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 | Extend a MRAmodelSet with relevant variable parameters |
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 a parameterised model from experiment files and the... |
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 functionnal 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 parameters... |
readMIDAS | Read a MIDAS file |
readNetworkAdj | Get an adjacency matrix from a file |
rebuildModel | Import a saved model with data files |
refit | Refit the model |
refitWithVariableParameter | Refit modelset by iterative relaxation of single parameters |
selectMinimalModel | Selection of a minimal model by the removal of non... |
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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