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

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... |

dNBabundsOld | A score function for the column components of the... |

dNBlibSizes | A score function for the row components of the independence... |

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 |

dNBllcolOld | A score function for the estimation of the column scores in... |

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 |

getDistCoord | Get coordinates of a distance object of n observations for... |

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 |

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... |

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 |

permanova | Perform a PERMANOVA analysis for group differences of a... |

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... |

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