bfw: Settings

In oeysan/bfw: Bayesian Framework for Computational Modeling

Settings

Description

main settings for bfw

Usage

bfw(
  job.title = NULL,
  job.group = NULL,
  jags.model,
  jags.seed = NULL,
  jags.method = NULL,
  jags.chains = NULL,
  custom.function = NULL,
  custom.model = NULL,
  params = NULL,
  saved.steps = 10000,
  thinned.steps = 1,
  adapt.steps = NULL,
  burnin.steps = NULL,
  initial.list = list(),
  custom.name = NULL,
  project.name = "Project",
  project.dir = "Results/",
  project.data = NULL,
  time.stamp = TRUE,
  save.data = FALSE,
  data.set = "AllData",
  data.format = "csv",
  raw.data = FALSE,
  run.robust = FALSE,
  merge.MCMC = FALSE,
  run.diag = FALSE,
  sep = ",",
  silent = FALSE,
  ...
)

Arguments

job.title	title of analysis, Default: NULL
job.group	for some hierarchical models with several layers of parameter names (e.g., latent and observed parameters), Default: NULL
jags.model	specify which module to use
jags.seed	specify seed to replicate a analysis, Default: NULL
jags.method	specify method for JAGS (e.g., parallel or simple), Default: NULL
jags.chains	specify specify number of chains for JAGS, Default: NULL
custom.function	custom function to use (e.g., defined function, external R file or string with function), Default: NULL
custom.model	define a custom model to use (e.g., string or text file (.txt), Default: NULL
params	define parameters to observe, Default: NULL
saved.steps	define the number of iterations/steps/chains in the MCMC simulations, Default: 10000
thinned.steps	save every kth step of the original saved.steps, Default: 1
adapt.steps	the number of adaptive iterations to use at the start of each simulation, Default: NULL
burnin.steps	the number of burnin iterations, NOT including the adaptive iterations to use for the simulation, Default: NULL
initial.list	initial values for analysis, Default: list()
custom.name	custom name of project, Default: NULL
project.name	name of project, Default: 'Project'
project.dir	define where to save data, Default: 'Results/'
project.data	define data to use for analysis (e.g., csv, rda, custom data.frame or matrix, or data included in package, Default: NULL
time.stamp	logical, indicating whether or not to append unix time stamp to file name, Default: TRUE
save.data	logical, indicating whether or not to save data, Default: FALSE
data.set	define subset of data, Default: 'AllData'
data.format	define what data format is being used, Default: 'csv'
raw.data	logical, indicating whether or not to use unprocessed data, Default: FALSE
run.robust	logical, indicating whether or not robust analysis, Default: FALSE
merge.MCMC	logical, indicating whether or not to merge MCMC chains, Default: FALSE
run.diag	logical, indicating whether or not to run diagnostics, Default: FALSE
sep	symbol to separate data (e.g., comma-delimited), Default: ','
silent	logical, indicating whether or not to run analysis without output, Default: FALSE
...	further arguments passed to or from other methods

Details

Settings act like the main framework for bfw, connecting function, model and JAGS.

Value

data from MCMC RunMCMC

See Also

head,modifyList,capture.output

oeysan/bfw documentation built on March 27, 2022, 7:41 p.m.