Package: seeds 0.9.1

Tobias Newmiwaka

seeds: Estimate Hidden Inputs using the Dynamic Elastic Net

Algorithms to calculate the hidden inputs of systems of differential equations. These hidden inputs can be interpreted as a control that tries to minimize the discrepancies between a given model and taken measurements. The idea is also called the Dynamic Elastic Net, as proposed in the paper "Learning (from) the errors of a systems biology model" (Engelhardt, Froelich, Kschischo 2016) <doi:10.1038/srep20772>. To use the experimental SBML import function, the 'rsbml' package is required. For installation I refer to the official 'rsbml' page: <https://bioconductor.org/packages/release/bioc/html/rsbml.html>.

Authors:Tobias Newmiwaka [aut, cre], Benjamin Engelhardt [aut]

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# Install 'seeds' in R:
install.packages('seeds', repos = c('https://newmi1988.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/newmi1988/seeds/issues

Datasets:
  • Model - Test dataset for demonstrating the bden algorithm.
  • res - Results from the uvb dataset for examples
  • uvbData - UVB signal pathway
  • uvbModel - An object of the odeModel Class

On CRAN:

20 exports 0.62 score 86 dependencies 2 scripts 134 downloads

Last updated 3 years agofrom:6925d92813. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 26 2024
R-4.5-winNOTEAug 26 2024
R-4.5-linuxNOTEAug 26 2024
R-4.4-winOKAug 26 2024
R-4.4-macNOTEAug 26 2024
R-4.3-winOKAug 26 2024
R-4.3-macNOTEAug 26 2024

Exports:BDENconfidenceBandsDENestiStateshiddenInputsimportSBMLnominalSolodeModeloutputEstimatesplotplotAnnoprintresultsSeedssetInitStatesetInputsetMeassetMeasFuncsetModelEquationsetParmssetSd

Dependencies:backportsbase64encbslibcachemcallrcheckmatecliclustercodacolorspacecpp11data.tableDerivdeSolvedigestdplyrevaluatefansifarverfastmapfontawesomeforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellmvtnormnlmennetpillarpkgconfigpracmaprocessxpspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcpprlangrmarkdownrpartrstudioapiRyacassassscalesstatmodstringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml

Seeds: Calculating the hidden inputs in a system

Rendered fromseeds.Rmdusingknitr::rmarkdownon Aug 26 2024.

Last update: 2020-06-25
Started: 2019-11-19

Readme and manuals

Help Manual

Help pageTopics
seeds: Estimate Hidden Inputs using the Dynamic Elastic Netseeds-package seeds
Bayesian Dynamic Elastic NetBDEN
Get the estimated confidence bands for the bayesian methodconfidenceBands confidenceBands,list,character,missing-method confidenceBands,list,character,numeric-method confidenceBands,resultsSeeds,character,missing-method
Create compilable c-code of a modelcreateCompModel
Greedy method for estimating a sparse solutionDEN
Get the estimated statesestiStates estiStates,list,missing-method estiStates,list,numeric-method estiStates,resultsSeeds,missing-method
Gibbs UpdateGIBBS_update
Get the estimated hidden inputshiddenInputs hiddenInputs,list,missing-method hiddenInputs,list,numeric-method hiddenInputs,resultsSeeds,missing-method
Import SBML Models using the Bioconductor package 'rsbml'importSBML
Calculates the Log Likelihood for a new sample given the current state (i.e. log[L(G|x)P(G)])LOGLIKELIHOOD_func
Componentwise Adapted Metropolis Hastings SamplerMCMC_component
Test dataset for demonstrating the bden algorithm.Model
Calculate the nominal solution of the modelnominalSol nominalSol,odeModel-method
A S4 class used to handle formatting ODE-Equation and calculate the needed functions for the seeds-algorithmodeEquations odeEquations-class
A class to store the important information of an model.odeModel odeModel-class
estimating the optimal control using the dynamic elastic netoptimal_control_gradient_descent
Get the estimated outputsoutputEstimates outputEstimates,list,missing-method outputEstimates,list,numeric-method outputEstimates,resultsSeeds,missing-method
Plot method for the S4 class resultsSeedsplot,resultsSeeds,missing-method
Create annotated plotplotAnno plotAnno,list-method plotAnno,resultsSeeds-method
A default printing function for the resultsSeeds classprint,resultsSeeds print,resultsSeeds-method
Results from the uvb dataset for examplesres
Results Class for the AlgorithmsresultsSeeds resultsSeeds-class
Set the vector with the initial (state) valuessetInitState setInitState,odeModel-method
Set the inputs of the model.setInput setInput,odeModel-method
set measurements of the modelsetMeas setMeas,odeModel-method
Set the measurement equation for the modelsetMeasFunc setMeasFunc,odeModel,function,logical-method setMeasFunc,odeModel,function,missing-method
Set the model equationsetModelEquation setModelEquation,odeModel-method
Set the model parameterssetParms setParms,odeModel,numeric-method
Set the standard deviation of the measurementssetSd setSd,odeModel-method
Automatic Calculation of optimal Initial ParametersSETTINGS
UVB signal pathwayuvbData
An object of the odeModel ClassuvbModel