GofCens (version 1.1)

kmPlot: Plot of the Kaplen-Meier and parametric estimations

Description

Function kmPlot is a function that generates a plot that combines a Kaplan-Meier survival curve and a parametric survival curve in the same graph. It is useful for comparing non-parametric survival estimates with the fitted parametric survival model.

Usage

# S3 method for default
kmPlot(times, cens = rep(1, length(times)), distr = "all6", colour = 1, 
       betaLimits = c(0, 1), igumb = c(10, 10), ggp = FALSE, m = NULL,
       prnt = TRUE, degs = 3, ...)
# S3 method for formula
kmPlot(formula, data, ...)

Value

If prnt = TRUE, the following output is returned:

Distribution

Distribution under study.

Parameters

List with the maximum likelihood estimates of the parameters of the distribution under study.

In addition, a list with the same contents is returned invisibly.

Arguments

times

Numeric vector of times until the event of interest.

cens

Status indicator (1, exact time; 0, right-censored time). If not provided, all times are assumed to be exact.

distr

A string specifying the name of the distribution to be studied. The possible distributions are the Weibull ("weibull"), the Gumbel ("gumbel"), the normal ("normal"), the lognormal ("lognormal"), the logistic ("logistic"), the loglogistic ("loglogistic"), the exponential ("exponential") and the beta ("beta") distribution. Default is "all6" and includes the fisrt 6 listed which are the most used distributions.

colour

Vector indicating the colours of the displayed plots.

betaLimits

Two-components vector with the lower and upper bounds of the Beta distribution. This argument is only required, if the beta distribution is considered.

igumb

Two-components vector with the initial values for the estimation of the Gumbel distribution parameters.

ggp

Logical to use or not the ggplot2 package to draw the plots. Default is FALSE.

m

Optional layout for the plots to be displayed.

prnt

Logical to indicate if the maximum likelihood estimates of the parameters should be printed. Default is TRUE.

degs

Integer indicating the number of decimal places of the numeric results of the output.

formula

A formula with a numeric vector as response (which assumes no censoring) or Surv object.

data

Data frame for variables in formula.

...

Optional arguments for function par, if ggp = FALSE.

Author

K. Langohr, M. Besalú, M. Francisco, G. Gómez.

Details

The parameter estimation is acomplished with the fitdistcens function of the fitdistrplus package.

References

Peterson Jr, Arthur V. Expressing the Kaplan-Meier estimator as a function of empirical subsurvival functions. In: Journal of the American Statistical Association 72.360a (1977): 854-858.

Examples

# Plots for complete data and default distributions
set.seed(123)
x <- rexp(1000, 0.1)
kmPlot(x)

# Plots for censored data using ggplot2
data(colon)
kmPlot(Surv(time, status) ~ 1, colon, distr= "lognormal", ggp = TRUE) 
  
# Plots for censored data from three distributions
data(nba)
kmPlot(Surv(survtime, cens) ~ 1, nba, distr = c("normal", "weibull", "lognormal"), 
       prnt = FALSE)