tidy.coxph {broom} | R Documentation |
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 cross models but is usually self-evident. If a model has several distinct types of components, you will need to specify which components to return.
## S3 method for class 'coxph' tidy(x, exponentiate = FALSE, conf.int = TRUE, conf.level = 0.95, ...)
x |
A |
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 |
conf.int |
Logical indicating whether or not to include a confidence
interval in the tidied output. Defaults to |
conf.level |
The confidence level to use for the confidence interval
if |
... |
Additional arguments. Not used. Needed to match generic
signature only. Cautionary note: Misspelled arguments will be
absorbed in |
A tibble::tibble with one row for each term and columns:
estimate |
estimate of slope |
std.error |
standard error of estimate |
statistic |
test statistic |
p.value |
p-value |
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
library(survival) cfit <- coxph(Surv(time, status) ~ age + sex, lung) 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()