allen.read.mcmc.chains: Read MCMC chains from Bayesian calibration software output
In tsdye/allen.archaeology: Allen\'s Interval Algebra for Archaeologists

allen.read.mcmc.chains

R Documentation

Read MCMC chains from Bayesian calibration software output

Description

Reads chains for two intervals from one or two csv files of MCMC output from a Bayesian calibration application. The function checks for missing or incorrect parameters and whether or not files exist. It exits with an error message if there are problems.

Usage

allen.read.mcmc.chains(
  mcmc.file,
  positions,
  mcmc.file.2 = NULL,
  positions.2 = NULL,
  names = c("Interval 1", "Interval 2"),
  app = "bcal",
  decimal = ".",
  separator = ",",
  quiet = "partial"
)

Arguments

`mcmc.file`	path to the csv file of MCMC output
`positions`	a vector of 2 or 4 column indices of mcmc.file
`mcmc.file.2`	optional path to another csv file of MCMC output
`positions.2`	a vector of 2 column indices of mcmc.file.2
`names`	a vector of two strings naming the intervals specified by the positions parameters(s)
`app`	one of 'bcal', 'oxcal', or 'chronomodel'
`decimal`	optional decimal character for Chronomodel output
`separator`	optional separator character for Chronomodel output
`quiet`	One of 'no' to allow messages and warnings, 'partial' (default) to suppress messages and allow warnings, or 'yes' to suppress messages and warnings.