Poisson Lognormal Models

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Documentation for package ‘PLNmodels’ version 1.2.1

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barents Barents fish data set
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.
extract_probs Extract edge selection frequency in bootstrap subsamples
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
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
mollusk Mollusk data set
Networkfamily An R6 Class to virtually represent a collection of network fits
oaks Oaks amplicon data set
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_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
rPLN PLN RNG
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
trichoptera Trichoptera data set
vcov.PLNfit Calculate Variance-Covariance Matrix for a fitted 'PLN()' model object
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