Man pages for davidkwca/inferTPBN
Infer Threshold PBNs from Timeseries Data.
| A | Add threshold parameters to network. |
| aToFunction | Turn threshold parameters into Boolean functions. |
| bestA | Jointly optimize all threshold parameters. |
| bestC | Find optimal probabilities for a set of regulatory functions. |
| bestPartialA | Optimize a subset of threshold parameters. |
| createNetwork | Create random threshold PBN. |
| FullRun | Complete run of network generation and inference. |
| inferPBN | Infer a Threshold PBN from a list of timeseries. |
| innovateGene | Greedily add new gene to regulatory function. |
| innovateGeneFunction | Add regulatory function to a gene. |
| innovateGeneUntilSaturated | Add new genes to regulatory set until no more improvement is... |
| Loss | Compute loss of the network on the timeseries. |
| LossGeneTimeseries | Computes the loss for a gene over a list of timeseries. |
| LossGeneTotal | Compute the total loss for a gene. |
| LossPriorGene | Compute the prior penalty for the network. |
| optimizeC | Optimize probabilities for regulatory functions to be used. |
| predict | Generate gene's next state given current state. |
| reproduce | Function to reproduce all data and plots. |
| setupPBN | Generate a random TPBN and a timeseries simulated from it. |
| simulateNetwork | Simulate a threshold PBN. |
| transformNetwork | Add TPBN parameters to a BoolNet network. |
