addLink                 Add a link on a compositional plot
arrayMult               Array multiplication
buildCentMat            A function to build a centering matrix based on
                        a dataframe
buildCompMat            Build the composition matrix for a certain
                        dimension m dimensions
buildConfMat            Build confounder design matrices with and
                        without intercepts
buildCovMat             A function to build the covariate matrix of the
                        constraints
buildEmptyJac           Prepare an empty Jacobian matrix, with useful
                        entries prefilled. In case of distribution
                        "gaussian", it returns the lhs matrix of the
                        linear system for finding the feature paramters
buildMarginalOffset     Build an offset matrix from an marginal model
                        object
buildMu                 A function to build the mu matrix
buildMuMargins          Build the marginal mu matrix
buildOffsetModel        Build a marginal offset matrix given a model
checkAlias              Check for alias structures in a dataframe, and
                        throw an error when one is found
checkMeanVarTrend       Quickly check if the mean variance trend
                        provides a good fit
checkMonotonicity       Check for monotonicity in compositional
                        datasets fro given dimensions
combi                   Perform model-based data integration
convPlot                Plot the convegrence of the different parameter
                        estimates in a line plot
deriv2LagrangianFeatures
                        The score function to estimate the latent
                        variables
deriv2LagrangianLatentVars
                        The jacobian function to estimate the latent
                        variables
deriv2LagrangianLatentVarsConstr
                        The score function to estimate the latent
                        variables
derivLagrangianFeatures
                        The score function to estimate the feature
                        parameters
derivLagrangianLatentVars
                        The score function to estimate the latent
                        variables
derivLagrangianLatentVarsConstr
                        The score function to estimate the latent
                        variables
estFeatureParameters    Estimate the feature parameters
estIndepModel           Estimate the independence model belonging to
                        one view
estLatentVars           Estimate the latent variables
estMeanVarTrend         Estimate a column-wise mean-variance trend
estOff                  Estimate the row/column parameters of the
                        independence model
extractCoords           Extract coordinates from fitted object
extractData             Helper function to extract data matrix from
                        phyloseq, expressionset objects etc. Also
                        filers out all zero rows
extractMat              A function to extract a data matrix from a
                        number of objects
filterConfounders       Filter out the effect of known confounders
getInflLatentVar        Extract the influence on the estimation of the
                        latent variable
gramSchmidtOrth         Gram schimdt orhtogonalize a with respect to b,
                        and normalize
indentPlot              Functions to indent the plot to include the
                        entire labels
inflPlot                A ggplot line plot showing the influences
influence.combi         Evaluate the influence function
jacConfounders          Jacobian when estimating confounder variables
jacConfoundersComp      Jacobian for conditioning under
                        compositionality
jacFeatures             Evaluate the jacobian for estimating the
                        feature parameters for one view
jacLatentVars           Evaluate the jacobian for estimating the latent
                        variable for one view
jacLatentVarsConstr     Evaluate the jacobian for estimating the latent
                        variable for one view for constrained
                        ordination
plot.combi              Make multiplots of the data integration object
polyHorner              Horner's method to evaluate a polynomial,
                        copied from the polynom package. the most
                        efficient way
predictSpline           A custom spline prediction function, extending
                        linearly with a slope such that prediction
                        never drops below first bisectant
prepareJacMat           prepare the jacobian matrix
prepareJacMatComp       prepare the jacobian for the latent variabels
                        compostional
prepareScoreMat         Prepare a helper matrix for score function
                        evaluation under quasi-likelihood
print.combi             Print an overview of a fitted combi x
quasiJacIndep           The jacobian for column offset estimation
quasiScoreIndep         Quasi score equations for column offset
                        parameters of sequence count data
rowMultiply             A function to efficiently row multiply a matrix
                        and a vector
scaleCoords             A helper function to rescale coordinates
scoreConfounders        Score functions for confounder variables
scoreConfoundersComp    Score equations for conditioning under
                        compositionality
scoreFeatureParams      Evaluate the score functions for the estimation
                        of the feature parameters for a single dataset
scoreLatentVars         Evaluate the score functions for the estimation
                        of the latent variables for a single dataset
seqM                    A small auxiliary function for the indices of
                        the lagrange multipliers
trimOnConfounders       Trim based on confounders to avoid taxa with
                        only zero counts
zhangMetabo             Metabolomes of mice that underwent Pulsed
                        Antibiotic Treatment (PAT) and controls
zhangMetavars           Baseline sample variables of PAT and control
                        mice
zhangMicrobio           Microbiomes of mice that underwent Pulsed
                        Antibiotic Treatment (PAT) and controls
