RunMCMC {bfw}

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