quasse-common {diversitree} R Documentation

## 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

[Package diversitree version 0.9-16 Index]