binseqtest-internal {binseqtest}

Internal functions

Description

Internal functions, not to be called by user

Usage

validAbparms(object)
validBound(object)
validBoundEst(object)
validBoundNBF(object)

abBindBothCalcK(object)
abtoBound(from)

pCalc(S,N,K,order,theta0=.5,alternative="two.sided",ponly=FALSE)
ciCalc(S,N,K,order,type="upper",alpha=0.025)

missNAbparms(ab,missN=NULL,...)

Arguments

object

object, usually a boundary of some class

from

an object of class abparms

S

vector of number of successes

N

vector of number of trials

K

vector of number of ways to reach each bounary point

order

vector of ordering of boundary points

theta0

null value of probability of success each binary random variable

alternative

character, either 'two.sided', 'less', or 'greater'

ponly

logical, should only the specific p-value type given by alternative be calculated

type

character, type of one-sided confidence interval to calculate, either 'upper' or 'lower'

alpha

numeric, amount of error to allow on the one side of the confidence interval

ab

object of class 'abparms'

missN

numeric vector, the N values where assessments are missed

...

arguments passed to other functions, not used

Details

The validXX functions check that the object is a valid member of the class XX. For example, validBound checks that a bound object is OK by sum the probability distribution using the N,S, and K values and checking that it is within computer error of 1. The validity checks are run automatically by the new() function as part of the S4 implementation.

The function abBindBothCalcK takes an abparms object and creates a bound object. It requires calculating K, which is the number of ways to reach each boundary point. It ignores the binding argument and assumes all boundaries are binding. The abtoBound function uses the binding argument to create either a bound object (for binding='both') or a boundNBF object otherwise. Users can use the as function to coerce an abparms object to a bound object.

The function pCalc takes a boundary and calculates p-values, and outputs a vector of p-values (ponly=TRUE) or list of 3 vectors (plower,pupper, pval).

The function cCalc takes a boundary and calculates one of the one sided confidence intervals as directed by the type argument (either 'upper' or 'lower').

The functions analyzeBound and analyzeBoundNBF take objects of the bound and boundNBF classes and create ones of the boundEst and boundNBFEst classes. This means basically that the confidence intervals and p-values are calculated that go with those bounds.

The functions getAlternative and getTSalpha get those parameters from the inputs.

The function missNAbparms modifies abparms objects to reflect missing assessments. This is the working function for the missN option in modify.