Computational benchmark

The covariance calculation is the most frequently repeated low-level operation during fitting and prediction. magp implements it in C++ through Rcpp. This page records a direct comparison with an independent R implementation of the same calculation.

Reproduce the benchmark

Clone the repository, install the development package, and run:

Rscript inst/benchmarks/benchmark-covariance-engine.R benchmark-output

The script creates fixed synthetic inputs, times both implementations, checks their largest absolute numerical difference, and records sessionInfo(). The complete script is included in the repository so that the comparison can be repeated on other computers.

Recorded result

results <- read.csv(system.file(
  "benchmarks",
  "covariance-engine-results.csv",
  package = "magp"
))
knitr::kable(
  results,
  digits = 4,
  caption = "Median elapsed time per covariance calculation."
)

Median elapsed time per covariance calculation.
mapping	rows	components	repetitions	r_seconds	rcpp_seconds	speedup	max_abs_difference
2d	180	8	3	0.125	0.0015	85.6164	0
full	180	8	3	0.151	0.0018	83.4254	0

speedup is the R time divided by the Rcpp time. Timing depends on the processor, R version, compiler, and system load, so the recorded values should not be treated as a universal performance guarantee. The max_abs_difference column is the direct numerical agreement check for the same inputs and parameters.

The benchmark session details are stored beside the result file:

session_file <- system.file(
  "benchmarks",
  "covariance-engine-session-info.txt",
  package = "magp"
)
cat(paste(readLines(session_file), collapse = "\n"))
#> R version 4.5.2 (2025-10-31)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Tahoe 26.5.2
#> 
#> Matrix products: default
#> BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
#> 
#> locale:
#> [1] C.UTF-8/C.UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8
#> 
#> time zone: America/New_York
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base
#> 
#> other attached packages:
#> [1] magp_0.12.0.9000
#> 
#> loaded via a namespace (and not attached):
#> [1] compiler_4.5.2 tools_4.5.2    Rcpp_1.1.2