Man pages for PLN-team/PLNmodels
Poisson Lognormal Models

barentsBarents fish data set
coefficient_pathExtract the regularization path of a PLNnetwork fit
coef.PLNfitExtract model coefficients
coef.PLNLDAfitExtracts model coefficients from objects returned by...
coef.PLNmixturefitExtract model coefficients
coef.ZIPLNfitExtract model coefficients
compute_offsetCompute offsets from a count data using one of several...
compute_PLN_starting_pointHelper function for PLN initialization.
extract_probsExtract edge selection frequency in bootstrap subsamples
fitted.PLNfitExtracts model fitted values from objects returned by 'PLN()'...
fitted.PLNmixturefitExtracts model fitted values from objects returned by...
fitted.ZIPLNfitExtracts model fitted values from objects returned by...
getBestModelBest model extraction from a collection of models
getModelModel extraction from a collection of models
molluskMollusk data set
NetworkfamilyAn R6 Class to virtually represent a collection of network...
oaksOaks amplicon data set
pipePipe operator
PLNPoisson lognormal model
PLNfamilyAn R6 Class to represent a collection of PLNfit
PLNfitAn R6 Class to represent a PLNfit in a standard, general...
PLNfit_diagonalAn R6 Class to represent a PLNfit in a standard, general...
PLNfit_fixedcovAn R6 Class to represent a PLNfit in a standard, general...
PLNfit_sphericalAn R6 Class to represent a PLNfit in a standard, general...
PLNLDAPoisson lognormal model towards Linear Discriminant Analysis
PLNLDAfitAn R6 Class to represent a PLNfit in a LDA framework
PLNLDAfit_diagonalAn R6 Class to represent a PLNfit in a LDA framework with...
PLNLDA_paramControl of a PLNLDA fit
PLNmixturePoisson lognormal mixture model
PLNmixturefamilyAn R6 Class to represent a collection of PLNmixturefit
PLNmixturefitAn R6 Class to represent a PLNfit in a mixture framework
PLNmixture_paramControl of a PLNmixture fit
PLNmodels-packagePLNmodels: Poisson Lognormal Models
PLNnetworkSparse Poisson lognormal model for network inference
PLNnetworkfamilyAn R6 Class to represent a collection of 'PLNnetworkfit's
PLNnetworkfitAn R6 Class to represent a PLNfit in a sparse inverse...
PLNnetwork_paramControl of PLNnetwork fit
PLN_paramControl of a PLN fit
PLNPCAPoisson lognormal model towards Principal Component Analysis
PLNPCAfamilyAn R6 Class to represent a collection of PLNPCAfit
PLNPCAfitAn R6 Class to represent a PLNfit in a PCA framework
PLNPCA_paramControl of PLNPCA fit
plot.NetworkfamilyDisplay various outputs (goodness-of-fit criteria,...
plot.PLNfamilyDisplay the criteria associated with a collection of PLN fits...
plot.PLNLDAfitLDA visualization (individual and/or variable factor map(s))...
plot.PLNmixturefamilyDisplay the criteria associated with a collection of...
plot.PLNmixturefitMixture visualization of a 'PLNmixturefit' object
plot.PLNnetworkfitExtract and plot the network (partial correlation, support or...
plot.PLNPCAfamilyDisplay the criteria associated with a collection of PLNPCA...
plot.PLNPCAfitPCA visualization (individual and/or variable factor map(s))...
plot.ZIPLNfit_sparseExtract and plot the network (partial correlation, support or...
predict_condPredict counts conditionally
predict.PLNfitPredict counts of a new sample
predict.PLNLDAfitPredict group of new samples
predict.PLNmixturefitPrediction for a 'PLNmixturefit' object
predict.ZIPLNfitPredict counts of a new sample
prepare_dataPrepare data for use in PLN models
rPLNPLN RNG
scRNASingle cell RNA-seq data
sigma.PLNfitExtract variance-covariance of residuals 'Sigma'
sigma.PLNmixturefitExtract variance-covariance of residuals 'Sigma'
sigma.ZIPLNfitExtract variance-covariance of residuals 'Sigma'
stability_selectionCompute the stability path by stability selection
standard_errorComponent-wise standard errors of B
trichopteraTrichoptera data set
vcov.PLNfitCalculate Variance-Covariance Matrix for a fitted 'PLN()'...
ZIPLNZero Inflated Poisson lognormal model
ZIPLNfitAn R6 Class to represent a ZIPLNfit
ZIPLNfit_diagonalAn R6 Class to represent a ZIPLNfit in a standard, general...
ZIPLNfit_fixedAn R6 Class to represent a ZIPLNfit in a standard, general...
ZIPLNfit_sparseAn R6 Class to represent a ZIPLNfit in a standard, general...
ZIPLNfit_sphericalAn R6 Class to represent a ZIPLNfit in a standard, general...
ZIPLNnetworkZero Inflated Sparse Poisson lognormal model for network...
ZIPLNnetworkfamilyAn R6 Class to represent a collection of ZIPLNnetwork
ZIPLNnetwork_paramControl of ZIPLNnetwork fit
ZIPLN_paramControl of a ZIPLN fit
PLN-team/PLNmodels documentation built on Oct. 13, 2024, 4:01 a.m.