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I've written a function that is a simulation, that outputs a vector of 100 elements, and I want to use the *apply functions to run the function many times and store the repeated output in a new vector for each time the simulation is run.

The function looks like:

J <- c(1:100) species_richness <- function(J){ a <- table(J) return(NROW(a)) } simulation <- function(J,gens,ploton=FALSE,v=0.1){ species_richness_output <- rep(NA,gens) for(rep in 1:gens){ index1 <- sample(1:length(J),1) if(runif(1,0,1) < v){ J[index1] <- (rep+100) } else{ index2 <- sample(1:length(J),1) while(index1==index2) { index2 <- sample(1:length(J),1) } J[index1] <- J[index2] } species_richness_output[rep] <- species_richness(J) } species_abundance <- function(J){ a <- table(J) return(a) } abuntable <- species_abundance(J) print(abuntable) octaves <- function(abuntable){ oct <- (rep(0,log2(sum(abuntable)))) for(i in 1:length(abuntable)){ oct2 <- floor(log2(abuntable[i])+1) oct[oct2] <- oct[oct2]+1 } print(oct) } # octaves(c(100,64,63,5,4,3,2,2,1,1,1,1)) if(ploton==TRUE){ hist(octaves(abuntable)) } print(species_richness(J)) return(J) } simulation(J, 10000,TRUE,v=0.1)

So that's my function, it takes J a vector I defined earlier, manipulates it, then returns: the newly simulated vector J of 100 elements a function called octave that categorises the new vector a histogram corresponding to the above "octave"

I have tried a number of variations: using lapply, mapply putting args=args_from_original_simulation

simulation_repeated <- c(mapply(list, FUN=simulation(args),times=10000))

but I keep getting an error with the match.fun part of the mapply function

Error in match.fun(FUN) : 'simulation(J, 10000, FALSE, 0.1)' is not a function, character or symbol

This is despite the simulation I have written showing as being saved as a function in the workspace.

Does anyone know what this error is pointing to?

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  • 2
    Maybe replicate is closer to what you're looking for...? Commented Jan 24, 2013 at 20:05
  • 3
    the sample code you've supplied looks FUBAR. Are your args varying from one simulation to the next? If not, than jorans got the right idea. Commented Jan 24, 2013 at 20:05
  • 1
    or r*ply from the ddply package Commented Jan 24, 2013 at 20:06
  • 2
    I'd also suggest you avoid naming variables with names of critical functions like args. If you supply a little more info, like the body of your simulation function and args you'll get a lot more specific answers. Commented Jan 24, 2013 at 20:06
  • i've gotten that error when passing in arguments to one of the pply functions before. Typically if you wrap the whole body in an anonymous function then it works. Commented Jan 24, 2013 at 20:21

1 Answer 1

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In this line:

simulation_repeated <- c(mapply(list, FUN=simulation(args),times=10000))

You are not giving a function to mapply. You are (essentially) passing the result of calling simulation(args) and simulation does not return a function.

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