R: Functional Form of Continuous Variable in Cox Proportional...

ggcoxfunctional {survminer} | R Documentation

## Functional Form of Continuous Variable in Cox Proportional Hazards Model

### Description

Displays graphs of continuous explanatory variable against martingale residuals of null cox proportional hazards model, for each term in of the right side of `formula`. This might help to properly choose the functional form of continuous variable in cox model (coxph). Fitted lines with lowess function should be linear to satisfy cox proportional hazards model assumptions.

### Usage

    ggcoxfunctional(formula, data = NULL, fit, iter = 0, f = 0.6,
      point.col = "red", point.size = 1, point.shape = 19, point.alpha = 1,
      xlim = NULL, ylim = NULL,
      ylab = "Martingale Residuals \nof Null Cox Model", title = NULL,
      caption = NULL, ggtheme = theme_survminer(), ...)

    ## S3 method for class 'ggcoxfunctional'
    print(x, ..., newpage = TRUE)

### Arguments

`formula` | a formula object, with the response on the left of a ~ operator, and the terms on the right. The response must be a survival object as returned by the Surv function.
`data` | a `data.frame` in which to interpret the variables named in the formula,
`fit` | an object of class coxph.object - created with coxph function.
`iter` | parameter of lowess.
`f` | parameter of lowess.
`point.col, point.size, point.shape, point.alpha` | color, size, shape and visibility to be used for points.
`xlim, ylim` | x and y axis limits e.g. xlim = c(0, 1000), ylim = c(0, 1).
`ylab` | y axis label.
`title` | the title of the final grob (`top` in arrangeGrob)
`caption` | the caption of the final grob (`bottom` in arrangeGrob)
`ggtheme` | function, ggplot2 theme name. Allowed values include ggplot2 official themes: see `theme`.
`...` | further arguments passed to the function `ggpar` for customizing the plot.
`x` | an object of class ggcoxfunctional
`newpage` | open a new page. See `grid.arrange`.

### Value

Returns an object of class `ggcoxfunctional` which is a list of ggplots.

### Functions

- `ggcoxfunctional`: Functional Form of Continuous Variable in Cox Proportional Hazards Model.

### Author(s)

Marcin Kosinski , m.p.kosinski@gmail.com

### Examples

    library(survival)
    data(mgus)
    res.cox <- coxph(Surv(futime, death) ~ mspike + log(mspike) + I(mspike^2) +
        age + I(log(age)^2) + I(sqrt(age)), data = mgus)
    ggcoxfunctional(res.cox,  data = mgus, point.col = "blue", point.alpha = 0.5)
    ggcoxfunctional(res.cox, data = mgus, point.col = "blue", point.alpha = 0.5,
                    title = "Pass the title", caption = "Pass the caption")

[Package survminer version 0.4.1 Index]