R2TEST - Ramos-Onsins & Rozas (R2) test
Syntax: [r2] = r2test(aln,rvalue)
Inputs:
aln - Alignment structure or sequence matrix
Outputs:
r2 - R_2 statistics
rvalue - (optional) 3 for R3 test, 4 for R4 test
Ramos-Onsins & Rozas (R2) test
Detects recent severe population growth (indicated by low r2 value)
This test is based on the difference between the number of singleton mutations and
the average number of nucleotide differences. The R2 statistic is defined as
\[
R_2 = \frac{{({{\sum\limits_{i = 1}^n {(U_i - k/2)} ^2 } \mathord{\left/
{\vphantom {{\sum\limits_{i = 1}^n {(U_i - k/2)} ^2 } n}} \right.
\kern-\nulldelimiterspace} n})^{1/2} }}{S}
\]
where $n$ is the sample size, $S$ the total number of segregating sites, $k$ the
average number of nucleotide differences between two sequences, and $U_i$ the
number of singleton mutations in sequence $i$. The rationale of this test is that
the expected numbers of singletons on a genealogy branch after a recent severe
population growth event is $k/2$; consequently, lower values of $R_2$ are expected
under this demographic scenario.
Two R2 related tests namely, R3 and R4. These statistics differ from the R2 test
in the power exponent values; in R3 and R4, the exponent values of 2 and 1/2 are
replaced by 3 and 1/3, and by 4 and 1/4, respectively.
REF: Ramos-Onsins SE, Rozas J.
Statistical properties of new neutrality tests against population growth.
Mol Biol Evol. 2002 Dec;19(12):2092-100.