Thanks for pointing me in the right direction.
Jostein
27. apr. 2015 17:31 skrev "Emmanuel Paradis" <emmanuel.para...@ird.fr>:
> Hi Jostein,
>
> Le 27/04/2015 14:44, Jostein Gohli a écrit :
>
>> Hi,
>>
>> I have some questions about the method from this paper:
>>
>> Paradis et al. (2013) Quantifying variation in speciation and extinction
>> rates with clade data. DOI: 10.1111/evo.12256
>>
>>
>>
>> #Some hypothetical data:
>>
>> SpeciesCount <- c(2,13,2,2,8,1,16)
>> Ages <- c(1,2,0.5,0.6,2,0.2,3)
>>
>> #And using the simplest model, assuming extinction rate = 0:
>>
>> halfdev <- function(p) {
>> if (p <= 0 || p >= 2) return(1e100)
>> -sum(dyule(SpeciesCount, p, Ages, log = TRUE))
>> }
>>
>> #optimizing with nlm:
>>
>> res <- nlm(halfdev, .1, hessian = TRUE)
>>
>> #Questions:
>> #The halfdev function is a -lnL function, so using the nlm function will
>> maximize
>> #the likelihood, correct?
>>
>
> Correct.
>
> #So, res$estimate is the estimate of lambda (for all clades) with the
>> highest likelihood?
>>
>
> Yes.
>
> #This means that I can use the following approach to get clade specific
>> estimates of speciation rate:
>>
>> lambdas <- -dyule(SpeciesCount, res$estimate, Ages, log = TRUE)
>>
>
> Not really. You are computing the respective contribution of each clade to
> the deviance function. This cannot be taken as clade-level estimates.
>
> # lambdas summarized with data
>> cbind(lambdas,SpeciesCount,Ages)
>>
>> # lambdas SpeciesCount Ages
>> # 1.4798877 2 1.0
>> # 3.6698954 13 2.0
>> # 1.4207890 2 0.5
>> # 1.3906988 2 0.6
>> # 3.0143270 8 2.0
>> # 0.2096531 1 0.2
>> # 3.8052613 16 3.0
>>
>> #And I can use these lambda values as a response variable in a pgls (or
>> #equivalent) for downstream analysis of speciation rates?
>>
>
> I guess you are looking for the Magallon-Sanderson estimate:
>
> log(SpeciesCount)/Ages
>
> HTH
>
> Best,
>
> Emmanuel
>
> Thanks in advance for all/any help.
>>
>> Jostein
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>> Searchable archive at
>> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>>
>>
>> Pour nous remonter une erreur de filtrage, veuillez vous rendre ici :
>> http://f.security-mail.net/3072htDHdU2
>>
>>
>>
>
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
