Man pages for parksw3/fitode
Tools for Ordinary Differential Equations Model Fitting
| apply_link | Apply link functions to model parameters |
| blowfly | Nicholson's blowfly data |
| bombay | Data from 1905 plague outbreak in Mumbai (formerly called... |
| check_link | Check link functions |
| coef-fitodeMCMC-method | Extract model coefficients from fitodeMCMC objects |
| coef-fitode-method | Extract model coefficients from fitode objects |
| confint-fitodeMCMC-method | Calculate credible intervals from fitodeMCMC objects for... |
| confint-fitode-method | Calculate confidence intervals from fitode objects for model... |
| dfun | Taylor expansion of digamma(a+b) for a>>b |
| dfun2 | Taylor expansion of trigamma(a+b) (?) for a>>b |
| Eval | S4 generic for evaluating an object |
| Eval-loglik.ode-method | Evaluate the log-likelihood model |
| fitode | Fit ordinary differential equations model |
| fitode-class | Class "fitode". Result of ode fitting based on Maximum... |
| fitodeMCMC | Fit ordinary differential equations model using MCMC |
| fitodeMCMC-class | Class "fitodeMCMC". Result of ode fitting based on Markov... |
| fixpar | Fix parameters of an ODE model |
| grad | S4 generic for computing a gradient |
| grad-loglik.ode-method | Evaluate the gradient of a likelihood model |
| grad-odemodel-method | Evaluate the gradients of a model |
| hessian | S4 generic for computing a hessian |
| initialize-loglik.ode-method | The initializer for loglik.ode |
| initialize-odemodel-method | Constructor method of "odemodel" class |
| initialize-prior.ode-method | the initializer for prior.ode |
| initialize-solution.ode-method | Constructor for solution.ode class |
| jacobian | S4 generic for computing a jacobian |
| jacobian-odemodel-method | Evaluate the jacobian of the gradients |
| logLik-fitode-method | Extract log-likelihood |
| loglik.ode-class | Class representing log-likelihood models used to fit ode... |
| logLik.sensitivity | Calculate the derivative of the log-likelihood function |
| make_prior | Make a list containing log prior density and its gradient |
| odemodel-class | Class "odemodel" representing ode models |
| ode.sensitivity | Calculate the derivative of the mean expression |
| ode.solve | solve ode models |
| phila1918 | 1918 Philadelphia flu data set |
| plot-fitodeMCMC-missing-method | Plot a fitodeMCMC object |
| plot-fitode-missing-method | Plot a fitode object |
| plot_internal | Internal function for plotting methods |
| predict-fitodeMCMC-method | Prediction function for fitodeMCMC objects |
| predict-fitode-method | Prediction function for fitode objects |
| prior.ode-class | Class representing prior models used to fit ode models |
| profile-fitode-method | Profile fitode objects |
| select_model | Select a log-likelihood model |
| select_prior | Select a prior model |
| set_link | Set up link functions for model parameters |
| show-fitodeMCMC-method | Show fitodeMCMC object |
| show-fitode-method | Show fitode objects |
| show-odemodel-method | Show the model |
| SierraLeone2014 | Data from 2014 Sierra Leone Ebola epidemic |
| simulate-fitode-method | simulate fitode objects |
| simulate_internal | Internal function for simulation models |
| simulate-odemodel-method | simulate model objects |
| solution.de-class | Class "solution.ode". Result of solving ode modeld... |
| stdEr-fitodeMCMC-method | Extract standard error from fitodeMCMC objects |
| stdEr-fitode-method | Extract standard error from fitode objects |
| summary-fitodeMCMC-method | Summarize fitodeMCMC object |
| summary-fitode-method | Summarize fitode object |
| Transform | S4 generic for transforming an object |
| Transform-loglik.ode-method | Transform the model |
| Transform-odemodel-method | Transform the model |
| Transform-prior.ode-method | Transform the prior model |
| tumorgrowth | Tumor growth data |
| update-fitodeMCMC-method | Update fitodeMCMC fits |
| update-fitode-method | Update fitode fits |
| vcov-fitodeMCMC-method | Extract variance-covariance matrix from fitodeMCMC objects |
| vcov-fitode-method | Extract variance-covariance matrix from fitode objects |
