Simulate data over a phylogeny, or sub section of a phylogeny, in order to reflect variable rates. Based on adding a constant to the tip data branch by branch and weighting by branch length and does not need to stretch the phylogeny. This is good for exponential rate decay, but pretty shoddy for delta at the moment - what it CAN do is do a good approximation of the delta relationship, but t isn't functioning as half life at the moment.
1 |
tree |
The tree that data is simulated on. |
node |
The node at which to make the changes. |
sig |
The standard deviation of the random component of the BM simulation. NOT sigma squared. |
a |
Initial rate increase before decay. If using the power decay this is, essentially, delta. |
t |
In "pwr" (delta) mode this is ROUGHLY the delta parameter. In "exp" earyl burst mode, it is the number of half lives for the decay to take place over. Essentially a high number means the rate decays rapidly, and a low one means it decays slowly. This is used rather than a rate parameter, since decay is relative to branch lengths, but half lives are not. |
decay |
Either "exp" (exponential) or "pwr" (power). The shape of the decay from the initial rate. |
dat |
If you want to use some data you already have and change it this way, put it here. |
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