R: Tidiers for coxph object

coxph_tidiers {broom} | R Documentation

## Tidiers for coxph object

### Description

Tidy the coefficients of a Cox proportional hazards regression model, construct predictions, or summarize the entire model into a single row.

### Usage

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

    ## S3 method for class 'coxph'
    augment(x, data = stats::model.frame(x), newdata,
      type.predict = "lp", type.residuals = "martingale", ...)

    ## S3 method for class 'coxph'
    glance(x, ...)

### Arguments

`x` | "coxph" object
`exponentiate` | whether to report the estimate and confidence intervals on an exponential scale
`conf.int` | confidence level to be used for CI
`...` | Extra arguments, not used
`data` | original data for `augment`
`newdata` | new data on which to do predictions
`type.predict` | type of predicted value (see `predict.coxph`)
`type.residuals` | type of residuals (see `residuals.coxph`)

### Details

When the modeling was performed with `na.action = "na.omit"` (as is the typical default), rows with NA in the initial data are omitted entirely from the augmented data frame. When the modeling was performed with `na.action = "na.exclude"`, one should provide the original data as a second argument, at which point the augmented data will contain those rows (typically with NAs in place of the new columns). If the original data is not provided to `augment` and `na.action = "na.exclude"`, a warning is raised and the incomplete rows are dropped.

### Value

`tidy` returns a data.frame with one row for each term, with columns

`estimate` | estimate of slope
`std.error` | standard error of estimate
`statistic` | test statistic
`p.value` | p-value

`augment` returns the original data.frame with additional columns added:

`.fitted` | predicted values
`.se.fit` | standard errors
`.resid` | residuals (not present if `newdata` is provided)

`glance` returns a one-row data.frame with statistics calculated on the cox regression.

### See Also

na.action

### Examples

    if (require("survival", quietly = TRUE)) {
        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()
    }

[Package broom version 0.4.4 Index]