Man pages for PLNmodels
Poisson Lognormal Models

coefficient_pathExtract the regularization path of a PLNnetwork fit
coef.PLNfitExtract model coefficients
coef.PLNLDAfitExtracts model coefficients from objects returned by 'PLNLDA'
compute_offsetCompute offsets from a count data using one of several...
extract_probsExtract edge selection frequency in bootstrap subsamples
fisherFisher information matrix for Theta
fitted.PLNfitExtracts model fitted values from objects returned by 'PLN'...
getBestModelBest model extraction from a collection of models
getModelModel extraction from a collection of models
molluskMollusk data set
pipePipe operator
PLNPoisson lognormal model
PLNfitAn R6 Class to represent a PLNfit in a standard, general...
PLNLDAPoisson lognormal model towards Linear Disciminant Analysis
PLNLDAfitAn R6 Class to represent a PLNfit in a LDA framework
PLNmodelsPLNmodels
PLNnetworkPoisson lognormal model towards sparse network inference
PLNnetworkfamilyAn R6 Class to represent a collection of PLNnetworkfit
PLNnetworkfitAn R6 Class to represent a PLNfit in a sparse inverse...
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
plot.PLNLDAfitLDA vizualiation (individual and/or variable factor map(s))...
plot.PLNnetworkfamilyDisplay various ouputs (goodness-of-fit criteria, robustness,...
plot.PLNnetworkfitExtract and plot the network (aprtial correlation, support or...
plot.PLNPCAfamilyDisplay the criteria associated with a collection of PLNPCA...
plot.PLNPCAfitPCA vizualiation (individual and/or variable factor map(s))...
predict.PLNfitPredict counts of a new sample
predict.PLNLDAfitPredict group of new samples
prepare_dataPrepare data for use in PLN models
prepare_data_from_biomPrepare data for use in PLN models from a biom object
prepare_data_from_phyloseqPrepare data for use in PLN models from a phyloseq object
rPLNPLN RNG
sigma.PLNfitExtract variance-covariance of residuals 'Sigma'
stability_selectionCompute the stability path by stability selection
standard_errorComponent-wise standard errors of Theta
trichopteraTrichoptera data set
vcov.PLNfitCalculate Variance-Covariance Matrix for a fitted 'PLN' model...
PLNmodels documentation built on May 17, 2019, 5:01 p.m.