Survival fitness function using the Restricted Mean Survival Time (RMST) of each group

Source: R/galgo.R

Survival fitness function using the Restricted Mean Survival Time (RMST) of each group as proposed by Dehbi & Royston et al. (2017).

surv_fitness(OS, clustclass, period)

Arguments

OS

a survival object with survival data of the patients evaluated
clustclass

a numeric vector with the group label for each patient
period

a number representing the period of time to evaluate in the RMST calculation

Value

The function computes the Harmonic mean of the differences between Restricted Mean Survival Time (RMST) of consecutive survival curves multiplied by the number of comparisons.

References

Dehbi Hakim-Moulay, Royston Patrick, Hackshaw Allan. Life expectancy difference and life expectancy ratio: two measures of treatment effects in randomized trials with non-proportional hazards BMJ 2017; 357 :j2250 https://www.bmj.com/content/357/bmj.j2250

Examples


# load example dataset
library(breastCancerTRANSBIG)
library(Biobase)
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:parallel’:
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
#>     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
#>     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
#>     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#>     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
#>     union, unique, unsplit, which.max, which.min
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
data(transbig)
Train <- transbig
rm(transbig)
#> Warning: object 'transbig' not found

clinical <- pData(Train)
OS <- survival::Surv(time = clinical$t.rfs, event = clinical$e.rfs)

surv_fitness(OS, clustclass = clinical$grade, period = 3650)
#> [1] 261.1064