survdiff_pairs: Pairwise 'survdiff' comparisons

In raredd/rawr: rawr miscellaneous

Pairwise survdiff comparisons

Description

Evaluate pairwise group differences in survival curves with survdiff.

Usage

survdiff_pairs(
  object,
  data = NULL,
  ...,
  method = p.adjust.methods,
  digits = getOption("digits")
)

Arguments

object	an object of class survdiff, survfit, or coxph alternatively, a formula in which case data must be provided
data	(optional) a data frame in which to interpret the variables named in object if given as a formula
...	additional arguments passed to survdiff such as na.action or rho to control the test
method	p-value correction method (default is 'holm'; see p.adjust
digits	integer indicating the number of decimal places to be used

Value

A list with three elements:

n	the number of subjects in each pair of groups
chi.sq	the chi-square statistic for a test of equality between pairs of groups
p.value	significance for each test. The lower and upper triangles of the matrix are uncorrected and adjusted, respectively, for multiple comparisons using method (the default is the Holm correction, see p.adjust)

See Also

coxph_pairs

survdiff; p.adjust; contrast from the rms package; pairwise.table

Examples

library('survival')
sdif <- survdiff(Surv(time, status) ~ sex, data = lung)
sfit <- survfit(Surv(time, status) ~ sex, data = lung)

stopifnot(identical(survdiff_pairs(sdif), survdiff_pairs(sfit)))


## numeric and integer variables will be treated as factor-like
sfit <- survfit(Surv(time, status) ~ extent, data = colon)
kmplot(sfit)
survdiff_pairs(sfit)

## compare
survdiff(Surv(time, status) ~ extent, data = colon[colon$extent %in% 1:2, ])
survdiff(Surv(time, status) ~ extent, data = colon[colon$extent %in% 2:3, ])
survdiff(Surv(time, status) ~ extent, data = colon[colon$extent %in% 3:4, ])
## etc ...


## for interactions, create a new variable with all levels
colon$int <- with(colon, interaction(sex, extent))
sfit <- survfit(Surv(time, status) ~ int, data = colon)
survdiff_pairs(sfit, rho = 1, method = 'BH')

## rawr >= 1.0.0 allows multiple variables
sfit <- survfit(Surv(time, status) ~ sex + extent, data = colon)
survdiff_pairs(sfit, rho = 1, method = 'BH')


## also allows for a formula to be passed (data arg required)
survdiff_pairs(Surv(time, status) ~ sex + extent, data = colon)


## strata will be ignored
sdif <- survdiff(Surv(time, status) ~ sex + strata(inst), data = lung)
survdiff_pairs(sdif)

raredd/rawr documentation built on March 4, 2024, 1:36 a.m.