quassecommon  R Documentation 
Utility functions for working with QuaSSE models. These
provide a minimal set of statevarying 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
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