updated version nr and date in Description

Revision 579 - Directory Listing
Modified Thu Apr 18 16:47:40 2013 UTC (6 years, 1 month ago) by maarten
fixed problem when calling sim() on a fitted (dep)mix model (this gave an error) by adding an "as" method to convert from (dep)mix.fitted to (dep)mix.sim

Revision 578 - Directory Listing
Modified Tue Jan 29 15:42:26 2013 UTC (6 years, 3 months ago) by ingmarvisser
minor stuff

Revision 577 - Directory Listing
Modified Tue Jan 29 14:11:02 2013 UTC (6 years, 3 months ago) by ingmarvisser
Minor changes related to R version 3.0.0 (these were released in version 1.2-2 of depmixS4).

Revision 574 - Directory Listing
Modified Mon Jan 14 16:27:57 2013 UTC (6 years, 4 months ago) by maarten
fixed bug when changing class to fitted

Revision 572 - Directory Listing
Modified Wed Nov 7 10:49:27 2012 UTC (6 years, 6 months ago) by maarten
- fixed problem with NA estimates of coefficients in GLM response models (these are now not used in the predict method)
- nobs now counts valid (nonmissing) observations using the y matrix, rather than from the density slot

Revision 571 - Directory Listing
Modified Tue Oct 2 10:27:44 2012 UTC (6 years, 7 months ago) by maarten
- fixed bug in summary.depmix compact (length was incorrect when names returns NULL for unnamed parameter vectors)

Revision 570 - Directory Listing
Modified Tue Sep 25 10:05:57 2012 UTC (6 years, 7 months ago) by ingmarvisser
summary additions

Revision 569 - Directory Listing
Modified Wed Sep 19 13:57:32 2012 UTC (6 years, 8 months ago) by maarten
- updated summary function to allow different response models

Revision 568 - Directory Listing
Modified Tue Sep 18 19:34:30 2012 UTC (6 years, 8 months ago) by maarten
adapted depmix summary method so that mlogit transition matrices are also displayed as probabilities 

Revision 567 - Directory Listing
Modified Tue Sep 18 11:01:46 2012 UTC (6 years, 8 months ago) by ingmarvisser
comments and stuff ...

Revision 566 - Directory Listing
Modified Tue Sep 18 08:36:03 2012 UTC (6 years, 8 months ago) by ingmarvisser
Changed variable 'corr' into a factor and added variable 'prev' for previous trial accuracy.

Revision 565 - Directory Listing
Modified Tue Aug 28 18:02:50 2012 UTC (6 years, 8 months ago) by maarten
- logLik now has a method="classification" option
- put computation of "posterior" inside em (still inside mix.fit and depmix.fit when using numerical optimization)
- updated help files

Revision 564 - Directory Listing
Modified Tue Aug 28 13:40:57 2012 UTC (6 years, 8 months ago) by maarten
updates voor classification likelihood

Revision 561 - Directory Listing
Modified Wed Aug 8 15:13:55 2012 UTC (6 years, 9 months ago) by ingmarvisser
Updated summary method for mix models to include sensible parameter names.

Revision 560 - Directory Listing
Modified Wed Aug 8 12:11:32 2012 UTC (6 years, 9 months ago) by ingmarvisser
- missing values were not treated in mix models in EM; fixed by a quick hack ...

Revision 559 - Directory Listing
Modified Wed Aug 8 11:03:44 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added an example with missing data to ?fit

Revision 558 - Directory Listing
Modified Wed Aug 8 10:48:56 2012 UTC (6 years, 9 months ago) by ingmarvisser
- fixed bug in fb (testing for is.na instead of is.nan)

Revision 557 - Directory Listing
Modified Mon Aug 6 09:08:31 2012 UTC (6 years, 9 months ago) by ingmarvisser
Changed N to n in various places in the vignette for consistency (thanks to Kuan Xu for noting).

Revision 556 - Directory Listing
Modified Tue Jul 31 16:19:28 2012 UTC (6 years, 9 months ago) by ingmarvisser
Minor changes related to classification likelihood and show/summary

Revision 555 - Directory Listing
Modified Tue Jul 31 14:23:14 2012 UTC (6 years, 9 months ago) by ingmarvisser
Made the exgauss example \dontrun{} as it causes trouble in R CMD check ...

Revision 554 - Directory Listing
Modified Mon Jul 30 15:08:06 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added changes about parameter names and summary/show methods.

Revision 553 - Directory Listing
Modified Mon Jul 30 14:38:17 2012 UTC (6 years, 9 months ago) by ingmarvisser
final (?) changes regarding parameter names, show and summary methods; output is now much more readable

Revision 552 - Directory Listing
Modified Mon Jul 30 12:33:44 2012 UTC (6 years, 9 months ago) by ingmarvisser
- changed parameters$coefficients from matrix to vector in multinomial identity models
- added names to those
- changed getpars such that it preserves names of parameters
- changed setpars such that it preserves names of parameters

Revision 551 - Directory Listing
Modified Thu Jul 26 13:46:55 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added the solnpcntrl and donlpcntrl arguments and default values to ?fit

Revision 550 - Directory Listing
Modified Thu Jul 26 13:25:19 2012 UTC (6 years, 9 months ago) by ingmarvisser
Threshold for small probabilities in multinom response and transInit set to 1e-6

Revision 549 - Directory Listing
Modified Thu Jul 26 13:24:47 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added solnp and donlp control arguments to the fit function.

Revision 548 - Directory Listing
Modified Thu Jul 26 11:41:54 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added NEWS for getmodel and changes in show/summary

Revision 547 - Directory Listing
Modified Thu Jul 26 11:41:10 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added help for getmodel; number=1 as default in getmodel

Revision 546 - Directory Listing
Modified Thu Jul 26 11:38:58 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added getmodel to namespace

Revision 545 - Directory Listing
Modified Thu Jul 26 09:10:38 2012 UTC (6 years, 9 months ago) by ingmarvisser
Removed the summary function of fitted models; the summary method is now identical to the summary method of non-fitted models (which was non-existent in earlier versions).

Revision 544 - Directory Listing
Modified Thu Jul 26 09:09:44 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added summary method for non-fitted models=identical to show function (except summary method has the compact argument, default to TRUE when using show.

Revision 543 - Directory Listing
Modified Wed Jul 25 16:01:06 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added compact=TRUE in show method for depmix objects to give shorter presentations; needs work

Revision 542 - Directory Listing
Modified Wed Jul 25 16:00:17 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added argument compact=TRUE to show method for fitted depmix objects to give shorter presentations for models without covariates.

Revision 541 - Directory Listing
Modified Wed Jul 25 14:57:32 2012 UTC (6 years, 9 months ago) by ingmarvisser
Replaced print by show for S4 objects

Revision 540 - Directory Listing
Modified Wed Jul 25 14:55:55 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added methods for getmodel generic for mix and depmix objects, eg getmodel(object,which="transition",state=2) gives the transition model for state 2 of a depmix object

Revision 539 - Directory Listing
Modified Wed Jul 25 14:54:45 2012 UTC (6 years, 9 months ago) by ingmarvisser
Added generic for getmodel, to get models from (dep)mix objects

Revision 538 - Directory Listing
Modified Wed Jul 25 07:18:27 2012 UTC (6 years, 9 months ago) by ingmarvisser
Changed print into show for 'print'ing prior, response and transition models in the show methods for mix and depmix objects

Revision 537 - Directory Listing
Modified Mon Jul 23 11:41:50 2012 UTC (6 years, 10 months ago) by ingmarvisser
Small transition parameters (<1e-5) in multinomial identity models are now set to zero.

Revision 536 - Directory Listing
Modified Thu Jul 19 13:51:11 2012 UTC (6 years, 10 months ago) by ingmarvisser
Zap small probabilities in multinom with identity link; probs<1e-5 are now set to zero.

