Helper functions for event history analysis with the survival package.
Install from GitHub repository.
library(devtools) install_github('junkka/ehahelper')
Make a data.frame of a survfit
or coxph
object for visualization with ggplot2.
library(ehahelper) library(survival) library(ggplot2) surv_object <- coxph(Surv(time, status) ~ strata(x), data = aml) ggplot(ggsurv(surv_object), aes(time, surv, color=strata)) + geom_step()
ggplot2 implementation for visualizing scaled Schoenfield residuals form a cox.zph object.
bladder1 <- bladder[bladder$enum < 5, ] fit <- coxph(Surv(stop, event) ~ (rx + size + number) * strata(enum) + cluster(id), bladder1) x <- cox.zph(fit, transform = "identity") gg_zph(x) gg_zph(x, log = TRUE)
Convert coxme objects to tidy format.
library(broom) library(coxme) fit <- coxme(Surv(y, uncens) ~ trt + (1|center), eortc) knitr::kable(tidy(fit, exp = T), digits = 3)
fit_g <- glance(fit) knitr::kable(as.data.frame(t(fit_g)), digits = 3)
Using a coxme model, add fitted values and standard errors to original dataset.
eortc_augmented <- augment(fit, eortc) knitr::kable(head(eortc_augmented))
Get predicted vales based on a mixed-effects Cox model, fitted using the coxme package. Extends the standard predict.coxme function by allowing for new data, and by calculating relative risks, either overall or within stratum.
new_data <- data.frame(trt = unique(eortc$trt)) predict_coxme(fit, newdata = new_data, type = "risk")
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