phangorn: discrete.gamma – R documentation

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discrete.gamma

Discrete Gamma function

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)

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.
`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 klaus.schliep@gmail.com

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

Phylogenetic Reconstruction and Analysis

v2.7.0

GPL (>= 2)

Authors

Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]

Initial release