bfw {bfw}

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