Handling of data formated as in the survival package for use in fitdistcens()
Surv2fitdistcens.RdProvide a function to prepare a data frame needed by fitdistcens() from data classically coded when using the Surv() function of the survival package
Usage
Surv2fitdistcens(time, time2, event,
type = c('right', 'left', 'interval', 'interval2'))Arguments
- time
for right censored data, this is the follow up time. For interval data, the first argument is the starting time for the interval.
- event
The status indicator, normally
0=alive,1=dead. Other choices areTRUE/FALSE(TRUE= death) or1/2(2=death). For interval censored data, the status indicator is0=right censored,1=event at time,2=left censored,3=interval censored. For factor data, assume that it has only two levels with the second level coding death.- time2
ending time of the interval for interval censored. Intervals are assumed to be open on the left and closed on the right, (start, end].
- type
character string specifying the type of censoring. Possible values are
"right","left","interval","interval2".
Details
Surv2fitdistcens makes a data.frame with two columns
respectively named left and right, describing each observed
value as an interval as required in fitdistcens():
the left column contains either NA
for left-censored observations, the left bound of the interval for
interval-censored observations, or the observed value for non-censored observations.
The right column contains either NA for right-censored observations,
the right bound of the interval for interval censored observations,
or the observed value for non-censored observations.
See also
See fitdistrplus for an overview of the package.
See fitdistcens for fitting of univariate distributions to censored data
and fremale for the full dataset used in examples below.
See Surv for survival objects which use the same arguments.
References
Delignette-Muller ML and Dutang C (2015), fitdistrplus: An R Package for Fitting Distributions. Journal of Statistical Software, 64(4), 1-34, doi:10.18637/jss.v064.i04 .
Examples
# (1) randomized fictive survival data - right-censored
#
origdata <- data.frame(rbind(
c( 43.01, 55.00, 0),
c( 36.37, 47.17, 0),
c( 33.10, 34.51, 0),
c( 71.00, 81.15, 1),
c( 80.89, 81.91, 1),
c( 67.81, 78.48, 1),
c( 73.98, 76.92, 1),
c( 53.19, 54.80, 1)))
colnames(origdata) <- c("AgeIn", "AgeOut", "Death")
# add of follow-up time (for type = "right" in Surv())
origdata$followuptime <- origdata$AgeOut - origdata$AgeIn
origdata
#> AgeIn AgeOut Death followuptime
#> 1 43.01 55.00 0 11.99
#> 2 36.37 47.17 0 10.80
#> 3 33.10 34.51 0 1.41
#> 4 71.00 81.15 1 10.15
#> 5 80.89 81.91 1 1.02
#> 6 67.81 78.48 1 10.67
#> 7 73.98 76.92 1 2.94
#> 8 53.19 54.80 1 1.61
### use of default survival type "right"
# in Surv()
survival::Surv(time = origdata$followuptime, event = origdata$Death, type = "right")
#> [1] 11.99+ 10.80+ 1.41+ 10.15 1.02 10.67 2.94 1.61
# for fitdistcens()
Surv2fitdistcens(origdata$followuptime, event = origdata$Death, type = "right")
#> left right
#> 1 11.99 NA
#> 2 10.80 NA
#> 3 1.41 NA
#> 4 10.15 10.15
#> 5 1.02 1.02
#> 6 10.67 10.67
