cindex.comp.meta: Function to compare two concordance indices

In survcomp: Performance Assessment and Comparison for Survival Analysis

Description

This function compares two lists of concordance indices computed from the same survival data by using the function concordance.index. The statistical test is a Student t test for dependent samples.

Usage

cindex.comp.meta(list.cindex1, list.cindex2, hetero = FALSE)

Arguments

list.cindex1	first list of concordance indices as returned by the concordance.index function.
list.cindex2	second list of concordance indices as returned by the concordance.index function.
hetero	if TRUE, a random effect model is use to compute the meta-estimators. Otherwise a fixed effect model is used.

Details

In meta-analysis, we estimate the statistic of interest in several independent datasets. It results a list of estimates such as list of concordance indices. The two lists of concordance indices must be computed from the same samples (and corresponding survival data). The function computes a meta-estimator for the correlations between the two scores and uses a Student t test for dependent samples.

Value

p.value	p-value from the Student t test for the comparison cindex1 > cindex2.
cindex1	meta-estimator of the first concordance index.
cindex2	meta-estimator of the second concordance index.

Author(s)

Benjamin Haibe-Kains

References

Cochrane, W. G. (1954) "The combination of estimates from different experiments", Biometrics, 10, pages 101–129.

Haibe-Kains, B. and Desmedt, C. and Sotiriou, C. and Bontempi, G. (2008) "A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?", Bioinformatics, 24, 19, pages 2200–2208.

See Also

concordance.index.

Examples

#first dataset
set.seed(12345)
age <- rnorm(100, 50, 10)
size <- rexp(100,1)
stime <- rexp(100)
cens <- runif(100,.5,2)
sevent <- as.numeric(stime <= cens)
stime <- pmin(stime, cens)
c1.1 <- concordance.index(x=age, surv.time=stime, surv.event=sevent,
  method="noether")
c2.1 <- concordance.index(x=size, surv.time=stime, surv.event=sevent,
  method="noether")
#second dataset
set.seed(54321)
age <- rnorm(110, 53, 10)
size <- rexp(110,1.1)
stime <- rexp(110)
cens <- runif(110,.55,2)
sevent <- as.numeric(stime <= cens)
stime <- pmin(stime, cens)
c1.2 <- concordance.index(x=age, surv.time=stime, surv.event=sevent,
  method="noether")
c2.2 <- concordance.index(x=size, surv.time=stime, surv.event=sevent,
  method="noether")
cindex.comp.meta(list.cindex1=list("cindex.age1"=c1.1, "cindex.age2"=c1.2),
  list.cindex2=list("cindex.size1"=c2.1, "cindex.size2"=c2.2))

Example output

Loading required package: survival
Loading required package: prodlim
$p.value
[1] 0.009257754

$cindex1
[1] 0.5551768

$cindex2
[1] 0.4726647

survcomp documentation built on Nov. 8, 2020, 4:54 p.m.