How to resample and remodel n times by vectorization? - r

Question

here's my for loop version of doing resample and remodel,
B <- 999
n <- nrow(butterfly)
estMat <- matrix(NA, B+1, 2)
estMat[B+1,] <- model$coef
for (i in 1:B) {
resample <- butterfly[sample(1:n, n, replace = TRUE),]
re.model <- lm(Hk ~ inv.alt, resample)
estMat[i,] <- re.model$coef
}
I tried to avoid for loop,
B <- 999
n <- nrow(butterfly)
resample <- replicate(B, butterfly[sample(1:n, replace = TRUE),], simplify = FALSE)
re.model <- lapply(resample, lm, formula = Hk ~ inv.alt)
re.model.coef <- sapply(re.model,coef)
estMat <- cbind(re.model.coef, model$coef)
It worked but didn't improve efficiency. Is there any approach I can do vectorization?
Sorry, not quite familiar with StackOverflow. Here's the dataset butterfly.
colony alt precip max.temp min.temp Hk
pd+ss 0.5 58 97 16 98
sb 0.8 20 92 32 36
wsb 0.57 28 98 26 72
jrc+jrh 0.55 28 98 26 67
sj 0.38 15 99 28 82
cr 0.93 21 99 28 72
mi 0.48 24 101 27 65
uo+lo 0.63 10 101 27 1
dp 1.5 19 99 23 40
pz 1.75 22 101 27 39
mc 2 58 100 18 9
hh 4.2 36 95 13 19
if 2.5 34 102 16 42
af 2 21 105 20 37
sl 6.5 40 83 0 16
gh 7.85 42 84 5 4
ep 8.95 57 79 -7 1
gl 10.5 50 81 -12 4

Answer 1

(Assuming butterfly$inv.alt <- 1/butterfly$alt)
You get the error because resample is not a list of resampled data.frames, which you can obtain with:
resample <- replicate(B, butterfly[sample(1:n, replace = TRUE),], simplify = FALSE)
The the following should work:
re.model <- lapply(resample, lm, formula = Hk ~ inv.alt)
To extract coefficients from a list of models, re.model$coef does work. The correct path to coefficients are: re.model[[1]]$coef, re.model[[2]]$coef, .... You can get all of them with the following code:
re.model.coef <- sapply(re.model, coef)
Then you can combined it with the observed coefficients:
estMat <- cbind(re.model.coef, model$coef)
In fact, you can put all of them into replicate:
re.model.coef <- replicate(B, {
bf.rs <- butterfly[sample(1:n, replace = TRUE),]
coef(lm(formula = Hk ~ inv.alt, data = bf.rs))
})
estMat <- cbind(re.model.coef, model$coef)