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EMC2: Extended Models of Choice 2:

The R package EMC2 provides tools to perform Bayesian hierarchical analyses of the following cognitive models: Diffusion Decision Model (DDM), Linear Ballistic Accumulator Model (LBA), Racing Diffusion Model (RDM), and Lognormal Racing Model (LNR). Specifically, the package provides functionality for specifying individual model designs, estimating the models, examining convergence as well as model fit through posterior prediction methods. It also includes various plotting functions and relative model comparison methods such as Bayes factors. In addition, users can specify their own likelihood function and perform non-hierarchical estimation. The package uses particle metropolis Markov chain Monte Carlo sampling. For hierarchical models, it uses efficient Gibbs sampling at the population level and supports a variety of covariance structures, extending the work of Gunawan and colleagues (2020).

Installation

To install the R package, and its dependencies you can use

install.packages("EMC2")

Or for the development version:

remotes::install_github("ampl-psych/EMC2",dependencies=TRUE)

Workflow Overview

Pictured below are the four phases of an EMC2cognitive model analysis with associated functions (in courier font).

 

 

For details, please see:

Stevenson, N., Donzallaz, M. C., Innes, R. J., Forstmann, B., Matzke, D., & Heathcote, A. (2024, January 30). EMC2: An R Package for cognitive models of choice. https://doi.org/10.31234/osf.io/2e4dq

Bug Reports, Contributing, and Feature Requests

If you come across any bugs, or have ideas for extensions of EMC2, you can add them as an issue here. If you would like to contribute to the package's code, please submit a pull request.

References

Stevenson, N., Donzallaz, M. C., Innes, R. J., Forstmann, B., Matzke, D., & Heathcote, A. (2024, January 30). EMC2: An R Package for cognitive models of choice. https://doi.org/10.31234/osf.io/2e4dq

Gunawan, D., Hawkins, G. E., Tran, M. N., Kohn, R., & Brown, S. D. (2020). New estimation approaches for the hierarchical Linear Ballistic Accumulator model. Journal of Mathematical Psychology, 96, 102368. https://doi.org/10.1016/j.jmp.2020.102368

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Version

Install

install.packages('EMC2')

Monthly Downloads

396

Version

2.1.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Maintainer

Niek Stevenson

Last Published

October 14th, 2024

Functions in EMC2 (2.1.0)

contr.decreasing

Contrast to enforce decreasing estimates
make_random_effects

Make random effects
make_data

Simulate data
merge_chains

Merge samples
pairs_posterior

Plot within-chain correlations
get_pars

Filter/manipulate parameters from emc object
run_sbc

Simulation-based calibration
plot_pars

Plots density for parameters
plot_prior

Title
get_data.emc

Get data
sampled_p_vector

Get model parameters from a design
run_bridge_sampling

Estimating Marginal likelihoods using WARP-III bridge sampling
parameters.emc

Returns a parameter type from an emc object as a data frame.
run_emc

Custom function for more controlled model estimation
make_emc

Make an emc object
plot.emc

Plot function for emc objects
predict.emc

Generate posterior predictives
prior

Prior specification
plot_defective_density

Plot defective densities for each subject and cell
plot_fit

Posterior predictive checks
mapped_par

Parameter mapping back to the design factors
posterior_summary.emc

Posterior quantiles
plot_sbc_hist

Plot the histogram of the observed rank statistics of SBC
recovery.emc

Recovery plots
get_BayesFactor

Bayes Factors
profile_plot

Likelihood profile plots
init_chains

Initialize chains
plot_relations

Plot relations
hypothesis.emc

Within-model hypothesis testing
subset.emc

Shorten an emc object
plot_sbc_ecdf

Plot the ECDF difference in SBC ranks
samples_LNR

An emc object of an LNR model of the Forstmann dataset using the first three subjects
summary.emc

Summary statistics for emc objects
LNR

The Log-Normal Race Model
chain_n

chain_n()
check.emc

Convergence checks for an emc object
compare

Information criteria and marginal likelihoods
DDM

The Diffusion Decision Model
EMC2-package

EMC2: Bayesian Hierarchical Analysis of Cognitive Models of Choice
contr.anova

Anova style contrast matrix
RDM

The Racing Diffusion Model
compare_subject

Information criteria for each participant
LBA

The Linear Ballistic Accumulator model
contr.increasing

Contrast to enforce increasing estimates
contr.bayes

Contrast to enforce equal prior variance on each level
fit.emc

Model estimation in EMC2
ess_summary.emc

Effective sample size
design

Specify a design and model
gd_summary.emc

Gelman-Rubin statistic
forstmann

Forstmann et al.'s data
credible.emc

Posterior credible interval tests