Poisson Lognormal Models

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Documentation for package ‘PLNmodels’ version 1.3.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS

Help Pages

A B C E F G I L M N O P R S T V Z

-- A --

AIC.PLNfit	Akaike Information Criterion for a fitted PLN model
AIC.ZIPLNfit	Akaike Information Criterion for a fitted ZIPLN model

-- B --

barents	Barents fish data set
BIC.PLNfit	Bayesian Information Criterion for a fitted PLN model
BIC.ZIPLNfit	Bayesian Information Criterion for a fitted ZIPLN model

-- C --

coef.PLNfit	Extract model coefficients
coef.PLNLDAfit	Extracts model coefficients from objects returned by 'PLNLDA()'
coef.PLNmixturefit	Extract model coefficients
coef.ZIPLNfit	Extract model coefficients
coefficient_path	Extract the regularization path of a PLNnetwork fit
compute_offset	Compute offsets from a count data using one of several normalization schemes
compute_PLN_starting_point	Helper function for PLN initialization.
compute_ZIPLN_starting_point	Helper function for ZIPLN initialization.

-- E --

extract_probs

Extract edge selection frequency in bootstrap subsamples

-- F --

fitted.PLNfit	Extracts model fitted values from objects returned by 'PLN()' and its variants
fitted.PLNmixturefit	Extracts model fitted values from objects returned by 'PLNmixture()' and its variants
fitted.ZIPLNfit	Extracts model fitted values from objects returned by 'ZIPLN()' and its variants

-- G --

getBestModel	Best model extraction from a collection of models
getBestModel.Networkfamily	Best model extraction from a collection of models
getBestModel.PLNmixturefamily	Best model extraction from a collection of models
getBestModel.PLNnetworkfamily	Best model extraction from a collection of models
getBestModel.PLNPCAfamily	Best model extraction from a collection of models
getBestModel.ZIPLNnetworkfamily	Best model extraction from a collection of models
getModel	Model extraction from a collection of models
getModel.Networkfamily	Model extraction from a collection of models
getModel.PLNmixturefamily	Model extraction from a collection of models
getModel.PLNnetworkfamily	Model extraction from a collection of models
getModel.PLNPCAfamily	Model extraction from a collection of models
getModel.ZIPLNnetworkfamily	Model extraction from a collection of models

-- I --

ICL	Integrated Classification Likelihood
ICL.PLNfit	Integrated Classification Likelihood
ICL.ZIPLNfit	Integrated Classification Likelihood

-- L --

logLik.PLNfit	Extract log-likelihood of a fitted PLN model
logLik.ZIPLNfit	Extract log-likelihood of a fitted ZIPLN model

