CalculateGdi: Calculate the genealogical divergence index (gdi)
In bomeara/phrapl: Phylogeography using Approximate Likelihood

Description Usage Arguments Author(s) Examples

This function calculates the genealogical divergence index (gdi) for a pair of taxa based on specified bi-directional migration rates (M) and a divergence time (t) estimated from a PHRAPL analysis. This index provides something similar to the genealogical sorting index (gsi), except for a given set of migration and divergence values instead of for a group on a tree. It also differs from the gsi in that it is calculated for a given pair of populations or taxa rather than for a single taxon in respect to the entire tree. The index is scaled to be between 0 and 1, where 0 = panmixia and 1 = strong divergence. Except when gdi is close to 1, there is a fairly high error, such that precision requires a large number of replicates (e.g., nreps = 10,000). We have incorporated the binom.confint function from the binom package to calculate a confidence interval if desired.

1 2	CalculateGdi(tau,migration.in,migration.out=NULL,nreps=10000,ciMethod="exact", msPath = system.file("msdir", "ms", package = "P2C2M"))

`tau`	The divergence time between two populations/groups.
`migration.in`	The migration rate into a population
`migration.out`	The migration rate out of a population. If this is not specified, migration rates are assumed to be symmetrical.
`nreps`	The number of genealogies to be simulated.
`ciMethod`	Which method to use to calculate a confidence interval for gdi. Any or all of eight methods for calculating a binomial confidence interval can be specified ("exact", "asymptotic", "agresti-coull", "wilson", "prop.test", "bayes", "logit", "cloglog", "probit", or "profile"). `ciMethod = "all"` will result in all eight being calculated. The default method is the Clopper-Pearson interval ("exact"). If `ciMethod=NULL`, only the gdi will be outputted.
`msPath`	Path to the local installation of ms; typing this string on the command line should result in ms running.