Package: fitode 0.1.1.9000

fitode: Tools for Ordinary Differential Equations Model Fitting

Methods and functions for fitting ordinary differential equations (ODE) model in 'R'. Sensitivity equations are used to compute the gradients of ODE trajectories with respect to underlying parameters, which in turn allows for more stable fitting. Other fitting methods, such as MCMC (Markov chain Monte Carlo), are also available.

Authors:Sang Woo Park [aut, cre], Ben Bolker [aut]

fitode_0.1.1.9000.tar.gz
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fitode_0.1.1.9000.tgz(r-4.4-any)fitode_0.1.1.9000.tgz(r-4.3-any)
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fitode.pdf |fitode.html✨
fitode/json (API)

# Install 'fitode' in R:
install.packages('fitode', repos = c('https://parksw3.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/parksw3/fitode/issues

Datasets:

On CRAN:

5.39 score 5 stars 31 scripts 141 downloads 24 exports 10 dependencies

Last updated 1 days agofrom:fa26ea2ccf. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macWARNINGOct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 30 2024

Exports:coefconfintdfundfun2EvalfitodefitodeMCMCgradhessianinitializejacobianlogLikode.solveodemodelplotpredictprofileshowsimulatestdErsummaryTransformupdatevcov

Dependencies:bbmlebdsmatrixcodaDerivdeSolvelatticeMASSMatrixmvtnormnumDeriv

Readme and manuals

Help Manual

Help pageTopics
Nicholson's blowfly datablowfly
Data from 1905 plague outbreak in Mumbai (formerly called Bombay)bombay
Extract model coefficients from fitode objectscoef,fitode-method coef.fitode
Extract model coefficients from fitodeMCMC objectscoef,fitodeMCMC-method coef.fitodeMCMC
Calculate confidence intervals from fitode objects for model parameters and their transformationsconfint,fitode-method confint.fitode
Calculate credible intervals from fitodeMCMC objects for model parameters and their transformationsconfint,fitodeMCMC-method confint.fitodeMCMC
Fit ordinary differential equations modelfitode
Class "fitode". Result of ode fitting based on Maximum Likelihood Estimationfitode-class
Fit ordinary differential equations model using MCMCfitodeMCMC
Class "fitodeMCMC". Result of ode fitting based on Markov Chain Monte Carlo (MCMC)fitodeMCMC-class
Constructor method of "odemodel" classinitialize,odemodel-method
Extract log-likelihoodlogLik,fitode-method logLik.fitode
Class representing log-likelihood models used to fit ode modelsloglik.ode-class
1918 Philadelphia flu data setphila1918
Internal function for plotting methodsplot_internal
Plot a fitode objectplot,fitode,missing-method plot,fitode-method plot.fitode
Plot a fitodeMCMC objectplot,fitodeMCMC,missing-method plot,fitodeMCMC-method
Prediction function for fitode objectspredict,fitode-method predict.fitode
Prediction function for fitodeMCMC objectspredict,fitodeMCMC-method predict.fitodeMCMC
Class representing prior models used to fit ode modelsprior.ode-class
Profile fitode objectsprofile,fitode-method profile.fitode
Data from 2014 Sierra Leone Ebola epidemicSierraLeone2014
Internal function for simulation modelssimulate_internal
simulate fitode objectssimulate,fitode-method
simulate model objectssimulate,odemodel-method
Extract standard error from fitode objectsstdEr,fitode-method stdEr.fitode
Extract standard error from fitodeMCMC objectsstdEr,fitodeMCMC-method stdEr.fitodeMCMC
Summarize fitode objectsummary,fitode-method summary.fitode
Summarize fitodeMCMC objectsummary,fitodeMCMC-method summary.fitodeMCMC
Tumor growth datatumorgrowth
Update fitode fitsupdate,fitode-method
Update fitodeMCMC fitsupdate,fitodeMCMC-method
Extract variance-covariance matrix from fitode objectsvcov,fitode-method vcov.fitode
Extract variance-covariance matrix from fitodeMCMC objectsvcov,fitodeMCMC-method vcov.fitodeMCMC