Fit and Simulate Model from Perturbation Data

addLayerLinks | Generate a list of links between two layers with a... |

addLink | add Link routine |

addPLinfos | Add the information provided by the profile likelihood in the... |

addVariableParameters | Search for and relax fixed coefficients of an MRAmodelSet to... |

aggregateDirectPaths | Aggregate the paths values for plotting |

cloneModel | Clone an MRAmodel or MRAmodelSet object |

computeFitScore | Compute the fitting scores of a model |

createDataSet | Import multiple files to create a group of models |

createModel | Creates and fits a parameterised model from experimental... |

createModelSet | Build an MRAmodelSet |

createSimulation | Create simulated data |

exportModel | Exports the model in a file |

extraction | Extraction of object from file or object |

extractModelCore | Extracts the data, the experimental design and the structure... |

extractSubmodels | Extract individual models from an MRAmodelSet |

fitmodel | Fit and simulate model from perturbation data |

generate_infos | Build infos vector from the parameters used to build the... |

generateToyDesign | Generate an experimental design for a toy network |

generateToyNetwork | Generate a fake network tab file |

getCombinationMatrix | Create a perturbation matrix |

getDirectPaths | Compute direct paths for a model |

getModelError | Compute the error of the model |

getParametersNames | Return the paths corresponding to each parameter |

getSamples | Get LHS samples |

getSimulation | Simulate the model for the experimental design used for the... |

importModel | Import model from a file |

initModel | Perform an initialisation of the model |

modelGroup | Constructor for modelGroup objects |

MRAmodel | Constructor for MRAmodel objects |

MRAmodelSet | Constructor for MRAmodelSet objects |

mul_path | Multiply two paths (list of links with exponent) |

niplotPL | Plots the functional relations between each non-identifiable... |

plotHeatmap | Plot a customized heatmap with a symmetrical scale that is... |

plotModelAccuracy | Plot heatmaps of the model simulation against the data... |

plotModelGraph | Plot the network used in the model |

plotModelParameters | Plot the parameters for a model or a list of models |

plotModelScores | Plot the fitting scores of the model |

plotModelScores.modelGroup | Plot the measurement scores for a group of models |

plotModelScores.MRAmodel | Plot the scores of each antibody |

plotModelSimulation | Plot the predictions by the model |

plotNetworkGraph | Plot a graph from an adjacency list |

plotParameters | Plot parameters |

plotParameters.modelGroup | Plot the parameters of the models |

plotResiduals | Plot the residual of each model in the group |

plotSimulation | Plot predictions generated by simulateModel One plot per... |

printParameters | Print the value of the parameters of the model |

profileLikelihood | Computes the profile likelihood and the parameter... |

readMIDAS | Read a MIDAS file |

readNetworkAdj | Get an adjacency matrix from a file |

rebuildModel | Import a saved model with data files |

refit | Fit a model using the parameter set from another model |

refitWithVariableParameter | Refit modelset by iterative relaxation of single parameters |

selectMinimalModel | Selection of a minimal model by iteratively removing... |

setVariableParameters | Set the variable parameters of a modelset |

simulateModel | Get the target simulations in a MIDAS design-like or list... |

suggestExtension | Tries to locally add one link each and returns a list of... |

testModel | Computes the fitting scores for a new parameter set |

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