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 |