In raredd/cmprsk2: cmprsk2

cmprsk2

Extensions for the cmprsk package.

See intro vignette

To install:

# install.packages('devtools')
devtools::install_github('raredd/cmprsk2', build_vignettes = TRUE)

library('cmprsk2')

options(width = 100)

library('knitr')
opts_chunk$set(fig.width = 10, fig.height = 8)

crr formula method

## model deaths with ltx and withdraw as competing events
cr1 <- crr2(Surv(futime, event(censored) == death) ~ age + sex + abo,
            data = transplant)

## include an all-cause death overall survival model
cr2 <- crr2(Surv(futime, event(censored) == death) ~ age + sex + abo,
            data = transplant,
            cox = Surv(futime, event == 'death') ~ age + sex + abo)

crr2 summary methods

summary(cr1)

library('htmlTable')
summary(
  cr2,
  html = TRUE, n = TRUE, ref = TRUE,
  htmlArgs = list(
    caption = 'CRR models.',
    rgroup = c('Age', 'Sex', 'Blood type'),
    rnames = c('+1 year change', 'Female', 'B', 'AB', 'O'),
    css.cell = 'white-space: nowrap; padding: 0px 5px 0px;'
  )
)

cuminc formula method

## can use same formula as crr2
ci1 <- cuminc2(Surv(futime, event(censored) == death) ~ abo,
               data = transplant)

## but event indicator is not required
ci2 <- cuminc2(Surv(futime, event(censored)) ~ sex,
               data = transplant)

cuminc2 summary methods

summary(ci1)

summary(ci1, times = 0:10 * 100)$est

cuminc plotting methods

par(mfrow = c(2, 2))

# ciplot(ci2)
plot(ci2, add = TRUE) ## equivalently

plot(ci2, split = 'event', add = TRUE, wh.events = 'est')


## convenience wrapper
par(mfrow = c(2, 2))
ciplot_by(
  rhs = 'sex', time = 'futime', event = 'event',
  data = transplant, by = 'abo', xlim = c(0, 1500),
  events = FALSE, single = FALSE, events.total = 2100
)

extras

## pairwise gray tests
cuminc_pairs(ci1)$p.value

timepoints2(
  ci2, html = TRUE,
  htmlArgs = list(
    caption = 'cuminc estimates at specific time points (<code>cuminc::timepoints</code>).'
  )
)

AIC(cr1$`CRR: death`)
sapply(cr1, BIC)
logLik(cr1$`CRR: death`)
deviance(cr1$`CRR: death`)

crrFits(cr1$`CRR: death`)
crrwald.test(cr1$`CRR: death`)

raredd/cmprsk2 documentation built on March 29, 2024, 5:34 a.m.