Rho using a file

This function calculates rho and kappa for a given testSet as defined by the file and columns (col1, col2), and returns a list containing both values. Called by rho.

rho.file(
  x,
  col1,
  col2,
  OcSBaserate = NULL,
  testSetBaserateInflation = 0,
  OcSLength = 10000,
  replicates = 800,
  ScSKappaThreshold = 0.9,
  ScSKappaMin = 0.4,
  ScSPrecisionMin = 0.6,
  ScSPrecisionMax = 1
)

Arguments

x	The observed kappa value, testSet or contingencyTable that will be tested with rho
col1	The first column from file
col2	The second column from file
OcSBaserate	The baserate of the observed codeSet (defaults to baserate of testSet or contingencyTable)
testSetBaserateInflation	The minimum baserate from the sampling procedure
OcSLength	The length of the observed codeSet
replicates	The number of simulated codeSets to use in the null hypothesis distribution for rho; similar to replicates in a Monte Carlo study
ScSKappaThreshold	The maximum kappa value used to generate simulated codeSets in the null hypothesis distribution for rho
ScSKappaMin	The minimum kappa value used to generate simulated codeSets in the null hypothesis distribution for rho
ScSPrecisionMin	The minimum precision to be used for generation of simulated codeSets in the null hypothesis distribution for rho
ScSPrecisionMax	The maximum precision to be used for generation of simulated codeSets in the null hypothesis distribution for rho

Value

rho for the given parameters

A list of the format:

rho

The rho of the codeSet

kappa

The Cohen's Kappa of the codeSet

See also

rho