Re: [R-sig-phylo] mixed phylogenetic model in MCMCglmm

2019-10-12 Thread Oscar Inostroza
Hi,
thank you for your attention. My data consists of 1820 observations
(species) grouped in 11 levels (I know that it is a lot!). I mean "crazy"
estimates because if I run the models separately for each level (i.e.
trimmed the database at each level), there is a very strong positive
relationship between x and y. However, when running the full model, the
slopes and intercepts are very different (e.g. negative or null slopes).

El sáb., 12 de oct. de 2019 a la(s) 03:51, HADFIELD Jarrod (
j.hadfi...@ed.ac.uk) escribió:

> Hi Oscar,
>
> The syntax and prior look fine. How many levels of group are there and
> what do you mean by crazy?
>
> Cheers,
>
> Jarrod
>
>
> > On 12 Oct 2019, at 04:54, Oscar Inostroza 
> wrote:
> >
> > I'm trying to run a mixed phylogenetic model using the function in the
> > MCMCglmm R package of the same name. In this model, I want to estimate
> > slopes and intercepts for each level of a given variable (modeled as a
> > random effect). I tried to run the model with the following code.
> However,
> > the estimates of slopes and intercepts for the random effect are crazy!
> > (i.e. when running separate models for each level, the results are
> > reasonable) There is something wrong with my code? (in the syntax of the
> > model, or likely in the prior specification)
> >
> > prior<- list(G=list(G1=list(V=1, nu=0.002), G2=list(V=diag(2), nu=2,
> > alpha.mu= rep(0,2), alpha.V=diag(1000,2,2))), R=list(V=1, nu=0.002))
> >
> > model<-MCMCglmm(y~x, random=~phylo +
> >
> us(1+x):group,family="gaussian",ginverse=list(phylo=inv.phylo$Ainv),prior=prior,data=data,nitt=nitt,burnin=burn,thin=thin,
> > pr=TRUE)
> >
> > Cheers
> >
> > p.s the same model, but in the syntax used by brms has the form:
> >
> > model <- brm(y ~ x +(1|phylo)+(1+x|group), cov_ranef = list(phylo = A)...
> >
> > (But it's too slow for my amount of data)
> >
> > --
> > Oscar
> >
> > [[alternative HTML version deleted]]
> >
> > ___
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> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
> The University of Edinburgh is a charitable body, registered in Scotland,
> with registration number SC005336.
>


-- 
Oscar Inostroza Michael
Biólogo
Magíster Ciencias (m) Zoología
Programa Doctorado en Sistemática y Biodiversidad
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7341

e-mail: oskinostr...@gmail.com
   oscarinostr...@udec.cl

Pagina Web: http://phyloevolecol.cl/inostroza-michael/

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[R-sig-phylo] mixed phylogenetic model in MCMCglmm

2019-10-11 Thread Oscar Inostroza
 I'm trying to run a mixed phylogenetic model using the function in the
MCMCglmm R package of the same name. In this model, I want to estimate
slopes and intercepts for each level of a given variable (modeled as a
random effect). I tried to run the model with the following code. However,
the estimates of slopes and intercepts for the random effect are crazy!
(i.e. when running separate models for each level, the results are
reasonable) There is something wrong with my code? (in the syntax of the
model, or likely in the prior specification)

prior<- list(G=list(G1=list(V=1, nu=0.002), G2=list(V=diag(2), nu=2,
alpha.mu= rep(0,2), alpha.V=diag(1000,2,2))), R=list(V=1, nu=0.002))

model<-MCMCglmm(y~x, random=~phylo +
us(1+x):group,family="gaussian",ginverse=list(phylo=inv.phylo$Ainv),prior=prior,data=data,nitt=nitt,burnin=burn,thin=thin,
pr=TRUE)

Cheers

p.s the same model, but in the syntax used by brms has the form:

model <- brm(y ~ x +(1|phylo)+(1+x|group), cov_ranef = list(phylo = A)...

