├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ └── rhub.yaml ├── .gitignore ├── .gitmodules ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── R2.R ├── RISK_CCFA.R ├── RcppExports.R ├── bassetfit_s3.R ├── driver-utils.R ├── fido.R ├── fido_transforms.R ├── fido_utils.R ├── fidofit_methods.R ├── fidofit_s3.R ├── fit_basset.R ├── fit_maltipoo.R ├── fit_orthus.R ├── fit_pibble.R ├── generics_s3.R ├── iqlr.R ├── kernels.R ├── mallard-data.R ├── mallard_family-data.R ├── maltipoo_sim.R ├── maltipoofit_s3.R ├── orthus_sim.R ├── orthus_transform_wrapper.R ├── pcrbias_mock-data.R ├── pibble_plotting.R └── pibble_sim.R ├── README.md ├── _pkgdown.yml ├── cleanup ├── configure ├── configure.ac ├── data ├── RISK_CCFA.RData ├── mallard.RData ├── mallard_family.RData └── pcrbias_mock.RData ├── docs ├── 404.html ├── articles │ ├── index.html │ ├── introduction-to-fido.html │ ├── mitigating-pcrbias.html │ ├── non-linear-models.html │ ├── non-linear-models_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-5-1.png │ ├── orthus.html │ └── picking_priors.html ├── authors.html ├── deps │ ├── Source_Code_Pro-0.4.9 │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQtM1rTEUc.woff2 │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQtMRrTEUc.woff2 │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQtMVrTEUc.woff2 │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQtMZrTEUc.woff2 │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQtMdrTEUc.woff2 │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQtMlrTA.woff2 │ │ ├── HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQtMprTEUc.woff2 │ │ └── font.css │ ├── Source_Sans_Pro-0.4.9 │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7jsDJT9g.woff2 │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7ksDJT9g.woff2 │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDI.woff2 │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7osDJT9g.woff2 │ │ ├── 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clr_array.html │ ├── coef.orthusfit.html │ ├── coef.pibblefit.html │ ├── conjugateLinearModel.html │ ├── convert_orthus_covariance.html │ ├── create_default_ilr_base.html │ ├── fido_package.html │ ├── fido_transforms.html │ ├── gather_array.html │ ├── index.html │ ├── kernels.html │ ├── lambda_to_iqlr.html │ ├── lmvgamma.html │ ├── lmvgamma_deriv.html │ ├── loglikMaltipooCollapsed.html │ ├── loglikPibbleCollapsed.html │ ├── mallard.html │ ├── mallard_family.html │ ├── maltipoo_fit.html │ ├── maltipoofit.html │ ├── metadata.html │ ├── miniclo.html │ ├── miniclo_array.html │ ├── mongrel-deprecated.html │ ├── name.html │ ├── name.orthusfit.html │ ├── name.pibblefit.html │ ├── name_dims.html │ ├── optimMaltipooCollapsed.html │ ├── optimPibbleCollapsed.html │ ├── orthus_fit.html │ ├── orthus_lr_transforms.html │ ├── orthus_sim.html │ ├── orthus_tidy_samples.html │ ├── orthusfit.html │ ├── pcrbias_mock.html │ ├── pibble_fit.html │ ├── pibble_sim.html │ ├── pibble_tidy_samples.html │ ├── pibblefit.html │ ├── plot.pibblefit-1.png │ ├── plot.pibblefit-2.png │ ├── plot.pibblefit.html │ ├── ppc.html │ ├── ppc.pibblefit-1.png │ ├── ppc.pibblefit.html │ ├── ppc_summary.html │ ├── predict.bassetfit.html │ ├── predict.pibblefit.html │ ├── print.orthusfit.html │ ├── print.pibblefit.html │ ├── r2.html │ ├── random_pibble_init.html │ ├── refit.html │ ├── req.html │ ├── req.maltipoofit.html │ ├── req.orthusfit.html │ ├── req.pibblefit.html │ ├── sample_prior.html │ ├── sample_prior.pibblefit-1.png │ ├── sample_prior.pibblefit.html │ ├── store_coord.html │ ├── summarise_posterior.html │ ├── summary.orthusfit.html │ ├── summary.pibblefit.html │ ├── uncollapsePibble.html │ ├── uncollapsePibble_sigmaKnown.html │ ├── verify.bassetfit.html │ ├── verify.html │ ├── verify.maltipoofit.html │ ├── verify.orthusfit.html │ └── verify.pibblefit.html ├── search.json └── sitemap.xml ├── fido.Rproj ├── inst ├── CITATION ├── extdata │ └── Kashyap2013 │ │ ├── README.txt │ │ ├── metabolites.csv │ │ └── microbe.rda ├── fido.png └── include │ ├── AdamOptim.h │ ├── LaplaceApproximation.h │ ├── MaltipooCollapsed.h │ ├── MatDist.h │ ├── MatDist_thread.h │ ├── MatrixAlgebra.h │ ├── MongrelModelClass.h │ ├── MultDirichletBoot.h │ ├── PibbleCollapsed.h │ ├── SpecialFunctions.h │ ├── fido.h │ └── fidoGenerated.h.in ├── maintainer.tex ├── man ├── RISK_CCFA.Rd ├── RISK_CCFA_otu.Rd ├── RISK_CCFA_sam.Rd ├── RISK_CCFA_tax.Rd ├── Y.Rd ├── access_dims.Rd ├── alr.Rd ├── alrInv.Rd ├── alrInv_array.Rd ├── alr_array.Rd ├── as.list.orthusfit.Rd ├── as.list.pibblefit.Rd ├── as.orthusfit.Rd ├── as.pibblefit.Rd ├── basset_fit.Rd ├── check_dims.Rd ├── clr_array.Rd ├── coef.orthusfit.Rd ├── coef.pibblefit.Rd ├── conjugateLinearModel.Rd ├── convert_orthus_covariance.Rd ├── create_default_ilr_base.Rd ├── fido_package.Rd ├── fido_transforms.Rd ├── gather_array.Rd ├── kernels.Rd ├── lambda_to_iqlr.Rd ├── lmvgamma.Rd ├── lmvgamma_deriv.Rd ├── loglikPibbleCollapsed.Rd ├── mallard.Rd ├── mallard_family.Rd ├── metadata.Rd ├── miniclo.Rd ├── miniclo_array.Rd ├── mongrel-deprecated.Rd ├── name.Rd ├── name.orthusfit.Rd ├── name.pibblefit.Rd ├── name_dims.Rd ├── optimPibbleCollapsed.Rd ├── orthus_fit.Rd ├── orthus_lr_transforms.Rd ├── orthus_sim.Rd ├── orthus_tidy_samples.Rd ├── orthusfit.Rd ├── pcrbias_mock.Rd ├── pibble_fit.Rd ├── pibble_sim.Rd ├── pibble_tidy_samples.Rd ├── pibblefit.Rd ├── plot.pibblefit.Rd ├── ppc.Rd ├── ppc.pibblefit.Rd ├── ppc_summary.Rd ├── predict.bassetfit.Rd ├── predict.pibblefit.Rd ├── print.orthusfit.Rd ├── print.pibblefit.Rd ├── r2.Rd ├── random_pibble_init.Rd ├── refit.Rd ├── req.Rd ├── req.orthusfit.Rd ├── req.pibblefit.Rd ├── sample_prior.Rd ├── sample_prior.pibblefit.Rd ├── store_coord.Rd ├── summarise_posterior.Rd ├── summary.orthusfit.Rd ├── summary.pibblefit.Rd ├── uncollapsePibble.Rd ├── uncollapsePibble_sigmaKnown.Rd ├── verify.Rd ├── verify.bassetfit.Rd ├── verify.orthusfit.Rd └── verify.pibblefit.Rd ├── src ├── ConjugateLinearModel.cpp ├── Makevars.in ├── Makevars.win ├── MaltipooCollapsed_LGH.cpp ├── MaltipooCollapsed_Optim.cpp ├── MatrixAlgebra.cpp ├── PibbleCollapsed_LGH.cpp ├── PibbleCollapsed_Optim.cpp ├── PibbleCollapsed_Uncollapse.cpp ├── PibbleCollapsed_Uncollapse_sigmaKnown.cpp ├── RcppExports.cpp ├── SpecialFunctions.cpp ├── test_LaplaceApproximation.cpp ├── test_MultDirichletBoot.cpp └── test_utils.cpp ├── tests ├── testthat.R └── testthat │ ├── .gitignore │ ├── Rplots.pdf │ ├── test-R2.R │ ├── test-baseFuns.R │ ├── test-basset.R │ ├── test-hessian.R │ ├── test-hvp.R │ ├── test-ilr.R │ ├── test-iqlr.R │ ├── test-kernels.R │ ├── test-laplaceapproximation.R │ ├── test-linesearch.R │ ├── test-maltipoo.R │ ├── test-matdist.R │ ├── test-mongrelfit-methods.R │ ├── test-multdirichletboot.R │ ├── test-numCores.R │ ├── test-orthus-transforms.R │ ├── test-orthus.R │ ├── test-pibble.R │ ├── test-sylvester-speedups.R │ ├── test-transforms.R │ └── test-utils.R └── vignettes ├── .gitignore ├── bibliography.bib ├── fido-lambda-all.png 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