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