[Mesquitelist] resent: BiSSE, notably simulation

[Andreas Prinzing]

Dear makers of mesquite

[I permit myself to resend this mail from October/16] 

Thank you for making Mesquite possible. 

I have a few questions on the BiSSE Speciation/extinction analyses. Probably
some are decidedly stupid (sorry in advanceà, but I hope that some make
sense. 


1. Methodological: can this more or less reasonably be applied to topologies
(i.e. no branch lengths)? Does rendering a topology ultrametric using for
instance Grafen's approach help? 


2. Functionning of Mesquite: 

2.1. In the "Analysis" in the BiSSE parameters menu:

=> I leave default parameters, i.e. "?" (as I want to find out) and "-" (as
I have no information on constraints). Right? 


2.2. In the "Hypothesis Testing", i.e. "Simulate trees and characters using
Trees & Diversification Characters in the Taxa&Trees menu, choosing the
BiSSE Trees & Characters as the simulator."

=> What do I set for "Rate 0 -> 1" and for "Rate 1-> 0" (mentioned in the
menu)? My choice, no specific rules to follow? 

=> I did not come across this option (mentioned in the manual): "Choose as
many taxa as in your data."  

=> Later in the "Choose New Bar & Line Chart": "make sure you choose the
matrix you just simulated...": there is a choice between *multiple*
simulated *trees* (not matrices): I use the last one? 

=> "Character value with Respective Tree" (in manual) is that "Character
value with current Tree" or "Character value with Tree" or "Character value
with Tree" (in the menu)? I guess it is the former. 

=> "Source of trees: Stored trees..." In the menu I was asked this question
before and not here. Suppose I am on the right track nevertheless? 

=> I am not asked a "value" but this is likely because I did not deal with
"BiSSE Ln likelihood difference". Right? 

=> I somewhat lost with: "BiSSE Parameters: Leave the parameters
unspecified, but set the constraints to be as in your UNCONSTRAINED model."
and then "BiSSE Parameters: Leave the parameters unspecified, but set the
constraints to be as in your CONSTRAINED model." (in the manual) This seems
to suggest the opposite things to do, and as this is only asked once in the
menu I can only do one thing. 

=> In the BiSSE parameters menu: I leave the "current values" to "?"? 


Thank you very much in advance!

Best regards
Andreas


    ++++++++++++++++++++++++++++++++++++++
    Andreas Prinzing, Prof.
    Equipe de Recherche "Ecologie de la Diversification"
Unité de Recherche "Ecobio" :  Ecosystèmes - Biodiversité - Evolution
Université Rennes 1 / Centre National de la Recherche Scientifique
Campus de Beaulieu, Bâtiment 14 A
35042 Rennes, France
    Tel : +33 2 23 23 67 12; fax: +33 2 23 23 50 26
    andreas.prinzing at univ-rennes1.fr
    http://ecobio.univ-rennes1.fr/Fiches_perso/Fiche.asp?pseudo=APrinzing
    http://ecobio.univ-rennes1.fr/Fiches_perso/Banque/publi1_APrinzing.doc