# Handling of data formated as in the survival package for use in fitdistcens() Provide a function to prepare a data frame needed by fitdistcens() from data classically coded when using the Surv() function of the survival package ```r 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 are `TRUE/FALSE` (`TRUE` = death) or `1/2` (`2`=death). For interval censored data, the status indicator is `0`=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. ## Returns `Surv2fitdistcens` returns a data.frame with two columns respectively named `left` and `right`. ## 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. Please visit the [Frequently Asked Questions](https://lbbe-software.github.io/fitdistrplus/articles/FAQ.html). ## References Delignette-Muller ML and Dutang C (2015), **fitdistrplus: An R Package for Fitting Distributions**. Journal of Statistical Software, 64(4), 1-34, tools:::Rd_expr_doi("https://doi.org/10.18637/jss.v064.i04") . ## Author(s) Christophe Dutang and Marie-Laure Delignette-Muller. ## Examples ```r # (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$AgeIn origdata ### use of default survival type "right" # in Surv() survival::Surv(time = origdata$followuptime, event = origdata$Death, type = "right") # for fitdistcens() Surv2fitdistcens(origdata$followuptime, event = origdata$Death, type = "right") # use of survival type "interval" # in Surv() survival::Surv(time = origdata$followuptime, time2 = origdata$followuptime, event = origdata$Death, type = "interval") # for fitdistcens() Surv2fitdistcens(time = origdata$followuptime, time2 = origdata$followuptime, event = origdata$Death, type = "interval") # use of survival type "interval2" origdata$survivalt1 <- origdata$followuptime origdata$survivalt2 <- origdata$survivalt1 origdata$survivalt2[1:3] <- Inf origdata survival::Surv(time = origdata$survivalt1, time2 = origdata$survivalt2, type = "interval2") Surv2fitdistcens(origdata$survivalt1, time2 = origdata$survivalt2, type = "interval2") # (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))) survival::Surv(time = d1$time, event = d1$ind, type = "left") Surv2fitdistcens(time = d1$time, event = d1$ind, type = "left") (d1bis <- data.frame(t1 = c(2, 5, 3, 7), t2 = c(2, 5, 3, 7), censtype = c(2, 1, 1, 1))) survival::Surv(time = d1bis$t1, time2 = d1bis$t2, event = d1bis$censtype, type = "interval") Surv2fitdistcens(time = d1bis$t1, time2 = d1bis$t2, event = d1bis$censtype, type = "interval") # 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))) survival::Surv(time = d2$t1, time2 = d2$t2, type = "interval2") Surv2fitdistcens(time = d2$t1, time2 = d2$t2, type = "interval2") (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))) survival::Surv(time = d2bis$t1, time2 = d2bis$t2, event = d2bis$censtype, type = "interval") Surv2fitdistcens(time = d2bis$t1, time2 = d2bis$t2, event = d2bis$censtype, type = "interval") ```

Surv2fitdistcens function