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dMod  

Dynamic Modeling and Parameter Estimation in ODE Models
View on CRAN: Click here


Download and install dMod package within the R console
Install from CRAN:
install.packages("dMod")

Install from Github:
library("remotes")
install_github("cran/dMod")

Install by package version:
library("remotes")
install_version("dMod", "1.0.2")



Attach the package and use:
library("dMod")
Maintained by
Daniel Kaschek
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-06-11
Latest Update: 2021-01-27
Description:
The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives. The methods used in dMod were published in Kaschek et al, 2019, .
How to cite:
Daniel Kaschek (2015). dMod: Dynamic Modeling and Parameter Estimation in ODE Models. R package version 1.0.2, https://cran.r-project.org/web/packages/dMod
Previous versions and publish date:
0.1 (2015-06-11 18:31), 0.3.1 (2016-05-18 17:26), 0.3.2 (2016-09-30 10:48), 0.4.2 (2018-08-09 14:50), 0.4 (2017-09-08 23:59), 1.0.0 (2019-04-24 00:12), 1.0.1 (2020-02-10 21:50)
Other packages that cited dMod R package
View dMod citation profile
Other R packages that dMod depends, imports, suggests or enhances
Functions, R codes and Examples using the dMod R package
Some associated functions: Id . P . Pexpl . Pimpl . Xd . Xf . Xs . Xt . Y . addReaction . as.data.frame.dMod . as.data.frame.eqnlist . as.eqnvec . as.eventlist . asjlist . as.parframe . as.parvec.parframe . attrs . blockdiagSymb . combine . compare . compile . confint.parframe . conservedQuantities . constraintExp2 . constraintL2 . controls . coordTransform . covariates . datalist . datapointL2 . define . dot . eqnlist . eqnvec . eventlist . expand.grid.alt . fitErrorModel . forcingsSymb . format.eqnvec . funC0 . getCoefficients . getConditions . getDerivs . getEquations . getFluxes . getLocalDLLs . getObservables . getParameters . getReactions . ggopen . grapes-.-times-grapes . jakstat . lbind . load.parlist . loadDLL . long2wide . lsdMod . match.fnargs . mname . modelname . msParframe . mstrust . nll . normL2 . nullZ . objframe . objlist . obsfn . odemodel . parfn . parframe . parlist . parvec . plot.datalist . plot.parlist . plotCombined . plotData . plotFluxes . plotPars . plotPaths . plotPrediction . plotProfile . plotResiduals . plotValues . plus-.datalist . plus-.fn . plus-jfn . plus-jlist . prdfn . prdframe . prdlist . predict.prdfn . print.eqnlist . print.eqnvec . print.parfn . print.parvec . print0 . priorL2 . profile . progressBar . reduceReplicates . repar . res . resolveRecurrence . rref . scale_color_dMod . scale_fill_dMod . stat.parlist . steadyStates . strelide . strpad . submatrix . subset.eqnlist . summary.eqnvec . symmetryDetection . theme_dMod . times-.fn . trust . unique.parframe . wide2long.data.frame . wide2long.list . wide2long.matrix . wide2long . write.eqnlist . wrss . 
Some associated R codes: classes.R . dMod.R . data.R . dataClass.R . eqnClass.R . eventClass.R . objClass.R . odeClass.R . parClass.R . parameters.R . plots.R . prdClass.R . prediction.R . statistics.R . steadyStates.R . strings.R . symbolics.R . symmetryDetection.R . tools.R . trust.R . trustL1.R .  Full dMod package functions and examples
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