Chapter-ready release

Final changes to structure and vignettes as a result of going through everything to write the first draft of the package paper.

Structural changes:

• Removed the specific prior for ind_y_0 as that was double-counting the first observation in the likelihood. The parameter ind_y_0 is still estimated in the data, but does not get a direct prior and instead has its prior constructed through the y_hat vector as do the other sizes.
• Removed y_0_obs as passed data because it isn't used in the model once the prior for ind_y_0 was removed.
• Data assignment, data generation, and testing code had to be re-worked to account for the removal of y_0_obs.
• Added a function to plot sizes over time as well as the DE plot function.

Vignette changes:

• Added the Here Be Dragons vignette that investigates an interaction between errors in numerical methods in the longitudinal model and the MCMC sampling.
• Re-worded and re-structured other vignettes to take advantage of the new size over time function.
• Included a set of posterior estimates for the Canham demo because running the fit takes a few hours.

What's Changed

• Maths vignette by @Tess-LaCoil in #44
• Vignette fonti by @Tess-LaCoil in #46
• Here be dragons by @Tess-LaCoil in #45
• Added a function to plot sizes over time in parallel with the DE plot… by @Tess-LaCoil in #48
• Paper writing by @Tess-LaCoil in #50

Full Changelog: 1.0...1.1

Full release.

Release version with initial set of vignettes set up and ready for ESA.

New name, new models

Added new models: power law, von Bertalanffy, and a linear DE with more direct parameterisation and wider priors than the vB model.

Also changed the name from rmot to hmde - hierarchical methods for differential equations.

What's Changed

• Power model add by @Tess-LaCoil in #13
• Update readme by @Tess-LaCoil in #16
• Vb model add by @Tess-LaCoil in #18
• Add datasets by @Tess-LaCoil in #19
• Revert "Vb model add" by @Tess-LaCoil in #20
• Ignore generate c/cpp files by @dfalster in #22
• Reduce testing os by @dfalster in #23
• Vb model add by @Tess-LaCoil in #25
• Added linear DE by @Tess-LaCoil in #26
• Name change by @Tess-LaCoil in #27
• Changed capitalisation for some files. by @Tess-LaCoil in #28

New Contributors

• @dfalster made their first contribution in #22

Full Changelog: 0.0.0.920...0.1.0

Canham Models

Canham model add (#12)

Added Canham model files, ensured they worked properly, and changed the structure of model testing slightly to check what the data structures are named as well.

* Added Canham files and code.

* Added current branch to CI testing workflow.

* Removed branch from CI testing workflow.

* Changed Canham data generation process to have 10 observations per individual, and corrected an error in the intitial size controls.

* Changed mnormt requirement structure.

* Changed testing structure to have specific names be checked for each model, including constant. Changed helper function to better iterate over parameter names.

Constant model

Constant (#10)

Finalised the testing structure for models with single and multiple individuals, using the constant growth model as the test case. 
- Generating a dataset to be loaded with the model in the fixtures.
- Running the chosen model on the first individual in the simulated data and test that the parameter estimate converges to a reasonable value (with 0.1 of the true value)
- Running the chosen model on multiple individuals and tests whether the output samples are of the right size for the number of chains, iterations, and parameters.

* Notation (#5)

* Updated notation and function structure in the multi individual constant model file for consistency. Updated rmot_run, rmot_models to reflect the changes.

* Removed old constant stan file and cleared out references to it in stanmodels.R, rmot.rmd.

* Updated ignore to exclude compiled binaries.

* Cleared out .o and .so files.

* Added develop branch as a trigger for PR

---------

Co-authored-by: Fonti Kar <[email protected]>

* Added single ind const model, updated rmot_models, rmot_run, rmot vignette. Need to do test files yet.

* Updated the single individual constant model stan file and the testing code.

* Added some comments to the model testing script.

* Expending tests: testing run

* Reorganise if statements

* Rename file to linear

* Added unit testing of model output for linear data.

* Re-added testing structure.

* Found problem with unit testing for const model outputs: object y_single/y_multi in global environment not being seen within rmot_assign_data function.

* Added internal testing data so no data is created within test_that() functions, y_single and y_multi are not evaluated globally #1

* Added internal testing data so no data is created within test_that() functions, y_single and y_multi are not evaluated globally #1

* Skip snapshots on CI

* Updated snaps

* Removed snaps as a testing framework and using expect_equal #1

* Removed skip_on_ci #1

* Updating roxygen version and package doc

* Updated code to generate testing data

* Moved helper code in generating fake data, removed internal testing data

* Updated rmot_assign and tests passing I think

* Completed testing workflow

* Added filepath to saving rds and updated TO DO in assign_data

* Set tolerance

* Updated version for checkout

* Added constant data generation and tests based on model output summary for single and multiple individuals. Tests all complete dynamically and when run in the testing console.

* Init comit for constant branch

* Tess helper funcs

* Regenerate test data using stan seed method

* using rstan::extract instead of summary

* Added constant as trigger

* Moved unique code back to make_constant.R

* Changed test data generation and single- and multi-individual testing structures for constant model.

* Fixed linear regression model testing.

* Resolving issues raised in pull request review: changed the set-up of the constant model and removed reference to the constant branch from R-CMD-checn.yaml.

---------

Co-authored-by: Fonti Kar <[email protected]>
Co-authored-by: Daniel Falster <[email protected]>

Stan template

Basic structure for simple Stan R package