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 |
dNBabunds |
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) |
dNBllcol |
A score function for the estimation of the column scores in an unconstrained RC(M) model |
dNBllcolNP |
Estimation of the parameters of a third degree GLM |
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 |
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 |
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-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 |