I get error "incorrect number of subscripts on matrix"

I am trying to perform a paired permutation t-test. I get an error " in t.star[r, ] <- res[[r]] : incorrect number of subscripts on matrix". Below is the code I wrote. Any pointers appreciated.

library(RVAideMemoire)
library(boot)
library(xlsx)


mydata <- read.xlsx("C:/data_bootstrap.xlsx",1)

results = boot(mydata,statistic=sample_mean,R=500) 

print (results)

sample_mean <- function(mydata, indices) {

  sam=mydata[indices,1]

  sam1=mydata[indices,2]
 
  
  bar = perm.t.test(sam,sam1,paired=TRUE,nperm=500)
 
return(bar)
 
}

Raw data, no need for the link:

structure(list(Random = c(11L, 10L, 11L, 11L, 10L, 10L, 36L, 11L, 10L, 16L, 16L, 10L, 16L, 10L, 16L, 10L, 11L, 11L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 10L, 10L, 10L, 11L), Statement = c(11L, 10L, 11L, 10L, 10L, 16L, 16L, 10L, 10L, 16L, 11L, 11L, 10L, 10L, 16L, 11L, 10L, 11L, 16L, 10L, 11L, 10L, 16L, 10L, 10L, 10L, 11L, 10L, 10L)), class = "data.frame", row.names = c(NA, -29L))

Solution

The boot() function requires its statistic argument to be a function that returns a vector. Your sample_mean function returns a list of class "htest" because that is the output of perm.t.test(). Based on the function name, I assume you want the estimate of the means of the differences from that test.

If you change your function to look as follows, the code works.

sample_mean <- function(mydata, indices) {
  
  sam=mydata[indices,1]
  
  sam1=mydata[indices,2]
  
  
  bar = perm.t.test(sam,sam1,paired=TRUE,nperm=500)
  
  return(bar$estimate)
}

If you want a different output from perm.t.test(), then swap $estimate for something else like $statistic or $p.value.

Here is an example of boot with R=10 (to be manageable):

results = boot(mydata,statistic=sample_mean,R=10) 
print(results)

ORDINARY NONPARAMETRIC BOOTSTRAP


Call:
boot(data = mydata, statistic = sample_mean, R = 10)


Bootstrap Statistics :
     original    bias    std. error
t1* 0.5172414 0.1206897    0.720067