MPTmultiverse v0.2-0

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Multiverse Analysis of Multinomial Processing Tree Models

Statistical or cognitive modeling usually requires a number of more or less arbitrary choices creating one specific path through a 'garden of forking paths'. The multiverse approach (Steegen, Tuerlinckx, Gelman, & Vanpaemel, 2016, <doi:10.1177/1745691616658637>) offers a principled alternative in which results for all possible combinations of reasonable modeling choices are reported. MPTmultiverse performs a multiverse analysis for multinomial processing tree (MPT, Riefer & Batchelder, 1988, <doi:10.1037/0033-295X.95.3.318>) models combining maximum-likelihood/frequentist and Bayesian estimation approaches with different levels of pooling (i.e., data aggregation). For the frequentist approaches, no pooling (with and without parametric or nonparametric bootstrap) and complete pooling are implemented using MPTinR <https://cran.r-project.org/package=MPTinR>. For the Bayesian approaches, no pooling, complete pooling, and three different variants of partial pooling are implemented using TreeBUGS <https://cran.r-project.org/package=TreeBUGS>. The main function is fit_mpt() who performs the multiverse analysis in one call.

Readme

MPTmultiverse

MPTmultiverse is an R package that provides functions for a multiverse analysis of multinomial processing tree (MPT) models. Note that the package is currently work in progress and should be considered alpha. If you experience problems, open an issue.

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. Travis-CI Build Status

Install

To install MPTmultiverse, make sure you already installed the devtools package via install.packages("devtools"). Moreover, you also need a to have JAGS installed: Go to http://mcmc-jags.sourceforge.net/ for instructions on how to install JAGS on your machine.

If these prerequisites are met, type devtools::install_github("mpt-network/MPTmultiverse") in your R console to install MPTmultiverse together with all required packages that it depends on. To make sure that you are using the latest versions of all packages, you should also run update.packages(ask = FALSE).

Usage

  1. Create a new folder that contains the following three files (cf. the subfolder vignettes/):
    1. The MPT model in the .eqn-format
      • The model should be parameterized including all equality constraints.
      • To encode fixed parameters (e.g., g=.50), replace the parameter in the eqn-file by constants.
    2. The data with individual frequencies as a .csv-file
    3. The file analysis.rmd(copied from the vignettes subfolder).
  2. Adjust the input options in analysis.rmd in the section "MPT model definition & Data". You have to specify the correct file names and the names of the columns in your data that contain a subject identifier and between-subjects conditions.
  3. Optionally, set some options (e.g., the number of bootstrap samples) via mpt_options()
  4. Run the analysis script (e.g., by knitting the .rmd file).

Current limitations

  • For the Bayesian models with "no-pooling" and "complete-pooling", no additional MCMC samples are drawn to achieve the desired level of convergence (e.g., Rhat < 1.05). This might be addressed in future versions of TreeBUGS. As a remedy, the number of MCMC iterations can be increased a priori (via mpt_options()).

All code in this repository is released under the GPL v2 or later license. All non-code materials is released under the CC-BY-SA license.

Functions in MPTmultiverse

Name Description
mpt_options Options Settings for MPT Comparison
plot.multiverseMPT Plot multiverseMPT
check_results Check results from a multiverse analysis
fit_mpt Multiverse Analysis for MPT Models
write_check_results Write check_results
write_results Write Results of Multiverse Analysis to csv-Files
get_pb_output Parametric Bootstrap for MPT
make_results_row Create
No Results!

Vignettes of MPTmultiverse

Name
NOT_USED/1_bayen_kuhlmann_2011.html
NOT_USED/2HTSM_Submodel4.eqn
NOT_USED/2_Smith_et_al_2011.rmd
NOT_USED/Kuhlmann_dl7.csv
NOT_USED/prospective_memory.eqn
NOT_USED/smith_et_al_2011.csv
introduction-bayen_kuhlmann_2011.rmd
No Results!

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Details

URL https://github.com/mpt-network/MPTmultiverse
BugReports https://github.com/mpt-network/MPTmultiverse/issues
LazyData yes
VignetteBuilder knitr
RoxygenNote 6.1.1
License GPL-2
NeedsCompilation no
Packaged 2019-03-11 21:24:50 UTC; henrik
Repository CRAN
Date/Publication 2019-03-11 23:52:42 UTC

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