├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENCE ├── NAMESPACE ├── NEWS.md ├── R ├── classes-fit.R ├── classes-model.R ├── classes-solver.R ├── classes-standecl.R ├── main-declarations.R ├── main-examples.R ├── main-functions.R ├── main-model.R ├── main-plot.R ├── main-solvers.R ├── odemodeling-package.R ├── utils-create_input.R ├── utils-misc.R ├── utils-stancode.R ├── utils-standecl.R └── zzz.R ├── README.md ├── data-raw └── lynxhare.R ├── data └── lynxhare.rda ├── dev ├── covr.R ├── exports.R ├── lint.R └── style.R ├── inst ├── CITATION └── template_functions.stan ├── man ├── AdaptiveOdeSolver.Rd ├── FixedNumStepsOdeSolver.Rd ├── OdeModel.Rd ├── OdeModelFit.Rd ├── OdeModelGQ.Rd ├── OdeModelMCMC.Rd ├── OdeSolver.Rd ├── StanArray.Rd ├── StanDeclaration.Rd ├── StanDimension.Rd ├── StanMatrix.Rd ├── StanParameter.Rd ├── StanTransformation.Rd ├── StanVariable.Rd ├── StanVector.Rd ├── StanVectorArray.Rd ├── compare_odefits.Rd ├── example_ode_model.Rd ├── lynxhare.Rd ├── ode_model.Rd ├── odemodeling-package.Rd ├── odesolvers.Rd ├── odesolvers_lists.Rd ├── plot_metric.Rd ├── stan_array.Rd ├── stan_dim.Rd ├── stan_matrix.Rd ├── stan_param.Rd ├── stan_transform.Rd ├── stan_var.Rd ├── stan_vector.Rd └── stan_vector_array.Rd ├── odemodeling.Rproj ├── tests ├── testthat.R └── testthat │ ├── test-classes-model.R │ ├── test-main-model.R │ ├── test-main-solvers.R │ ├── test-main_declarations.R │ ├── test-utils-stancode.R │ ├── test-workflow-gsir.R │ ├── test-workflow-lv.R │ └── test-workflow-tmdd.R └── vignettes ├── .gitignore └── tutorial.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jtimonen/odemodeling/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jtimonen/odemodeling/HEAD/.gitignore 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