Release Chapter-ready release · traitecoevo/hmde

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