GCD calculation

[dajmcdon]

I'm not entirely sure what the use case for gcd_num() is, but is it worth implementing differently? We don't currently import Rcpp (which the second version uses):

d <- sample(1:1000, 1000, TRUE)

microbenchmark::microbenchmark(
  epiprocess = epiprocess:::gcd_num(d),
  rtestim = rtestim:::gcd(d)
)
#> Warning in microbenchmark::microbenchmark(epiprocess = epiprocess:::gcd_num(d),
#> : less accurate nanosecond times to avoid potential integer overflows
#> Unit: microseconds
#>        expr       min         lq      mean    median       uq      max neval
#>  epiprocess 12249.816 12346.0635 17960.673 12423.984 14510.54 484596.5   100
#>     rtestim    19.024    24.2515  5672.601    34.973    51.66 563304.5   100

^{Created on 2024-03-06 with reprex v2.1.0}

[dsweber2]

That mean median comparison though.

When I search for gcd_num, the only time it shows up is in guess_period, where it is handed a list of diffs between dates, converted to numeric. So I'd expect it to run once per loop of epix_process, which doesn't seem likely to eat too much time.

The lack of tests may mean there's a bug lurking, so that would be a potential gain from switching over to a non-DIY implementation.