Re: [R-sig-phylo] compar.ou

2013-10-29 Thread sandra goutte
Thank you Marguerite. Looking at OUwie and OUCH/SLOUCH, i see that alpha is estimated along the other parameters, whereas in Hansen 1997 and other papers it is suggested that this would lead to very large standard errors. Is that problem resolved in these functions? Best, Sandra. 2013/10/26

Re: [R-sig-phylo] compar.ou

2013-10-29 Thread Brian O'Meara
In at least the OUwie paper we spent a lot of time doing simulations to determine this empirically (this may have been examined in other papers, too, though none come to mind). Alpha can be estimated, but sometimes with scarily large standard errors (but not always). This property should hold for

Re: [R-sig-phylo] compar.ou

2013-10-29 Thread Cecile Ane
FYI, we have some theory to explain why alpha has large standard errors and in which conditions. As Brian says, it comes with a flat likelihood with respect with alpha. http://dx.doi.org/10.1214/13-AOS1105 or http://www.stat.wisc.edu/~ane/publis/2013HoAne_AoS.pdf On 10/29/2013 09:46 AM, Brian

Re: [R-sig-phylo] compar.ou

2013-10-29 Thread Marguerite Butler
Hi Sandra and others, You can also assess confidence using parametric bootstrap, a procedure which we generally recommend for all users. ouch has built-in facilities to do so (the bootstrap() and simulate() functions in addition to update() ). I think there are examples in my tutorial. If

Re: [R-sig-phylo] Error in OUwie

2013-10-29 Thread Brian O'Meara
The error happens after it does the calculation for the point estimates, so it's likely happening when it starts doing the calculations to look at the curvature at the solution (to see if it's a maximum rather than a saddle point and to get an estimate of standard errors). Doing OU1 -