[R-meta] Questions about phylogenetic meta-analisys

[Rafael Rios]

Dear Wolfgang,

Thank you a lot! I was able to conduct the phylogenetic meta-analysis. Your
explanations were very clear.

Best wishes,

Rafael R. Moura.
*scientia amabilis*

Doutorando da Pós-graduação em Ecologia e Conservação de Recursos Naturais
Universidade Federal de Uberlândia, Uberlândia, MG, Brasil

ORCID: http://orcid.org/0000-0002-7911-4734
Currículo Lattes:
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4244908A8
Research Gate: https://www.researchgate.net/profile/Rafael_Rios_Moura2


<http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4244908A8>

2017-10-01 17:50 GMT-03:00 Viechtbauer Wolfgang (SP) <
wolfgang.viechtbauer at maastrichtuniversity.nl>:

> Please always cc the mailing list.
>
> I took a look at the datasets you sent to me; meta.csv does not contain a
> variable called 'field' and the 'species' variable is actually called
> 'species1', but I could work around that.
>
> Based on your example, I noticed an issue with rma.mv() which caused some
> checks on the 'R' argument not being run as intended. That has been fixed
> in the 'devel' version; see here:
>
> http://www.metafor-project.org/doku.php/installation#development_version
>
> Please install that and try again. When you try to fit the model, you will
> then get the error:
>
> There are levels in 'species1' for which there are no rows/columns in the
> corresponding 'R' matrix.
>
> As the error will tell you, h1$species contains some levels that are not
> represented in the 'phylo' matrix. I did a bit of checking and this appears
> to due to these species:
>
> [1] Zygiella_x-notata_ott504327
> [2] Neolamprologus_pulcher_--Daffodil--_ott311695
> [3] Dugesia_sp_06_MR-2009_ott859610
>
> Make sure that these are also contained in 'phylo' and that the
> row/columnnames are spelled exactly in the same way. rma.mv() doesn't try
> to do some kind of fuzzy matching, but expects 1-1 matches between the
> levels of the variable specified via the 'random' argument and the
> dimension names of the corresponding matrix specified via 'R'.
>
> By the way, 'phylo' appears to be a distance matrix (at least, the
> diagonal elements are all 0's, so this strongly suggests that this is what
> it is). But 'R' should be used to specify covariance/correlation matrices.
>
> As for your other question: As I mentioned, the second argument is for
> specifying the sampling variances, not the standard errors. The sampling
> variances are the square of the standard errors. I don't know what you mean
> by 'May you provide your calculation of standard error?' Each outcome
> measure has a different formula for the standard errors (and hence sampling
> variance), so I don't know what you are asking here.
>
> Best,
> Wolfgang
>
> -----Original Message-----
> From: Rafael Rios [mailto:biorafaelrm at gmail.com]
> Sent: Thursday, 28 September, 2017 4:22
> To: Viechtbauer Wolfgang (SP)
> Subject: Re: Questions about phylogenetic meta-analisys
>
> ATTACHMENT(S) REMOVED: phylo.csv | meta.csv
>
> Dear Wolfgang,
>
> Thank you for the contributions. My data follows on attached. "meta.csv"
> is my dataset, and "phylo.csv" is the phylogenetic distance matrix. Both
> files were saved as CSV (MS-DOS) format.
>
> I have another doubt. You said that I should use rma.mv(zf, sezf^2, ...).
> However, my advisor said that most meta-analists frequently confound
> standard error with variance. So, we must use rma.mv(zf, sezf, ...). Is
> that true? May you provide your calculation of standard error? Thank you!
>
> Best wishes,
>
> Rafael R. Moura.
> scientia amabilis
>
> Doutorando da Pós-graduação em Ecologia e Conservação de Recursos Naturais
> Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
>
> ORCID: http://orcid.org/0000-0002-7911-4734
> Currículo Lattes: http://buscatextual.cnpq.br/buscatextual/
> visualizacv.do?id=K4244908A8
> Research Gate: https://www.researchgate.net/profile/Rafael_Rios_Moura2
>
> 2017-09-27 18:40 GMT-03:00 Viechtbauer Wolfgang (SP) <
> wolfgang.viechtbauer at maastrichtuniversity.nl>:
> Dear Rafael,
>
> First of all, 'sezf' sounds like these are standard errors. The second
> argument of rma.mv() (and rma()/rma.uni()) is for the *sampling
> variances* (the square of the standard errors). So, you should use: rma.mv(zf,
> sezf^2, ...).
>
> This aside, I cannot diagnose what the problem is without a reproducible
> example or at least more information. Could you at least post:
>
> unique(h1$species)
> class(phylo)
> dimnames(phylo)
>
> Best,
> Wolfgang
>
> -----Original Message-----
> From: Rafael Rios [mailto:biorafaelrm at gmail.com]
> Sent: Wednesday, 27 September, 2017 20:49
> To: r-sig-meta-analysis at r-project.org; Viechtbauer Wolfgang (SP)
> Subject: Questions about phylogenetic meta-analisys
>
> Dear Dr. Wolfgang Viechtbauer and other meta-analysists,
>
> I am trying to conduct a phylogenetic meta-analysis using function rma.mv
> with the following format:
>
> meta1=rma.mv(zf, sezf, mods= ~phylum,
>              random = list (~1|study, ~1|species, ~1|field),
>              R=list(species=phylo),
>              data = h1)
>
> Where I have a moderator (phylum) and three random variables (study,
> species and if it was an observational or experimental study). We included
> phylogenetic correlation matrix (phylo) in argument R. However, I found the
> following error message: "Error in R[[j]][s.levels[[j]], s.levels[[j]]] :
> subscript out of bounds". I also tryied to use a matrix with phylogenetic
> distances, but I found the same error. I hope that this e-mail finds you
> well.
>
> Best wishes,
>
> Rafael R. Moura.
> scientia amabilis
>
> Doutorando da Pós-graduação em Ecologia e Conservação de Recursos Naturais
> Universidade Federal de Uberlândia, Uberlândia, MG, Brasil
>
> ORCID: http://orcid.org/0000-0002-7911-4734
> Currículo Lattes: http://buscatextual.cnpq.br/buscatextual/
> visualizacv.do?id=K4244908A8
> Research Gate: https://www.researchgate.net/profile/Rafael_Rios_Moura2
>

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