(But it's too slow for my amount of data)

-- 
Oscar

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[R-sig-phylo] Phylogenetic varying slopes and intercepts model

2019-09-10 Thread Oscar Inostroza
Hi, everybody

I’m trying to fit a phylogenetic model to model the relationship between x
and y (eg. lmer syntax: y~x +(1|species), species with their respective
var-covar matrix). Given that species are grouped into major categories
(families, orders, etc), What is the correct way to account for this
hierarchical structure, while estimating slopes and random intercepts for
one of those categories? For example, if I want the estimates of slopes and
intercepts for each level of the family category: what is the correct way?

a) y~x+(1|species)+(1+x|family), ## varying intercept-slope by family
(family added as another random effect),

b) y~x+(1+x|family/species) ## varying intercept-slope by family,
accounting for the fact that species are grouped into family,

or simply I have to add the family category as a fixed effect:

c) y~x+family+(1+family|species)

Best,


-- 
Oscar

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Re: [R-sig-phylo] GeoSSE question

2015-04-14 Thread Oscar Inostroza
thank you very much for your answers

2015-04-11 12:37 GMT-03:00 Santiago Sanchez santiago.snc...@gmail.com:
 Hello Oscar,

 GeoSSE itself cannot be extended to include more than 3 states. What you 
 could do is set up a  ClaSSE model that is equivalent to GeoSSE with more 
 than 3 states. In the ClaSSE help page there is an example that can give you 
 an idea of how to do this.

 Cheers,
 Santiago


 Santiago Sanchez-Ramirez
 Ecology and Evolutionary Biology, University of Toronto
 Natural History (Mycology), Royal Ontario Museum
 100 Queen's Park
 Toronto, ON
 M5S 2C6
 Canada
 +1 416 586 8025
 Website: www.sites.google.com/site/santiagosnchezrmirez/


 Message: 4
 Date: Sat, 11 Apr 2015 04:13:54 -0300
 From: Oscar Inostroza oskinostr...@gmail.com
 To: r-sig-phylo@r-project.org
 Subject: [R-sig-phylo] GeoSSE question
 Message-ID:
CADG1FwswSVqEWCnZ1ZTmPptDcpXq0Ln7s80AWR-4eK45=vk...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Hi all,
 Im writing to ask aabout Geosse function (Goldberg et al, 2011; Syst
 Biol) implemented in the diversitree. R package.  Is possible to
 extend extend this function to consider more than two areas? If anyone
 knows and I could help me, I would be very grateful

 best regards

 --
 Oscar Inostroza Michael
 Bi?logo
 Programa Magister Ciencias (m) Zoolog?a
 Laboratorio de Ecolog?a Evolutiva y Filoinform?tica
 Facultad de Ciencias Naturales Y Oceanogr?ficas
 Universidad de Concepci?n
 Barrio Universitario s/n, Casilla 160-C
 Concepci?n, CHILE

 Fono Oficina: (56) 41 - 220 - 7325

 e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl



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-- 
Oscar Inostroza Michael
Biólogo
Programa Magister Ciencias (m) Zoología
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 - 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] GeoSSE question

2015-04-11 Thread Oscar Inostroza
Hi all,
Im writing to ask aabout Geosse function (Goldberg et al, 2011; Syst
Biol) implemented in the diversitree. R package.  Is possible to
extend extend this function to consider more than two areas? If anyone
knows and I could help me, I would be very grateful

best regards

-- 
Oscar Inostroza Michael
Biólogo
Programa Magister Ciencias (m) Zoología
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 - 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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Re: [R-sig-phylo] PGLS with discrete binary independent variable?

2014-11-13 Thread Oscar Inostroza
your question can be evaluated using generalised linear mixed models
(GLMM). For this, a excellent R alternative is MCMCglmm program,
developed by Hadfield (2010).

Chers

Hadfield JD (2010). MCMC methods for Multi-response Generalised Linear
Mixed Models: The MCMCglmm R Package. Journal of Statistical Software,
33(2), 1-22.

2014-11-13 15:03 GMT-03:00 Brian A. Gill gillbri...@gmail.com:
 Dear list members.

 I am working on a comparative phylogenetic analysis.

 My independent variable is latitude (discrete binary; Colorado or Ecuador)
 and my dependent variable is elevation range breadth in meters (continuous).

 It seems that independent contrasts are not appropriate because they
 require two continuous variables.

 Does anyone know if a PGLS approach is valid with these trait types?

 Would this not effectively be trying to do a regression between two points
 because of the discrete binary independent variable?

 I'm unable to find any examples in the literature dealing with this
 scenario, but found an example here:

 http://tmfujis.wordpress.com/2013/08/22/phylogenetic-regression-part-1/

 Thanks!


