cr17 (version 0.1.0)

summarizeCR: Competing Risks Models Summary

Description

Generates summarized report, including visualisation of survival and cumulative incidences curves, diagnostic tables and p-values of tests comparing models between groups.

Usage

summarizeCR(time, risk, group, cens = NULL, rho = 0, target = NULL,
  type = "kaplan-meier", conf.int = 0.95, conf.type = "log",
  ggtheme = theme_minimal(), titleSurv = "Survival curves",
  titleCuminc = "Cumulative incidence functions", xtitle = "Time",
  ytitleSurv = "Probability of survivng up to time t",
  ytitleCuminc = "Cumulative incidences", legendtitle = "Group",
  riskTabTitle = "Number at risk", eventTabTitle = "Number of events")

Arguments

time

vector with times of an event or follow-up, must be numeric.

risk

vector with type of event, can be numeric or factor/character.

group

vector with group variable, can be numeric or factor/character.

cens

value of 'risk' indicating censored observation (if NULL, the first value of 'risk' vector will be taken).

rho

rho parameter from Fleming-Harrington Test.

target

point in time, in which the confidence bounds should be plotted (default NULL, no confidence bounds plotted).

type

type of survival curve to be fitted. Possible values are "kaplan-meier" (default), "fleming-harrington" or "fh2".

conf.int

conf.int level of two-sided confidence interval (default = 0.95).

conf.type

type of confidence interval. Possilble values: "none", "plain", "log" (default), "log-log".

ggtheme

ggtheme to be used in plots (default: theme_minimal()).

titleSurv

a title of a survival curves plot (default: "Survival curves").

titleCuminc

a title of a cumulative incidences plot (default: "Cumulative incidence functions").

xtitle

a title of x axis of survival curves and cumulative incidences plots(default: "Time").

ytitleSurv

a title of y axis of survial curves plot (default: "Probability of survivng up to time t").

ytitleCuminc

a title of y axis (default: "Cumulative incidences").

legendtitle

a title of a legend (default: "Group").

riskTabTitle

a title of table with number at risk.

eventTabTitle

a title of table with number of events.

Value

Results of all functions implemented in the package summarised in an one-page report.

Examples

# NOT RUN {
summarizeCR(time = LUAD$time/365, risk = LUAD$event, group = LUAD$gender, cens = "alive")

summarizeCR(time = LUAD$time, risk = LUAD$event, group = LUAD$gender, cens = "alive",
target = 1200, type = "fleming-harrington",  conf.int = 0.99, conf.type = "log-log",
ggtheme = theme_bw())

summarizeCR(time = LUAD$time, risk = LUAD$event, group = LUAD$gender, cens = "alive", rho = 1,
target = 800, type = "kaplan-meier", ggtheme = theme_gray(), titleSurv = "Survival analysis",
titleCuminc = "Competing risks models", xtitle = "Days", ytitleSurv = "Survival curves",
ytitleCuminc = "Cumulative incidence functions", legendtitle = "Gender")

# }