run_emc {EMC2} | R Documentation |
Although typically users will rely on fit
, this function can be used for more fine-tuned specification of estimation needs.
The function will throw an error if a stage is skipped,
the stages have to be run in order ("preburn", "burn", "adapt", "sample").
More details can be found in the fit
help files (?fit
).
run_emc(
emc,
stage,
stop_criteria,
p_accept = 0.8,
step_size = 100,
verbose = FALSE,
verboseProgress = FALSE,
fileName = NULL,
particles = NULL,
particle_factor = 50,
cores_per_chain = 1,
cores_for_chains = length(emc),
max_tries = 20,
n_blocks = 1
)
emc |
An emc object |
stage |
A string. Indicates which stage is to be run, either |
stop_criteria |
A list. Defines the stopping criteria and for which types of parameters these should hold. See |
p_accept |
A double. The target acceptance probability of the MCMC process. This fine-tunes the width of the search space to obtain the desired acceptance probability. Defaults to .8 |
step_size |
An integer. After each step, the stopping requirements as
specified by |
verbose |
Logical. Whether to print messages between each step with the current status regarding the stop_criteria. |
verboseProgress |
Logical. Whether to print a progress bar within each step or not. Will print one progress bar for each chain and only if cores_for_chains = 1. |
fileName |
A string. If specified will autosave emc at this location on every iteration. |
particles |
An integer. How many particles to use, default is |
particle_factor |
An integer. |
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 |
An integer. How many cores to use across chains.
Defaults to the number of chains. the total number of cores used is equal to |
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. |
n_blocks |
An integer. Number of blocks. Will block the parameter chains such that they are updated in blocks. This can be helpful in extremely tough models with a large number of parameters. |
An emc object
## Not run:
# First define a design
design_DDMaE <- design(data = forstmann,model=DDM,
formula =list(v~0+S,a~E, t0~1, s~1, Z~1, sv~1, SZ~1),
constants=c(s=log(1)))
# Then make the emc, we've omitted a prior here for brevity so default priors will be used.
emc <- make_emc(forstmann, design)
# Now for example we can specify that we only want to run the "preburn" phase
# for MCMC 200 iterations
emc <- run_emc(emc, stage = "preburn", stop_criteria = list(iter = 200))
## End(Not run)