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zkamvar avatar zkamvar commented on June 25, 2024

I'm working on the function to estimate round robin frequencies in place, but I'm having trouble passing ASAN at my comparison function for qsort.

The error it gives me:

mlg_counter.c:61:10: runtime error: member access within null pointer of type 'struct mask'

All I want to do is cast it into a char *. @JonahBrooks, do you have any pointers (pun VERY intended)?

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zkamvar avatar zkamvar commented on June 25, 2024

The issue above has been fixed and the results are fantastic as compared to doing the same thing in base R:

Setup:

# Function for counting the number of round robin mlgs per locus
rr <- function(x){
        mask <- seq(ncol(x))
        res  <- vector(mode = "integer", length = ncol(x))
        for (i in mask){
                res[i] <- nrow(unique(x[, -i, drop = FALSE]))
        }
        return(res)
}

x <- matrix(sample(0:2, 6660, rep = TRUE), nrow = 666, ncol = 10)
library('microbenchmark')
library('poppr')
res <- microbenchmark(rr(x), .Call("mlg_round_robin", x, PACKAGE = "poppr"))
res
Unit: milliseconds
                                           expr        min         lq        mean     median         uq       max neval  
                                          rr(x) 199.243444 220.686884  241.518477 229.980039 245.227290 569.22988   100  
 .Call("mlg_round_robin", x, PACKAGE = "poppr")   4.213625   4.396508    6.976769   4.925717   5.974037  50.60142   100

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zkamvar avatar zkamvar commented on June 25, 2024

I've added a function to estimate round robin allele frequencies in the mlg-counter branch called rraf()

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zkamvar avatar zkamvar commented on June 25, 2024

I've added both pgen() and psex() and I've documented Stacy's name on the functions, now I just need to add her name to the Authors@R field in the Description.

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