GramSchmidt             Gram-Schmidt orthogonalization of vectors
JacCol_constr           Jacobian of the constrained analysis with
                        linear response function.
JacCol_constr_noLab     The jacobian of the response function without
                        taxon labels
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
NBjacobianAbundsOld     Jacobian for the column components of the
                        independence model
NBjacobianColNP         Jacobian function for the estimation of a third
                        degree GLM
NBjacobianColOld        Jacobian for the estimation of the column
                        scores
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
RCM                     Wrapper function for the RCM() function
RCM_NB                  Fit the RC(M) model with the negative binomial
                        distribution.
Zeller                  Microbiomes of colorectal cancer patients and
                        healthy controls
addOrthProjection       This function adds orthogonal projections to a
                        given plot
arrayprod               An auxiliary R function to 'array' multiply an
                        array with a vector, kindly provided by Joris
                        Meys
buildCentMat            A function to build a centering matrix based on
                        a dataframe
buildConfMat            A function to build the confounder matrices
buildConfMat,character-method
                        buildConfMat.character
buildConfMat,data.frame-method
                        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 when one is found
constrCorresp           Constrained correspondence analysis with
                        adapted powers
correctXMissingness     Replace missing entries in X by their
                        expectation to set their contribution to the
                        estimating equations to zero
dLR_nb                  A function that returns the value of the
                        partial derivative of the log-likelihood ratio
                        to alpha, keeping the response functions fixed
dNBabundsOld            A score function for the column components of
                        the independence model (mean relative
                        abundances)
dNBlibSizes             A score function for the row components of the
                        independence model (library sizes)
dNBllcolNP              Estimation of the parameters of a third degree
                        GLM
dNBllcolOld             A score function for the estimation of the
                        column scores in an unconstrained RC(M) model
dNBllcol_constr         The score function of the response function for
                        1 taxon at the time
dNBllcol_constr_noLab   The score function of the general response
                        function
dNBllrow                A score function of the NB for the row scores
dNBpsis                 A score function for the psi of a given
                        dimension
deviances               A function to extract deviances for all
                        dimension, including after filtering on
                        confounders
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 labels
estNPresp               Estimate the taxon-wise response functions
                        non-parametrically
extractCoord            A function to extract plotting coordinates,
                        either for plot.RCM or to export to other
                        plotting software
extractE                A function to extract a matrix of expected
                        values for any dimension of the fit
filterConfounders       Filters out the effect of known confounders.
                        This is done by fitting interactions of every
                        taxon with the levels of the confounders. It
                        returns a modified offset matrix for the
                        remainder of the fitting procedure.
getDevMat               ACalculate the matrix of deviance residuals
getDevianceRes          A function to calculate the matrix of deviance
                        residuals.
getDistCoord            Get coordinates of a distance object of n
                        observations for the provided indices
getInflCol              A function to extract the influence for a given
                        parameter index
getInflRow              Extract the influence of all observations on a
                        given row score
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
liks                    Calculate the log-likelihoods of all possible
                        models
permanova               Perform a PERMANOVA analysis for group
                        differences of a predefined cofactor using the
                        pseudo F-statistic
plot.RCM                Plot RC(M) ordination result with the help of
                        ggplot2
plotRespFun             Plot the non-parametric response functions
residualPlot            Make residual plots
respFunJacMat           Calculates the Jacobian of the parametric
                        response functions
respFunScoreMat         Derivative of the Lagrangian of the parametric
                        response function
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
