NEWS

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MPTinR 1.14

• Released July 2021 Significant User Visible Changes o check.mpt() now returns the order of both trees and categories required for fitting for EQN model files. This can be used to determine the required ordering of the data. Bugfixes o ** MPTinR VERSION 1.13.x **

MPTinR 1.13

• Released August 2020 Significant User Visible Changes o Bugfixes o MPTinR now warns in case of over-parameterised models estimated using the hessian and suggests deactivating it. ** MPTinR VERSION 1.12.x **

MPTinR 1.12

• Released December 2019 Significant User Visible Changes o This is a maintenance update to address CRAN issues, which does not add any new features. o Removed all links to my now defunct homepage at the University of Freiburg. Bugfixes o MPTinR now uses a proper NAMESPACE file (i.e., all exported functions are listed individually) o select.mpt() should work even if the entered objects have a class attribute of length two. ** MPTinR VERSION 1.10.x **

MPTinR 1.10

• Released July 2015 Significant User Visible Changes and new Features o added 850 ROCs used in the meta-analysis of Klauer and Kellen (2015), see ?roc6. Bugfixes o The changes made to the FIA calculation for summed data in version 1.7 were incorrect. FIA for multiple data sets simply needs to be summed to correspond to FIA when these data sets were fitted in a super-model (with separate parameters for each data set). Consequently, the old behavior of simply summing FIA was restored in both fit.mpt et al. and select.mpt. Vignette was updated to show this. o all functions from default packages imported. o FIA for first data set was sometimes incorrectly treated as different from get.mpt.fia (or fit.mpt). ** MPTinR VERSION 1.9.x **

MPTinR 1.8

• Released June 2015 Significant User Visible Changes and new Features o added updated version of the MPTinR paper as vignette. o removed URL (site was not updated anymore). Bugfixes o select.mpt was still giving wrong FIA values for multiple data sets (used G^2 instead of 0.5*G^2). o the summed FIA value in the output from fit.mpt and the like was also incorrect (also used G^2 instead of 0.5*G^2) ** MPTinR VERSION 1.8.x **
• Released April 2015 Significant User Visible Changes and new Features o Bugfixes o bug that prevented inequalities to be correctly taken into account for calculation of FIA is corrected (Thanks to Christoph Klauer for noticing this). This bug was introduced in version 1.6. o prepare.mpt.fia was not working, fixed. ** MPTinR VERSION 1.7.x **

MPTinR 1.7

• Released March 2015 Significant User Visible Changes and new Features o less messages if show.messages == FALSE. Bugfixes o summed BIC and FIA values were calculated incorrectly (i.e., the individual values were simply summed which is incorrect due to the non-linear nature of the log(n) term). This is now corrected for both the output of fit.mpt (et al.) and select.mpt (for which now summed BIC and FIA are always calculated anew for multiple data sets). o removed note in documentation that gen.X functions are rather new. They are well tested by now. o bmpt.fia should now work without snowfall without throwing a warning. ** MPTinR VERSION 1.6.x **

MPTinR 1.6

• Released October 2014 Significant User Visible Changes and new Features o numDeriv is now only imported and not attached. o names for models passed to select.mpt are now automatically determined via match.call(). o changed the maintainer email address. Bugfixes o C++ code now uses Rcpp attributes. o A bug prohibiting computation of FIA for models without inequality restrictions and with DEBUG flags enabled when compiling should now be resolved. The computation causing it is skipped when no inequalities are present. o calculating FIA via fit.model did not work for individual data sets. o get.mpt.fia: added examples outside dontrun{} blocks running simple fia tests, with and without inequalities. o all calls to snowfall prefaced with snowfall:: to avoid CRAN NOTEs. ** MPTinR VERSION 1.5.x **

MPTinR 1.5

• Released August 2014 Significant User Visible Changes and new Features o added numDeriv argument to fit functions (fit.mpt, fit.model, & fit.mptinr) which allows to deactivate numerical estimation of hessian (for calculation of CIs) as it may be extremely time consuming. Bugfixes o ** MPTinR VERSION 1.4.x **

MPTinR 1.4

• Released May 2014 Significant User Visible Changes and new Features o Bugfixes o repaired mConst argument and FIA function. ** MPTinR VERSION 1.3.x **

