R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #
> # Testing reference implementation (R) versus unrolled loop (c) and openmp version (c)
> # copyright (c) 2016-2020 - Danny Arends, Pjotr Prins, Gudrun Brockmann and Rob Williams
> # last modified Apr, 2016
> # first written Apr, 2016
> #
> 
> library(ctl)
Loading required package: MASS
Loading required package: parallel
Loading required package: qtl
> 
> n.perm <- 20
> n.ind <- 200
> n.phe <- 200
> 
> time.ref <- 0
> time.cor <- 0
> time.omp <- 0
> 
> time.all <- matrix(NA, 0, 3, dimnames = list(c(), c("ref", "cor", "omp")))
> for(i in 1:n.perm) {
+   x <- runif(n.ind)                                   # Random x vector
+   Y <- matrix(runif(n.ind * n.phe), n.ind, n.phe)     # Random Y matrix
+ 
+   s.ref <- proc.time()[3]                             # Start time
+   res.ref <- round(cor(x, Y), 6)                      # Run analysis
+   time.ref <- time.ref + (proc.time()[3] - s.ref)     # Add time information
+ 
+   s.cor <- proc.time()[3]
+   res.cor <- round(correlation(x, Y), 6)
+   time.cor <- time.cor + (proc.time()[3] - s.cor)
+ 
+   s.omp <- proc.time()[3]
+   res.omp  <- round(openmp(2, x, Y)$res, 6)
+   time.omp <- time.omp + (proc.time()[3] - s.omp)
+ 
+   cat(time.ref, time.cor, time.omp, "\n")
+ 
+   time.all <- rbind(time.all, c(time.ref, time.cor, time.omp))
+ 
+   if(!all(res.ref == res.cor)) stop("ref != cor\n")   # When results differ, stop
+   if(!all(res.ref == res.omp)) stop("ref != mp\n")    # When results differ, stop
+ }
0 0 0 
0 0 0 
0 0 0 
0 0 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0 0.01 0 
0.01 0.01 0 
> 
> boxplot(time.all)
> plot(time.all[,"ref"], time.all[,"cor"])
> plot(time.all[,"ref"], time.all[,"omp"])
> 
> proc.time()
   user  system elapsed 
   0.28    0.12    0.34