tidy.coxph: Tidy a(n) coxph object

View source: R/survival-coxph-tidiers.R

tidy.coxphR Documentation

Tidy a(n) coxph object

Description

Tidy summarizes information about the components of a model. A model component might be a single term in a regression, a single hypothesis, a cluster, or a class. Exactly what tidy considers to be a model component varies across models but is usually self-evident. If a model has several distinct types of components, you will need to specify which components to return.

Usage

## S3 method for class 'coxph'
tidy(x, exponentiate = FALSE, conf.int = FALSE, conf.level = 0.95, ...)

Arguments

x

A coxph object returned from survival::coxph().

exponentiate

Logical indicating whether or not to exponentiate the the coefficient estimates. This is typical for logistic and multinomial regressions, but a bad idea if there is no log or logit link. Defaults to FALSE.

conf.int

Logical indicating whether or not to include a confidence interval in the tidied output. Defaults to FALSE.

conf.level

The confidence level to use for the confidence interval if conf.int = TRUE. Must be strictly greater than 0 and less than 1. Defaults to 0.95, which corresponds to a 95 percent confidence interval.

...

Additional arguments. Not used. Needed to match generic signature only. Cautionary note: Misspelled arguments will be absorbed in ..., where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass conf.lvel = 0.9, all computation will proceed using conf.level = 0.95. Two exceptions here are:

  • tidy() methods will warn when supplied an exponentiate argument if it will be ignored.

  • augment() methods will warn when supplied a newdata argument if it will be ignored.

Value

A tibble::tibble() with columns:

estimate

The estimated value of the regression term.

p.value

The two-sided p-value associated with the observed statistic.

statistic

The value of a T-statistic to use in a hypothesis that the regression term is non-zero.

std.error

The standard error of the regression term.

See Also

tidy(), survival::coxph()

Other coxph tidiers: augment.coxph(), glance.coxph()

Other survival tidiers: augment.coxph(), augment.survreg(), glance.aareg(), glance.cch(), glance.coxph(), glance.pyears(), glance.survdiff(), glance.survexp(), glance.survfit(), glance.survreg(), tidy.aareg(), tidy.cch(), tidy.pyears(), tidy.survdiff(), tidy.survexp(), tidy.survfit(), tidy.survreg()

Examples



# load libraries for models and data
library(survival)

# fit model
cfit <- coxph(Surv(time, status) ~ age + sex, lung)

# summarize model fit with tidiers
tidy(cfit)
tidy(cfit, exponentiate = TRUE)

lp <- augment(cfit, lung)
risks <- augment(cfit, lung, type.predict = "risk")
expected <- augment(cfit, lung, type.predict = "expected")

glance(cfit)

# also works on clogit models
resp <- levels(logan$occupation)
n <- nrow(logan)
indx <- rep(1:n, length(resp))
logan2 <- data.frame(
  logan[indx, ],
  id = indx,
  tocc = factor(rep(resp, each = n))
)

logan2$case <- (logan2$occupation == logan2$tocc)

cl <- clogit(case ~ tocc + tocc:education + strata(id), logan2)

tidy(cl)
glance(cl)

library(ggplot2)

ggplot(lp, aes(age, .fitted, color = sex)) +
  geom_point()

ggplot(risks, aes(age, .fitted, color = sex)) +
  geom_point()

ggplot(expected, aes(time, .fitted, color = sex)) +
  geom_point()


broom documentation built on Aug. 30, 2022, 1:07 a.m.