NEWS.md

In jtimonen/odemodeling: Building, fitting, and validating Bayesian ODE models in 'Stan'

Version 0.2

odemodeling 0.2.2

• Improves documentation.
• Exports example_ode_model().

odemodeling 0.2.0

• Adds the $diagnose() method for the OdeModel class.
• Stores the results of diagnose and stansummaryin the OdeModelMCMC class instances.

Version 0.1

odemodeling 0.1.0

• Exposes the $reliability() method for the OdeModelMCMC class. Adds a recompute_loglik argument for it.
• Improves the tutorial vignette.
• A feature that is still missing is ability to create stan_transforms that both depend on the ODE solution AND have effect on model likelihood. This is because transformed parameters block is created so that the ODE solution is always second last and log likelihood last.

Early development versions

odemodeling 0.0.22

• Fixes the order of transformed parameters so that the ODE solution is always second last and log likelihood last.

odemodeling 0.0.21

• Fix a bug in plot_r_eff() which plotted the wrong metric.

odemodeling 0.0.20

• Edits the $reliability() method for the OdeModelMCMC class so that it only ever compares OdeModelGQ objects due to possible i/o information loss.

odemodeling 0.0.19

• Only internal improvements in tests.

odemodeling 0.0.18

• Adds plot_metric() and other plotting functions.

odemodeling 0.0.17

• Removes accidentally duplicated code and improves test coverage.

odemodeling 0.0.16

• Fixes the output of the $sample_manyconf() method of OdeModel class.
• Adds the compute_reliability_metrics() function.
• Adds an initial version of the $reliability() method for the OdeModelMCMC class.

odemodeling 0.0.15

• Adds more result extraction and plotting methods for OdeModelFits.
• Makes it easier to extract initial state y0 always in the same format, no matter if it is a parameter, data, or transformation.

odemodeling 0.0.14

• Includes lynxhare data.
• Adds Lotka-Volterra model to example models.

odemodeling 0.0.13

• Renames the $simulate() method to $gqs() and implement it also for OdeModel.
• Implements the useful $make_params() method for OdeModel.

odemodeling 0.0.12

• Changes data vector y0 to vector y0 in ODE solver function signatures so it is possible to have initial state be parameter.
• Adds the name argument to example_ode_model() and adds the tmdd example.

odemodeling 0.0.11

• Simplifies and makes stan_param() and stan_transform() less vulnerable to errors.
• With ode_model(), it is now possible to create also a model where odefun_vars and loglik_vars are empty lists.

odemodeling 0.0.10

• Includes ode_model() for creating models.
• Includes stan_var(), stan_param() etc. for model specification.
• Includes rk45(), bdf(), midpoint(), rk4() etc. for solver specification.
• Includes the OdeModel and OdeModelMCMC and OdeModelGQ R6 classes.
• Implements parameter sampling via the $sample() method of the OdeModel class.
• Implements generating quantities with possibly different solver or solver configuration (the $simulate() method of OdeModelMCMC class)
• Implemented other useful methods of OdeModelMCMC and OdeModelGQ classes are for example $extract_unflattened(), $extract_odesol(), $plot_odesol(), $dim() and $dim_odesol().
• Implements some comparison functions between OdeModelMCMC and OdeModelGQ objects, such as log_ratios(), psis(), max_abs_odesol_diff() and max_abs_loglik_diff().

jtimonen/odemodeling documentation built on Sept. 15, 2024, 4:29 a.m.