problem running mixed model including a phylogeny suggested in vignette "Covariance structure"
The short answer is that the *values* of the names are OK, but the *order* is wrong (setdiff() only checks that the values are equivalent, not the order). I will try to add some better tests/diagnostics to the code. On Thu, Mar 13, 2025 at 12:10?PM Pablo Inchausti
<pablo.inchausti.f at gmail.com> wrote:
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 Ecolog?a Centro Universitario Regional del Este Universidad de la Rep?blica, 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 [[alternative HTML version deleted]]
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