phylopairs:Comparative Analyses of Lineage-Pair Traits
Facilitates the testing of causal relationships among lineage-pair traits in a phylogenetically informed context.
Lineage-pair traits are characters that are defined for pairs
of lineages instead of individual taxa. Examples include the
strength of reproductive isolation, range overlap, competition
coefficient, diet niche similarity, and relative hybrid
fitness. Users supply a lineage-pair dataset and a phylogeny.
'phylopairs' calculates a covariance matrix for the
pairwise-defined data and provides built-in models to test for
relationships among variables while taking this covariance into
account. Bayesian sampling is run through built-in 'Stan'
programs via the 'rstan' package. The various models and
methods that this package makes available are described in
Anderson et al. (In Review), Coyne and Orr (1989)
<doi:10.1111/j.1558-5646.1989.tb04233.x>, Fitzpatrick (2002)
<doi:10.1111/j.0014-3820.2002.tb00860.x>, and Castillo (2007)
<doi:10.1002/ece3.3093>.