Revision 535 - Directory Listing
Modified Fri Jun 22 19:16:36 2012 UTC (6 years, 11 months ago) by maarten
- in EM with hard classification: needed to explicitly set factor levels in formula for computation of gamma.
-changed example slightly (seemed to give problems without defining the model again)

Revision 534 - Directory Listing
Modified Fri Jun 22 18:55:28 2012 UTC (6 years, 11 months ago) by maarten
- changed version to 1.3-0
- added example of classification likelihood in "depmix" help file (still needs vignette)

Revision 533 - Directory Listing
Modified Fri Jun 22 17:21:33 2012 UTC (6 years, 11 months ago) by maarten
- implementation of classification likelihood in EM complete (still needs thorough testing)

Revision 532 - Directory Listing
Modified Thu Jun 21 17:55:49 2012 UTC (6 years, 11 months ago) by maarten
- added xi computation to classification likelihood (still needs correct logL)

Revision 531 - Directory Listing
Modified Thu Jun 21 14:12:50 2012 UTC (6 years, 11 months ago) by maarten
added classification likelihood in em.control and EM for mix and depmix models

Revision 529 - Directory Listing
Modified Wed Jun 20 14:45:45 2012 UTC (6 years, 11 months ago) by ingmarvisser
minor update to documentation ...

Revision 528 - Directory Listing
Modified Wed Jun 20 14:29:05 2012 UTC (6 years, 11 months ago) by maarten
- deleted classification likelihood from em.control

Revision 527 - Directory Listing
Modified Wed Jun 20 09:36:24 2012 UTC (6 years, 11 months ago) by ingmarvisser
Changes in Rd and vignette et cetera for the 'missing data release' 1.2-0

Revision 526 - Directory Listing
Modified Mon Jun 18 17:48:10 2012 UTC (6 years, 11 months ago) by ingmarvisser
bug fix met data check

Revision 525 - Directory Listing
Modified Sun Jun 17 21:58:22 2012 UTC (6 years, 11 months ago) by ingmarvisser
Removed the is.null(data) from condition that tests for trivial formula (~1) as it causes that the dimension of the return value of the dens function is incompatible with other functions (which expect short return values when the model is stationary=homogeneous in time).

Revision 524 - Directory Listing
Modified Fri Jun 15 14:51:13 2012 UTC (6 years, 11 months ago) by ingmarvisser
Added comments to NEWS and help files about missing values.

Revision 523 - Directory Listing
Modified Fri Jun 15 14:37:52 2012 UTC (6 years, 11 months ago) by maarten
- changed back to only change NA to 1 in B (and not NaN) in "fb" 
- using explicit argument calls in logLik

Revision 522 - Directory Listing
Modified Fri Jun 15 14:18:01 2012 UTC (6 years, 11 months ago) by ingmarvisser
Made argument name for argument stationary explicit in function call to fb from logLik as this was causing an error (...)
Changed default optimization criterion for donlp2 to 1e-6

Revision 521 - Directory Listing
Modified Fri Jun 15 13:27:09 2012 UTC (6 years, 11 months ago) by ingmarvisser
Added classification argument to em.depmix

Revision 520 - Directory Listing
Modified Fri Jun 15 12:19:38 2012 UTC (6 years, 11 months ago) by ingmarvisser
Corrected version, nojss option enforced.

Revision 519 - Directory Listing
Modified Fri Jun 15 11:32:12 2012 UTC (6 years, 11 months ago) by maarten
- in fb, missing cases are now only NA, not NaN
- in logLik, default method is now "fb" (for speed as this is implemented in C)

Revision 518 - Directory Listing
Modified Thu Jun 14 18:46:05 2012 UTC (6 years, 11 months ago) by maarten
- started with classification likelihood (done for mix models, not for depmix models)
- still needs to be tested!

Revision 517 - Directory Listing
Modified Tue Jun 12 14:31:19 2012 UTC (6 years, 11 months ago) by ingmarvisser
Updated help page of em.control to explain the procedure for generating starting values using the Dirichlet distribution.

Revision 516 - Directory Listing
Modified Tue Jun 12 13:14:18 2012 UTC (6 years, 11 months ago) by ingmarvisser
Added subsection on missing data to the vignette as well as a table with possible response models.

Revision 515 - Directory Listing
Modified Thu May 10 20:08:59 2012 UTC (7 years ago) by ingmarvisser
Changed the default max iterations in EM to 500.

Revision 514 - Directory Listing
Modified Thu Apr 26 19:53:50 2012 UTC (7 years ago) by maarten
- started adding functionality for NA's in responses (NEEDS TO BE TESTED PROPERLY!!!)

Revision 513 - Directory Listing
Modified Fri Mar 30 10:44:05 2012 UTC (7 years, 1 month ago) by ingmarvisser
Made generation of gamma values to lead to more extreme values.

Revision 512 - Directory Listing
Modified Thu Mar 29 10:02:43 2012 UTC (7 years, 1 month ago) by maarten
- random gamma starting values in EM now uses a dirichlet distribution
- TODO: specify dispersion as a parameter in em.options()

Revision 511 - Directory Listing
Modified Fri Mar 16 13:17:11 2012 UTC (7 years, 2 months ago) by ingmarvisser
Changed latex options to reduce file size.

Revision 510 - Directory Listing
Modified Thu Mar 15 19:19:30 2012 UTC (7 years, 2 months ago) by ingmarvisser
Compacted vignette pdf added

Revision 509 - Directory Listing
Modified Thu Mar 15 19:18:17 2012 UTC (7 years, 2 months ago) by ingmarvisser
Remove vignette pdf because too large

Revision 508 - Directory Listing
Modified Thu Mar 15 13:41:41 2012 UTC (7 years, 2 months ago) by ingmarvisser
Changes to make the package compatible with 2.15.0

Revision 507 - Directory Listing
Modified Mon Mar 5 14:08:41 2012 UTC (7 years, 2 months ago) by ingmarvisser
Added Rdonlp2, again, to the Suggests field.

Revision 506 - Directory Listing
Modified Wed Feb 29 09:20:34 2012 UTC (7 years, 2 months ago) by ingmarvisser
Upped version nr to 1.1-1 and removed suggestion of Rdonlp as this no longer compiles properly.

Revision 503 - Directory Listing
Modified Thu Nov 3 13:19:54 2011 UTC (7 years, 6 months ago) by ingmarvisser
Reintroduced Rdonlp2 support which does seem to work ...

Revision 502 - Directory Listing
Modified Wed Nov 2 14:28:53 2011 UTC (7 years, 6 months ago) by ingmarvisser
Various minor changes for compatibility with R 2.14.0

Revision 501 - Directory Listing
Modified Tue Nov 1 13:21:04 2011 UTC (7 years, 6 months ago) by ingmarvisser
Fixed a documentation error in ?responses.

Revision 500 - Directory Listing
Modified Tue Nov 1 11:56:53 2011 UTC (7 years, 6 months ago) by ingmarvisser
Updated NEWS file with version 1.1-0 info; removed ddens code as it does not provide any speed improvements.

Revision 499 - Directory Listing
Modified Thu Oct 27 13:34:56 2011 UTC (7 years, 6 months ago) by ingmarvisser
Added several examples: Poisson switching data (generated data), S & P 500 returns data, multinomial data with n>1 and different for different time points (artificial data).

Revision 498 - Directory Listing
Modified Wed Oct 26 15:36:23 2011 UTC (7 years, 6 months ago) by ingmarvisser
Added error message about missing data.

Revision 497 - Directory Listing
Modified Wed Oct 26 13:31:18 2011 UTC (7 years, 6 months ago) by ingmarvisser
Fixed a bug in the relative stopping criterion for EM, this time for good.

Revision 496 - Directory Listing
Modified Tue Oct 25 12:41:38 2011 UTC (7 years, 6 months ago) by ingmarvisser
Fixed a bug in the relative stopping criterion for EM (which resulted in no iterations in some cases with large positive loglikelihoods).

Revision 495 - Directory Listing
Modified Mon Oct 24 20:15:16 2011 UTC (7 years, 6 months ago) by ingmarvisser
Removed Rdonlp2 optimization option as Rdonlp2 does not install anymore.

