Description Usage Arguments Value Author(s) Examples
A function to fit coalescent models to a given phylogenetic tree.
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phy |
A phylogenetic tree. |
Model |
A Model choice from const (constant population size), expo (exponetial growth),expan (expansion growth), log (logistic growth), step (piecewise constant), pexpan (piecewise expansion growth) and plog (piecewise logistic growth). |
start |
Initial values for the parameters to be optimized over. |
lower, |
upper Bounds on the variables. |
Rcpp |
Calculation is based on C++ code when it is True and on R code when it is False. |
MCMC |
MCMC simulation is run when it is true, and not run when it is False. The default prior is uniform given the lower and upper. |
sig |
MCMC simulation step size. |
run |
Number of MCMC simulation. |
Parameters estimation of a given model, loglikelihood and AIC
Fei Xiang (xf3087@gmail.com)
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