Closed LauravanHolstein closed 1 year ago
Hi Laura,
This error caused by the latest numpy version has been already fixed a week ago. Please download the latest PyRate version.
Your understanding is correct: Self diversity dependence is always indicated by 0_0, i.e. Gl0_0, Wl0_0, Gm0_0, and Wm0_0.
Gl0_1 can never be diversity dependence.
How did you run the MBD analysis with the LTT as single predictor? The only possibility to do so is an empty folder for -var
(i.e., without any text files in it). Then, correctly, you do not get any Gl0_1 because self diversity is the only predictor.
Best, Torsten
Hi Torsten,
You're right - tried plotting today and all good. Thank you for this!
Right - my mistake, I put the whole clade's LTT text file as the single predictor in the predictor folder. Will repeat the analysis without it!
Many thanks as always, Laura
Hi!
Final question for now (I hope!). I got the following error while trying to plot the results of a MBD analysis:
I'm running PyRate on a Mac M1, and these are the data (although I got the same error with a different dataset, so unlikely this is the consequence of weird data input).
Also, just to check my sanity, in Tracer the Gl0_0 estimate refers to the correlation parameter for self diversity dependence of speciation (and Wl0_0 to the shrinkage factor for self diversity dependence of speciation, etc), right? With the ...0_1, ...0_2, etc, estimates referring to parameters for supplied predictors 1, 2, etc?
The reason I ask is that, when I ran MBD with a single predictor, the LTT output of the whole clade, I got very different correlation parameters for Gl0_0 and Gl0_1 (-8.31 and 1.62, respectively). I assumed that these would be the same or similar, as GI0_1 would essentially be self diversity dependence in this case, right? I must be understanding it wrong!
Many thanks, Laura