The km.outcomes function is part of the conf package. The
Kaplan-Meier product-limit estimator (KMPLE) is used to estimate the
survivor function for a data set of positive values in the presence of
right censoring1. The km.outcomes function
generates a matrix with all possible combinations of observed failures
and right-censored values and the resulting support values for the
Kaplan-Meier product-limit estimator for a sample of size n. The function has only the sample
size n as its argument.
The km.outcomes function is accessible following
installation of the conf package:
install.packages("conf")
library(conf)The KMPLE is a nonparametric estimate of the survival function from a data set of lifetimes that includes right-censored observations and is used in a variety of application areas. For simplicity, we will refer to the object of interest generically as the item and the event of interest as the failure.
Let n denote the number of items on test. For a given n, there are 2n + 1 − 1 different possible outcomes (failure times or censoring times) for observing an experiment at a specific time of interest. For any combination of failure or censored times at a specific time, the KMPLE can be calculated. The KMPLE of the survival function S(t) is given by $$ \hat{S}(t) = \prod\limits_{i:t_i \leq t}\left( 1 - \frac{d_i}{n_i}\right), $$ for t ≥ 0, where t1, t2, …, tk are the times when at least one failure is observed (k is an integer between 1 and n, which is the number of distinct failure times in the data set), d1, d2, …, dk are the number of failures observed at times t1, t2, …, tk, and n1, n2, …, nk are the number of items at risk just prior to times t1, t2, …, tk. It is common practice to have the KMPLE “cut off” after the largest time recorded if it corresponds to a right-censored observation2. The KMPLE drops to zero after the largest time recorded if it is a failure; the KMPLE is undefined, however, after the largest time recorded if it is a right-censored observation.
The support values are calculated for each number of observed events between times 0 and the observation time, listed in column l for each combination of failure times or censoring times up to that time. The columns labeled as d1, d2, ..., dn list a 0 if the event corresponds to a censored observation and a 1 if the event corresponds to a failure.
The support values are listed numerically in the S(t) column, and in order to keep the support values as exact fractions, the numerators and denominators are stored separately in the output columns named num and den.
To illustrate a simple case, consider the KMPLE for the experiment when there are n = 4 items on test.
Let’s consider an experiment where failures occur at times t = 1 and t = 3, and right censorings occur at times t = 2 and t = 4. In this setting, the KMPLE is
where NA indicates that the KMPLE is undefined3.
library(conf)
# display the outcomes and KMPLE for n = 4 items on test
n = 4
km.outcomes(n)
#> l d1 d2 d3 d4 S(t) num den
#> [1,] 0 -1 -1 -1 -1 1.0000000 1 1
#> [2,] 1 0 NA NA NA 1.0000000 1 1
#> [3,] 1 1 NA NA NA 0.7500000 3 4
#> [4,] 2 0 0 NA NA 1.0000000 1 1
#> [5,] 2 1 0 NA NA 0.7500000 3 4
#> [6,] 2 0 1 NA NA 0.6666667 2 3
#> [7,] 2 1 1 NA NA 0.5000000 6 12
#> [8,] 3 0 0 0 NA 1.0000000 1 1
#> [9,] 3 1 0 0 NA 0.7500000 3 4
#> [10,] 3 0 1 0 NA 0.6666667 2 3
#> [11,] 3 1 1 0 NA 0.5000000 6 12
#> [12,] 3 0 0 1 NA 0.5000000 1 2
#> [13,] 3 1 0 1 NA 0.3750000 3 8
#> [14,] 3 0 1 1 NA 0.3333333 2 6
#> [15,] 3 1 1 1 NA 0.2500000 6 24
#> [16,] 4 0 0 0 0 NA NA NA
#> [17,] 4 1 0 0 0 NA NA NA
#> [18,] 4 0 1 0 0 NA NA NA
#> [19,] 4 1 1 0 0 NA NA NA
#> [20,] 4 0 0 1 0 NA NA NA
#> [21,] 4 1 0 1 0 NA NA NA
#> [22,] 4 0 1 1 0 NA NA NA
#> [23,] 4 1 1 1 0 NA NA NA
#> [24,] 4 0 0 0 1 0.0000000 0 1
#> [25,] 4 1 0 0 1 0.0000000 0 4
#> [26,] 4 0 1 0 1 0.0000000 0 3
#> [27,] 4 1 1 0 1 0.0000000 0 12
#> [28,] 4 0 0 1 1 0.0000000 0 2
#> [29,] 4 1 0 1 1 0.0000000 0 8
#> [30,] 4 0 1 1 1 0.0000000 0 6
#> [31,] 4 1 1 1 1 0.0000000 0 24If we observe the experiment at time t0 = 2.5, Ŝ(t) = 3/4 and is represented by row 5 where l = 2 events have occurred: one failure d1 = 1 and one censored item d2 = 0. Notice that d3 and d4 are NA since they have not been observed yet. If instead, we choose t0 = 4.5, Ŝ(t) = NA and is represented by row 21 where l = 4 events have occurred: first was a failure d1 = 1, second was a censored item d2 = 0, third was a failure d3 = 1, and the fourth and last item was a censored d4 = 0.
Looking at the above output from the Specific Example, the first row corresponds to choosing a time value t0 that satisfies 0 < t0 < 1, which is associated with an observation time prior to the occurrence of an observed failure or censoring time. That is, l = 0 events have occurred, and -1’s are listed to represent these initialized values. All n items are on test and Ŝ(t) = 1.
For the second row, l = 1 event has occurred and that event is a censored item d1 = 0. We have not observed any of the other items so they are listed as NA’s.
The third row shows the case when only l = 1 event has occurred and that event is a failure; that is, d1 = 1. Again, we have not observed any of the other items so they are listed as NA’s.
For more information on how the Ŝ(t) values are generated, please refer to the vignette titled km.support which is available via the link on the conf package webpage.
In addition, the functions km.pmf and
km.surv, which are also part of the conf package, have
dependencies on km.outcomes.
Kaplan, E. L., and Meier, P. (1958), “Nonparametric Estimation from Incomplete Observations,” Journal of the American Statistical Association, 53, 457–481.↩︎
Kalbfleisch, J. D., and Prentice, R. L. (2002), The Statistical Analysis of Failure Time Data (2nd ed.), Hoboken, NJ: Wiley.↩︎
Qin Y., Sasinowska H. D., Leemis L. M. (2023), “The Probability Mass Function of the Kaplan–Meier Product–Limit Estimator,” The American Statistician, 77 (1), 102–110.↩︎