| addOrthProjection | This function adds orthogonal projections to a given plot |
| arrayprod | An auxiliary R function to 'array' multiply an array with a... |
| buildCentMat | A function to build a centering matrix based on a dataframe |
| buildConfMat | A function to build the confounder matrices |
| buildConfMat.character | buildConfMat.character |
| buildConfMat.data.frame | buildConfMat.data.frame |
| buildCovMat | A function to build the covariate matrix of the constraints |
| buildDesign | A function to build the design matrix |
| checkAlias | Check for alias structures in a dataframe, and throw an error... |
| constrCorresp | Constrained correspondence analysis with adapted powers |
| correctXMissingness | Replace missing entries in X by their expectation to set... |
| deviances | A function to extract deviances for all dimension, including... |
| dLR_nb | A function that returns the value of the partial derivative... |
| dNBabunds | A score function for the column components of the... |
| dNBlibSizes | A score function for the row components of the independence... |
| dNBllcol | A score function for the estimation of the column scores in... |
| dNBllcol_constr | The score function of the response function for 1 taxon at... |
| dNBllcol_constr_noLab | The score function of the general response function |
| dNBllcolNP | Estimation of the parameters of a third degree GLM |
| dNBllrow | A score function of the NB for the row scores |
| dNBpsis | A score function for the psi of a given dimension |
| ellipseCoord | A function that returns the coordinates of an ellipse |
| estDisp | Estimate the overdispersion |
| estNBparams | A function to estimate the taxon-wise NB-params |
| estNBparamsNoLab | A function to estimate the NB-params ignoring the taxon... |
| estNPresp | Estimate the taxon-wise response functions non-parametrically |
| extractCoord | A function to extract plotting coordinates, either for... |
| extractE | A function to extract a matrix of expected values for any... |
| filterConfounders | Filters out the effect of known confounders. This is done by... |
| getDevianceRes | A function to calculate the matrix of deviance residuals. |
| getDevMat | ACalculate the matrix of deviance residuals |
| getInflCol | A function to extract the influence for a given parameter... |
| getInflRow | Extract the influence of all observations on a given row... |
| getInt | Integrate the spline of an vgam object |
| getLogLik | Extract the logged likelihood of every count |
| getModelMat | A function to construct a model matrix of a certain degree |
| getRowMat | Return a matrix of row scores |
| heq_nb | Define linear equality constraints for env. gradient |
| heq_nb_jac | The jacobian of the linear equality constraints |
| indentPlot | Functions to indent the plot to include the entire labels |
| inertia | Calculate the log-likelihoods of all possible models |
| JacCol_constr | Jacobian of the constrained analysis with linear response... |
| JacCol_constr_noLab | The jacobian of the response function without taxon labels |
| liks | Calculate the log-likelihoods of all possible models |
| LR_nb | Get the value of the log-likelihood ratio of alpha |
| LR_nb_Jac | A function that returns the Jacobian of the likelihood ratio |
| NBalphaInfl | Calculate the components of the influence functions |
| NBcolInfl | The influence function for the column scores |
| NBjacobianAbunds | Jacobian for the column components of the independence model |
| NBjacobianCol | Jacobian for the estimation of the column scores |
| NBjacobianColNP | Jacobian function for the estimation of a third degree GLM |
| NBjacobianLibSizes | Jacobian for the raw components of the independence model |
| NBjacobianPsi | Jacobian for the psi of a given dimension |
| NBjacobianRow | A jacobian function of the NB for the row scores |
| NBpsiInfl | The influence function for the psis |
| NBrowInfl | The influence function for the row scores |
| plot.RCM | Plot RC(M) ordination result with the help of ggplot2 |
| plotRespFun | Plot the non-parametric response functions |
| RCM | Wrapper function for the RCM() function |
| RCM_NB | Fit the RC(M) model with the negative binomial distribution. |
| residualPlot | Make residual plots |
| respFunJacMat | Calculates the Jacobian of the parametric response functions |
| respFunScoreMat | Derivative of the Lagrangian of the parametric response... |
| rowMultiply | A function to efficiently row multiply a matrix and a vector |
| seq_k | A small auxiliary function for the length of the lambdas |
| trimOnConfounders | Trim based on confounders to avoid taxa with only zero counts |
| Zeller | Microbiomes of colorectal cancer patients and healthy... |
