CompareKM: Compare KM curve of full population vs. BEP

In lengning/gClinBiomarker: gClinBiomarker: an R package for clinical biomarker analyses

Description

This function provides K-M curves to compare full population vs. BEP.

Usage

CompareKM(data, tte, cens, trt = NULL, bep, bep.indicator = 1,
  bep.name = "Biomarker Evaluable", itt.name = "All",
  col.itt = "palegreen4", col.bep = "lightpink2", col.ci = "lightcyan",
  shaded.ci = TRUE, xlim = NULL, xat = NULL, ylab = paste(tte,
  "Survival Probability"), xlab = "Time", main = "",
  surv.conf.type = "plain", pdf.name = NULL, pdf.param = list(height = 5),
  par.param = list(mar = c(4, 4, 3, 2)), ...)

Arguments

data	Input data frame. Rows are patients and columns are variables (e.g. demographics variables, time to event variables, biomarker variables, treatment indicator, etc.). One patient per row.
tte	column name that indicates the time to event variable
cens	column name that indicates the censoring variable associated to tte. 1 indicates event and 0 indicates censoring
trt	name of the treatment column. If trt is specified, the analysis will be performed within treatment arm. if it is NULL, the comparison will be performed using all samples.
bep	name of the column which indicates biomarker evaluable population. If it is null, patients who have non NA records in biomarker variable will be used as BEP.
bep.indicator	In the subpopulation column, which value is used to define the biomarker evaluable population.
bep.name	preferred display name of the biomarker evaluable population. If it is NULL, bep will be used.
itt.name	preferred display name of the full population (e.g. ITT). If it is NULL, "All" will be used.
col.itt, col.bep, col.ci	Color for itt curve, bep curve and confidence interval curve (CI)
shaded.ci	Whether add background shade to disply CI
xlim, xat, ylab, xlab, main	see plot
surv.conf.type	confidence interval type. Default is "plain". see conf.type in survfit
pdf.name	name of output pdf file. If it is NULL (default), the plots will be displayed but not saved as pdf
pdf.param	A list of parameters that define pdf graphics device. See pdf. for example, pdf.param=list(width=10, height=5)
par.param	A list of parameters that define graphcial parameters. See par. for example, par.param=list(mfrow=c(3,1), mar=c(4,4,3,2))
...	additional parameters for plot

Note

This function generates KM curves to compare full population vs BEP, within each treatment arm.

Author(s)

Ning Leng [e-mail], Alexey Pronin [e-mail], and previous team members (see DESCRIPTION)

Examples

data(input)
sample.data <- input
CompareKM(data=sample.data, tte="OS",cens="OS.event", main="OS ITT", bep="BEP")

lengning/gClinBiomarker documentation built on May 9, 2019, 2:55 p.m.