MPTinR 1.3

• Released April 2014 Significant User Visible Changes and new Features o added args.fia argument to fit.mpt and fit.model to pass arguments to get.mpt.fia (such as mConst, see below). o added function lbmpt.to.mpt to transform a model in LBMPT into model equations (thanks to Quentin Gronau and Franz Dietrich). o added restrictions argument to make.mpt.cf. o added example on how to fit a confidence rating SDT model to ?fit.model. Bugfixes o added mConst argument to bmpt.fia (+ get.mpt.fia) to avoid numerical underflows with huge models when calculating FIA. see: http://stackoverflow.com/q/20529407/28957 (this argument should be used carefully). o check.model argument in fit.model was also responsible for certain sanity checks in the objective et al. This frequently led to errors which are now silently dropped. ** MPTinR VERSION 1.2.x **

MPTinR 1.2

• Released November 2013 Significant User Visible Changes and new Features o Most warnings (e.g., concerning unsuccessful optimization with analytic gradient) are now messages. o Added error message when the objective function did not evaluate successfully with the given starting values. o restrictions to constants can now be set to any value (not anymore restricted to be within 0 and 1). o fit.model and gen.predictions (et al.) have argument check.model which allows to suppress the check if the expected values of a model sum to 1. Bugfixes o Removed bug that crashed the main functions when Hessian function failed to produce reasonable results. o FIA calculation could fail when determinant of Fisher matrix was below 0 as it did not take the absolute value (as does the original code by Wu et al.). This should be fixed now and FIA again works for all (BMPT) models. o check.mpt doesn't fail anymore if any of the predictions is NA or NaN. o Removed bug that crashed MPTinR when fitting a model with a single free parameter to multiple datasets (bug reported by Alberto Mirisola) o fit.mpt gives a warning when FIA fails due to model not being a BMPT (instead of failing). ** MPTinR VERSION 1.1.x **

MPTinR 1.1

• Released May 2013 Significant User Visible Changes and new Features o Calculation of FIA uses RcppEigen for dramatic speed improvements (thanks to Christian Mueller). o FIA calculation can also be parallelized, see bmpt.fia (but even in fit.mpt or fit.model, if multicore is not "none", or in get.mpt.fia) o documentation now says that extra brackets will distort FIA calculation (Thanks to Joachim Vandekerckhove and EJ Wagenmakers) o added possibility to specify individual bounds for random starting values (via two element list). o multicore fitting now uses load balancing. o select.mpt shows how often p < .05 when results consists of multiple data sets. (p.smaller.05) Bugfixes o Added note that LLKs do not include factorial constant of the multinomial PMF. o (hopefully) repaired bug in make.mdt() with matrix/data.frame ** MPTinR VERSION 1.0.x **

MPTinR 1.0

• Released January 2013 Significant User Visible Changes and new Features o added function plot.prediction for plotting obersved versus predicted data. o added fia.penalty to information criteria output and to select.mpt. o added G.Square, df, and p to output of select.mpt o argument dataset added to select.mpt. Allows to select only certain datasets for the comparison (argument may be of length > 1). o added CITATION file (as our Behavior Research Methods paper finally came out) Bugfixes o select.mpt works now if some some models (with multiple datasets) were fitted with fit.aggregated = FALSE. o select.mpt returns the aggregated GoF (G^2, df, p) when output = "full" o You can now pose an order restriction on variables that may also be restricted to be equal to others. E.g., the following restriction is allowed list("G2 < G3 < G5", "G1 = G2", "G4 = G5") and produces the desired results, see r-forge/MPTinR/bugs/restrictionsbug.order.R Note that in this case G1 would be marked as inequality restricted instead of equality restricted (which is not the case for G4). ** MPTinR VERSION 0.9.x **

MPTinR 0.9

• Released July 2012 Significant User Visible Changes and new Features o added functions gen.data, sample.data and gen.predictions for bootstrapping, generating data and predictions. o coments in model and restrictions files are now treated as in R: Everything to the right of a # is ignored and NOT the whole line! o MPTinR is now byte compiled. o make.mdt can now handle a matrix or data.frames building a big mdt file. Bugfixes o fixed bug when obtaining fia from textConnection also for fit.model() ** MPTinR VERSION 0.8.x **

