fitness_landscape_manual

Manually construct a simple fitness landscape. Does not actually use the tree::fitness_landscape function.

library(tree)

Starting rain here is close to the equilibrium from scripts/equilibrium.R -- because the function is actually not terrifically smooth, it's not really the equilbrium seed rain, but close enough for our purposes.

p <- ebt_base_parameters()

p$add_strategy(new(Strategy))

p$seed_rain <- 22.2533930672727

schedule <- build_schedule(p)

## 1: Splitting {41} times (141)
## 2: Splitting {32} times (182)
## 3: Splitting {20} times (214)
## 4: Splitting {11} times (234)

schedule$use_ode_times <- TRUE

Now, let's get a view of the fitness landscape with respect to one parameter.

lma <- p[[1]]$parameters[["lma"]]

n_mutants <- 11

Add the mutants; they will all be introduced with a seed rain of 1, though they will not influence the environent at all. p_with_mutants <- p$copy() Add a vector of new lmas. There will be n_mutants+1 mutant strategy, because we're adding the resident in as a mutant too for checking. p_with_mutants$add_strategy_mutant(new(Strategy, list(lma=lma))) for (i in seq(lma * 0.1, lma * 1.2, length.out=n_mutants)) { p_with_mutants$add_strategy_mutant(new(Strategy, list(lma=i))) }

lma_mutant <- c(lma, seq(lma * 0.1, lma * 1.2, length.out=n_mutants))

p_with_mutants <- expand_parameters("lma", lma_mutant, p)

schedule_with_mutants <- expand_schedule(schedule, p_with_mutants$n_mutants)

And run, producing only seed rain. The resident seed rain should be unchanged here.

Unfortunately this is very slow!

ebt_with_mutants <- run_ebt(p_with_mutants, schedule_with_mutants)

seed_rain_mutant <- ebt_with_mutants$seed_rains

lma_v <- sapply(seq_len(p_with_mutants$size),
                function(i) p_with_mutants[[i]]$parameters[["lma"]])

all.equal(lma_v, c(lma, lma_mutant))

## [1] TRUE

plot(lma_v[-(1:2)], seed_rain_mutant[-(1:2)], log="y")

points(lma_v[[1]], seed_rain_mutant[[1]] / p$seed_rain[[1]],
       col="red", pch=19)

points(lma_v[[2]], seed_rain_mutant[[2]],
       col="blue", pch=19, cex=.5)

w_mutant <- log(seed_rain_mutant)

plot(lma_v[-(1:2)], w_mutant[-(1:2)])

points(lma_v[[1]], w_mutant[[1]] - log(p$seed_rain[[1]]),
       col="red", pch=19)

points(lma_v[[2]], w_mutant[[2]], col="blue", pch=19, cex=.5)