cci.strat {currentSurvival}

Estimates Stratified Current Cumulative Incidence (CCI) and Common Cumulative Incidence (comCI) Functions

Description

This is an internal function and is not usually called by user.
This function estimates the stratified 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 stratified common cumulative incidence (comCI) function. Moreover, statistical test can be applied to compare the risk groups.

Usage

cci.strat(data, stratf = NULL, maxx = NULL, com.est = TRUE, 
          conf.int = FALSE, conf.int.level = NULL, 
          no.iter = NULL, points = NULL, fig = TRUE, 
          pvals = FALSE, pval.test = NULL)

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)

stratf

stratification factor (maximum number of stratification levels is 8 because of figure clarity)

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.

pvals

a logical value indicating whether p-values for the comparison of stratified curves at pre-defined time points should be computed. The default value is FALSE.

pval.test

a type of a test that will be used for the computation of p-values. Possible values are “naive”, “log”, “loglog”. The default value is “loglog”.

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

pval

p-values for the comparison of point estimates at the defined time points

summary

summary of input data

Author(s)

Eva Janousova, Tomas Pavlik
Institute of Biostatistics and Analyses
Masaryk University, Brno, Czech Republic
[e-mail]

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.

See Also

cci

Examples

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