Benchmarking results

This page provides benchmark results of several standard net survival routines implemented in this package. Note that the runtime also depends on other packages, in particular on RateTables.jl.

Take numbers displayed here carefully

All the following benchmarks are run on github action contunous integration platform, which is a very slow computing engine. Thus, these numbers may not represent your local performance. A locally ran version of these benchmarks in availiable on the github readme, and the below code blocks can be used to check performance on your own hardware.

Benchmarks w.r.t. `relsurv`

This first set of benchmark compares standard functionalities with their implementation in relsurv. Below numbers gives runtime mulitpliers w.r.t. R::relsurv, computed on github action CI.

using RateTables, NetSurvival, RCall, DataFrames

function test_surv(r_method,::Type{E}, stratified) where E
    if stratified
        jl = @timed fit(E, @formula(Surv(time,status)~sex), colrec, slopop)
        @rput r_method
        r = @timed R"""
            rez = relsurv::rs.surv(survival::Surv(time, stat) ~ sex, rmap=list(age = age, sex = sex, year = diag), data = relsurv::colrec, ratetable = relsurv::slopop, method = r_method, add.times=1:8149)
        """
    else
        jl = @timed fit(E, @formula(Surv(time,status)~1), colrec, slopop)
        @rput r_method
        r = @timed R"""
            rez = relsurv::rs.surv(survival::Surv(time, stat) ~ 1, rmap=list(age = age, sex = sex, year = diag), data = relsurv::colrec, ratetable = relsurv::slopop, method = r_method, add.times=1:8149)
        """
    end
    return r.time / jl.time
end

function test_graffeo(stratified)
    if stratified
        jl = @timed fit(GraffeoTest, @formula(Surv(time,status)~stage+Strata(sex)), colrec, slopop)
        r = @timed R"""
        rez = relsurv::rs.diff(survival::Surv(time, stat) ~ stage + survival::strata(sex), rmap=list(age = age, sex = sex, year = diag), data = relsurv::colrec, ratetable = relsurv::slopop)
        """
    else
        jl = @timed fit(GraffeoTest, @formula(Surv(time,status)~stage), colrec, slopop)
        r = @timed R"""
        rez = relsurv::rs.diff(survival::Surv(time, stat) ~ stage, rmap=list(age = age, sex = sex, year = diag), data = relsurv::colrec, ratetable = relsurv::slopop)
        """
    end
    return r.time / jl.time
end
test_all(stratified) = [
    test_surv("pohar-perme", PoharPerme, stratified),
    test_surv("ederer1", EdererI, stratified),
    test_surv("ederer2", EdererII, stratified),
    test_surv("hakulinen", Hakulinen, stratified),
    test_graffeo(stratified),
]
test_all() = DataFrame(
    Algorithm = ["Pohar Perme", "EdererI", "EdererII", "Hakulinen", "Graffeo's LRT"],
    unstratified = test_all(false),
    stratified = test_all(true)
)
rez = test_all()
rez = test_all() # discard first run.

# note: to obtain the pretty printing from the readme, you need to install PrettyTables.jl and do :
# using PrettyTables
# pretty_table(rez, backend = Val(:markdown))

rez

5×3 DataFrame

Row	Algorithm	unstratified	stratified
	String	Float64	Float64
1	Pohar Perme	6.9655	6.34096
2	EdererI	3.19294	1.92697
3	EdererII	12.54	9.77578
4	Hakulinen	10.1448	6.80201
5	Graffeo's LRT	9.45116	14.3843

Benchmarking across time

The following charts provide a glimpse of NetSurvival.jl's performance along time, also ran on github CI:

Benchmarking results

Benchmarks w.r.t. relsurv

Benchmarking across time

Benchmarks w.r.t. `relsurv`