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ggcoxdiagnostics

Diagnostic Plots for Cox Proportional Hazards Model with ggplot2

Description

Displays diagnostics graphs presenting goodness of Cox Proportional Hazards Model fit, that can be calculated with coxph function.

Usage

ggcoxdiagnostics(
  fit,
  type = c("martingale", "deviance", "score", "schoenfeld", "dfbeta", "dfbetas",
    "scaledsch", "partial"),
  ...,
  linear.predictions = type %in% c("martingale", "deviance"),
  ox.scale = ifelse(linear.predictions, "linear.predictions", "observation.id"),
  hline = TRUE,
  sline = TRUE,
  sline.se = TRUE,
  hline.col = "red",
  hline.size = 1,
  hline.alpha = 1,
  hline.yintercept = 0,
  hline.lty = "dashed",
  sline.col = "blue",
  sline.size = 1,
  sline.alpha = 0.3,
  sline.lty = "dashed",
  point.col = "black",
  point.size = 1,
  point.shape = 19,
  point.alpha = 1,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ggtheme = ggplot2::theme_bw()
)

Arguments

`fit`	an object of class coxph.object - created with coxph function.
`type`	the type of residuals to present on Y axis of a diagnostic plot. The same as in residuals.coxph: character string indicating the type of residual desired. Possible values are `"martingale", "deviance", "score", "schoenfeld", "dfbeta", "dfbetas"` and `"scaledsch"`. Only enough of the string to determine a unique match is required.
`...`	further arguments passed to `residuals.coxph` or to the function `ggpar` for customizing the plot.
`linear.predictions`	(deprecated, see `ox.scale`) a logical value indicating whether to show linear predictions for observations (`TRUE`) or just indexed of observations (`FALSE`) on X axis.
`ox.scale`	one value from `c("linear.predictions", "observation.id", "time")`. It defines what will be presented on OX scale. Possible values: y hat for `"linear.predictions"`, Id of an observation for `"observation.id"` or Time for `"time"`.
`hline`	a logical - should the horizontal line be added to highlight the `Y=0` level.
`sline, sline.se`	a logical - should the smooth line be added to highlight the local average for residuals.
`hline.col, hline.size, hline.lty, hline.alpha, hline.yintercept`	color, size, linetype, visibility and Y-axis coordinate to be used for geom_hline. Used only when `hline = TRUE`.
`sline.col, sline.size, sline.lty, sline.alpha`	color, size, linetype and visibility to be used for geom_smooth. Used only when `sline = TRUE`.
`point.col, point.size, point.shape, point.alpha`	color, size, shape and visibility to be used for points.
`title, subtitle, caption`	main title, subtitle and caption.
`ggtheme`	function, ggplot2 theme name. Default value is ggplot2::theme_bw(). Allowed values include ggplot2 official themes: see `theme`.

Value

Returns an object of class ggplot.

Functions

ggcoxdiagnostics: Diagnostic Plots for Cox Proportional Hazards Model with ggplot2

Author(s)

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

Examples

library(survival)
coxph.fit2 <- coxph(Surv(futime, fustat) ~ age + ecog.ps, data=ovarian)
ggcoxdiagnostics(coxph.fit2, type = "deviance")

ggcoxdiagnostics(coxph.fit2, type = "schoenfeld", title = "Diagnostic plot")
ggcoxdiagnostics(coxph.fit2, type = "deviance", ox.scale = "time")
ggcoxdiagnostics(coxph.fit2, type = "schoenfeld", ox.scale = "time",
                 title = "Diagnostic plot", subtitle = "Data comes from survey XYZ",
                 font.subtitle = 9)
ggcoxdiagnostics(coxph.fit2, type = "deviance", ox.scale = "linear.predictions",
                 caption = "Code is available here - link", font.caption = 10)
ggcoxdiagnostics(coxph.fit2, type = "schoenfeld", ox.scale = "observation.id")
ggcoxdiagnostics(coxph.fit2, type = "scaledsch", ox.scale = "time")

survminer

Drawing Survival Curves using 'ggplot2'

v0.4.9

GPL-2

Authors

Alboukadel Kassambara [aut, cre], Marcin Kosinski [aut], Przemyslaw Biecek [aut], Scheipl Fabian [ctb]

Initial release

2021-03-09