bone: Bone marrow treatemtn survival data

In gamair: Data for 'GAMs: An Introduction with R'

Description

Data from Klein and Moeschberger (2003), for 23 patients with non-Hodgkin's lymphoma.

Usage

data(bone)

Format

A data frame with 3 columns and 23 rows. Each row refers to one patient. The columns are:

t

Time of death, relapse or last follow up after treatment, in days.

d

1 for death or relapse. 0 otherwise.

trt

2 level factor. allo or auto depending on treatment recieved.

Details

The data were collected at the Ohio State University bone marrow transplant unit. The allo treatment is bone marrow transplant from a matched sibling donor. The auto treatment consists of bone marrow removal and replacement after chemotherapy.

Source

Klein and Moeschberger (2003).

References

Klein and Moeschberger (2003) Survival Analysis: techniques for censored and truncated data.

Wood, S.N. (2017) Generalized Additive Models: An Introduction with R

Examples

## example of fitting a Cox PH model as a Poisson GLM... 
## First a function to convert data frame of raw data
## to data frame of artificial data...

psurv <- function(surv,time="t",censor="d",event="z") {
## create data frame to fit Cox PH as Poisson model.
## surv[[censor]] should be 1 for event or zero for censored.   
  if (event %in% names(surv)) warning("event name already in use in data frame")
  surv <- as.data.frame(surv)[order(surv[[time]]),] ## ascending time order
  et <- unique(surv[[time]][surv[[censor]]==1]) ## unique times requiring record
  es <- match(et,surv[[time]]) ## starts of risk sets in surv
  n <- nrow(surv); t <- rep(et,1+n-es) ## times for risk sets
  st <- cbind(0,surv[unlist(apply(matrix(es),1,function(x,n) x:n,n=n)),])
  st[st[[time]]==t&st[[censor]]!=0,1] <- 1 ## signal events 
  st[[time]] <- t ## reset time field to time for this risk set
  names(st)[1] <- event
  st
} ## psurv

## Now fit the model...
require(gamair)
data(bone);bone$id <- 1:nrow(bone)
pb <- psurv(bone); pb$tf <- factor(pb$t)
## Note that time factor tf should go first to ensure
## it has no contrasts applied... 
b <- glm(z ~ tf + trt - 1,poisson,pb)
drop1(b,test="Chisq") ## test for effect - no evidence

## martingale and deviance residuals
chaz <- tapply(fitted(b),pb$id,sum) ## cum haz by subject
mrsd <- bone$d - chaz
drsd <- sign(mrsd)*sqrt(-2*(mrsd + bone$d*log(chaz)))

## Estimate and plot survivor functions and standard
## errors for the two groups...

te <- sort(unique(bone$t[bone$d==1])) ## event times

## predict survivor function for "allo"...
pd <- data.frame(tf=factor(te),trt=bone$trt[1])
fv <- predict(b,pd)
H <- cumsum(exp(fv)) ## cumulative hazard
plot(stepfun(te,c(1,exp(-H))),do.points=FALSE,ylim=c(0,1),xlim=c(0,550),
     main="black allo, grey auto",ylab="S(t)",xlab="t (days)")
## add s.e. bands...     
X <- model.matrix(~tf+trt-1,pd)
J <- apply(exp(fv)*X,2,cumsum)
se <- diag(J%*%vcov(b)%*%t(J))^.5
lines(stepfun(te,c(1,exp(-H+se))),do.points=FALSE,lty=2)
lines(stepfun(te,c(1,exp(-H-se))),do.points=FALSE,lty=2)

## same for "auto"...
pd <- data.frame(tf=factor(te),trt=bone$trt[23])
fv <- predict(b,pd); H <- cumsum(exp(fv))
lines(stepfun(te,c(1,exp(-H))),col="grey",lwd=2,do.points=FALSE)
X <- model.matrix(~tf+trt-1,pd)
J <- apply(exp(fv)*X,2,cumsum)
se <- diag(J%*%vcov(b)%*%t(J))^.5
lines(stepfun(te,c(1,exp(-H+se))),do.points=FALSE,lty=2,col="grey",lwd=2)
lines(stepfun(te,c(1,exp(-H-se))),do.points=FALSE,lty=2,col="grey",lwd=2)

gamair documentation built on Aug. 23, 2019, 5:03 p.m.