README.md

In dfriend21/fstCpp: What the Package Does in One 'Title Case' Line

Simple R package that exports a single C++ function called wcCpp(). It calculates overall and per-locus F-statistics (FIT, FST, and FIS) as well as pairwise FST. It uses the formulas given in Weir and Cockerham (1984).

I wrote this because existing functions in R (i.e. Fst() from pegas; wc() and pairwise.WCfst() from hierfstat) are not fast - this function runs considerably faster.

Below are the results of benchmarking the functions using a dataset of 1937 individuals with 20 loci, 289 alleles, and 5 populations.

  expression                      median `itr/sec` mem_alloc n_itr total_time
1 wcCpp(alls, pp)                35.94ms    27.7     465.8KB    14   504.83ms
2 pegas::Fst(loc)                  2.36s     0.424    64.7MB     1      2.36s
3 hierfstat::wc(hf)                 2.1s     0.477    86.9MB     1       2.1s
4 hierfstat::pairwise.WCfst(hf)    9.88s     0.101   442.8MB     1      9.88s

Weir, B. S. and Cockerham, C. C. (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358–1370.

dfriend21/fstCpp documentation built on Feb. 7, 2022, 9:13 a.m.