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| 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 |
| extractMat-method | 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 |