discrete.gamma: Discrete Gamma and Beta distribution

In phangorn: Phylogenetic Reconstruction and Analysis

Discrete Gamma and Beta distribution

Description

discrete.gamma internally used for the likelihood computations in pml or optim.pml. It is useful to understand how it works for simulation studies or in cases where .

Usage

discrete.gamma(alpha, k)

discrete.beta(shape1, shape2, k)

plot_gamma_plus_inv(shape = 1, inv = 0, k = 4, discrete = TRUE,
  cdf = TRUE, append = FALSE, xlab = "x", ylab = ifelse(cdf, "F(x)",
  "f(x)"), xlim = NULL, verticals = FALSE, edge.length = NULL,
  site.rate = "gamma", ...)

plotRates(obj, cdf.color = "blue", main = "cdf", ...)

Arguments

alpha	Shape parameter of the gamma distribution.
k	Number of intervals of the discrete gamma distribution.
shape1, shape2	non-negative parameters of the Beta distribution.
shape	Shape parameter of the gamma distribution.
inv	Proportion of invariable sites.
discrete	logical whether to plot discrete (default) or continuous pdf or cdf.
cdf	logical whether to plot the cumulative distribution function or density / probability function.
append	logical; if TRUE only add to an existing plot.
xlab	a label for the x axis, defaults to a description of x.
ylab	a label for the y axis, defaults to a description of y.
xlim	the x limits of the plot.
verticals	logical; if TRUE, draw vertical lines at steps.
edge.length	Total edge length (sum of all edges in a tree).
site.rate	Indicates what type of gamma distribution to use. Options are "gamma" (Yang 1994) and "gamma_quadrature" using Laguerre quadrature approach of Felsenstein (2001)
...	Further arguments passed to or from other methods.
obj	an object of class pml
cdf.color	color of the cdf.
main	a main title for the plot.

Details

These functions are exported to be used in different packages so far only in the package coalescentMCMC, but are not intended for end user. Most of the functions call C code and are far less forgiving if the import is not what they expect than pml.

Value

discrete.gamma returns a matrix.

Author(s)

Klaus Schliep [e-mail]

See Also

pml.fit, stepfun, pgamma, pbeta,

Examples

discrete.gamma(1, 4)

old.par <- par(no.readonly = TRUE)
par(mfrow = c(2,1))
plot_gamma_plus_inv(shape=2, discrete = FALSE, cdf=FALSE)
plot_gamma_plus_inv(shape=2, append = TRUE, cdf=FALSE)

plot_gamma_plus_inv(shape=2, discrete = FALSE)
plot_gamma_plus_inv(shape=2, append = TRUE)
par(old.par)

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.