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fitode: Fitting ordinary differential equations (ODE) models in R

devtools::install_github("parksw3/fitode")

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Version

Install

install.packages('fitode')

Monthly Downloads

39

Version

0.1.1

License

GPL (>= 2)

Maintainer

Sang Woo Park

Last Published

October 29th, 2022

Functions in fitode (0.1.1)

Eval,loglik.ode-method

Evaluate the log-likelihood model

Apply link functions to model parameters

coef,fitodeMCMC-method

Extract model coefficients from fitodeMCMC objects

logLik,fitode-method

Extract log-likelihood

coef,fitode-method

Extract model coefficients from fitode objects

predict,fitodeMCMC-method

Prediction function for fitodeMCMC objects

summary,fitodeMCMC-method

Summarize fitodeMCMC object

prior.ode-class

Class representing prior models used to fit ode models

Transform,odemodel-method

Transform the model

S4 generic for transforming an object

Tumor growth data

Nicholson's blowfly data

Transform,prior.ode-method

Transform the prior model

S4 generic for computing a jacobian

S4 generic for evaluating an object

SierraLeone2014

Data from 2014 Sierra Leone Ebola epidemic

Class "fitode". Result of ode fitting based on Maximum Likelihood Estimation

Transform,loglik.ode-method

Transform the model

Fit ordinary differential equations model

profile,fitode-method

Profile fitode objects

S4 generic for computing a hessian

ode.sensitivity

Calculate the derivative of the mean expression

Make a list containing log prior density and its gradient

Check link functions

initialize,loglik.ode-method

The initializer for loglik.ode

fitodeMCMC-class

Class "fitodeMCMC". Result of ode fitting based on Markov Chain Monte Carlo (MCMC)

simulate,fitode-method

simulate fitode objects

Select a log-likelihood model

show,odemodel-method

Fit ordinary differential equations model using MCMC

Taylor expansion of digamma(a+b) for a>>b

confint,fitode-method

Calculate confidence intervals from fitode objects for model parameters and their transformations

Taylor expansion of trigamma(a+b) (?) for a>>b

grad,odemodel-method

Evaluate the gradients of a model

S4 generic for computing a gradient

confint,fitodeMCMC-method

Calculate credible intervals from fitodeMCMC objects for model parameters and their transformations

logLik.sensitivity

Calculate the derivative of the log-likelihood function

loglik.ode-class

Class representing log-likelihood models used to fit ode models

initialize,solution.ode-method

Constructor for solution.ode class

jacobian,odemodel-method

Evaluate the jacobian of the gradients

Internal function for plotting methods

initialize,odemodel-method

Constructor method of "odemodel" class

initialize,prior.ode-method

the initializer for prior.ode

plot,fitode,missing-method

Plot a fitode object

plot,fitodeMCMC,missing-method

Plot a fitodeMCMC object

vcov,fitode-method

Extract variance-covariance matrix from fitode objects

show,fitodeMCMC-method

Show fitodeMCMC object

solution.ode-class

Class "solution.ode". Result of solving ode modeld with/without sensitivity equations

stdEr,fitode-method

Extract standard error from fitode objects

vcov,fitodeMCMC-method

Extract variance-covariance matrix from fitodeMCMC objects

show,fitode-method

Show fitode objects

Fix parameters of an ODE model

predict,fitode-method

Prediction function for fitode objects

solve ode models

grad,loglik.ode-method

Evaluate the gradient of a likelihood model

summary,fitode-method

Summarize fitode object

stdEr,fitodeMCMC-method

Extract standard error from fitodeMCMC objects

simulate,odemodel-method

simulate model objects

Set up link functions for model parameters

update,fitode-method

Update fitode fits

simulate_internal

Internal function for simulation models

update,fitodeMCMC-method

Update fitodeMCMC fits

Class "odemodel" representing ode models

Select a prior model