twostageTE (version 1.3)

stageTwoAnalysis: Stage two analysis

Description

Wrapper function for twoStageTE that users can directly call on their data.

Usage

stageTwoAnalysis(stageOne, explanatory, response, type = "IR-wald",  level = 0.95, combineData=FALSE)

Arguments

stageOne

Object returned from calling the function stageOneAnalysis

explanatory

Explanatory sample points

response

Observed responses at the explanatory sample points

type

String input of either "IR-wald" (default), "IR-likelihood" or "locLinear"

level

Confidence level (defaults to 0.95)

combineData

Optional boolean input on whether to combine data from both stages. Default is FALSE.

Value

List:

L1

Lower bound of CI

U1

Upper bound of CI

estimate

Threshold estimate

level

Confidence level

X1

First stage explanatory variable

Y1

First stage response variable

X2

Second stage explanatory variable

Y2

Second stage response variable

L2

Ssecond stage lower bound of CI

U2

Second stage upper bound of CI

call

Method Call

sigmaSq

Estimate of variance

deriv_d0

Derivative estimate

class

twostageTE

Examples

X=runif(25, 0,1)
Y=X^2+rnorm(n=length(X), sd=0.1)
oneStage_IR=stageOneAnalysis(X, Y, 0.25, type="IR-wald", 0.99)
X2=runif(75,oneStage_IR$L1 ,oneStage_IR$U1)
Y2=X2^2+rnorm(n=length(X2), sd=0.1)
twoStage_IR = stageTwoAnalysis(oneStage_IR, X2, Y2, type="IR-wald", 0.95)

## The function is currently defined as
function (stageOne, explanatory, response, type = "IR-wald", 
    level = 0.95, combineData = FALSE) 
{
    cl1 <- match.call(expand.dots = TRUE)
    Y_0 = stageOne$threshold
    C_1 = stageOne$C_1
    gamma1=1/3
    if (combineData) {
	explanatory = c(explanatory , 
	    stageOne$X1[stageOne$X1 > stageOne$L1 & stageOne$X1 < stageOne$U1])
	response = c(response , 
	    stageOne$Y1[stageOne$X1 > stageOne$L1 & stageOne$X1 < stageOne$U1])		
    }
    if (type == "IR-wald") {
        CI = waldConfidenceInterval_ir_stageTwo(explanatory, 
            response, Y_0, level = level, gamma1 = gamma1, C_1 = C_1, 
            n1 = length(stageOne$X1))
        return(structure(list(L2 = CI$lower, U2 = CI$upper, estimate = CI$estimate, 
            threshold = Y_0, level = level, X1 = stageOne$X1, 
            Y1 = stageOne$Y1, X2 = explanatory, Y2 = response, 
            L1 = stageOne$L1, U1 = stageOne$U1, call = cl1, sigmaSq = CI$sigmaSq, 
            deriv_d0 = CI$deriv_d0), class = "twostageTE"))
    }
    else if (type == "IR-likelihood") {
        CI = likelihoodConfidenceInterval(explanatory, response, 
            Y_0, level = level)
        return(structure(list(L2 = CI$lower, U2 = CI$upper, estimate = CI$estimate, 
            threshold = Y_0, level = level, X1 = stageOne$X1, 
            Y1 = stageOne$Y1, X2 = explanatory, Y2 = response, 
            L1 = stageOne$L1, U1 = stageOne$U1, call = cl1, sigmaSq = CI$sigmaSq, 
            deriv_d0 = CI$deriv_d0), class = "twostageTE"))
    }
    else if (type == "SIR") {
        CI = waldConfidenceInterval_sir_stageTwo(explanatory = explanatory, 
            response = response, Y_0 = Y_0, gamma1 = gamma1, 
            C_1 = C_1, level = level)
        return(structure(list(L2 = CI$lower, U2 = CI$upper, estimate = CI$estimate, 
            threshold = Y_0, level = level, X1 = stageOne$X1, 
            Y1 = stageOne$Y1, X2 = explanatory, Y2 = response, 
            L1 = stageOne$L1, U1 = stageOne$U1, call = cl1, sigmaSq = CI$sigmaSq, 
            deriv_d0 = CI$deriv_d0), class = "twostageTE"))
    }
    else if (type == "locLinear") {
        CI = linearBootstrapConfidenceInterval_stageTwo(explanatory = explanatory, 
            response = response, Y_0 = Y_0, level = level)
        return(structure(list(L2 = CI$lower, U2 = CI$upper, estimate = CI$estimate, 
            threshold = Y_0, level = level, X1 = stageOne$X1, 
            Y1 = stageOne$Y1, X2 = explanatory, Y2 = response, 
            L1 = stageOne$L1, U1 = stageOne$U1, call = cl1, sigmaSq = CI$sigmaSq, 
            deriv_d0 = CI$deriv_d0), class = "twostageTE"))
    }
    else error("stageOneAnalysis: type should be either 
        'IR-wald','IR-likelihood', 'SIR', or 'locLinear'")
  }