Revision 493 - Directory Listing
Modified Thu Sep 22 09:26:35 2011 UTC (7 years, 8 months ago) by ingmarvisser
Added a NAMESPACE file (required starting with R version 2.14.0). 

Fixed a bug in bootstrap which was using a $ to access a field of 
an S3 object, and added an example of using bootstrap to the ?fitdmm 
help page.

Revision 492 - Directory Listing
Modified Tue Sep 20 14:47:56 2011 UTC (7 years, 8 months ago) by ingmarvisser
Trial to add Namespace to depmix, failed so far ...

Revision 491 - Directory Listing
Modified Fri Sep 16 11:46:54 2011 UTC (7 years, 8 months ago) by ingmarvisser
Fixed a bug which led to an error when specifying multigroup models 
in which one or more groups had a 1-state model (fixed by adding a 
drop=FALSE in function mgdmm). 
Removed an invisible (and unnecessary) directory.

Revision 489 - Directory Listing
Modified Fri Sep 2 13:56:24 2011 UTC (7 years, 8 months ago) by ingmarvisser
Changed line endings to Unix consistently.

Revision 488 - Directory Listing
Modified Thu Sep 1 15:16:58 2011 UTC (7 years, 8 months ago) by ingmarvisser
Added documentation for the useC argument in fb/forwardbackward and corrected the PACKAGE argument to the .C call.

Revision 487 - Directory Listing
Modified Thu Sep 1 10:32:58 2011 UTC (7 years, 8 months ago) by ingmarvisser
Corrected a typo in the vignette; updated version nr in Description and package help file.

Revision 486 - Directory Listing
Modified Wed Aug 17 14:39:43 2011 UTC (7 years, 9 months ago) by ingmarvisser
Added an error message for unrecognized arguments to em.control() (which could result in models that never converge)

Revision 485 - Directory Listing
Modified Wed Jul 6 14:32:53 2011 UTC (7 years, 10 months ago) by ingmarvisser
Added sanity check for the case that nstates=1 combined with non-trivial transition model.

Revision 484 - Directory Listing
Modified Tue Jun 28 16:07:04 2011 UTC (7 years, 10 months ago) by maarten
- added a fix for models without covariates/intercepts. In responseGLM and responseMVN the function setpars now exits when length(value) == 0. In setpars.depmix, a check is added whether npar > 0. 

Revision 483 - Directory Listing
Modified Mon Jun 27 09:40:42 2011 UTC (7 years, 10 months ago) by ingmarvisser
Added sensible error message in case (fit) method is wrongly specified.

Revision 482 - Directory Listing
Modified Thu Jun 23 20:50:17 2011 UTC (7 years, 11 months ago) by ingmarvisser
Removed call to C-code for apply.

Revision 481 - Directory Listing
Modified Thu Jun 23 08:40:15 2011 UTC (7 years, 11 months ago) by ingmarvisser
Changed dependence to R 2.13.0 because of reliance on nobs generic which is available from that version.

Revision 480 - Directory Listing
Modified Wed Jun 22 20:23:51 2011 UTC (7 years, 11 months ago) by ingmarvisser
Added now working C-code to replace an often apply'd call to flatten an array into a matrix in function fb (5-fold improvement for this operation, but total time savings is limited).

Revision 479 - Directory Listing
Modified Wed Jun 22 13:18:25 2011 UTC (7 years, 11 months ago) by ingmarvisser
Added c-function for computing some intermediate results in log likelihood computation that are taking loads of time (not finished yet).

Revision 478 - Directory Listing
Modified Wed Jun 22 11:51:04 2011 UTC (7 years, 11 months ago) by ingmarvisser
Remove & delete matrix header & code files.

Revision 477 - Directory Listing
Modified Wed Jun 22 11:50:09 2011 UTC (7 years, 11 months ago) by ingmarvisser
Cleaned some comments in the C-code and removed the now obsolete matrix header and code files.

Revision 476 - Directory Listing
Modified Wed Jun 22 11:37:02 2011 UTC (7 years, 11 months ago) by ingmarvisser
Made useC=TRUE the default so it is always used when optimizing models and computing the likelihood

Revision 475 - Directory Listing
Modified Wed Jun 22 10:25:43 2011 UTC (7 years, 11 months ago) by ingmarvisser
Added conditionals for the homogeneous case in the C-code; working correctly.

Revision 474 - Directory Listing
Modified Wed Jun 22 10:06:22 2011 UTC (7 years, 11 months ago) by ingmarvisser
Removed all intermediate variables in computation of alpha, beta and xi.

Revision 473 - Directory Listing
Modified Wed Jun 22 09:24:11 2011 UTC (7 years, 11 months ago) by ingmarvisser
Optimized computation of alpha (removed intermediate computations); working correctly.

Revision 472 - Directory Listing
Modified Wed Jun 22 08:59:11 2011 UTC (7 years, 11 months ago) by ingmarvisser
Working version of C-code for alpha, beta and xi variables (not optimezed yet).

Revision 471 - Directory Listing
Modified Tue Jun 21 20:50:33 2011 UTC (7 years, 11 months ago) by ingmarvisser
C-code for backward variables now correct.

Revision 470 - Directory Listing
Modified Tue Jun 21 13:29:11 2011 UTC (7 years, 11 months ago) by ingmarvisser
Initial set up of loop for backwards variables

Revision 469 - Directory Listing
Modified Tue Jun 21 13:06:22 2011 UTC (7 years, 11 months ago) by ingmarvisser
C-code now return correct forward variables and scaling values; also added an interface function for mix/lca models to the fb function.

Revision 468 - Directory Listing
Modified Mon Jun 20 12:42:27 2011 UTC (7 years, 11 months ago) by ingmarvisser
Loop over cases and times for forward variables now complete (still to add for the mix case, ie no transition model).

Revision 467 - Directory Listing
Modified Mon Jun 20 08:01:49 2011 UTC (7 years, 11 months ago) by ingmarvisser
Minor changes to C-code, changed default to useC=FALSE for now.

Revision 466 - Directory Listing
Modified Mon Jun 20 07:38:00 2011 UTC (7 years, 11 months ago) by ingmarvisser
Upped version to 1.1-0 for next release which is to have c-code forward backward computations for speed improvement.

Revision 465 - Directory Listing
Modified Sun Jun 19 21:07:06 2011 UTC (7 years, 11 months ago) by ingmarvisser
Initial set up for C code of forward backward algorithm.

Revision 464 - Directory Listing
Modified Fri Jun 17 13:25:47 2011 UTC (7 years, 11 months ago) by ingmarvisser
Added c function and R .C(alls) to it to eventually compute the forward/backward variables with for performance improvement.

Revision 462 - Directory Listing
Modified Thu Jun 16 12:11:50 2011 UTC (7 years, 11 months ago) by ingmarvisser
Final changes to news and description for release 1.0-4

Revision 461 - Directory Listing
Modified Wed Jun 15 12:33:00 2011 UTC (7 years, 11 months ago) by ingmarvisser
Removed ntimes attribute from speed data (and adapted examples and tests accordingly), updated reference on speed data help page to Dutilh et al. (2011).

Revision 460 - Directory Listing
Modified Wed Jun 15 10:26:59 2011 UTC (7 years, 11 months ago) by ingmarvisser
This time really using nobs generic from stats4.

Revision 458 - Directory Listing
Modified Fri Apr 22 07:43:57 2011 UTC (8 years, 1 month ago) by ingmarvisser
Fixed a bug in simulation of Gaussian response models (which was returning all nans).

Revision 457 - Directory Listing
Modified Tue Mar 22 13:55:22 2011 UTC (8 years, 2 months ago) by ingmarvisser
Updated NEWS file ...

Revision 456 - Directory Listing
Modified Tue Mar 22 12:02:48 2011 UTC (8 years, 2 months ago) by ingmarvisser
Using AIC/BIC/logLik/nobs generics from stats/stats4 rather than defining them anew (which gave clashes with other packages that did the same).

