quasse-common: Support Functions for QuaSSE Models

In diversitree: Comparative 'Phylogenetic' Analyses of Diversification

Support Functions for QuaSSE Models

Description

Utility functions for working with QuaSSE models. These provide a minimal set of state-varying functions, suitable for use with make.quasse, and simulation assistance functions for use with tree.quasse.

This is currently poorly explained!

Usage

constant.x(x, c)
sigmoid.x(x, y0, y1, xmid, r)
stepf.x(x, y0, y1, xmid)
noroptimal.x(x, y0, y1, xmid, s2)

make.linear.x(x0, x1)

make.brownian.with.drift(drift, diffusion)

Arguments

x	Character state
c	Constant.
y0	y value at very small x (limit as x tends to negative infinity)
y1	y value at very large x (limit as x tends to infinity). For noroptimal.x, this is the y value at xmid.
xmid	Midpoint (inflection point) of sigmoid or step function
r	Rate at which exponential decay occurs or sigmoid changes - higher values are steeper
s2	Variance of the normal distribution specified by noroptimal.x.
x0	Lower x limit for the linear function: y will take value at x0 for all x smaller than this
x1	Upper x limit for the linear function: y will take value at x1 for all x greater than this
drift	Rate of drift
diffusion	Rate of diffusion (positive)

Details

The linear function returned by (make.linear.x) will go to zero wherever negative. This may not always be desired, but is required for valid likelihood calculations under QuaSSE.

Author(s)

Richard G. FitzJohn

diversitree documentation built on Oct. 2, 2024, 9:13 a.m.