Estimates for groups within fixed effects & also: enough info for estimating variance? MCMCglmm

Hi Jarrod,

Thanks so much for your reply & patience with my lack of stats/math saavy.

If fitting the model to include us(Znnd):species, I'm unsure of how to
specify the prior. Based on your Course Notes, I've tried:
priorI= list(R = list(V = 1, nu = 0, fix = 1), G = list(G1 = list(V =
diag(2) * 0.02, nu = 2),
+                  G2 = list(V = 1,nu = 0.002)))


Where (G1 = list(V = diag(2) * 0.02, nu = 2) represents a 2 X 2 matrix
of distances between individuals X species Is this the correct matrix
size, since Znnd is continuous? It was hard to extrapolate from the
us(1+time:chick) data as there were only two time points per
chick...but I understand that with categorical predictors, you would
have a matrix that is the size of the number of categories.

Would it be possible to walk me through how to specify nu? For
example, the difference between specifying nu=dim(V)+1 vs nu=dim(V)? I
see us() examples with both and am unclear as to their relative merits
other than their both being attempting  to be uninformative?

Also, my response variable contains high replication (>1000) for the
majority of species but very low replication for a few (16, 20, 24),
and is very skewed towards having more zeroes than ones overall.

I have yet to follow up on your suggestions for part 2.

Many thanks,

Andrea



Quoting Jarrod Hadfield <j.hadfield at ed.ac.uk>:

> Hi,
>
> 1/ It is not a good idea to remove the intercept in this instance.
> It is forcing the regressions to go through the origin so that when
> Zdbh and Znnd are zero the probability of being in either class is
> 50:50 (0 on the logit scale). The random effects are not deviations
> from the first species but deviations from the average species. Only
> with fixed effects are the contrasts (usually) with the first level.
> If you want random slopes you need to replace ~species with
> us(Znnd):species but with only 23 species and a categorical response
> you will probably not get very precise estimates.
>
> 2/ i.i.d species effects are often hard to separate from
> phylogenetically correlated species effects, and the phylogenetic
> heritability (aka Pagel's lambda) is often poorly estimated. This is
> particularly the case with categorical response variables and you
> have the added difficulty that numerical issues are often
> encountered if there is support for heritabilities close to one.
> Presumably there is variation in the outcome within species? If you
> do encounter numerical problems then you can use trunc=TRUE in the
> call to MCMCglmm which keeps the latent variable from going into
> extreme-probability territory or you can assume the heritability=1
> by using MCMCgmmRAM:
>
> http://jarrod.bio.ed.ac.uk/MCMCglmmRAM_2.24.tar.gz
>
> If you have a lot of replication within species (?) my feeling is
> that you can probably get away with fitting both terms.
>
> Cheers,
>
> Jarrod
>
>
>
>
>
> On 05/03/2018 17:08, Drager, Andrea Pilar wrote:
>>
>> Hi all,
>>
>> I've fitted a model with a binary response at the individual level,
>> two continuous fixed effects (measured at the individual level but
>> containing info on 23 species), and a single random effect of
>> "species". My model is mixing well and the results fit the data,
>> but what I am really interested in is getting estimates for the
>> fixed effect by species, rather than globally.
>>
>> It is my understanding (per a 2016 reply to a post to this list:
>> parameter estimates for all factor levels MCMCglmm) that by
>> suppressing the intercept here, I am estimating the first "level"
>> (one species?) for each effect, and that the remaining effects are
>> deviations from these levels.  How do I code random slopes and
>> intercepts for species within each of the fixed effects, rather
>> than deviations from a common distribution?
>>
>> priorS = list(R = list(V = 1, nu = 0, fix = 1),  G = list(G1 =
>> list(V = 1, nu = 0.002)))
>>
>> smodel <-MCMCglmm(fl~  -1 + Zdbh + Znnd,
>>                   random = ~ species,
>>                   family = "categorical", verbose=F, pr = TRUE,
>> start=list(QUASI=FALSE),
>>                   data=IHF,prior=priorS,
>>                   nitt=500000,burnin=5000,thin=100)
>>
>>
>> A second part of the question is that I would like to include a
>> random effect to measure the influence of phylogenetic
>> autocorrelation. I know how to code this using a distance matrix
>> (see below), however, I am concerned that statistically, "species"
>> and "phylo" may not have enough information to partition the
>> variance in a meaningful way. Perhaps running three models
>> (random=species, random=phylo, random=species + phylo) and
>> comparing goodness-of-fit could be useful? I would greatly
>> appreciate any insight. Many thanks!
>>
>> prior = list(R = list(V = 1, nu = 0, fix = 1), G = list(G1 = list(V
>> = 1,nu = 0.002),
>> G2=list(V=1,nu=0.002)))
>>
>> model <-MCMCglmm(fl ~ Zdbh_mm + Znnd,
>>                  random = ~species + phylo,
>>                  family = "categorical", verbose=F, pr = TRUE,
>> start=list(QUASI=FALSE),
>> ginverse=list(phylo=inv.phylo$Ainv),data=IHF,prior=prior,
>>                  nitt=500000,burnin=5000,thin=100)
>> Andrea Pilar Drager
>> PhD. student
>> Ecology and Evolutionary Biology, Rice University
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
R-sig-mixed-models Info Page - ETH Zurich<https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
stat.ethz.ch
Your email address: Your name (optional): You may enter a privacy password below. This provides only mild security, but should prevent others from messing ...



>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.


Andrea Pilar Drager
PhD. student
Ecology and Evolutionary Biology, Rice University


-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: not available
URL: <https://stat.ethz.ch/pipermail/r-sig-mixed-models/attachments/20180307/d3cf5bc7/attachment-0001.ksh>