-- M --

microcosm	Cow microbiome data set
mollusk	Mollusk data set

-- N --

Networkfamily

An R6 Class to virtually represent a collection of network fits

-- O --

oaks	Oaks amplicon data set

-- P --

PLN	Poisson lognormal model
PLNfamily	An R6 Class to represent a collection of PLNfit
PLNfit	An R6 Class to represent a PLNfit in a standard, general framework
PLNfit_diagonal	An R6 Class to represent a PLNfit in a standard, general framework, with diagonal residual covariance
PLNfit_fixedcov	An R6 Class to represent a PLNfit in a standard, general framework, with fixed (inverse) residual covariance
PLNfit_genpop	An R6 Class to represent a PLNfit with a residual covariance structured by a fixed correlation matrix (e.g. a genetic relationship matrix), motivated by population genetics
PLNfit_spherical	An R6 Class to represent a PLNfit in a standard, general framework, with spherical residual covariance
PLNLDA	Poisson lognormal model towards Linear Discriminant Analysis
PLNLDAfit	An R6 Class to represent a PLNfit in a LDA framework
PLNLDAfit_diagonal	An R6 Class to represent a PLNfit in a LDA framework with diagonal covariance
PLNLDAfit_spherical	An R6 Class to represent a PLNfit in a standard, general framework, with diagonal residual covariance
PLNLDA_param	Control of a PLNLDA fit
PLNmixture	Poisson lognormal mixture model
PLNmixturefamily	An R6 Class to represent a collection of PLNmixturefit
PLNmixturefit	An R6 Class to represent a PLNfit in a mixture framework
PLNmixture_param	Control of a PLNmixture fit
PLNnetwork	Sparse Poisson lognormal model for network inference
PLNnetworkfamily	An R6 Class to represent a collection of 'PLNnetworkfit's
PLNnetworkfit	An R6 Class to represent a PLNfit in a sparse inverse covariance framework
PLNnetwork_param	Control of PLNnetwork fit
PLNPCA	Poisson lognormal model towards Principal Component Analysis
PLNPCAfamily	An R6 Class to represent a collection of PLNPCAfit
PLNPCAfit	An R6 Class to represent a PLNfit in a PCA framework
PLNPCA_param	Control of PLNPCA fit
PLN_param	Control of a PLN fit
plot.Networkfamily	Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (either 'PLNnetworkfamily' or 'ZIPLNnetworkfamily')
plot.PLNfamily	Display the criteria associated with a collection of PLN fits (a PLNfamily)
plot.PLNLDAfit	LDA visualization (individual and/or variable factor map(s)) for a 'PLNPCAfit' object
plot.PLNmixturefamily	Display the criteria associated with a collection of PLNmixture fits (a PLNmixturefamily)
plot.PLNmixturefit	Mixture visualization of a 'PLNmixturefit' object
plot.PLNnetworkfamily	Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (either 'PLNnetworkfamily' or 'ZIPLNnetworkfamily')
plot.PLNnetworkfit	Extract and plot the network (partial correlation, support or inverse covariance) from a 'PLNnetworkfit' object
plot.PLNPCAfamily	Display the criteria associated with a collection of PLNPCA fits (a PLNPCAfamily)
plot.PLNPCAfit	PCA visualization (individual and/or variable factor map(s)) for a 'PLNPCAfit' object
plot.ZIPLNfit_sparse	Extract and plot the network (partial correlation, support or inverse covariance) from a 'ZIPLNfit_sparse' object
plot.ZIPLNnetworkfamily	Display various outputs (goodness-of-fit criteria, robustness, diagnostic) associated with a collection of network fits (either 'PLNnetworkfamily' or 'ZIPLNnetworkfamily')
predict.PLNfit	Predict counts of a new sample
predict.PLNLDAfit	Predict group of new samples
predict.PLNmixturefit	Prediction for a 'PLNmixturefit' object
predict.ZIPLNfit	Predict counts of a new sample
predict_cond	Predict counts conditionally
predict_cond.PLNfit	Predict counts conditionally
prepare_data	Prepare data for use in PLN models

-- R --

rPLN

PLN RNG

-- S --

scRNA	Single cell RNA-seq data
sigma.PLNfit	Extract variance-covariance of residuals 'Sigma'
sigma.PLNmixturefit	Extract variance-covariance of residuals 'Sigma'
sigma.ZIPLNfit	Extract variance-covariance of residuals 'Sigma'
stability_selection	Compute the stability path by stability selection
standard_error	Component-wise standard errors of B
standard_error.PLNfit	Component-wise standard errors of B
standard_error.PLNfit_fixedcov	Component-wise standard errors of B
standard_error.PLNmixturefit	Component-wise standard errors of B
standard_error.PLNnetworkfit	Component-wise standard errors of B
standard_error.PLNPCAfit	Component-wise standard errors of B

-- T --

trichoptera

Trichoptera data set

-- V --

vcov.PLNfit

Calculate Variance-Covariance Matrix for a fitted 'PLN()' model object

-- Z --

ZIPLN	Zero Inflated Poisson lognormal model
ZIPLNfit	An R6 Class to represent a ZIPLNfit
ZIPLNfit_diagonal	An R6 Class to represent a ZIPLNfit in a standard, general framework, with diagonal residual covariance
ZIPLNfit_fixed	An R6 Class to represent a ZIPLNfit in a standard, general framework, with fixed (inverse) residual covariance
ZIPLNfit_sparse	An R6 Class to represent a ZIPLNfit in a standard, general framework, with sparse inverse residual covariance
ZIPLNfit_spherical	An R6 Class to represent a ZIPLNfit in a standard, general framework, with spherical residual covariance
ZIPLNnetwork	Zero Inflated Sparse Poisson lognormal model for network inference
ZIPLNnetworkfamily	An R6 Class to represent a collection of ZIPLNnetwork
ZIPLNnetwork_param	Control of ZIPLNnetwork fit
ZIPLN_param	Control of a ZIPLN fit