Estimate Hidden Inputs using the Dynamic Elastic Net
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Documentation for package ‘seeds’ version 0.9.1
- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
Help Pages
| seeds-package | seeds: Estimate Hidden Inputs using the Dynamic Elastic Net |
| BDEN | Bayesian Dynamic Elastic Net |
| confidenceBands | Get the estimated confidence bands for the bayesian method |
| confidenceBands-method | Get the estimated confidence bands for the bayesian method |
| createCompModel | Create compilable c-code of a model |
| DEN | Greedy method for estimating a sparse solution |
| estiStates | Get the estimated states |
| estiStates-method | Get the estimated states |
| GIBBS_update | Gibbs Update |
| hiddenInputs | Get the estimated hidden inputs |
| hiddenInputs-method | Get the estimated hidden inputs |
| importSBML | Import SBML Models using the Bioconductor package 'rsbml' |
| LOGLIKELIHOOD_func | Calculates the Log Likelihood for a new sample given the current state (i.e. log[L(G|x)P(G)]) |
| MCMC_component | Componentwise Adapted Metropolis Hastings Sampler |
| Model | Test dataset for demonstrating the bden algorithm. |
| nominalSol | Calculate the nominal solution of the model |
| nominalSol-method | Calculate the nominal solution of the model |
| odeEquations | A S4 class used to handle formatting ODE-Equation and calculate the needed functions for the seeds-algorithm |
| odeEquations-class | A S4 class used to handle formatting ODE-Equation and calculate the needed functions for the seeds-algorithm |
| odeModel | A class to store the important information of an model. |
| odeModel-class | A class to store the important information of an model. |
| optimal_control_gradient_descent | estimating the optimal control using the dynamic elastic net |
| outputEstimates | Get the estimated outputs |
| outputEstimates-method | Get the estimated outputs |
| plot-method | Plot method for the S4 class resultsSeeds |
| plotAnno | Create annotated plot |
| plotAnno-method | Create annotated plot |
| print,resultsSeeds | A default printing function for the resultsSeeds class |
| print-method | A default printing function for the resultsSeeds class |
| res | Results from the uvb dataset for examples |
| resultsSeeds | Results Class for the Algorithms |
| resultsSeeds-class | Results Class for the Algorithms |
| seeds | seeds: Estimate Hidden Inputs using the Dynamic Elastic Net |
| setInitState | Set the vector with the initial (state) values |
| setInitState-method | Set the vector with the initial (state) values |
| setInput | Set the inputs of the model. |
| setInput-method | Set the inputs of the model. |
| setMeas | set measurements of the model |
| setMeas-method | set measurements of the model |
| setMeasFunc | Set the measurement equation for the model |
| setMeasFunc-method | Set the measurement equation for the model |
| setModelEquation | Set the model equation |
| setModelEquation-method | Set the model equation |
| setParms | Set the model parameters |
| setParms-method | Set the model parameters |
| setSd | Set the standard deviation of the measurements |
| setSd-method | Set the standard deviation of the measurements |
| SETTINGS | Automatic Calculation of optimal Initial Parameters |
| uvbData | UVB signal pathway |
| uvbModel | An object of the odeModel Class |