[WIP] v0.12.0

[juniperlsimonis]

portalcast updates model scripts according to controls_model

• Previously, if you changed any controls of a prefab model, you had to manually re-write the models using fill_models before running portalcast.
• Using fill_models would result in hand-made scripts being overwritted, so a specific function (update_models) for updating the models was created.
• update_models by default only updates the models listed in the controls_model input, to avoid overwriting model scripts. To change this behavior and also update all of the prefab models' scripts, set update_prefab_models = TRUE. This is particularly handy when changing a global (with respect to model scripts) argument: main, quiet, verbose, or arg_checks.
• addresses

Messaging around trying to use not-complete directory improved

• Indication now made that a component of the directory is missing and suggestion is made to run create_dir.
• addresses

Patching data set bug in plotting

• There was a bug with matching the interpolated to the non interpolated data sets within the ensembling, which has been fixed.
• addresses

Updated messaging

• Moved most of the messaging into tidied functions.

Changed behavior of prep_rodents_table and prep_rodents

• Now there is no start_moon argument, and all of the data prior to end_moon are returned.
• This aligns the rodents prep functions with the other (moons, covariates) prep functions.
• Facilitates use of data prior to start_moon in forecasting models (e.g., for distributions of starting state variables).
• Requires that model functions now explicitly trim the rodents table being used. This has been added to all prefab models.

Fixed codecov targets

• Previous targets were restrictively high due to earlier near-perfect coverage.
• A codecov.yml file is now included in the repo (and ignored for the R build) which sets the target arbitrarily at the still-quite-high-but-not-restrively-so 95%.
• It can be changed if needed in the future.

Simple EDM model added

• addresses

JAGS infrastructure added

• Using the runjags package, with extensive access to the API of run.jags via a control_runjags list (see runjags_control).
• Currently in place with a very simple random walk model.
• addresses

Prepared rodents table includes more content

• Expanded back in time to the start.
• Added effort columns (all default options in prefab_rodents_controls have effort = TRUE).

Updated adding a model and data vignette

• Added section at the end about just extending existing models to new data sets.
• addresses

[codecov]

Codecov Report

Merging #141 into master will decrease coverage by 0.05%.
The diff coverage is 97.15%.

@@            Coverage Diff             @@
##           master     #141      +/-   ##
==========================================
- Coverage   99.38%   99.32%   -0.06%     
==========================================
  Files          20       20              
  Lines        3070     3134      +64     
==========================================
+ Hits         3051     3113      +62     
- Misses         19       21       +2

Impacted Files	Coverage Δ
R/portalcast.R	100% <100%> (+2.27%)	⬆️
R/process_casts.R	99.47% <100%> (ø)	⬆️
R/fill_dir.R	100% <100%> (ø)	⬆️
R/setup_dir.R	100% <100%> (ø)	⬆️
R/prepare_models.R	99.56% <100%> (+0.03%)	⬆️
R/cast_covariates.R	100% <100%> (ø)	⬆️
R/download.R	99.36% <100%> (ø)	⬆️
R/ensembling.R	98.88% <100%> (-1.12%)	⬇️
R/prepare_rodents.R	99.55% <100%> (ø)	⬆️
R/utilities.R	99.14% <100%> (ø)	⬆️
... and 6 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update c66cc46...7f03411. Read the comment docs.