MPTinR 0.8

• Released February - May 2012 Significant User Visible Changes and new Features o fit.mpt and fit.model (see version 0.7.0) are now just wrappers around the new function fit.mptinr. They produce the appropirate objective, gradient, hessian, and prediction function to fit the model. o fit.model contains an example of how to fit a SDT. see ?fit.model. Dont forget to set lower.bound and upper.bound when fitting non-MPT models. o fit.mptinr is a new function that takes an arbitrary objective function and possibly a gradient, hessian and prediction function to fit categorical data (see examples in ?fit.model). o fitting for MPT and similar models is done using a gradient function, which significantly improves fitting speed. In the rare cases where fitting fails using the gradient a numerical gradient is still used (with warning). o The Hessian Matrix for MPTs and similar models is now symbolically derived yielding an exact Hessian matrix (before it was numerically estimated leading to incorrect Hessians whean paramaters were exactly at the boundary). o fitting is now based on nlminb instead of optim's L-BFGS-B (using L-BFGS-B is available in fit.mpt.old) o models and restrictions can now be specified using textConnections instead of only external files. See examples in ?fit.mpt and especially ?fit.model. restrictions can be specified as a list of characters. o added make.mdt, a function to make .mdt data files which can be read by multiTree or HMMTree. o new argument show.messages added to the fitting function (default = TRUE). If FALSE the time messeages around the fitting algorithm are suppressed. o expanded check.mpt functionality (now gives number of categories and number of independent categories) o all fitting functions have the argument fit.aggregated to indicate whether or not the aggregated data (for multiple datasets) should be fitted. Default is TRUE o summary.llks was renamed to fitting.runs o model.info now gives the rank of the Fisher Matrix (instead of the rank of the Hessian Matrix). Bugfixes o resolved small bug when fitting using multicore = "individual" o no more warning message if CIs cannot be computed. o select.mpt now compares aggregated FIA for output = "full" o select.mpt now rounds information criteria before determining number of best fits o no more warnings by cell counts below 5 (seems unprincipled) o fixed bug when restricted parameters were not in the original model (now throws a warning, thanks to Alex) ** MPTinR VERSION 0.7.0 **

MPTinR 0.7.0

• Released January 2012 Significant User Visible Changes o now contains fit.model() a copy of fit.mpt() with arguments for lower and upper bounds for the parameters. You should be able to fit a lot more models with this function. (fit.model() is slightly slower than fit.mpt() for MPTs) New Features / Bugfixes o MPTinR should now allow easy model files with all types of operators (not only + - *) and even R functions (e.g., pnorm, ...) via the function fit.model() ** MPTinR VERSION 0.6.5 **

MPTinR 0.6.5 (2011-11-22)

• Released June 2011 Significant User Visible Changes o New Features / Bugfixes o added a parameter to specify the starting values for the fitting routine (in fit.mpt) ** MPTinR VERSION 0.6.4 **

MPTinR 0.6.4

• Released June 2011 Significant User Visible Changes o New Features / Bugfixes o added URL to DESCRIPTION file. o corrected more problems in bmpt.fia when using small models that were related to differences in matrix functionality of Matlab and R (the problem is R's default of '[', drop = TRUE). ** MPTinR VERSION 0.6.3 **

MPTinR 0.6.3

• Released April 2011 Significant User Visible Changes o get.mpt.fia modified such that bmpt.fia is only called as often as there are differences in the hank.join parameters (i.e., only if the ratio between the trees differ, not the ns). As a consequence, CFIA is calculated as part of get.mpt.fia. Furthermore, CIs of CFIA are not returned by get.mpt.fia. o fit.mpt adjusted to use the optimization of get.mpt.fia (see above) for multi-individual fit. That is, fit.mpt now calls get.mpt.fia only once (previous were two calls, one for for individual data, one for aggregated data). o objective function in fit.mpt vectorized (previous was using for-loop). Obtained speed up: ~40%. New Features / Bugfixes o bmpt.fia fixed to deal with models without restricted parameters (was necessary as we did not use en empty matrix correctly) o Corrected a bug that lead to a wrong labeling of restricted parameters in the mean parameter table for multi-individual fit when using sort.param = TRUE. o Corrected a bug in the R implementation of bmpt.fia, when only one parameter was fixed.