forsearch_cph: Create Statistics of Forward Search in a Cox Proportional...

In forsearch: Diagnostic Analysis Using Forward Search Procedure for Various Models

Create Statistics of Forward Search in a Cox Proportional Hazard Database

Description

Prepares summary statistics at each stage of forward search for subsequent plotting.

Usage

forsearch_cph(alldata, formula.rhs, nofactform, initial.sample=1000, 
      skip.step1=NULL, ties = "efron", maxdisturb=.01, proportion=TRUE, 
      unblinded=TRUE, begin.diagnose= 100, verbose=TRUE)

Arguments

alldata	Data frame whose first 3 columns are Observation, event.time, and status, and whose last columns are independent variables. Factor variables must be defined in advance.
formula.rhs	The right hand side of a formula object (omit tilde '~')
nofactform	Formula, omitting all factor variables
initial.sample	Number of observations in Step 1 of forward search
skip.step1	NULL or a vector of integers for observations to be included in Step 1
ties	Method for handling ties in event time, "efron", "breslow" or "exact"; see survival::coxph
maxdisturb	Amount of maximum disturbance to add to each event time to prevent ties
proportion	Logical. TRUE causes running of survival::cox.zph on each stage
unblinded	TRUE causes printing of presumed analysis structure
begin.diagnose	Numeric. Indicates where in code to begin printing diagnostics. 0 prints all; 100 prints none
verbose	TRUE causes function identifier to display before and after run

Details

Step 1 requires one additional observation to be included in database to prevent failure of Wald statistic in Step 2 calculation of coxph function

Value

LIST

Rows in stage	Observation numbers of rows included at each stage
Number of model parameters	Number of fixed coefficients in Cox model
Fixed parameter estimates	Vector of parameter estimates at each stage
Wald Test	Vector of Wald tests at each stage
LogLikelihood	Vector of null and overall coefficients log likelihoods at each stage
Likelihood ratio test	Vector of LRTs at each stage
Leverage	Matrix of leverage of each observation at each stage
Call	Call to this function

Author(s)

William R. Fairweather

References

Atkinson, A and M Riani. Robust Diagnostic Regression Analysis, Springer, New York, 2000.

Examples

Observation <- 1:60
xx1 <- runif(60)
xx2 <- runif(60)
treat <- c(rep("A",30),rep("B",20),rep("C",10))
treat <- as.factor(treat)
event.time <- trunc(100*runif(60))
statusx <- c(rep(1,22),rep(0,8),rep(1,17),rep(0,3),rep(1,6),rep(0,4))
index3 <- sample(1:60,60)
xindep <- data.frame(Observation,event.time,status=statusx,xx1,xx2,treat)
formula.rhs <- "xx1 + xx2 + treat"
coxph.out05 <- forsearch_cph(alldata=xindep, formula.rhs=formula.rhs, 
    nofactform="xx1 + xx2", skip.step1=NULL, ties="efron", initial.sample=500, 
    begin.diagnose=100)

forsearch documentation built on April 4, 2025, 5:52 a.m.