cci.nostrat {currentSurvival} R Documentation

## Estimates Current Cumulative Incidence (CCI) and Common Cumulative Incidence (comCI) Functions Without Stratification

### Description

This is an internal function and is not usually called by user.
This function estimates the unstratified current cumulative incidence (CCI), i.e. the probability that a patient is alive and in any disease remission after initiating his or her therapy. Optionally, this function estimates the unstratified common cumulative incidence (comCI) function.

### Usage

cci.nostrat(data, maxx = NULL, com.est = TRUE, conf.int = FALSE,
conf.int.level = NULL, no.iter = NULL,
points = NULL, fig = TRUE)


### Arguments

 data a matrix with ascending times from therapy initiation to occurrence of individual events (in days, i.e. positive integer values), total follow-up times from therapy initiation to data cut-off date (in days), and censoring indicators; the size of the data matrix is n times (2*r+2), where n is the number of patients and r is the maximum number of disease remissions achieved by patients; the data matrix consists of the following columns: data[,1] is the time from therapy initiation to achievement of the first disease remission data[,2] is the time from therapy initiation to loss of the first disease remission data[,3] is the time from therapy initiation to achievement of the second disease remission ... data[,2*r-1] is the time from therapy initiation to achievement of the rth disease remission data[,2*r] is the time from therapy initiation to loss of the rth disease remission data[,2*r+1] is the follow-up time (time from the therapy initiation to death or to the date of last contact with a patient) data[,2*r+2] is the censoring indicator (1..patient died, 0..patient is censored) maxx maximum follow-up time calculated from therapy initiation in days (defining time period for which the point estimates will be computed and curves will be plotted). Setting maxx smaller than the maximum follow-up time enables creating plots without fluctuating curve ends that may be caused by small number of patients. The default value is the maximum follow-up time (i.e. max(data[,2*r+1])). com.est a logical value indicating whether common cumulative incidence function should be estimated. The default value is TRUE. conf.int a logical value indicating whether confidence interval for the function(s) should be estimated. The default value is FALSE. conf.int.level two-sided confidence interval level (must be in range 0.9 and 0.99). The default value is 0.95. no.iter a number of bootstrap iterations for confidence interval computation (must be in range between 10 and 10,000). The default value is 100. points time points in which the point estimates will be computed (in months). The default values are 0, 12, 24, ..., floor(maxx/(365/12)). fig a logical value indicating whether a figure should be plotted. The default value is TRUE.

### Value

a list containing the following elements:

 no.risk numbers of patients at risk at the defined time points pest a matrix of point estimates (accompanied with confidence intervals) at the defined time points pest.day a matrix of point estimates (accompanied with confidence intervals) at each day of the follow-up time summary summary of input data

### Author(s)

Eva Janousova, Tomas Pavlik
Institute of Biostatistics and Analyses
Masaryk University, Brno, Czech Republic
janousova@iba.muni.cz

### References

Pavlik T., Janousova E., Pospisil Z., et al. (2011). Estimation of current cumulative incidence of leukaemia-free patients and current leukaemia-free survival in chronic myeloid leukaemia in the era of modern pharmacotherapy. BMC Med Res Methodol 11:140.

cci
# This is an internal function and is not usually called by user.