Add a progress bar to boot function in R

Question

I am trying to add a progress bar to a bootstrap function in R. I tried to make the example function as simple as possible (hence i'm using mean in this example).

library(boot)
v1 <- rnorm(1000)
rep_count = 1

m.boot <- function(data, indices) {
  d <- data[indices]
  setWinProgressBar(pb, rep_count)
  rep_count <- rep_count + 1
  Sys.sleep(0.01)
  mean(d, na.rm = T) 
  }

tot_rep <- 200
pb <- winProgressBar(title = "Bootstrap in progress", label = "",
                     min = 0, max = tot_rep, initial = 0, width = 300)
b <- boot(v1, m.boot, R = tot_rep)
close(pb)

The bootstrap functions properly, but the problem is that the value of rep_count does not increase in the loop and the progress bar stays frozen during the process.

If I check the value of rep_count after the bootstrap is complete, it is still 1.

What am i doing wrong? maybe the boot function does not simply insert the m.boot function in a loop and so the variables in it are not increased?

Thank you.

Answer 1

You could use the package progress as below:

library(boot)
library(progress)

v1 <- rnorm(1000)

#add progress bar as parameter to function
m.boot <- function(data, indices, prog) {
  
  #display progress with each run of the function
  prog$tick()
  
  d <- data[indices]
  Sys.sleep(0.01)
  mean(d, na.rm = T) 
  
}

tot_rep <- 200

#initialize progress bar object
pb <- progress_bar$new(total = tot_rep + 1) 

#perform bootstrap
boot(data = v1, statistic = m.boot, R = tot_rep, prog = pb)

I haven't quite figured out yet why it's necessary to set the number of iterations for progress_bar to be +1 the total bootstrap replicates (parameter R), but this is what was necessary in my own code, otherwise it throws an error. It seems like the bootstrap function is run one more time than you specify in parameter R, so if the progress bar is set to only run R times, it thinks the job is finished before it really is.