 Brian



 --
 Brian A. Gill

 VISIT MY WEBSITE:
 http://gillbriana.wix.com/brian-gill

 FOLLOW ME ON TWITTER:
 @CSUBrianGill

 Colorado State University Biology
 1878 Campus Delivery
 Fort Collins, CO 80523

 970-215-7037

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-- 
Oscar Inostroza Michael
Biólogo
Programa Magister Ciencias (m) Zoología
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 - 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] trouble with quasse function

2013-11-22 Thread Oscar Inostroza
hello all!!
I am writing to know if anyone can help me. I have tried to model the
effect of a continuous variable both on rates of speciation and extinction. I
have No problems for the rate of speciation. However when I try to model
extinction rates, especially for the hump model ((f.h -make.b1
(constant.x, noroptimal.x), and i try to fin de ML of this function (mle.h
find.mle (nodrift (f.h), p.h, control = control, verbose = 0) throws me the
following error:
Error in f (y, len, pars, t0): Integration failure at step 0

Who knows what might be happening and how to fix it?

in advance thank you very much!!



-- 
Oscar Inostroza Michael
Biólogo
Programa Magister Ciencias (m) Zoología
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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Re: [R-sig-phylo] ancestral estimation under OU model

2013-11-08 Thread Oscar Inostroza
thank you very much for your quick response!!!

regards


2013/11/8 Liam J. Revell liam.rev...@umb.edu

 Hi Oscar.

 You can fit the OU model using (for example) fitContinuous in the geiger
 package, transform your tree using the fitted value of alpha, and then
 estimate ancestral states using BM. This will give you the same ancestral
 states as if you simultaneously fit the OU model to the tree.

 For instance:

 ## load packages
 library(phytools)
 library(geiger)
 ## fit OU model
 fit-fitContinuous(tree,x,model=OU)
 ## transform tree, could use transform.phylo
 ou-ouTree(tree,alpha=fit$opt$alpha)
 ## fit ancestral states, could use ace, anc.ML, etc.
 asr-fastAnc(ou,x)

 Let us know if this helps. Liam

 Liam J. Revell, Assistant Professor of Biology
 University of Massachusetts Boston
 web: http://faculty.umb.edu/liam.revell/
 email: liam.rev...@umb.edu
 blog: http://blog.phytools.org


 On 11/8/2013 6:52 PM, Oscar Inostroza wrote:

 Hi All

 Currently ancestral state reconstruction for continuous characters is done
 only in Brownian motion or BM wthit a trend (e.g. phytools; Liam Revell).
 So
 I would ask , is there any way to estimate ancestral states (continuous
 data) for each node of a phylogenetic tree under other model like OU?

 thanks in advance!!



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-- 
Oscar Inostroza Michael
Biólogo
Programa Magister Ciencias (m) Zoología
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] phylogenetic correlation between multistate character

2013-09-17 Thread Oscar Inostroza-Michael
Hello everyone!, I Hope you are very fine. I write to know if anyone 
knows of any method that allows to study the correlated evolution of 
multistate characters?


greetings and thanks in advance

--
Oscar Inostroza Michael
Biólogo
Programa Magister Ciencias (m) Zoología
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE
 
Fono Oficina: (56) 41 - 220 – 7325


e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] Problem with fitContinuous function

2013-07-17 Thread oscar inostroza
Dear list

Im trying to use the function fitContinuous implemented in Geiger (Harmon
et al., 2008) to adjust the different macroevolutionay models to my data
set. However, when run the models trend and OU the resuls show the
following error: Parameter estimates appear at bounds (beta to trend model
and alpha to OU model). anyone know why this happens and how to fix it?

p.s. the problem persists even when I apply a transformation to the data
(e.g. log)

-- 
Oscar Inostroza Michael
Biólogo
Programa Magister Ciencias (m) Zoología
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] parallelize diversitree

2013-03-16 Thread oscar inostroza
Hi all user

Hello to all members, I write to ask if someone could guide me how to
parallelize the program diversitree. This because I tried to run the
function quasse, but it is computationally intensive. I have a MacPro
with 12 cores, so what I would use all this capacity to perform these
analyzes

Greetings and thanks in advance



-- 
Oscar Inostroza Michael
Biólogo
Programa Magister Ciencias (m) Zoología
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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Re: [R-sig-phylo] assigning branch lengths to supertree

2013-02-27 Thread oscar inostroza
Thank you very much for your  help Jonathan and Alejandro

cheers

2013/2/27 Jonathan Eastman jonathan.east...@gmail.com:
 Hey Oscar,

 I saw your post on Rsigphylo, and I wanted to let you know that I've got a
 method for doing just what you need.  The attached files include
 installation instructions (README.pdf) and a tutorial for the method.  I'd
 be happy to address particular questions that you might have.

