Documentation should show turning non-freq-dep to freq-dep for interventions and the "trick" of the dummy fitness

[rdiaz02]

Example:

### Non-freq-dep-fitness
rT <- data.frame(parent = c("Root", rep("TP53", 2)),
                 child = c("TP53", "MDM2", "ATM"),
                 s = 0.5,
                 sh = c(-Inf, 0, 0),
                 typeDep = "MN")

epvecx <- c("TP53:MDM2" = -0.4)

FitEff <- allFitnessEffects(rT = rT, epistasis = epvecx)

set.seed(1)
ex3 <- oncoSimulIndiv(
    FitEff,
    model = "McFLD",
    mu = 1e-4,
    sampleEvery = 0.01,
    initSize = 5000,
    finalTime = 100,
    onlyCancer = FALSE
)


### Turning the first example into something you can intervene

#### What are the fitnesses?

(allgf <- evalAllGenotypes(FitEff, addwt = TRUE))

#### Write as freq-dep-fitess

rTfdf <- allgf
rTfdf[, 2] <- as.character(rTfdf[, 2])
colnames(rTfdf)[2] <- "Fitness"

## Add a dummy expression so fdf works
rTfdf[1, 2] <- "1 + 0 * n_"

rTF <- allFitnessEffects(genotFitness = rTfdf,
                         frequencyDependentFitness = TRUE,
                         frequencyType = "abs")

## Of course, much slower than the non-fdf, but identical
set.seed(1)
ex3F <- oncoSimulIndiv(
    rTF,
    model = "McFLD",
    mu = 1e-4,
    sampleEvery = 0.01,
    initSize = 5000,
    finalTime = 100,
    onlyCancer = FALSE
)

par(mfrow = c(2, 1))
plot(ex3, show = "genotypes")
plot(ex3F, show = "genotypes")

#### Create intervention

## To make effects more visible, a stronger effect
ix <- list(
    list(ID = "i1",
         Trigger = "T > 10",
         WhatHappens = "n_TP53_ATM = n_TP53_ATM*0.5",
         Periodicity = 1,
         Repetitions = Inf
         )
)

ixF <- createInterventions(ix, rTF)

set.seed(1)
ex3ixF <- oncoSimulIndiv(
    rTF,
    model = "McFLD",
    mu = 1e-4,
    sampleEvery = 0.01,
    initSize = 5000,
    finalTime = 100,
    onlyCancer = FALSE,
    interventions = ixF)

par(mfrow = c(2, 1))
plot(ex3F, show = "genotypes")
plot(ex3ixF, show = "genotypes")

(This is example is an answer to a question from Sara Verde Camacho, student of PRSTR, 2024-25)