Description Usage Arguments Value Examples
Generates summarized report, including visualisation of survival and cumulative incidences curves, diagnostic tables and p-values of tests comparing models between groups.
1 2 3 4 5 6 7 | 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")
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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. |
Results of all functions implemented in the package summarised in an one-page report.
1 2 3 4 5 6 7 8 9 10 | 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")
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