Revision 454 - Directory Listing
Modified Tue Feb 15 13:25:07 2011 UTC (8 years, 3 months ago) by ingmarvisser
Updates for version 1.0-2; minor bug fix release.

Revision 453 - Directory Listing
Modified Tue Feb 15 13:24:16 2011 UTC (8 years, 3 months ago) by ingmarvisser
Fixed a bug in simulation of binomial responses.

Revision 449 - Directory Listing
Modified Tue Jan 25 14:37:21 2011 UTC (8 years, 3 months ago) by ingmarvisser
Added a meaningful error message in the EM algorithm for lca/mixture 
    models in case the initial log likelihood is NA (thanks to Matthias
    Ihrke for pointing this out).

Revision 448 - Directory Listing
Modified Tue Nov 23 13:13:55 2010 UTC (8 years, 5 months ago) by ingmarvisser
Final minor changes (NEWS, DESCRIPTION etc) for release 1.0-1

Revision 447 - Directory Listing
Modified Tue Nov 23 12:18:16 2010 UTC (8 years, 6 months ago) by ingmarvisser
Added an error message for multinomial response models with n>1 and link='mlogit' as this case is not handled.

Revision 446 - Directory Listing
Modified Tue Nov 23 08:55:45 2010 UTC (8 years, 6 months ago) by ingmarvisser
Fixed a bug in multinomial response models with n>1; parameters were not normalized such that they did not sum to unity in those cases.

Revision 445 - Directory Listing
Modified Thu Nov 11 15:12:13 2010 UTC (8 years, 6 months ago) by ingmarvisser
Added a check for bad likelihoods when generating starting values.

Revision 444 - Directory Listing
Modified Wed Oct 20 11:01:22 2010 UTC (8 years, 7 months ago) by ingmarvisser
Added function em.control that returns the list of em control parameters. This makes future additions to this list easier and gives less clutter in the function definition of fit. The default for EM is now to use random start values.

Revision 443 - Directory Listing
Modified Tue Oct 19 15:08:36 2010 UTC (8 years, 7 months ago) by ingmarvisser
Removed reference to boot package as this produced a warning (invlogit function now defined directly in the test file.)

Revision 442 - Directory Listing
Modified Tue Oct 19 15:07:40 2010 UTC (8 years, 7 months ago) by ingmarvisser
Removed doctype lines as these produce warnings under R 2.12.0

Revision 441 - Directory Listing
Modified Tue Oct 19 15:06:58 2010 UTC (8 years, 7 months ago) by ingmarvisser
Upped to version nr 1.0-1,  bug fix release and updates relating to R 2.12.0

Revision 436 - Directory Listing
Modified Wed Aug 4 19:08:03 2010 UTC (8 years, 9 months ago) by ingmarvisser
Release 1.0-0 of depmixS4, now including vignette and refs to it.

Revision 435 - Directory Listing
Modified Wed Aug 4 14:43:09 2010 UTC (8 years, 9 months ago) by ingmarvisser
Added vignette to version 1.0-0

Revision 434 - Directory Listing
Modified Wed Aug 4 14:39:00 2010 UTC (8 years, 9 months ago) by ingmarvisser
Updated news/readme etc

Revision 430 - Directory Listing
Modified Mon Jul 5 14:05:25 2010 UTC (8 years, 10 months ago) by ingmarvisser
Updated vignette to depmixS4.

Revision 428 - Directory Listing
Modified Thu Jul 1 20:47:29 2010 UTC (8 years, 10 months ago) by ingmarvisser
More minor edits (convergence message)

Revision 426 - Directory Listing
Modified Thu Jul 1 20:20:08 2010 UTC (8 years, 10 months ago) by ingmarvisser
Cleaned up comments, minor edits to messages.

Revision 424 - Directory Listing
Modified Wed Jun 30 22:23:49 2010 UTC (8 years, 10 months ago) by ingmarvisser
Added vignette source and pdf to the inst/doc directory

Revision 422 - Directory Listing
Modified Wed Jun 30 15:12:37 2010 UTC (8 years, 10 months ago) by ingmarvisser
Added vignette file

Revision 421 - Directory Listing
Modified Wed Jun 30 15:11:22 2010 UTC (8 years, 10 months ago) by ingmarvisser
updates to Description et cetera for release 1.0-0

Revision 418 - Directory Listing
Modified Mon Jun 21 14:32:28 2010 UTC (8 years, 11 months ago) by ingmarvisser
Took care of (harmless) coercion warning (all(dc)) and added require("Rdonlp2") in using that method for optimization.

Revision 417 - Directory Listing
Modified Thu Jun 3 12:27:14 2010 UTC (8 years, 11 months ago) by ingmarvisser
fixed a bug in setting the lower and upper bounds for normal response parameters in GLMresponse

Revision 414 - Directory Listing
Modified Tue May 11 13:27:33 2010 UTC (9 years ago) by ingmarvisser
Release 0.9-0 updates

Revision 413 - Directory Listing
Modified Fri Apr 23 15:20:17 2010 UTC (9 years, 1 month ago) by ingmarvisser
Fixed a bug in multinomial models with n>1

Revision 411 - Directory Listing
Modified Wed Mar 10 16:08:33 2010 UTC (9 years, 2 months ago) by ingmarvisser
Minor code cleanups

Revision 410 - Directory Listing
Modified Wed Mar 10 16:07:53 2010 UTC (9 years, 2 months ago) by ingmarvisser
Minor codoc issues.

Revision 409 - Directory Listing
Modified Wed Mar 10 16:07:16 2010 UTC (9 years, 2 months ago) by ingmarvisser
Updated citation info

Revision 408 - Directory Listing
Modified Wed Mar 10 16:07:00 2010 UTC (9 years, 2 months ago) by ingmarvisser
Updated version nr (now at 1.0-0 !)

Revision 406 - Directory Listing
Modified Wed Mar 10 15:46:08 2010 UTC (9 years, 2 months ago) by maarten
- removed warning messages from dm_dmvnorm; now checks whether eigenvalues of the covariance matrix are >= 0 and if not, returns NaN without warning

Revision 405 - Directory Listing
Modified Tue Mar 9 19:12:49 2010 UTC (9 years, 2 months ago) by maarten
- added random.start option to EM
- fit method now has an em.control argument

Revision 404 - Directory Listing
Modified Tue Mar 9 16:21:10 2010 UTC (9 years, 2 months ago) by ingmarvisser
Added error message in case ntimes in response models and in prior model are in conflict

Revision 403 - Directory Listing
Modified Tue Mar 9 12:43:42 2010 UTC (9 years, 2 months ago) by ingmarvisser
Copied trunk to pkg directory

Revision 402 - Directory Listing
Modified Tue Mar 9 12:40:49 2010 UTC (9 years, 2 months ago) by ingmarvisser
Emptied pkg directory depmixS4

Revision 341 - Directory Listing
Modified Fri Feb 5 10:28:17 2010 UTC (9 years, 3 months ago) by ingmarvisser
added gamlss* to suggests field to make the example in makeDepmix work

Revision 340 - Directory Listing
Modified Mon Feb 1 13:15:12 2010 UTC (9 years, 3 months ago) by ingmarvisser
Copied trunk to pkg directory depmixS4

Revision 338 - Directory Listing
Modified Mon Feb 1 13:12:22 2010 UTC (9 years, 3 months ago) by ingmarvisser
empty depmixS4 pkg directory

Revision 316 - Directory Listing
Modified Tue Jan 19 12:37:01 2010 UTC (9 years, 4 months ago) by ingmarvisser
Changed version number and CHANGES file.

Revision 314 - Directory Listing
Modified Tue Jan 19 12:29:20 2010 UTC (9 years, 4 months ago) by ingmarvisser
Changed definition of a few c++ pointers to conform to standards.

