gelman: Potential scale reduction factor

In ggdmc: Cognitive Models

Potential scale reduction factor

Description

gelman function calls the function, gelman.diag in the coda package to calculates PSRF.

Usage

gelman(
  x,
  hyper = FALSE,
  start = 1,
  end = NA,
  confidence = 0.95,
  transform = TRUE,
  autoburnin = FALSE,
  multivariate = TRUE,
  split = TRUE,
  subchain = FALSE,
  nsubchain = 3,
  digits = 2,
  verbose = FALSE,
  ...
)

hgelman(
  x,
  start = 1,
  end = NA,
  confidence = 0.95,
  transform = TRUE,
  autoburnin = FALSE,
  split = TRUE,
  subchain = FALSE,
  nsubchain = 3,
  digits = 2,
  verbose = FALSE,
  ...
)

Arguments

x	posterior samples
hyper	a Boolean switch, indicating posterior samples are from hierarchical modeling
start	start iteration
end	end iteration
confidence	confident inteval
transform	turn on transform
autoburnin	turn on auto burnin
multivariate	multivariate Boolean switch
split	split whether split mcmc chains; When split is TRUE, the function doubles the number of chains by spliting into 1st and 2nd halves.
subchain	whether only calculate a subset of chains
nsubchain	indicate how many chains in a subset
digits	print out how many digits
verbose	print more information
...	arguments passing to coda gelman.diag.

Examples

## Not run: 
rhat1 <- hgelman(hsam); rhat1
rhat2 <- hgelman(hsam, end = 51); rhat2
rhat3 <- hgelman(hsam, confidence = .90); rhat3
rhat4 <- hgelman(hsam, transform = FALSE); rhat4
rhat5 <- hgelman(hsam, autoburnin = TRUE); rhat5
rhat6 <- hgelman(hsam, split = FALSE); rhat6
rhat7 <- hgelman(hsam, subchain = TRUE); rhat7
rhat8 <- hgelman(hsam, subchain = TRUE, nsubchain = 4);
rhat9 <- hgelman(hsam, subchain = TRUE, nsubchain = 4,
digits = 1, verbose = TRUE);

hat1 <- gelman(hsam[[1]], multivariate = FALSE); hat1
hat2 <- gelman(hsam[[1]], hyper = TRUE, verbose = TRUE); hat2
hat3 <- gelman(hsam, hyper = TRUE, verbose = TRUE); hat3
hat4 <- gelman(hsam, multivariate = TRUE, verbose = FALSE);
hat5 <- gelman(hsam, multivariate = FALSE, verbose = FALSE);
hat6 <- gelman(hsam, multivariate = FALSE, verbose = TRUE);
hat7 <- gelman(hsam, multivariate = T, verbose = TRUE);

## End(Not run)

ggdmc documentation built on April 13, 2025, 5:09 p.m.