MI.ci: Cumulative incidence estimation for interval censored...

In MIICD: Multiple Imputation for Interval Censored Data

Description

Uses multiple imputation to compute the cumulative incidence function for interval censored competing risks data

Usage

MI.ci(k, m, data, status, trans, cens.code, conf.int = F, alpha = 0.05)

Arguments

k	An integer, indicates the number of iteration to perform
m	An integer, indicates the number of imputation to perform at each iteration
status	The name of the column where status are to be found
trans	Denomination of the event of interest in the status column
data	The input data (see details)
conf.int	Logical, computes the confidence interval
cens.code	Censor indicator in the status column of the data
alpha	Parametrize the confidence interval width

Details

This function uses a multiple imputation approach to estimate a cumulative incidence function for interval censored competing risks data. Estimates are computed using Rubin's rules (Rubin (1987)). The cumulative incidence is computed as the mean of cumulative incidences over imputations. The variance is computed at each point by combining the within imputation variance and the between imputation variance augmented by an inflation factor to take into account the finite number of imputations. At each iteration, the cumulative incidence is updated and multiple imputation is performed using the updated estimate. If conf.int is required, the log-log transformation is used to compute the lower confidence interval.

Print and plot methods are available to handle results.

The data must contain at last three columns: left, right and status. For interval censored data, the left and right columns indicates lower and upper bounds of intervals, respectively. Inf in the right column stands for right censored observations. When an observation is right censored, the status column must contain the censor indicator specified by cens.code. The transition of interest must be specified by the trans parameter.

Value

est A data frame with estimates

... Other objects

Author(s)

Marc Delord <[e-mail]>

References

Delord, M. & Genin, E. Multiple Imputation for Competing Risks Regression with Interval Censored Data Journal of Statistical Computation and Simulation, 2015

PAN, Wei. A Multiple Imputation Approach to Cox Regression with Interval-Censored Data. Biometrics, 2000, vol. 56, no 1, p. 199-203.

Rubin, D. B. (1987). Multiple imputation for nonresponse in surveys.

Schenker, N. and Welsh, A. (1988). Asymptotic results for multiple imputation. The Annals of Statistics pages 1550-1566.

Tanner, M. A. and Wong, W. H. (1987). An application of imputation to an estimation problem in grouped lifetime analysis. Technometrics 29, 23-32.

Wei, G. C., & Tanner, M. A. (1991). Applications of multiple imputation to the analysis of censored regression data. Biometrics, 47(4), 1297-1309.

See Also

Surv, survfit

Examples

res <- MI.ci(k = 5,  m = 5, status = 'status',  trans = 1 , data = ICCRD,
 conf.int = TRUE, cens.code = 0 , alpha = 0.05)
 res
 print(res)
 plot(res)

Example output

Cumulative incidence estimation for interval censored data using data augmentation and multiple imputation

Call:
MI.ci(k = 5, m = 5, data = ICCRD, status = "status", trans = 1, 
    cens.code = 0, conf.int = TRUE, alpha = 0.05)

Interval-censored response for cumulative incidence estimation:

No.Observation: 150 
Patern:
                          type
Cause                      exact interval-censored right-censored
  1                            0                64              0
  2                           37                 0              0
  unknown (right-censored)     0                 0             49

$est
A 134 x 5 data frame of required estimates
         time        prev          sd          uci         lci
1 0.000000000 0.000000000 0.000000000 0.000000e+00 0.000000000
3 0.009716295 0.001481481 0.003919217 5.358738e-07 0.009163005
4 0.021007201 0.002962963 0.004912195 3.819121e-05 0.012590687
5 0.022201890 0.002962963 0.004912195 3.819121e-05 0.012590687
6 0.126768750 0.002962963 0.004912195 3.819121e-05 0.012590687
7 0.150446887 0.005925926 0.004679300 9.731537e-04 0.015097186

Cumulative incidence estimation for interval censored data using data augmentation and multiple imputation

Call:
MI.ci(k = 5, m = 5, data = ICCRD, status = "status", trans = 1, 
    cens.code = 0, conf.int = TRUE, alpha = 0.05)

Interval-censored response for cumulative incidence estimation:

No.Observation: 150 
Patern:
                          type
Cause                      exact interval-censored right-censored
  1                            0                64              0
  2                           37                 0              0
  unknown (right-censored)     0                 0             49

$est
A 134 x 5 data frame of required estimates
         time        prev          sd          uci         lci
1 0.000000000 0.000000000 0.000000000 0.000000e+00 0.000000000
3 0.009716295 0.001481481 0.003919217 5.358738e-07 0.009163005
4 0.021007201 0.002962963 0.004912195 3.819121e-05 0.012590687
5 0.022201890 0.002962963 0.004912195 3.819121e-05 0.012590687
6 0.126768750 0.002962963 0.004912195 3.819121e-05 0.012590687
7 0.150446887 0.005925926 0.004679300 9.731537e-04 0.015097186

MIICD documentation built on May 2, 2019, 11:01 a.m.