Extrait l'argument de fonction local à utiliser globalement dans R

Question

J'ai créé une fonction dans R ayant plusieurs arguments. J'aimerais pouvoir appeler ces arguments globalement, à utiliser en dehors de la fonction.

Comment cela peut-il être fait facilement? Je pense peut-être que match.fun() et match.arg() seraient ce qui est nécessaire ici. Ai-je raison?

Ma fonction est la suivante:

HAC.sim <- function(K, N, Hstar, p, probs, perms = 10000){ 

specs <- 1:N 

### Set up a container to hold the identity of each individual from each permutation 

pop <- array(dim = c(c(perms, N), K)) 

### Create an ID for each haplotype 

haps <- as.character(1:Hstar) 

### Assign probabilities of occurrence to each haplotype, ensure they sum to 1 
### This is where we assume we "know" the distribution of haplotypes 
### Here, I have assumed they all occur with equal frequency, but you can change this to   assume some dominant ones and some rare ones, whatever you want 

# probs <- rep(1/Hstar, Hstar) 
probs <- c(0.45, 0.45, rep(0.10/8, 8)) 

### Generate permutations, we assume each permutation has N individuals, and we sample those individuals' haplotypes from our probabilities 

# If K > 1, haplotypes are partitioned into equally-sized subpopulations/demes 
# Can change number of haplotypes in each subpopulation and re-run simulation 
# For each additional, K, add new Ki and new pop[j ,, i] in loop 

for(j in 1:perms){ 
    for(i in 1:K){ 
     if(i == 1){ 
      pop[j, specs, i] <- sample(haps, size = N, replace = TRUE, prob = probs) 
     } 
      else{ 
       pop[j ,, 1] <- sample(haps[K1], size = N, replace = TRUE, prob = probs[K1]) 
       pop[j ,, 2] <- sample(haps[K2], size = N, replace = TRUE, prob = probs[K2]) 
     } 
    } 
} 

### Make a matrix to hold the 1:N individuals from each permutation 

HAC.mat <- array(dim = c(c(perms, N), K)) 

for(k in specs){ 
    for(j in 1:perms){ 
     for(i in 1:K){ 
      ind.index <- sample(specs, size = k, replace = FALSE) ## which individuals will we sample 
      hap.plot <- pop[sample(1:nrow(pop), size = 1, replace = TRUE), ind.index, sample(1:K, size   = 1, replace = TRUE)] ## pull those individuals from a permutation 
      HAC.mat[j, k, i] <- length(unique(hap.plot)) ## how many haplotypes did we get for a given sampling intensity (k) from each ### permutation (j) 
     } 
    } 
} 

### Calculate the mean and CI for number of haplotypes at each sampling intensity (j) 

means <- apply(HAC.mat, MARGIN = 2, mean) 
lower <- apply(HAC.mat, MARGIN = 2, function(x) quantile(x, 0.025)) 
upper <- apply(HAC.mat, MARGIN = 2, function(x) quantile(x, 0.975)) 

d <- data.frame(specs, means, lower, upper) 

### Plot the curve and frequency barplot 

par(mfrow = c(1, 2)) 

for(i in 1:K){ 
    if(i == 1){ 
     plot(specs, means, type = "n", xlab = "Specimens sampled", ylab = "Unique haplotypes", ylim = c(1, Hstar)) 
     polygon(x = c(specs, rev(specs)), y = c(lower, rev(upper)), col = "gray") 
     lines(specs, means, lwd = 2) 
     HAC.bar <- barplot(N*probs, xlab = "Unique haplotypes", ylab = "Specimens sampled", names.arg = 1:Hstar) 
    } 
    else{ 
     plot(specs, means, type = "n", xlab = "Specimens sampled", ylab = "Unique haplotypes", ylim = c(1, max(HAC.mat))) 
     polygon(x = c(specs, rev(specs)), y = c(lower, rev(upper)), col = "gray") 
     lines(specs, means, lwd = 2) 
     HAC.bar <- barplot(N*probs[get(paste0("K", i))], xlab = "Unique haplotypes", ylab = "Specimens sampled", names.arg = get(paste0("K",i))) 
    } 
} 

## Measures of Closeness ## 

cat("\n Mean number of haplotypes sampled: " , max(means)) 
cat("\n Mean number of haplotypes not sampled: " , Hstar - max(means)) 
cat("\n Proportion of haplotypes sampled: " , max(means)/Hstar) 
cat("\n Proportion of haplotypes not sampled: " , (Hstar - max(means))/Hstar) 

cat("\n") 

cat("\n Mean estimate of N*: ", (p*N*Hstar)/max(means)) 

} 

HAC.sim(K = 1, N = 100, Hstar = 10, p = 0.95, probs = probs, perms = 10000) 

Je voudrais l'argument « p » être disponible pour passer à une autre fonction. Dois-je simplement utiliser l'ellipse (...) dans ma fonction pour spécifier des arguments supplémentaires?

Answer 1

Si je comprends bien ce que vous demandez, cela montre comment assigner aux valeurs de l'environnement global les arguments d'une fonction.

> ls() 
character(0) 
> fn <- function(a, b, c) { 
    global_a <<- a 
    global_b <<- b 
    global_c <<- c 
    a*b*c 
} 
> ls() 
[1] "fn" 
> fn(2, 3, 4) 
[1] 24 
> ls() 
[1] "fn"  "global_a" "global_b" "global_c" 
> global_a 
[1] 2 

Cependant, je fortement vous encourage à trouver une alternative autour de ce que vous essayez de résoudre, parce que ce genre d'approche peut conduire à beaucoup de maux de tête sur la route.

Vous pouvez passer les arguments comme un attribut à vos résultats si vous êtes intéressé par seulement quelques-uns des paramètres par exemple:

fn_attr <- function(a, b, c) { 
    res <- a * b * c 
    attr(res, "args") <- list(a = a, c = c) 
    res 
} 

> foo <- fn_attr(2, 3, 4) 
> attr(foo, "args")$a 

ou obtenez toutes les valeurs des arguments:

fn_attr_all <- function(a, b, c) { 
    args_vals <- as.list(environment()) 
    res <- a * b * c 
    attr(res, "args") <- args_vals 
    res 
}