# quasse-common: Support Functions for QuaSSE Models In diversitree: Comparative 'Phylogenetic' Analyses of Diversification

 quasse-common 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

diversitree documentation built on May 29, 2024, 4:38 a.m.