Revision 312 - Directory Listing
Modified Mon Nov 2 16:04:02 2009 UTC (9 years, 6 months ago) by ingmarvisser
Upped version number and related change in Readme and Changes files

Revision 311 - Directory Listing
Modified Mon Nov 2 16:03:12 2009 UTC (9 years, 6 months ago) by ingmarvisser
repaired broken documentation link

Revision 284 - Directory Listing
Modified Wed Jul 8 14:11:59 2009 UTC (9 years, 10 months ago) by ingmarvisser
Updated 'Changes' and 'Description' files.

Revision 283 - Directory Listing
Modified Wed Jul 8 14:08:53 2009 UTC (9 years, 10 months ago) by ingmarvisser
Adapted help files for R 2.9.1

Revision 282 - Directory Listing
Modified Wed Jul 8 14:06:54 2009 UTC (9 years, 10 months ago) by ingmarvisser
Changed the call to npsol code, which now uses an option file for setting iteration limit and other optional control parameters.

Revision 281 - Directory Listing
Modified Wed Jul 8 11:45:10 2009 UTC (9 years, 10 months ago) by ingmarvisser
added depmix files to depmix subdirectory in pkg directory

Revision 279 - Directory Listing
Modified Wed Jul 8 11:24:53 2009 UTC (9 years, 10 months ago) by ingmarvisser
Moved depmixS4 files into subdirectory within the pkg directory

Revision 278 - Directory Listing
Modified Wed Jul 8 11:22:09 2009 UTC (9 years, 10 months ago) by ingmarvisser
add depmix and depmixS4 directories so that good old depmix also finds a home on r-forge

Revision 277 - Directory Listing
Modified Fri Jun 26 11:55:27 2009 UTC (9 years, 10 months ago) by ingmarvisser
Fixed a codoc issue in mix.sim-class.Rd

Revision 275 - Directory Listing
Modified Wed Jun 24 19:39:58 2009 UTC (9 years, 10 months ago) by ingmarvisser
Copied files from trunk to pkg directory.

Revision 274 - Directory Listing
Modified Wed Jun 24 19:37:12 2009 UTC (9 years, 10 months ago) by ingmarvisser
Delete files in pkg directory for new release.

Revision 273 - Directory Listing
Modified Thu Jun 18 11:53:47 2009 UTC (9 years, 11 months ago) by maarten
fixed bug in fit(responseGLMMULTINOMIAL): starting weights were set incorrectly

Revision 264 - Directory Listing
Modified Tue Apr 21 10:14:46 2009 UTC (10 years, 1 month ago) by ingmarvisser
Copied trunk to pkg directory for release 0.2-1

Revision 263 - Directory Listing
Modified Tue Apr 21 10:10:24 2009 UTC (10 years, 1 month ago) by ingmarvisser
Copied pkg to trunk directory

Revision 262 - Directory Listing
Modified Fri Feb 20 09:42:15 2009 UTC (10 years, 3 months ago) by ingmarvisser
Fixed encoding problem in AIC.Rd

Revision 260 - Directory Listing
Modified Wed Feb 18 12:53:42 2009 UTC (10 years, 3 months ago) by ingmarvisser
Copied from: trunk revision 259
Moved trunk version to pkg directory

Revision 259 - Directory Listing
Modified Wed Feb 18 12:47:03 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Added tag for release 0.2-0

Revision 258 - Directory Listing
Modified Wed Feb 18 12:14:39 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Added refs to the AIC/BIC help page

Revision 257 - Directory Listing
Modified Wed Feb 18 12:06:04 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Changed order of examples in responses.Rd to match the order of models listed, and added some comments

Revision 256 - Directory Listing
Modified Wed Feb 18 11:59:24 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Added link to responses help page from GLMresponse help page

Revision 255 - Directory Listing
Modified Wed Feb 18 11:50:45 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Added example of the use of conrows argument to fit help page (rev 255)

Revision 254 - Directory Listing
Modified Wed Feb 18 11:28:39 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Changed model numbers in example on the fit help page to be more consistent

Revision 253 - Directory Listing
Modified Wed Feb 18 11:16:59 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Fixed bug in nlin (bug nr 309), working correctly now, revision 253

Revision 252 - Directory Listing
Modified Wed Feb 18 10:28:06 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Updated to do list; moved new feature requests to a tracker as well as doc issues and bugs

Revision 251 - Directory Listing
Modified Tue Feb 17 16:09:56 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Added newx (newdata) argument for predict method of transInit objects (useful in eg plotting logit functions depending on covariates)

Revision 250 - Directory Listing
Modified Tue Feb 17 14:22:50 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Fixed a bug in setting starting values of transInit models

Revision 249 - Directory Listing
Modified Tue Feb 17 10:35:00 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Added help file for mix.sim class

Revision 248 - Directory Listing
Modified Tue Feb 17 10:27:43 2009 UTC (10 years, 3 months ago) by ingmarvisser
Original Path: trunk
Updated help files for mix classes and updated to do list

Revision 244 - Directory Listing
Modified Wed Nov 26 20:05:09 2008 UTC (10 years, 5 months ago) by ingmarvisser
Original Path: trunk
updated individual paper

Revision 229 - Directory Listing
Modified Mon Oct 20 12:14:40 2008 UTC (10 years, 7 months ago) by maarten
Original Path: trunk
- fixed new bug in GLMresponse with starting values
- GLMresponse still needs thorough checking! 

Revision 228 - Directory Listing
Modified Thu Oct 9 23:16:41 2008 UTC (10 years, 7 months ago) by maarten
Original Path: trunk
- fixed problem in GLMresponse with family=binomial() (treated parameters as matrix)
- in GLMbinomial, starting values are no longer automatically transformed with an inverse link (now only for bi/multi-nomial, if prob=true and only for intercept 

Revision 227 - Directory Listing
Modified Sun Sep 7 21:10:51 2008 UTC (10 years, 8 months ago) by maarten
Original Path: trunk
- fixed bug in dens and logDens methods of BINOMresponse (missing size argument)

Revision 226 - Directory Listing
Modified Fri Sep 5 11:55:08 2008 UTC (10 years, 8 months ago) by ingmarvisser
Original Path: trunk
added prob=TRUE support for binomial models in GLMresponse

Revision 225 - Directory Listing
Modified Tue Aug 26 21:39:56 2008 UTC (10 years, 8 months ago) by maarten
Original Path: trunk
- fixed problem with n>1 in multinomial fitting and simulation
- fixed related (potential) bug in binomial

Revision 224 - Directory Listing
Modified Tue Aug 26 13:16:23 2008 UTC (10 years, 8 months ago) by ingmarvisser
Original Path: trunk
Added simulate functie voor mix models

Revision 223 - Directory Listing
Modified Wed Aug 20 14:03:10 2008 UTC (10 years, 9 months ago) by ingmarvisser
Original Path: trunk
Restructured test files; added tests for response models; added .Rout.save files so errors are checked in R CMD check

Revision 221 - Directory Listing
Modified Mon Aug 11 09:21:28 2008 UTC (10 years, 9 months ago) by ingmarvisser
Original Path: trunk
Fixed a bug in show method for GLMresponse models

Revision 219 - Directory Listing
Modified Fri Aug 1 14:27:11 2008 UTC (10 years, 9 months ago) by ingmarvisser
Original Path: trunk
Added some comments

Revision 218 - Directory Listing
Modified Fri Aug 1 14:24:08 2008 UTC (10 years, 9 months ago) by ingmarvisser
Original Path: trunk
Changed predict method to deal with multinomial(identity) objects.

Revision 217 - Directory Listing
Modified Fri Aug 1 14:23:17 2008 UTC (10 years, 9 months ago) by ingmarvisser
Original Path: trunk
Changed show method to deal with multinomial(identity) objects.

Revision 216 - Directory Listing
Modified Fri Aug 1 11:56:47 2008 UTC (10 years, 9 months ago) by ingmarvisser
Original Path: trunk
Fixed bug in viterbi.

