autoplot.predictCSC: Plot Predictions From a Cause-specific Cox Proportional...

Description Usage Arguments Value See Also Examples

View source: R/autoplot.predictCSC.R

Description

Plot predictions from a Cause-specific Cox proportional hazard regression.

Usage

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## S3 method for class 'predictCSC'
autoplot(
  object,
  ci = object$se,
  band = object$band,
  plot = TRUE,
  smooth = FALSE,
  digits = 2,
  alpha = NA,
  group.by = "row",
  reduce.data = FALSE,
  ...
)

Arguments

object

Object obtained with the function predictCox.

ci

[logical] If TRUE display the confidence intervals for the predictions.

band

[logical] If TRUE display the confidence bands for the predictions.

plot

[logical] Should the graphic be plotted.

smooth

[logical] Should a smooth version of the risk function be plotted instead of a simple function?

digits

[integer] Number of decimal places.

alpha

[numeric, 0-1] Transparency of the confidence bands. Argument passed to ggplot2::geom_ribbon.

group.by

[character] The grouping factor used to color the prediction curves. Can be "row", "strata", or "covariates".

reduce.data

[logical] If TRUE only the covariates that does take indentical values for all observations are displayed.

...

Additional parameters to cutomize the display.

Value

Invisible. A list containing:

See Also

predict.CauseSpecificCox to compute risks based on a CSC model.

Examples

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library(survival)
library(rms)
library(ggplot2)
library(prodlim)

#### simulate data ####
set.seed(10)
d <- sampleData(1e2, outcome = "competing.risks")
seqTau <- c(0,unique(sort(d[d$event==1,time])), max(d$time))

#### CSC model ####
m.CSC <- CSC(Hist(time,event)~ X1 + X2 + X6, data = d)

pred.CSC <- predict(m.CSC, newdata = d[1:2,], time = seqTau, cause = 1, band = TRUE)
autoplot(pred.CSC, alpha = 0.2)

#### stratified CSC model ####
m.SCSC <- CSC(Hist(time,event)~ strata(X1) + strata(X2) + X6,
              data = d)
pred.SCSC <- predict(m.SCSC, time = seqTau, newdata = d[1:4,],
                     cause = 1, keep.newdata = TRUE, keep.strata = TRUE)
autoplot(pred.SCSC, group.by = "strata")

Example output

riskRegression version 2020.02.05
Loading required package: Hmisc
Loading required package: lattice
Loading required package: Formula
Loading required package: ggplot2

Attaching package:HmiscThe following objects are masked frompackage:base:

    format.pval, units

Loading required package: SparseM

Attaching package:SparseMThe following object is masked frompackage:base:

    backsolve

riskRegression documentation built on Jan. 13, 2021, 11:12 a.m.