R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Wally plots to assess calibration of a risk or survival...

wallyPlot

R Documentation

Wally plots to assess calibration of a risk or survival prediction

Description

Wally plots to assess calibration of a risk or survival prediction

Usage

wallyPlot(object, time, formula, data, cause = 1, q = 10, ylim,
  hanging = FALSE, seed = NULL, mar = c(4.1, 4.1, 2, 2), colbox = "red",
  type = "risk", pseudo = FALSE, verbose = TRUE, ...)

Arguments

`object`	Probabilistic survival predictions or probabilistic event risk predictions evaluated at `time` for the subjects in `data`. Either given in form of a numeric vector of probabilistic predictions or as an object which in the survival setting has a `predictSurvProb` method and in the competing risks setting has a `predictEventProb` method.
`time`	Time interest for evaluating calibration of the predictions.
`formula`	A survival or event history formula. The left hand side is used to compute the expected event status. If `formula` is `missing`, try to extract a formula from the first element in object.
`data`	A data frame in which to validate the prediction models and to fit the censoring model. If `data` is missing, try to extract a data set from the first element in object.
`cause`	For competing risks settings the cause of interest.
`q`	The number of quantiles. Defaults to 10.
`ylim`	Limits of y-axis. If missing the function tries to find appropriate limits based on the simulated and real data.
`hanging`	If `TRUE`, hang bars corresponding to observed frequencies at the value of the corresponding prediction.
`seed`	A seed value to make results reproducible.
`mar`	Plot margins passed to par.
`colbox`	Color of the box which identifies the real data calibration plot.
`type`	For survival models only: show either "risk" or "survival".
`pseudo`	Logical. Determines the method for estimating expected event frequencies. See `calPlot`. Default is `FALSE`.
`verbose`	If `TRUE` warn about missing formula and data.
`...`	Further arguments passed to `calPlot`.

Value

List of simulated and real data.

Author(s)

Paul F. Blanche <paul.blanche@univ-ubs.fr> and Thomas A. Gerds <tag@biostat.ku.dk>

Examples


# Survival setting
library(prodlim)
library(survival)
set.seed(180)
d = SimSurv(180)
f = coxph(Surv(time,status)~X1+X2,data=d)
## Not run: 
wallyPlot(f,
          time=4,
          q=10,
          type="risk",
          data=d,
          formula=Surv(time,status)~1)
 wallyPlot(f,
          time=4,
          q=10,
          hanging=TRUE,
          type="survival",
          data=d,
          formula=Surv(time,status)~1)

## End(Not run)

# Competing risks setting
library(prodlim)
library(survival)
library(riskRegression)
set.seed(180)
d2 = SimCompRisk(180)
f2 = CSC(Hist(time,event)~X1+X2,data=d2)
## Not run: 
wallyPlot(f2,
          time=5,
          q=3,
          hanging=TRUE,
          data=d2,
          formula=Hist(time,event)~1)
          

## End(Not run)

Wally plots to assess calibration of a risk or survival prediction

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Results