Revision 215 - Directory Listing
Modified Tue Jul 29 14:35:28 2008 UTC (10 years, 9 months ago) by ingmarvisser
Original Path: trunk
Fixed minor bug in depmix.fit (included drop=FALSE somewhere to deal with models with a single linear constraint)

Revision 214 - Directory Listing
Modified Wed Jul 2 11:53:50 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
simulate(depmix) now takes stationarity of transInit model into account

Revision 213 - Directory Listing
Modified Wed Jul 2 10:00:57 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
simulate(depmix) now forces init@x to be a matrix

Revision 212 - Directory Listing
Modified Tue Jul 1 22:07:39 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Added example to simulate (which does not work now)

Revision 210 - Directory Listing
Modified Tue Jul 1 14:08:44 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
setpars no longer renames elements in parameter list
splitted getpars(mix) into getpars(mix) and getpars(depmix)

Revision 208 - Directory Listing
Modified Tue Jul 1 12:32:38 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
added my name to a few help files ;-)

Revision 207 - Directory Listing
Modified Tue Jul 1 12:26:10 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
added alias to response-classes

Revision 206 - Directory Listing
Modified Tue Jul 1 12:09:18 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
added export MVNresponse class

Revision 205 - Directory Listing
Modified Tue Jul 1 11:15:39 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
fixed formatting problem in responses.Rd (resolves warnings in R CMD CHECK)

Revision 203 - Directory Listing
Modified Tue Jul 1 09:05:14 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
fixed comments in responses.Rd

Revision 202 - Directory Listing
Modified Tue Jul 1 08:59:49 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
fixed remaining bug in responseMVN related to invsigma

Revision 200 - Directory Listing
Modified Mon Jun 30 10:49:05 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
deleted obsolete simulate file

Revision 199 - Directory Listing
Modified Mon Jun 30 10:47:09 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
put simulate methods in corresponding class files
added separate depmixsim file

Revision 198 - Directory Listing
Modified Mon Jun 30 10:21:14 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Additions to the NEWS file

Revision 197 - Directory Listing
Modified Mon Jun 30 09:56:10 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Added generic for simulate

Revision 196 - Directory Listing
Modified Mon Jun 30 09:41:27 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Added help file for makeDepmix

Revision 195 - Directory Listing
Modified Mon Jun 30 09:10:45 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Fixed a bug in show method for GLMresponse

Revision 194 - Directory Listing
Modified Sat Jun 28 09:33:57 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Updated NEWS, added more changes of the upcoming release 0.2-0
Updated README (changed on section on transition from old to new depmix)

Revision 193 - Directory Listing
Modified Fri Jun 27 11:12:10 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
- added MASS dependency (for mvrnorm)
- MVNresponse example in responses now uses mvrnorm

Revision 192 - Directory Listing
Modified Fri Jun 27 09:03:30 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
added "dots" to simulate(transInit) for consistency

Revision 191 - Directory Listing
Modified Thu Jun 26 14:20:46 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Fixed documentation error in simulate.Rd

Revision 190 - Directory Listing
Modified Thu Jun 26 00:14:14 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
- fixed simulate documentation and simulate methods (times argument rather than time)

Revision 189 - Directory Listing
Modified Wed Jun 25 14:42:17 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Solved various codoc issues

Revision 188 - Directory Listing
Modified Wed Jun 25 14:03:51 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
commit.txt

Revision 187 - Directory Listing
Modified Wed Jun 25 13:58:37 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Added function nlin to extract the number of linear constraints in fitted models; to be used in computing the number of free parameters (eg for likelihood testing)

Revision 186 - Directory Listing
Modified Tue Jun 24 21:02:54 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk


Revision 185 - Directory Listing
Modified Tue Jun 24 16:04:19 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
- added function to generate MVNresponse models
- fixed MVNnorm fit function (now also works without weights
- TODO: setpars function

Revision 184 - Directory Listing
Modified Tue Jun 24 15:35:27 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
- fixed bug in NORMresponse (now also works without weights)

Revision 183 - Directory Listing
Modified Tue Jun 24 14:23:39 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Added examples to responses.Rd

Revision 182 - Directory Listing
Modified Tue Jun 24 14:15:26 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Added default w=NULL in the fit function for NORMresponse objects

Revision 181 - Directory Listing
Modified Tue Jun 24 13:11:04 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
changed fit for GLM to be in line with others in the package (used if(missing(w)) w <- NULL rather than default w=NULL

Revision 180 - Directory Listing
Modified Tue Jun 24 13:09:15 2008 UTC (10 years, 10 months ago) by maarten
Original Path: trunk
- fixed bug in multinomial fit (for number categories, nnet.default now uses softmax=TRUE rather than entropy=TRUE) 

Revision 179 - Directory Listing
Modified Tue Jun 24 13:07:52 2008 UTC (10 years, 10 months ago) by ingmarvisser
Original Path: trunk
Added default w=NULL in the fit function for GLMresponse objects

Revision 178 - Directory Listing
Modified Fri Jun 20 13:38:08 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Changed getpars and setpars to deal with mix objects correctly; changed examples in depmix.fit.Rd

Revision 176 - Directory Listing
Modified Wed Jun 18 08:30:32 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
Renamed remotely

Revision 175 - Directory Listing
Modified Wed Jun 18 07:51:47 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Changed alias in depmix.sim help file; updated to do list

Revision 174 - Directory Listing
Modified Tue Jun 17 15:09:10 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
opzetje voor de responses.Rd help file

Revision 173 - Directory Listing
Modified Tue Jun 17 14:35:09 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
fixed mismatch in simulate.Rd

Revision 172 - Directory Listing
Modified Tue Jun 17 14:31:08 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
added depmix.sim help

Revision 171 - Directory Listing
Modified Tue Jun 17 14:11:27 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Fixed a bug in dens function for binomial models

Revision 170 - Directory Listing
Modified Tue Jun 17 12:52:04 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Added prob argument to setpars for multinom models (internal use only)

Revision 169 - Directory Listing
Modified Tue Jun 17 12:24:16 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Added mix-class.Rd and mix.fitted-class.Rd help files and fixed some codoc issues

Revision 168 - Directory Listing
Modified Tue Jun 17 10:31:00 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Fixed bug in setpars for multinomial models (again)

Revision 167 - Directory Listing
Modified Tue Jun 17 10:06:32 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
changed BINOMresponse so that n>1 is now contained in y matrix as a second column.

Revision 166 - Directory Listing
Modified Tue Jun 17 09:34:30 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Fixed bug in setpars for multinomial models

Revision 165 - Directory Listing
Modified Tue Jun 17 08:48:16 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Fixed bug in makeResponseModels to give a sensible error if the number of start values is incorrect

Revision 164 - Directory Listing
Modified Fri Jun 13 16:05:45 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
set transpose before setpars in fit MULTINOMresponse (as in fit transInit). But there is still a problem in setpars...

Revision 163 - Directory Listing
Modified Fri Jun 13 15:37:20 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
added simulate in methods (deleted it from normal functions)

Revision 162 - Directory Listing
Modified Fri Jun 13 15:27:20 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
- commented simulate generic

Revision 161 - Directory Listing
Modified Fri Jun 13 15:06:32 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
- fixed bug in creation of multinom with a factor response

Revision 160 - Directory Listing
Modified Fri Jun 13 14:23:51 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
- fixed bug in GLM when response is a 2 column matrix

Revision 159 - Directory Listing
Modified Fri Jun 13 14:21:52 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Added some things to the NAMESPACE

Revision 158 - Directory Listing
Modified Fri Jun 13 14:08:02 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
- fixed bug in multinom

Revision 157 - Directory Listing
Modified Thu Jun 12 13:44:52 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
- changed EM so that a simpler routine (not fb) is used for mix models

Revision 156 - Directory Listing
Modified Wed Jun 11 21:06:46 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Added mix class for mixture and latent class models

Revision 155 - Directory Listing
Modified Wed Jun 11 10:26:32 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Deleted depmixNew-test2.R as these are moved to a dontrun section in the examples of fit

Revision 154 - Directory Listing
Modified Wed Jun 11 09:49:48 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Deleted depmixNew-test3.R as these are all in the examples of fit

