rho.file {rhoR}

Rho using a file

Description

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.

Usage

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