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

214

Version

3.3.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Maintainer

Niek Stevenson

Last Published

December 2nd, 2025

Functions in EMC2 (3.3.0)

compare_subject

Information Criteria For Each Participant
contr.anova

Anova Style Contrast Matrix
chain_n

MCMC Chain Iterations
forstmann

Forstmann et al.'s Data
gd_summary.emc

Gelman-Rubin Statistic
check.emc

Convergence Checks for an emc Object
credible.emc

Posterior Credible Interval Tests
fit.emc

Model Estimation in EMC2
compare

Information Criteria and Marginal Likelihoods
factor_diagram

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

Posterior Quantiles
group_design

Create Group-Level Design Matrices
get_trend_pnames

Get parameter types from trend object
get_BayesFactor

Bayes Factors
get_data.emc

Get Data
cut_factors

Cut Factors Based on Credible Loadings
design

Specify a Design and Model
get_pars

Filter/Manipulate Parameters from emc Object
get_prior.emc

Get Prior
convolve_design_matrix

Convolve Events with HRF to Construct Design Matrices
ess_summary.emc

Effective Sample Size
contr.increasing

Contrast Enforcing Increasing Estimates
design_fmri

Create fMRI Design for EMC2 Sampling
high_pass_filter

Apply High-Pass Filtering to fMRI Data
make_random_effects

Generate Subject-Level Parameters
get_design.emc.prior

Get Design
get_group_design.emc.prior

Get Group Design
merge_chains

Merge Samples
model_averaging

Model Averaging
make_data

Simulate Data
make_emc

Make an emc Object
plot.emc

Plot Function for emc Objects
plot_density

Plot Defective Densities
make_SEM_diagram

Make SEM Diagram
pairs_posterior

Plot Within-Chain Correlations
hypothesis.emc

Within-Model Hypothesis Testing
init_chains

Initialize Chains
plot.emc.design

Plot method for emc.design objects
plot_delta

Plot Difference of Cumulative Distribution Functions
make_sem_structure

Define Structural Equation Model (SEM) Matrices
plot_cdf

Plot Defective Cumulative Distribution Functions
parameters.emc.prior

Return Data Frame of Parameters
plot_design.emc.design

Plot Design
plot_caf

Plot conditional accuracy functions
plot_pars

Plots Density for Parameters
mapped_pars

Parameter Mapping Back to the Design Factors
plot_ss_if

Plot Inhibition Functions
plot_ss_srrt

Plot Mean SRRT
make_trend

Create a trend specification for model parameters
plot.emc.prior

Plot a prior
plot_sbc_ecdf

Plot the ECDF Difference in SBC Ranks
plot_stat

Plot Statistics on Data
plot_trend

Plots trends over time
profile_plot

Likelihood Profile Plots
prior_help

Prior Specification Information
rotate_loadings

Rotate loadings based on posterior median
reshape_events

Reshape events data for fMRI analysis
recovery.emc

Recovery Plots
register_trend

Register a custom C++ trend kernel
run_bridge_sampling

Estimating Marginal Likelihoods Using WARP-III Bridge Sampling
plot_sbc_hist

Plot the Histogram of the Observed Rank Statistics of SBC
run_emc

Fine-Tuned Model Estimation
plot_relations

Plot Group-Level Relations
run_hyper

Run a Group-level Model.
trend_help

Get help information for trend kernels and bases
update2version

Update EMC Objects to the Current Version
subset.emc

Shorten an emc Object
split_timeseries

Split fMRI Timeseries Data by ROI Columns
summary.emc

Summary Statistics for emc Objects
summary.emc.design

Summary method for emc.design objects
sampled_pars

Get Model Parameters from a Design
samples_LNR

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

Generate Posterior/Prior Predictives
summary.emc.group_design

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

Summary method for emc.prior objects
plot_design_fmri

Plot fMRI Design Matrix
plot_fmri

Plot fMRI peri-stimulus time courses
prior

Specify Priors for the Chosen Model
run_sbc

Simulation-Based Calibration
RDM

The Racing Diffusion Model
DDM

The Diffusion Decision Model
EMC2-package

EMC2: Bayesian Hierarchical Analysis of Cognitive Models of Choice
MRI

GLM model for fMRI data
LBA

The Linear Ballistic Accumulator model
align_loadings

Reorder MCMC Samples of Factor Loadings
LNR

The Log-Normal Race Model
MRI_AR1

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

Gaussian Signal Detection Theory Model for Binary Responses
DDMGNG

The GNG (go/nogo) Diffusion Decision Model
auto_thin.emc

Automatically Thin an emc Object
contr.bayes

Contrast Enforcing Equal Prior Variance on each Level
contr.decreasing

Contrast Enforcing Decreasing Estimates