Preliminaries | Requirements | Data set | Mathematical background | Covariates and offsets | Optimization by Variational inference | Analysis of trichoptera data with a PLN model | A PLN model with latent main effects | Adjusting a fit | The PLNfit object | Field access | GLM-like interface | Observation weights | Accounting for covariates and offsets | Covariance models (full, diagonal, spherical) | References

Preliminaries | Requirements | Data set | Mathematical background | Covariates and offsets | Parametrization of the covariance of the mixture models | Optimization by Variational inference | Analysis of trichoptera data with a PLN-mixture model | A mixture model with a latent main effects for the Trichoptera data set | Adjusting a collection of fits | Structure of PLNmixturefamily | Model selection | Structure of PLNmixturefit | Specific fields | plot method | predict method | References

Preliminaries | The trichoptera data set | Formatting | Table of counts (abundancies) | Covariates (external meteorological effect, groups) | Offsets and the compositionality issue | References

Preliminaries | Requirements | Data set | Mathematical background | Covariates and offsets | Optimization by Variational inference | Analysis of trichoptera data with a PLNPCA model | A model with latent main effects for the Trichoptera data set | Adjusting a collection of fits | Structure of PLNPCAfamily | Model selection of rank $q$ | Structure of PLNPCAfit | Additional visualization | Projecting new data in the PCA space | A model accounting for meteorological covariates | References

Preliminaries | Format description | Computing offsets | Building data frame using prepare_data | Importing data from biom and phyloseq objects using prepare_data_from_[phyloseq|biom] | Reading from a biom file | Reading from a phyloseq-class object | Mathematical details about the offsets | Total Sum Scaling | Cumulative Sum Scaling | Relative Log Expression | Geometric Mean of Pairwise Ratio | Wrench normalisation | References

Preliminaries | Requirements | Data set | Mathematical background | Covariates and offsets | Alternating optimization | Analysis of trichoptera data with a PLNnetwork model | Adjusting a collection of network - a.k.a. a regularization path | Structure of PLNnetworkfamily | Exploring the path of networks | Model selection issue: choosing a network | Structure of a PLNnetworkfit | References

Preliminaries | Requirements | Data set | Mathematical background | Covariates and offsets | Prediction | Optimization by Variational inference | Analysis of trichoptera data with a PLN-LDA model | A model with main effects and no covariates | Structure of PLNLDAfit | Specific fields | plot method | predict method | A model with latent main effects and meteorological covariates | References

Preliminaries | Requirements | Data set | Mathematical background | Analysis of microcosm with ZIPLN | Comparing zero-inflation parameterizations | Inspecting the fit | Sparse network inference with ZIPLNnetwork | References