Learn R Programming

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:.

 

 

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

Copy Link

Version

Install

install.packages('EMC2')

Monthly Downloads

301

Version

3.2.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Maintainer

Niek Stevenson

Last Published

June 27th, 2025

Functions in EMC2 (3.2.0)

contr.increasing

Contrast Enforcing Increasing Estimates
gd_summary.emc

Gelman-Rubin Statistic
convolve_design_matrix

Convolve Events with HRF to Construct Design Matrices
forstmann

Forstmann et al.'s Data
factor_diagram

Factor diagram plot #Makes a factor diagram plot. Heavily based on the fa.diagram function of the psych package.
design_fmri

Create fMRI Design for EMC2 Sampling
get_prior.emc

Get Prior
get_trend_pnames

Get parameter types from trend object
get_design.emc.prior

Get Design
get_pars

Filter/Manipulate Parameters from emc Object
ess_summary.emc

Effective Sample Size
group_design

Create Group-Level Design Matrices
pairs_posterior

Plot Within-Chain Correlations
chain_n

MCMC Chain Iterations
high_pass_filter

Apply High-Pass Filtering to fMRI Data
model_averaging

Model Averaging
compare_subject

Information Criteria For Each Participant
contr.anova

Anova Style Contrast Matrix
make_data

Simulate Data
make_emc

Make an emc Object
credible.emc

Posterior Credible Interval Tests
make_random_effects

Generate Subject-Level Parameters
make_trend

Create a trend specification for model parameters
plot_design.emc.design

Plot Design
plot_design_fmri

Plot fMRI Design Matrix
cut_factors

Cut Factors Based on Credible Loadings
plot_fmri

Plot fMRI peri-stimulus time courses
plot_pars

Plots Density for Parameters
design

Specify a Design and Model
get_BayesFactor

Bayes Factors
get_data.emc

Get Data
mapped_pars

Parameter Mapping Back to the Design Factors
predict.emc.prior

Generate Posterior/Prior Predictives
trend_help

Get help information for trend kernels and bases
merge_chains

Merge Samples
prior

Specify Priors for the Chosen Model
update2version

Update EMC Objects to the Current Version
run_bridge_sampling

Estimating Marginal Likelihoods Using WARP-III Bridge Sampling
plot_cdf

Plot Defective Cumulative Distribution Functions
plot_density

Plot Defective Densities
prior_help

Prior Specification Information
run_emc

Fine-Tuned Model Estimation
samples_LNR

LNR Model of Forstmann Data (First 3 Subjects)
subset.emc

Shorten an emc Object
summary.emc

Summary Statistics for emc Objects
profile_plot

Likelihood Profile Plots
fit.emc

Model Estimation in EMC2
parameters.emc.prior

Return Data Frame of Parameters
split_timeseries

Split fMRI Timeseries Data by ROI Columns
plot.emc.design

Plot method for emc.design objects
plot.emc.prior

Plot a prior
plot.emc

Plot Function for emc Objects
reshape_events

Reshape events data for fMRI analysis
plot_sbc_ecdf

Plot the ECDF Difference in SBC Ranks
recovery.emc

Recovery Plots
credint.emc.prior

Posterior Quantiles
plot_relations

Plot Group-Level Relations
hypothesis.emc

Within-Model Hypothesis Testing
init_chains

Initialize Chains
plot_sbc_hist

Plot the Histogram of the Observed Rank Statistics of SBC
plot_stat

Plot Statistics on Data
summary.emc.design

Summary method for emc.design objects
summary.emc.prior

Summary method for emc.prior objects
sampled_pars

Get Model Parameters from a Design
run_sbc

Simulation-Based Calibration
MRI

GLM model for fMRI data
DDMGNG

The GNG (go/nogo) Diffusion Decision Model
MRI_AR1

Create an AR(1) GLM model for fMRI data
DDM

The Diffusion Decision Model
EMC2-package

EMC2: Bayesian Hierarchical Analysis of Cognitive Models of Choice
LNR

The Log-Normal Race Model
LBA

The Linear Ballistic Accumulator model
RDM

The Racing Diffusion Model
SDT

Gaussian Signal Detection Theory Model for Binary Responses
align_loadings

Reorder MCMC Samples of Factor Loadings
contr.decreasing

Contrast Enforcing Decreasing Estimates
contr.bayes

Contrast Enforcing Equal Prior Variance on each Level
auto_thin.emc

Automatically Thin an emc Object
check.emc

Convergence Checks for an emc Object
compare

Information Criteria and Marginal Likelihoods