Man pages for CenterForStatistics-UGent/RCM
Fit row-column association models with the negative binomial distribution for the microbiome

addOrthProjectionThis function adds orthogonal projections to a given plot
arrayprodAn auxiliary R function to 'array' multiply an array with a...
buildCentMatA function to build a centering matrix based on a dataframe
buildConfMatA function to build the confounder matrices
buildCovMatA function to build the covariate matrix of the constraints
buildDesignA function to build the design matrix
checkAliasCheck for alias structures in a dataframe, and throw an error...
constrCorrespConstrained correspondence analysis with adapted powers
correctXMissingnessReplace missing entries in X by their expectation to set...
deviancesA function to extract deviances for all dimension, including...
dLR_nbA function that returns the value of the partial derivative...
dNBabundsOldA score function for the column components of the...
dNBlibSizesA score function for the row components of the independence...
dNBllcol_constrThe score function of the response function for 1 taxon at...
dNBllcol_constr_noLabThe score function of the general response function
dNBllcolNPEstimation of the parameters of a third degree GLM
dNBllcolOldA score function for the estimation of the column scores in...
dNBllrowA score function of the NB for the row scores
dNBpsisA score function for the psi of a given dimension
ellipseCoordA function that returns the coordinates of an ellipse
estDispEstimate the overdispersion
estNBparamsA function to estimate the taxon-wise NB-params
estNBparamsNoLabA function to estimate the NB-params ignoring the taxon...
estNPrespEstimate the taxon-wise response functions non-parametrically
extractCoordA function to extract plotting coordinates, either for...
extractEA function to extract a matrix of expected values for any...
filterConfoundersFilters out the effect of known confounders. This is done by...
getDevianceResA function to calculate the matrix of deviance residuals.
getDevMatACalculate the matrix of deviance residuals
getDistCoordGet coordinates of a distance object of n observations for...
getInflColA function to extract the influence for a given parameter...
getInflRowExtract the influence of all observations on a given row...
getIntIntegrate the spline of an vgam object
getLogLikExtract the logged likelihood of every count
getModelMatA function to construct a model matrix of a certain degree
getRowMatReturn a matrix of row scores
GramSchmidtGram-Schmidt orthogonalization of vectors
heq_nbDefine linear equality constraints for env. gradient
heq_nb_jacThe jacobian of the linear equality constraints
indentPlotFunctions to indent the plot to include the entire labels
inertiaCalculate the log-likelihoods of all possible models
JacCol_constrJacobian of the constrained analysis with linear response...
JacCol_constr_noLabThe jacobian of the response function without taxon labels
liksCalculate the log-likelihoods of all possible models
LR_nbGet the value of the log-likelihood ratio of alpha
LR_nb_JacA function that returns the Jacobian of the likelihood ratio
NBalphaInflCalculate the components of the influence functions
NBcolInflThe influence function for the column scores
NBjacobianAbundsOldJacobian for the column components of the independence model
NBjacobianColNPJacobian function for the estimation of a third degree GLM
NBjacobianColOldJacobian for the estimation of the column scores
NBjacobianLibSizesJacobian for the raw components of the independence model
NBjacobianPsiJacobian for the psi of a given dimension
NBjacobianRowA jacobian function of the NB for the row scores
NBpsiInflThe influence function for the psis
NBrowInflThe influence function for the row scores
permanovaPerform a PERMANOVA analysis for group differences of a...
plot.RCMPlot RC(M) ordination result with the help of ggplot2
plotRespFunPlot the non-parametric response functions
RCMWrapper function for the RCM() function
RCM_NBFit the RC(M) model with the negative binomial distribution.
residualPlotMake residual plots
respFunJacMatCalculates the Jacobian of the parametric response functions
respFunScoreMatDerivative of the Lagrangian of the parametric response...
rowMultiplyA function to efficiently row multiply a matrix and a vector
seq_kA small auxiliary function for the length of the lambdas
trimOnConfoundersTrim based on confounders to avoid taxa with only zero counts
ZellerMicrobiomes of colorectal cancer patients and healthy...
CenterForStatistics-UGent/RCM documentation built on April 24, 2023, 8:26 p.m.