 Jon



-- 
Oscar Inostroza Michael
Biólogo
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] assign branch length to supertree

2013-02-26 Thread oscar inostroza
hello ausers
I write hoping that you can help me. I did a supertree by hand,
however I would like to assign branch lengths values according to a
phylogeny of the same group that I made. this can be done, ie, assign
a value to each branch length according to my phylogeny with some R
program?

thank you very much beforehand

-- 
Oscar Inostroza Michael
Biólogo
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] diversification analysis questions

2012-11-09 Thread oscar inostroza
Hi all
I write to ask a simple question, anyone know how to plot the
parameters obtained by applying the different diversification models
implemented in the program laser  of Rabosky ??.

if anyone can guide me would be very nice

cheers!

-- 
Oscar Inostroza Michael
Biólogo
Laboratorio de Ecología Evolutiva y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] urgent question

2011-09-27 Thread oscar inostroza
hello to all users
First I explain what I do.

I'm working on the evolution of the social structure
of a particular insect. I want to evaluate whether the coloanial
(independent variable, contonous) size of the species predicts the  social
structure(variable discrete with 4 states) in such insects. for this I fit
a GLMM in the program MCMCglmm of R, since my response variable is
discrete with 4 states. the problem lies is not good as well
adjusted prior to  model.

the model I'm trying to implement is the following:

 model - MCMCglmm (EstructuraSOC ~ Colonysize -1,
random = ~ animal
rcov = ~ us (trait): units,
family = categorical
Prior = list (R = list (fix = 1, V = 0.25 * (I + J), n = 3), G = list (G1 =
list (V = diag (4), n = 4), G2 = list (V = diag (4), n = 4)))
data = Data,
pedigree= Apistree ,
nitt = 60,
burnin = 10,
thin = 100)

with I = J = 3 (since they are 4 categories). to implement this model throws
me the following error:

  V is the wrong dimension for Some priorG / priorR elements.

I have little experience in the use of R or less of MCMCglmm, so if anyone
can help me in the structure of the model, as in the prior adjustment would
be very nice.

regards

p.s. if someone is willing to help to contact me for inclusion in the
job so, since it only needed to submit to a journal ISI  of the area
-- 
Oscar Inostroza Michael
Biólogo
Laboratorio de Ecología Molecular y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] urgent question

2011-09-27 Thread oscar inostroza
hello to all users
First I explain what I do.

I'm working on the evolution of the social structure
of a particular insect. I want to evaluate whether the coloanial
(independent variable, contonous) size of the species predicts the  social
structure(variable discrete with 4 states) in such insects. for this I fit
a GLMM in the program MCMCglmm of R, since my response variable is
discrete with 4 states. the problem lies is not good as well
adjusted prior to  model.

the model I'm trying to implement is the following:

 model - MCMCglmm (EstructuraSOC ~ Colonysize -1,
random = ~ animal
rcov = ~ us (trait): units,
family = categorical
Prior = list (R = list (fix = 1, V = 0.25 * (I + J), n = 3), G = list (G1 =
list (V = diag (4), n = 4), G2 = list (V = diag (4), n = 4)))
data = Data,
pedigree= Apistree ,
nitt = 60,
burnin = 10,
thin = 100)

with I = J = 3 (since they are 4 categories). to implement this model throws
me the following error:

  V is the wrong dimension for Some priorG / priorR elements.

I have little experience in the use of R or less of MCMCglmm, so if anyone
can help me in the structure of the model, as in the prior adjustment would
be very nice.

regards

p.s. if someone is willing to help to contact me for inclusion in the
job so, since it only needed to submit to a journal ISI  of the area
-- 
Oscar Inostroza Michael
Biólogo
Laboratorio de Ecología Molecular y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl




-- 
Oscar Inostroza Michael
Biólogo
Laboratorio de Ecología Molecular y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

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[R-sig-phylo] help

2011-09-26 Thread oscar inostroza
Hi

i have a litlle question. i try work on MCMCglmm packages for evalute if
exist a evolutionary relationship between a discrete multiestate
variable(response) and a continuous variable, but a i have a problem, when
run the model the program give me the error : can't scale non-ultrametric
trees, so i try ocuping a ultrametric tree, but the program give me other
error: the tree dont have branch length.
so I'm very confused why i need a ultrametric tree or a tree with branches
length ??

if someone can guide me I will be very grateful




-- 
Oscar Inostroza Michael
Biólogo
Laboratorio de Ecología Molecular y Filoinformática
Facultad de Ciencias Naturales Y Oceanográficas
Universidad de Concepción
Barrio Universitario s/n, Casilla 160-C
Concepción, CHILE

Fono Oficina: (56) 41 - 220 – 7325

e-mail: oskinostr...@gmail.com
  oscarinostr...@udec.cl

[[alternative HTML version deleted]]

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