tests/pspline.R

library(survival)
#
# Tests with the pspline function, to verify the prediction aspects
#
options(na.action=na.exclude)
aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)

spfit <- coxph(Surv(time, status) ~ pspline(age) + ph.ecog, lung)

spfit2 <- coxph(Surv(time, status) ~ pspline(age) + ph.ecog, lung, x=TRUE)
x2 <- model.matrix(spfit)
all.equal(spfit2$x, x2)

keep <- (lung$age < 60)
x3 <- model.matrix(spfit, data=lung[keep,])  
attr(x3, 'assign') <- NULL #subscripting loses the assign attr below
all.equal(napredict(spfit$na.action,x2)[keep,], x3)

p2 <- predict(spfit, newdata=lung[keep,])
aeq(p2, predict(spfit)[keep])


p3 <- survfit(spfit)
p4 <- survfit(spfit, newdata=lung[1:2,])
temp <- scale(x2[1:2,], center=spfit$means, scale=FALSE)%*% coef(spfit)
aeq(p3$time, p4$time)
aeq(outer(-log(p3$surv), exp(temp), '*'), -log(p4$surv))

# Check out model.frame
spfit3 <- coxph(Surv(time, status) ~ pspline(age) + sex, lung,
                model=TRUE)  #avoid the missing value
m2 <- model.frame(spfit3, data=lung[keep,])
all.equal(m2, spfit3$model[keep,], check.attributes=FALSE)

#
# Test of residuals, in response to a reported bug.  
# These are three progam paths that should all lead to the same C routine
fit <- coxph(Surv(tstart, tstop, status) ~ sex + treat + pspline(age), cgd)
fit2 <- coxph(Surv(tstart, tstop, status) ~ fit$linear, cgd, iter=0, init=1)
fit3 <- coxph(Surv(tstart, tstop, status) ~ offset(fit$linear), cgd)
all.equal(fit$resid, fit2$resid)
all.equal(fit$resid, fit3$resid)

# 
# Check using coxph.detail. The matrix multiply below only is
#  valid for the breslow approximation.
fit4 <-  coxph(Surv(tstart, tstop, status) ~ sex + treat + pspline(age),
               cgd, ties='breslow')
dt <- coxph.detail(fit4, riskmat=TRUE)

# the results of coxph.detail used to be in time order, now are in data set
#  order
rscore <- exp(fit4$linear)
exp4 <- (rscore *dt$riskmat) %*% dt$hazard
r4 <- cgd$status - exp4
aeq(r4, fit4$resid)

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survival documentation built on Aug. 24, 2021, 5:06 p.m.