Revision 153 - Directory Listing
Modified Tue Jun 10 22:01:03 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Documentation updates (added cross links and the like)

Revision 152 - Directory Listing
Modified Tue Jun 10 15:22:18 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
More minor changes

Revision 151 - Directory Listing
Modified Tue Jun 10 15:14:02 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
More minor changes in documentation

Revision 150 - Directory Listing
Modified Tue Jun 10 14:17:13 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Minor changes in documentation

Revision 149 - Directory Listing
Modified Tue Jun 10 14:09:26 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Added forwardbackward, user accessible function to get the forward and backward variables

Revision 148 - Directory Listing
Modified Tue Jun 10 13:16:50 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Renamed veterbi2.R to viterbi.R (this is the one in use)

Revision 147 - Directory Listing
Modified Tue Jun 10 13:14:35 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Removed two of three viterbi versions

Revision 146 - Directory Listing
Modified Tue Jun 10 12:34:29 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Moved test files to test dir

Revision 145 - Directory Listing
Modified Tue Jun 10 12:33:38 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Updated test files

Revision 144 - Directory Listing
Modified Tue Jun 10 08:03:20 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Dontshow example added

Revision 143 - Directory Listing
Modified Mon Jun 9 23:16:11 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk


Revision 142 - Directory Listing
Modified Mon Jun 9 14:38:38 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Dontshow example added

Revision 141 - Directory Listing
Modified Mon Jun 9 14:22:51 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Restructured help files somewhat

Revision 140 - Directory Listing
Modified Mon Jun 9 13:08:25 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
- updated simulate method.
- simulate(response,nsim,...) now returns a (T*nsim)*ncol(response@y) matrix
- simulate(depmix,nsim,...) now returns an object of class depmix.sim with additional slot for states

Revision 139 - Directory Listing
Modified Mon Jun 9 12:01:32 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Added a NEWS file with a record of major changes

Revision 138 - Directory Listing
Modified Mon Jun 9 11:59:20 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Added simulate as a generic so the trunk version builds again

Revision 137 - Directory Listing
Modified Mon Jun 9 11:55:55 2008 UTC (10 years, 11 months ago) by ingmarvisser
Original Path: trunk
Changed responseGLMGAMMA.r to responseGLMGAMMA.R (note the capital)

Revision 136 - Directory Listing
Modified Thu May 29 10:50:55 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk


Revision 135 - Directory Listing
Modified Thu May 29 10:40:53 2008 UTC (10 years, 11 months ago) by maarten
Original Path: trunk
- added Poisson and Gamma GLMresponse models
- reorganized simulate methods

Revision 134 - Directory Listing
Modified Wed May 21 10:18:43 2008 UTC (11 years ago) by maarten
Original Path: trunk
- fixed simulate method, now works but still needs proper checking

Revision 133 - Directory Listing
Modified Wed May 21 08:47:49 2008 UTC (11 years ago) by maarten
Original Path: trunk
- fixed new error in GLMMULTINOM.R 

Revision 132 - Directory Listing
Modified Wed May 21 00:04:29 2008 UTC (11 years ago) by maarten
Original Path: trunk
- fixed EM, now works on Test 4 in depmixNew-test1.R :-)

Revision 131 - Directory Listing
Modified Tue May 20 16:41:14 2008 UTC (11 years ago) by maarten
Original Path: trunk


Revision 128 - Directory Listing
Modified Tue May 20 10:42:09 2008 UTC (11 years ago) by maarten
Original Path: trunk
Renamed remotely

Revision 127 - Directory Listing
Modified Tue May 20 09:30:40 2008 UTC (11 years ago) by maarten
Original Path: trunk
 -fixed bug in simulate.r

Revision 126 - Directory Listing
Modified Tue May 20 07:31:27 2008 UTC (11 years ago) by ingmarvisser
Original Path: trunk
Put most functions into separate R files (part 2)

Revision 124 - Directory Listing
Modified Fri May 16 20:40:03 2008 UTC (11 years ago) by maarten
Original Path: trunk
-added simulation method for several models

Revision 123 - Directory Listing
Modified Fri May 9 15:24:09 2008 UTC (11 years ago) by ingmarvisser
Original Path: trunk
Remove responses.R (which has become empty)

Revision 122 - Directory Listing
Modified Fri May 9 15:23:14 2008 UTC (11 years ago) by ingmarvisser
Original Path: trunk
Put most functions into separate R files

Revision 119 - Directory Listing
Modified Fri May 9 10:50:01 2008 UTC (11 years ago) by ingmarvisser
Original Path: trunk
minor changee

Revision 118 - Directory Listing
Modified Fri May 9 10:49:41 2008 UTC (11 years ago) by ingmarvisser
Original Path: trunk
minor changee

Revision 117 - Directory Listing
Modified Fri May 2 16:38:36 2008 UTC (11 years ago) by maarten
Original Path: trunk
corrected error (only in trunk version)

Revision 116 - Directory Listing
Modified Thu Mar 27 22:27:52 2008 UTC (11 years, 1 month ago) by ingmarvisser
Original Path: trunk
Removed .Rhistory

Revision 115 - Directory Listing
Modified Thu Mar 27 22:26:51 2008 UTC (11 years, 1 month ago) by ingmarvisser
Original Path: trunk
Added srcll directory with tests for C-code for lystig and fb

Revision 114 - Directory Listing
Modified Thu Mar 27 22:25:06 2008 UTC (11 years, 1 month ago) by ingmarvisser
Original Path: trunk
Moved apply(dens etc) into fb and lystig, updated todo

Revision 111 - Directory Listing
Modified Tue Mar 25 09:48:02 2008 UTC (11 years, 1 month ago) by ingmarvisser
Original Path: trunk
Added readme

Revision 110 - Directory Listing
Modified Tue Mar 25 09:23:33 2008 UTC (11 years, 1 month ago) by ingmarvisser
Original Path: trunk
Updated depmix-intro.pdf

Revision 109 - Directory Listing
Modified Sun Mar 23 15:18:12 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Fighting with svn

Revision 108 - Directory Listing
Modified Sun Mar 23 15:17:07 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Final changes

Revision 107 - Directory Listing
Modified Sun Mar 23 15:16:22 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Final changes

Revision 106 - Directory Listing
Modified Sun Mar 23 15:07:33 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Final minor changes

Revision 102 - Directory Listing
Modified Sun Mar 23 14:39:25 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Moved latest version to pkg directory

Revision 101 - Directory Listing
Modified Sun Mar 23 14:29:34 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Moved latest version to pkg directory

Revision 99 - Directory Listing
Modified Sun Mar 23 14:11:15 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Final minor changes

Revision 98 - Directory Listing
Modified Fri Mar 21 23:45:47 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Speeded up EM a little bit

Revision 97 - Directory Listing
Modified Fri Mar 21 16:13:42 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added example file for viterbi and added viterbi2 with different scaling

Revision 96 - Directory Listing
Modified Thu Mar 20 22:30:09 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Moving file to pkg for release

Revision 95 - Directory Listing
Modified Thu Mar 20 11:55:31 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk
- fixed bug in Viterbi (for stationary models)

Revision 94 - Directory Listing
Modified Thu Mar 20 11:34:45 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
updated namespace file

Revision 93 - Directory Listing
Modified Thu Mar 20 11:32:06 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Changed hmm into object etc, not working unfortunately ...

