quasse-common {diversitree} | R Documentation |
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!
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)
x |
Character state |
c |
Constant. |
y0 |
y value at very small |
y1 |
y value at very large |
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
|
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) |
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.
Richard G. FitzJohn