Poisson Lognormal Models


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Documentation for package ‘PLNmodels’ version 0.11.6

Help Pages

coef.PLNfit Extract model coefficients
coef.PLNLDAfit Extracts model coefficients from objects returned by 'PLNLDA()'
coef.PLNmixturefit 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
extract_probs Extract edge selection frequency in bootstrap subsamples
fisher Fisher information matrix for Theta
fisher.PLNfit Fisher information matrix for Theta
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
getBestModel 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
getModel 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
mollusk Mollusk data set
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
PLNLDA Poisson lognormal model towards Linear Discriminant Analysis
PLNLDAfit An R6 Class to represent a PLNfit in a LDA framework
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
PLNmodels PLNmodels
PLNnetwork Poisson lognormal model towards sparse network inference
PLNnetworkfamily An R6 Class to represent a collection of PLNnetworkfit
PLNnetworkfit An R6 Class to represent a PLNfit in a sparse inverse covariance framework
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
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 PLNnetwork fits (a 'PLNnetworkfamily')
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
predict.PLNfit Predict counts of a new sample
predict.PLNLDAfit Predict group of new samples
predict.PLNmixturefit Prediction for a 'PLNmixturefit' object
prepare_data Prepare data for use in PLN models
rPLN PLN RNG
sigma.PLNfit Extract variance-covariance of residuals 'Sigma'
sigma.PLNmixturefit Extract variance-covariance of residuals 'Sigma'
stability_selection Compute the stability path by stability selection
standard_error Component-wise standard errors of Theta
standard_error.PLNfit Component-wise standard errors of Theta
trichoptera Trichoptera data set
vcov.PLNfit Calculate Variance-Covariance Matrix for a fitted 'PLN()' model object