Revision 92 - Directory Listing
Modified Thu Mar 20 11:05:16 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
More minor changes

Revision 91 - Directory Listing
Modified Wed Mar 19 21:45:52 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
More minor changes

Revision 90 - Directory Listing
Modified Wed Mar 19 21:17:55 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added links in help files and other minor stuff

Revision 88 - Directory Listing
Modified Tue Mar 18 16:22:11 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Updated test files and other minor changes

Revision 87 - Directory Listing
Modified Tue Mar 18 15:35:08 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added help for llratio

Revision 86 - Directory Listing
Modified Tue Mar 18 10:44:18 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Codoc changes

Revision 85 - Directory Listing
Modified Mon Mar 17 22:59:04 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Minor changes in help files

Revision 84 - Directory Listing
Modified Mon Mar 17 22:35:32 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added help files internal, fitted class and response classes

Revision 83 - Directory Listing
Modified Mon Mar 17 15:39:29 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added NAMESPACE file

Revision 82 - Directory Listing
Modified Mon Mar 17 15:38:32 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Minor changes, mostly in documentation

Revision 81 - Directory Listing
Modified Thu Mar 13 00:36:20 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk
- fixed binomial response model (hopefully...needs some testing)

Revision 80 - Directory Listing
Modified Sat Mar 8 13:07:54 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Minor changes

Revision 79 - Directory Listing
Modified Fri Mar 7 16:26:14 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Updated help files and other minor changes

Revision 78 - Directory Listing
Modified Fri Mar 7 16:16:50 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Updated help files and other minor changes

Revision 77 - Directory Listing
Modified Fri Mar 7 15:35:47 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Minor changes

Revision 76 - Directory Listing
Modified Fri Mar 7 15:34:14 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Minor changes

Revision 75 - Directory Listing
Modified Fri Mar 7 15:25:15 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Renamed data sets to .rda instead of .Rda (won't work otherwise ...) 

Revision 74 - Directory Listing
Modified Fri Mar 7 15:24:51 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Renamed data sets to .rda instead of .Rda (won't work otherwise ...) 

Revision 73 - Directory Listing
Modified Fri Mar 7 15:06:18 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added help files for data sets

Revision 72 - Directory Listing
Modified Fri Mar 7 14:52:10 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Updated help files and removed some errors in them the package now builds

Revision 71 - Directory Listing
Modified Fri Mar 7 14:40:09 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Moved generics into allGenerics.R and cleaned up comments etc

Revision 70 - Directory Listing
Modified Fri Mar 7 14:39:32 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Moved generics into allGenerics.R

Revision 69 - Directory Listing
Modified Fri Mar 7 14:20:46 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Deleted all redundant files

Revision 68 - Directory Listing
Modified Fri Mar 7 14:14:55 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Deleted all redundant files

Revision 67 - Directory Listing
Modified Fri Mar 7 13:51:41 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Minor changes (comments and sourc()'s etc

Revision 66 - Directory Listing
Modified Fri Mar 7 13:45:15 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Moved necessary files into R directory

Revision 65 - Directory Listing
Modified Fri Mar 7 13:28:37 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added R directory

Revision 64 - Directory Listing
Modified Fri Mar 7 13:12:36 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
minor changes

Revision 63 - Directory Listing
Modified Fri Mar 7 13:11:54 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
llratio now gives positive ratio ...

Revision 62 - Directory Listing
Modified Fri Mar 7 12:56:05 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Updated balance scale example to work with EM

Revision 61 - Directory Listing
Modified Fri Mar 7 10:51:11 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk
- fixed problem with multinomial fit (especially for init models)

Revision 60 - Directory Listing
Modified Fri Mar 7 09:47:57 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added convergence message to return object

Revision 59 - Directory Listing
Modified Fri Mar 7 09:22:06 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Renamed viterbi to .R instead of .r

Revision 58 - Directory Listing
Modified Fri Mar 7 09:21:34 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Renamed viterbi to .R instead of .r

Revision 57 - Directory Listing
Modified Thu Mar 6 23:39:46 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk
- em function in EM.R now works with depmix objects
- depmix-test3EM.R is now example with depmix models, one with intercept only (works ok) and one with a covariate (doesn't work)

Revision 56 - Directory Listing
Modified Thu Mar 6 17:34:46 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk


Revision 55 - Directory Listing
Modified Thu Mar 6 17:32:42 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk
- viterbi now handles hmmModel
- added EM3.R and depmix-test3EM3.R as example of EM with viterbi states for maximisation of trinModel...doesn't work either :(

Revision 54 - Directory Listing
Modified Thu Mar 6 15:44:05 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Minor changes

Revision 53 - Directory Listing
Modified Thu Mar 6 15:15:41 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Balance scale example with new code

Revision 52 - Directory Listing
Modified Thu Mar 6 15:14:26 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Minor changes

Revision 51 - Directory Listing
Modified Thu Mar 6 15:08:58 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Updated help files

Revision 50 - Directory Listing
Modified Thu Mar 6 11:29:41 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added em optimization example for latent class model of balance scale data

Revision 49 - Directory Listing
Modified Thu Mar 6 11:28:56 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Changed reestimation of initial parameters for multiple cases

Revision 48 - Directory Listing
Modified Thu Mar 6 10:40:42 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added support for dealing with timeseries of length 1, ie for latent class models

Revision 47 - Directory Listing
Modified Thu Mar 6 10:38:48 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added support for dealing with timeseries of length 1, ie for latent class models

Revision 46 - Directory Listing
Modified Wed Mar 5 16:15:20 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Example now works with EM on stationary model

Revision 45 - Directory Listing
Modified Wed Mar 5 16:14:16 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added option for stationary models in EM update of transition matrix, see example file: depmix-test3EM2.R

Revision 44 - Directory Listing
Modified Wed Mar 5 00:32:03 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk
- fixed fit(trinModel), so EM works, but likelihood still goes down!
- added viterbi algorithm (will still need ntimes etc)

Revision 43 - Directory Listing
Modified Wed Mar 5 00:31:15 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk
Removed file/folder

Revision 42 - Directory Listing
Modified Tue Mar 4 23:41:54 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added file with description of response-class

Revision 41 - Directory Listing
Modified Tue Mar 4 23:31:01 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added descriptions for accessor functions

Revision 40 - Directory Listing
Modified Tue Mar 4 23:02:33 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Minor changes

Revision 39 - Directory Listing
Modified Tue Mar 4 23:01:47 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added help file response.Rd (not quite finished)

Revision 38 - Directory Listing
Modified Tue Mar 4 22:20:30 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added working example of contraints on balance scale data model and usage of likelihood ratio test

Revision 37 - Directory Listing
Modified Tue Mar 4 22:16:47 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added balance scale data set

Revision 36 - Directory Listing
Modified Tue Mar 4 22:16:15 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added balance scale data set

Revision 35 - Directory Listing
Modified Tue Mar 4 22:08:41 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Updated aliases and title/description

Revision 34 - Directory Listing
Modified Tue Mar 4 22:05:18 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added help for llratio, loglikelihood ratio test of two fitted models

Revision 33 - Directory Listing
Modified Tue Mar 4 22:00:32 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added help for logLik, AIC and BIC methods

Revision 32 - Directory Listing
Modified Tue Mar 4 21:43:00 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added help for logLik, AIC and BIC methods

Revision 30 - Directory Listing
Modified Tue Mar 4 16:22:24 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Update of balance scale example with new depmix class and fit functions

Revision 29 - Directory Listing
Modified Tue Mar 4 00:42:56 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk


Revision 28 - Directory Listing
Modified Tue Mar 4 00:42:21 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk


Revision 27 - Directory Listing
Modified Sun Mar 2 21:45:49 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added help file for depmix.fit function

Revision 25 - Directory Listing
Modified Sun Mar 2 20:39:40 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added accessor functions ntimes, nstates and nresp

Revision 24 - Directory Listing
Modified Sun Mar 2 20:38:32 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Added detailed depmix class description

Revision 22 - Directory Listing
Modified Sun Mar 2 17:16:07 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Updated help file for creating depmix models

Revision 20 - Directory Listing
Modified Sun Mar 2 09:03:06 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Removed R directory and put all files in trunk

Revision 18 - Directory Listing
Modified Sun Mar 2 08:37:18 2008 UTC (11 years, 2 months ago) by ingmarvisser
Original Path: trunk
Moved files into trunk directory

Revision 17 - Directory Listing
Added Sat Mar 1 20:28:39 2008 UTC (11 years, 2 months ago) by maarten
Original Path: trunk
- added trunk, tags, and branches folders

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