Man pages for combi
Compositional omics model based visual integration

addLinkAdd a link on a compositional plot
arrayMultArray multiplication
buildCentMatA function to build a centering matrix based on a dataframe
buildCompMatBuild the composition matrix for a certain dimension m...
buildConfMatBuild confounder design matrices with and without intercepts
buildCovMatA function to build the covariate matrix of the constraints
buildEmptyJacPrepare an empty Jacobian matrix, with useful entries...
buildMarginalOffsetBuild an offset matrix from an marginal model object
buildMuA function to build the mu matrix
buildMuMarginsBuild the marginal mu matrix
buildOffsetModelBuild a marginal offset matrix given a model
checkAliasCheck for alias structures in a dataframe, and throw an error...
checkMeanVarTrendQuickly check if the mean variance trend provides a good fit
checkMonotonicityCheck for monotonicity in compositional datasets fro given...
combiPerform model-based data integration
convPlotPlot the convegrence of the different parameter estimates in...
deriv2LagrangianFeaturesThe score function to estimate the latent variables
deriv2LagrangianLatentVarsThe jacobian function to estimate the latent variables
deriv2LagrangianLatentVarsConstrThe score function to estimate the latent variables
derivLagrangianFeaturesThe score function to estimate the feature parameters
derivLagrangianLatentVarsThe score function to estimate the latent variables
derivLagrangianLatentVarsConstrThe score function to estimate the latent variables
estFeatureParametersEstimate the feature parameters
estIndepModelEstimate the independence model belonging to one view
estLatentVarsEstimate the latent variables
estMeanVarTrendEstimate a column-wise mean-variance trend
estOffEstimate the row/column parameters of the independence model
extractCoordsExtract coordinates from fitted object
extractDataHelper function to extract data matrix from phyloseq,...
extractMatA function to extract a data matrix from a number of objects
filterConfoundersFilter out the effect of known confounders
getInflLatentVarExtract the influence on the estimation of the latent...
gramSchmidtOrthGram schimdt orhtogonalize a with respect to b, and normalize
indentPlotFunctions to indent the plot to include the entire labels
inflPlotA ggplot line plot showing the influences
influence.combiEvaluate the influence function
jacConfoundersJacobian when estimating confounder variables
jacConfoundersCompJacobian for conditioning under compositionality
jacFeaturesEvaluate the jacobian for estimating the feature parameters...
jacLatentVarsEvaluate the jacobian for estimating the latent variable for...
jacLatentVarsConstrEvaluate the jacobian for estimating the latent variable for...
plot.combiMake multiplots of the data integration object
polyHornerHorner's method to evaluate a polynomial, copied from the...
predictSplineA custom spline prediction function, extending linearly with...
prepareJacMatprepare the jacobian matrix
prepareJacMatCompprepare the jacobian for the latent variabels compostional
prepareScoreMatPrepare a helper matrix for score function evaluation under...
print.combiPrint an overview of a fitted combi x
quasiJacIndepThe jacobian for column offset estimation
quasiScoreIndepQuasi score equations for column offset parameters of...
rowMultiplyA function to efficiently row multiply a matrix and a vector
scaleCoordsA helper function to rescale coordinates
scoreConfoundersScore functions for confounder variables
scoreConfoundersCompScore equations for conditioning under compositionality
scoreFeatureParamsEvaluate the score functions for the estimation of the...
scoreLatentVarsEvaluate the score functions for the estimation of the latent...
seqMA small auxiliary function for the indices of the lagrange...
trimOnConfoundersTrim based on confounders to avoid taxa with only zero counts
zhangMetaboMetabolomes of mice that underwent Pulsed Antibiotic...
zhangMetavarsBaseline sample variables of PAT and control mice
zhangMicrobioMicrobiomes of mice that underwent Pulsed Antibiotic...
combi documentation built on Nov. 8, 2020, 5:34 p.m.