├── .Rbuildignore ├── .gitignore ├── CITATION.cff ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── TMBtrait.R ├── VP.gllvm.R ├── aicc.gllvm.R ├── anova.gllvm.R ├── coef.gllvm.R ├── coefplot.gllvm.R ├── confint.gllvm.R ├── ecoCoefs.gllvm.R ├── getEnvironCov.gllvm.R ├── getLV.gllvm.R ├── getLoadings.gllvm.R ├── getPredictErr.gllvm.R ├── getResidualCor.gllvm.R ├── getResidualCov.gllvm.R ├── gllvm.R ├── gllvm.TMB.R ├── gllvm.VA.R ├── gllvm.auxiliary.R ├── gllvm.iter.R ├── gllvm.makeform.R ├── glmmVA.R ├── goodnessOfFit.gllvm.R ├── logLik.gllvm.R ├── ordiplot.gllvm.R ├── phyloplot.gllvm.R ├── plot.gllvm.R ├── plotVP.gllvm.R ├── predict.gllvm.R ├── predictLVs.gllvm.R ├── print.gllvm.R ├── randomCoefplot.R ├── residuals.gllvm.R ├── se.gllvm.R ├── simulate.gllvm.R ├── summary.gllvm.R ├── update.gllvm.R ├── vcov.gllvm.R └── zzz.R ├── README.md ├── data ├── Skabbholmen.RData ├── beetle.RData ├── eSpider.RData ├── fungi.RData ├── kelpforest.RData └── microbialdata.RData ├── docs ├── 404.html ├── articles │ ├── F4.png │ ├── F4coef.png │ ├── VP1-1.png │ ├── VP2-1.png │ ├── Xcovar-1.png │ ├── bigplot-1.png │ ├── coefsP-1.png │ ├── corrplot-1.png │ ├── fixuGLLVM-1.png │ ├── index.html │ ├── lvAR-1.png │ ├── ordip6_1-1.png │ ├── ordip6_3-1.png │ ├── ordiplot1-1.png │ ├── plotrow-1.png │ ├── rcoefs-1.png │ ├── specord-1.png │ ├── vignette1.html │ ├── vignette1_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-13-2.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-18-2.png │ │ │ ├── unnamed-chunk-18-3.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-19-2.png │ │ │ ├── unnamed-chunk-19-3.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ └── unnamed-chunk-26-2.png │ ├── vignette2.html │ ├── vignette2_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ ├── unnamed-chunk-8-2.png │ │ │ ├── unnamed-chunk-8-3.png │ │ │ └── unnamed-chunk-9-1.png │ ├── vignette3.html │ ├── vignette3_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-11-10.png │ │ │ ├── unnamed-chunk-11-2.png │ │ │ ├── unnamed-chunk-11-3.png │ │ │ ├── unnamed-chunk-11-4.png │ │ │ ├── unnamed-chunk-11-5.png │ │ │ ├── unnamed-chunk-11-6.png │ │ │ ├── unnamed-chunk-11-7.png │ │ │ ├── unnamed-chunk-11-8.png │ │ │ ├── unnamed-chunk-11-9.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── vignette4.html │ ├── vignette4_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-11-2.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── vignette5.html │ ├── vignette5_files │ │ └── figure-html │ │ │ ├── curves-1.png │ │ │ └── quad_plot-1.png │ ├── vignette6.html │ ├── vignette7.html │ ├── vignette8.html │ ├── vignette8_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ └── unnamed-chunk-5-1.png │ └── vignette9.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── AICc.html │ ├── Skabbholmen.html │ ├── VP.gllvm-1.png │ ├── VP.gllvm.html │ ├── anova.gllvm.html │ ├── beetle.html │ ├── coefplot.gllvm-1.png │ ├── coefplot.gllvm.html │ ├── confint.gllvm.html │ ├── eSpider.html │ ├── ecoCoefs.html │ ├── fungi.html │ ├── getEnvironCov.gllvm.html │ ├── getLV.gllvm.html │ ├── getLoadings.gllvm.html │ ├── getPredictErr.gllvm.html │ ├── getResidualCor.gllvm.html │ ├── getResidualCov.gllvm.html │ ├── gllvm-1.png │ ├── gllvm-10.png │ ├── gllvm-11.png │ ├── gllvm-12.png │ ├── gllvm-13.png │ ├── gllvm-14.png │ ├── gllvm-15.png │ ├── gllvm-16.png │ ├── gllvm-17.png │ ├── gllvm-18.png │ ├── gllvm-19.png │ ├── gllvm-2.png │ ├── gllvm-3.png │ ├── gllvm-4.png │ ├── gllvm-5.png │ ├── gllvm-6.png │ ├── gllvm-7.png │ ├── gllvm-8.png │ ├── gllvm-9.png │ ├── gllvm.html │ ├── goodnessOfFit.html │ ├── index.html │ ├── kelpforest.html │ ├── logLik.gllvm.html │ ├── microbialdata.rd │ ├── ordiplot.gllvm-1.png │ ├── ordiplot.gllvm.html │ ├── phyloplot.gllvm.html │ ├── plot.gllvm.html │ ├── predict.gllvm.html │ ├── predictLVs.gllvm.html │ ├── randomCoefplot.gllvm.html │ ├── residuals.gllvm.html │ ├── se.gllvm.html │ ├── simulate.gllvm.html │ ├── summary.gllvm.html │ ├── update.gllvm.html │ └── vcov.gllvm.html └── sitemap.xml ├── gllvm.Rproj ├── inst └── CITATION ├── man ├── AICc.Rd ├── Skabbholmen.Rd ├── VP.gllvm.Rd ├── anova.gllvm.Rd ├── beetle.Rd ├── coefplot.gllvm.Rd ├── confint.gllvm.Rd ├── eSpider.Rd ├── ecoCoefs.Rd ├── fungi.Rd ├── getEnvironCov.gllvm.Rd ├── getLV.gllvm.Rd ├── getLoadings.gllvm.Rd ├── getPredictErr.gllvm.Rd ├── getResidualCor.gllvm.Rd ├── getResidualCov.gllvm.Rd ├── gllvm.Rd ├── glmmVA.Rd ├── goodnessOfFit.Rd ├── kelpforest.Rd ├── logLik.gllvm.Rd ├── microbialdata.rd ├── ordiplot.gllvm.Rd ├── phyloplot.gllvm.Rd ├── plot.gllvm.Rd ├── predict.gllvm.Rd ├── predictLVs.gllvm.Rd ├── randomCoefplot.gllvm.Rd ├── residuals.gllvm.Rd ├── se.gllvm.Rd ├── simulate.gllvm.Rd ├── summary.gllvm.Rd ├── update.gllvm.Rd └── vcov.gllvm.Rd ├── src ├── Makevars ├── distrib.h ├── gllvm.cpp └── utils.h ├── tests ├── testthat.R └── testthat │ └── test-fitgllvm.R └── vignettes ├── F4.png ├── F4coef.png ├── RRGLM.RData ├── RRGLMb1.RData ├── VP1-1.png ├── VP2-1.png ├── 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