#> 7 2.94 2.94
#> 8 1.61 1.61
# use of survival type "interval"
# in Surv()
survival::Surv(time = origdata$followuptime, time2 = origdata$followuptime,
event = origdata$Death, type = "interval")
#> [1] 11.99+ 10.80+ 1.41+ 10.15 1.02 10.67 2.94 1.61
# for fitdistcens()
Surv2fitdistcens(time = origdata$followuptime, time2 = origdata$followuptime,
event = origdata$Death, type = "interval")
#> left right
#> 1 11.99 NA
#> 2 10.80 NA
#> 3 1.41 NA
#> 4 10.15 10.15
#> 5 1.02 1.02
#> 6 10.67 10.67
#> 7 2.94 2.94
#> 8 1.61 1.61
# use of survival type "interval2"
origdata$survivalt1 <- origdata$followuptime
origdata$survivalt2 <- origdata$survivalt1
origdata$survivalt2[1:3] <- Inf
origdata
#> AgeIn AgeOut Death followuptime survivalt1 survivalt2
#> 1 43.01 55.00 0 11.99 11.99 Inf
#> 2 36.37 47.17 0 10.80 10.80 Inf
#> 3 33.10 34.51 0 1.41 1.41 Inf
#> 4 71.00 81.15 1 10.15 10.15 10.15
#> 5 80.89 81.91 1 1.02 1.02 1.02
#> 6 67.81 78.48 1 10.67 10.67 10.67
#> 7 73.98 76.92 1 2.94 2.94 2.94
#> 8 53.19 54.80 1 1.61 1.61 1.61
survival::Surv(time = origdata$survivalt1, time2 = origdata$survivalt2,
type = "interval2")
#> [1] 11.99+ 10.80+ 1.41+ 10.15 1.02 10.67 2.94 1.61
Surv2fitdistcens(origdata$survivalt1, time2 = origdata$survivalt2,
type = "interval2")
#> left right
#> 1 11.99 NA
#> 2 10.80 NA
#> 3 1.41 NA
#> 4 10.15 10.15
#> 5 1.02 1.02
#> 6 10.67 10.67
#> 7 2.94 2.94
#> 8 1.61 1.61
# (2) Other examples with various left, right and interval censored values
#
# with left censored data
(d1 <- data.frame(time = c(2, 5, 3, 7), ind = c(0, 1, 1, 1)))
#> time ind
#> 1 2 0
#> 2 5 1
#> 3 3 1
#> 4 7 1
survival::Surv(time = d1$time, event = d1$ind, type = "left")
#> [1] 2- 5 3 7
Surv2fitdistcens(time = d1$time, event = d1$ind, type = "left")
#> left right
#> 1 NA 2
#> 2 5 5
#> 3 3 3
#> 4 7 7
(d1bis <- data.frame(t1 = c(2, 5, 3, 7), t2 = c(2, 5, 3, 7),
censtype = c(2, 1, 1, 1)))
#> t1 t2 censtype
#> 1 2 2 2
#> 2 5 5 1
#> 3 3 3 1
#> 4 7 7 1
survival::Surv(time = d1bis$t1, time2 = d1bis$t2,
event = d1bis$censtype, type = "interval")
#> [1] 2- 5 3 7
Surv2fitdistcens(time = d1bis$t1, time2 = d1bis$t2,
event = d1bis$censtype, type = "interval")
#> left right
#> 1 NA 2
#> 2 5 5
#> 3 3 3
#> 4 7 7
# with interval, left and right censored data
(d2 <- data.frame(t1 = c(-Inf, 2, 3, 4, 3, 7), t2 = c(2, 5, 3, 7, 8, Inf)))
#> t1 t2
#> 1 -Inf 2
#> 2 2 5
#> 3 3 3
#> 4 4 7
#> 5 3 8
#> 6 7 Inf
survival::Surv(time = d2$t1, time2 = d2$t2, type = "interval2")
#> [1] 2- [2, 5] 3 [4, 7] [3, 8] 7+
Surv2fitdistcens(time = d2$t1, time2 = d2$t2, type = "interval2")
#> left right
#> 1 NA 2
#> 2 2 5
#> 3 3 3
#> 4 4 7
#> 5 3 8
#> 6 7 NA
(d2bis <- data.frame(t1 = c(2, 2, 3, 4, 3, 7), t2 = c(2, 5, 3, 7, 8, 7),
censtype = c(2,3,1,3,3,0)))
#> t1 t2 censtype
#> 1 2 2 2
#> 2 2 5 3
#> 3 3 3 1
#> 4 4 7 3
#> 5 3 8 3
#> 6 7 7 0
survival::Surv(time = d2bis$t1, time2 = d2bis$t2,
event = d2bis$censtype, type = "interval")
#> [1] 2- [2, 5] 3 [4, 7] [3, 8] 7+
Surv2fitdistcens(time = d2bis$t1, time2 = d2bis$t2,
event = d2bis$censtype, type = "interval")
#> left right
#> 1 NA 2
#> 2 2 5
#> 3 3 3
#> 4 4 7
#> 5 3 8
#> 6 7 NA