fit: Model Estimation in EMC2

In EMC2: Bayesian Hierarchical Analysis of Cognitive Models of Choice

Model Estimation in EMC2

Description

General purpose function to estimate models specified in EMC2.

Usage

## S3 method for class 'emc'
fit(
  emc,
  stage = NULL,
  iter = 1000,
  stop_criteria = NULL,
  search_width = 1,
  step_size = 100,
  verbose = TRUE,
  fileName = NULL,
  particle_factor = 50,
  cores_per_chain = 1,
  cores_for_chains = length(emc),
  max_tries = 20,
  thin = FALSE,
  ...
)

fit(emc, ...)

Arguments

emc	An emc object created with make_emc, or a path to where the emc object is stored.
stage	A string. Indicates which stage to start the run from, either preburn, burn, adapt or sample. If unspecified, it will run the subsequent stage (if there is one).
iter	An integer. Indicates how many iterations to run in the sampling stage.
stop_criteria	A list. Defines the stopping criteria and for which types of parameters these should hold. See the details and examples section.
search_width	A double. Tunes target acceptance probability of the MCMC process. This fine-tunes the width of the search space to obtain the desired acceptance probability. 1 is the default width, increases lead to broader search.
step_size	An integer. After each step, the stopping requirements as specified by stop_criteria are checked and proposal distributions are updated. Defaults to 100.
verbose	Logical. Whether to print messages between each step with the current status regarding the stop_criteria.
fileName	A string. If specified, will auto-save emc object at this location on every iteration.
particle_factor	An integer. particle_factor multiplied by the square root of the number of sampled parameters determines the number of particles used.
cores_per_chain	An integer. How many cores to use per chain. Parallelizes across participant calculations. Only available on Linux or Mac OS. For Windows, only parallelization across chains (cores_for_chains) is available.
cores_for_chains	An integer. How many cores to use across chains. Defaults to the number of chains. The total number of cores used is equal to cores_per_chain * cores_for_chains.
max_tries	An integer. How many times should it try to meet the finish conditions as specified by stop_criteria? Defaults to 20. max_tries is ignored if the required number of iterations has not been reached yet.
thin	A boolean. If TRUE will automatically thin the MCMC samples, closely matched to the ESS. Can also be set to a double, in which case 1/thin of the chain will be removed (does not have to be an integer).
...	Additional optional arguments

Details

stop_criteria is either a list of lists with names of the stages, or a single list in which case its assumed to be for the sample stage (see examples). The potential stop criteria to be set are:

selection (character vector): For which parameters the stop_criteria should hold

mean_gd (numeric): The mean Gelman-Rubin diagnostic across all parameters in the selection

max_gd (numeric): The max Gelman-Rubin diagnostic across all parameters in the selection

min_unique (integer): The minimum number of unique samples in the MCMC chains across all parameters in the selection

min_es (integer): The minimum number of effective samples across all parameters in the selection

omit_mpsrf (Boolean): Whether to include the multivariate point-scale reduction factor in the Gelman-Rubin diagnostic. Default is FALSE.

iter (integer): The number of MCMC samples to collect.

The estimation is performed using particle-metropolis within-Gibbs sampling. For sampling details see:

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

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

Value

An emc object

Examples

# Define a design first
ADmat <- matrix(c(-1/2,1/2),ncol=1,dimnames=list(NULL,"d"))
# We also define a match function for lM
matchfun=function(d)d$S==d$lR

# Drop most subjects for speed
dat <- forstmann[forstmann$subjects %in% unique(forstmann$subjects)[1:2],]
dat$subjects <- droplevels(dat$subjects)

design_LNR <- design(data = dat,model=LNR,matchfun=matchfun,
                     formula=list(m~lM,s~1,t0~1),
                     contrasts=list(m=list(lM=ADmat)))
# Before fit can be called, we first need to make an emc object
LNR_s <- make_emc(dat, design_LNR, rt_resolution = 0.05, n_chains = 2)
# Run fit, here illustrating how to use stop_criteria (also for speed purposes)
LNR_s <- fit(LNR_s, cores_for_chains = 1, stop_criteria = list(
  preburn = list(iter = 10), burn = list(mean_gd = 2.5), adapt = list(min_unique = 20),
  sample = list(iter = 25, max_gd = 2)), verbose = FALSE, particle_factor = 30, step_size = 25)

EMC2 documentation built on April 11, 2025, 5:50 p.m.