[R-sig-ME] problem running mixed model including a phylogeny suggested in vignette "Covariance structure"

[Pablo Inchausti]

Hi,
I have been trying to run the mixed model incorporating a phylogeny that is
suggested in
https://cran.r-project.org/web/packages/glmmTMB/vignettes/covstruct.html
(section Proptional). I have encountered errors that I cannot resolve and
hence this post.

This is what I did:
require(ade4); require(ape); require(glmmTMB)

data(carni70) # loads the data

carnidat <- data.frame(species = rownames(carni70$tab), carni70$tab)

phylo <- read.tree(text=carni70$tre) # reads the phylogeny

A <- vcv(phylo) # uses package ape to calculate the var-covar matrix from
the phylogeny

# verifies whether the species names of  rows and columns of var-covar
phylogenetic matrix are the same as those in the dataframe

setdiff(carnidat$species, rownames(A)) # No!. I then correct them.

carnidat$species=gsub("_", ".", carnidat$species) # corrects all species
names

setdiff(colnames(A), rownames(A)) # final check. All is fine.

setdiff(carnidat$species, rownames(A)) # another final check. All is fine.

carnidat$dummy <- factor(1) # a dummy grouping variable must be added to
the dataset

Then I ran the model:

fit_phylo=glmmTMB(log(range)~log(size)+propto(0+species|dummy, A),
data= carnidat)

And I obtain the following error message:

Error: column or row names of the matrix do not match the terms.
Expecting names:
‘speciesAtelocynus.microtis’‘speciesBassariscus.alleni’‘
speciesBassariscus.astutus’‘
speciesBassariscus.beddardi’‘speciesBassariscus.gabbii’‘speciesBassariscus.lasius’‘speciesBassariscus.pauli’‘
speciesBassariscus.sumichrasti’‘speciesCanis.latrans’‘speciesCanis.lupus’‘speciesCerdocyon.

(This is much longer, but one can get the idea)

Just in case, the same model does run using the package brms.

I would appreciate very much any suggestion that you might have.
Thanks in advance.
Cheers
Pablo

> sessionInfo()R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS


Attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] glmmTMB_1.1.10 ape_5.8

loaded via a namespace (and not attached):
 [1] nlme_3.1-166        TH.data_1.1-2       estimability_1.5.1
reformulas_0.3.0    xtable_1.8-4
 [6] minqa_1.2.8         zoo_1.8-12          TMB_1.9.15
lme4_1.1-35.5       grid_4.4.3
[11] MASS_7.3-61         mvtnorm_1.3-1       numDeriv_2016.8-1.1
compiler_4.4.3      multcomp_1.4-26
[16] codetools_0.2-20    sandwich_3.1-1      emmeans_1.10.5
coda_0.19-4.1       Rcpp_1.0.13
[21] mgcv_1.9-1          rstudioapi_0.16.0   lattice_0.22-6
digest_0.6.37       nloptr_2.1.1
[26] Rdpack_2.6.1        parallel_4.4.3      splines_4.4.3
rbibutils_2.3       Matrix_1.7-0
[31] tools_4.4.3         boot_1.3-31         survival_3.7-0


>

-- 
*Pablo Inchausti*
Profesor de Ecología
Centro Universitario Regional del Este
Universidad de la República,
Avenida Cachimba del Rey
Maldonado, Departamento de Maldonado CP 20100
Uruguay
*Phone*: +598.42.25.53.26 interno 602

*Website*: https://sites.google.com/view/pablo-inchausti/iniciostart
<https://sites.google.com/view/pablo-inchausti//iniciostart>

*Book/Libro Statistical Modeling with R websites: *

*https://sites.google.com/view/statistical-modeling-with-r/home
<https://sites.google.com/view/statistical-modeling-with-r/home>*
*https://global.oup.com/booksites/content/9780192859013/
<https://global.oup.com/booksites/content/9780192859013/>*

*Canal YouTube* Pablo Inchausti Estadistica: @PabloIEstadistica
https://www.youtube.com/channel/UCKCknL2o8rzr7uumT-GDi7Q/a

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