phangorn (version 2.5.5)

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, ...)

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 wether to plot discrete (default) or continous pdf or cdf.

cdf

logical wether to plot the cummulative 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

ogical; if TRUE, draw vertical lines at steps.

…

Further arguments passed to or from other methods.

Value

discrete.gamma returns a matrix.

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.

See Also

pml.fit, stepfun

Examples

# NOT RUN {
discrete.gamma(1, 4)

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(mfrow = c(1,1))

# }