Fit row-column association models with the negative binomial distribution for the microbiome

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Documentation for package ‘RCM’ version 1.18.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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	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 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
deviances	A function to extract deviances for all dimension, including after filtering on confounders
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
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.
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 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
GramSchmidt	Gram-Schmidt orthogonalization of vectors
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 function.
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
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
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-method	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 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
Zeller	Microbiomes of colorectal cancer patients and healthy controls