RunMCMC: Run MCMC

In bfw: Bayesian Framework for Computational Modeling

Run MCMC

Description

Conduct MCMC simulations using JAGS

Usage

RunMCMC(
  jags.model,
  params = NULL,
  name.list,
  data.list,
  initial.list = list(),
  run.contrasts = FALSE,
  use.contrast = "between",
  contrasts = NULL,
  custom.contrast = NULL,
  run.ppp = FALSE,
  k.ppp = 10,
  n.data,
  credible.region = 0.95,
  save.data = FALSE,
  ROPE = NULL,
  merge.MCMC = FALSE,
  run.diag = FALSE,
  param.diag = NULL,
  sep = ",",
  monochrome = TRUE,
  plot.colors = c("#495054", "#e3e8ea"),
  graphic.type = "pdf",
  plot.size = "15,10",
  scaling = 100,
  plot.aspect = NULL,
  vector.graphic = FALSE,
  point.size = 12,
  font.type = "serif",
  one.file = TRUE,
  ppi = 300,
  units = "in",
  layout = "a4",
  layout.inverse = FALSE,
  ...
)

Arguments

jags.model	specify which module to use
params	define parameters to observe, Default: NULL
name.list	list of names
data.list	list of data
initial.list	initial values for analysis, Default: list()
run.contrasts	logical, indicating whether or not to run contrasts, Default: FALSE
use.contrast	choose from "between", "within" and "mixed". Between compare groups at different conditions. Within compare a group at different conditions. Mixed compute all comparisons, Default: "between",
contrasts	define contrasts to use for analysis (defaults to all) , Default: NULL
custom.contrast	define contrasts for custom models , Default: NULL
run.ppp	logical, indicating whether or not to conduct ppp analysis, Default: FALSE
k.ppp	run ppp for every kth length of MCMC chains, Default: 10
n.data	sample size for each parameter
credible.region	summarize uncertainty by defining a region of most credible values (e.g., 95 percent of the distribution), Default: 0.95
save.data	logical, indicating whether or not to save data, Default: FALSE
ROPE	define range for region of practical equivalence (e.g., c(-0.05 , 0.05), Default: NULL
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
param.diag	define parameters to use for diagnostics, default equals all parameters, Default: NULL
sep	symbol to separate data (e.g., comma-delimited), Default: ','
monochrome	logical, indicating whether or not to use monochrome colors, else use DistinctColors, Default: TRUE
plot.colors	range of color to use, Default: c("#495054", "#e3e8ea")
graphic.type	type of graphics to use (e.g., pdf, png, ps), Default: 'pdf'
plot.size	size of plot, Default: '15,10'
scaling	scale size of plot, Default: 100
plot.aspect	aspect of plot, Default: NULL
vector.graphic	logical, indicating whether or not visualizations should be vector or raster graphics, Default: FALSE
point.size	point size used for visualizations, Default: 12
font.type	font type used for visualizations, Default: 'serif'
one.file	logical, indicating whether or not visualizations should be placed in one or several files, Default: TRUE
ppi	define pixel per inch used for visualizations, Default: 300
units	define unit of length used for visualizations, Default: 'in'
layout	define a layout size for visualizations, Default: 'a4'
layout.inverse	logical, indicating whether or not to inverse layout (e.g., landscape) , Default: FALSE
...	further arguments passed to or from other methods

Value

list containing MCMC chains , MCMC chains as matrix , summary of MCMC, list of name used, list of data, the jags model, running time of analysis and names of saved files

See Also

runjags.options,run.jags detectCores as.mcmc.list,varnames rbind.fill cor,cov,sd mvrnorm write.table

bfw documentation built on March 18, 2022, 6:19 p.m.