portalcasting v0.55.0

Reorganizing the app pointing

• Now having a single app.R file in the top level of the directory simplifies the issue around where the files are for the app
• This replaces the global.R, ui.R, and server.R files

portalcasting v0.54.0

Adding sandbox and production version of update_ functions.

Adding Pat as an author

Pointing the dockerfile to the current build SHA

• Previously, we were using default settings for remotes::install_github, which actually points to HEAD, when testing the build and push for the docker action. that was fine (although not great) when we were only running that action on tagged version releases, as the main branch was typically up-to-date with the tag and such, but this isn't exact and it also means any testing of the build on a PR was actually still grabbing from main, which is not what we want.
• We now use the SHA for the specific event that triggers the build by passing it into the docker file as an ARG

portalcasting v0.53.0

Removing temporary patch for backwards compatibility

portalcasting v0.52.0

Patching evaluations issues

• The table was too big as was for github standard, so removing columns of repeated content that can be grabbed from metadata

portalcasting v0.51.1

minor patches to deal with pkgdown site building

portalcasting v0.51.0

Major updates to pkgdown site

• Shift to bootstrap 5

Include CI tests of \dontrun examples and eval=FALSE vignettes

• Because of the long run time of some of the code, we wrap most documentation examples and vignette code in a way to prevent evaluation in real-time. As a result, much of the documentation code isn't run and therefore would not break builds if it would error.
• To address this, we add two scripts in the new inst/extra_testing folder and a github action runner for each.

Added CITATION file

• Cites the JOSS paper.

Bringing the app code into the package

• Improves robustness of building the app (includes code and dependencies in the docker image, allows for unit testing app components, etc.)
• Also allows users to spin-up a local version with run_web_app() pointed to main

Using arrow to speed up reading and writing files

Evaluation figures now read from evaluations file

• Avoids computing evaluations while generating plots

Elimination of model-named functions

• The models are now implemented using cast on their fit and cast elements in their control lists
• Only models the need new functions have them (meta_tsglm and fit_runjags) for fitting
• forecast method used generally now for cast function
  • introduction of forecast methods for tsglm and runjags objects

Shifting covariates to a daily-level build initial step

• need to shift this to level daily so we can manage when a newmoon is split between historic and forecast days

Putting species under dataset in the models' controls lists

• This is more articulated and allows for finer control to help avoid fitting issues, etc.

Moving arguments into functionalities

• cast_date is not an argument anymore, just filled automatically
• dataset arguments are also being removed as possible to streamline (just pull from model controls)

Model functions are now species-level

• To facilitate a lot of downstream functionality, we're breaking up the model functions to operate on the species-level rather than the dataset-level, according to the new control lists
• Species that were failing the nb GARCH models (s or not) have been removed, since that throws a warning and then fits a Poisson version, and we are now fitting Poisson versions of everyone.

process_model_output replaces save_cast_output and various model processing bits

• provides a much more general way to produce a forecast that can be integrated in the system, leveraging the metadata files

casts metadata table includes new column

• species
• to facilitate backwards compatibility, filled with NA for previous tables if missing when loaded

updates to prefab models to 13 time steps forward (addressing issue 297)

• pevGARCH, nbGARCH, nbsGARCH all get past_mean set to 13
• all models set with lead_time of 13

new models

• sAutoArima
• sNaiveArima
• pGARCH
• psGARCH

new functions

• update_dir is an "update-flavored" setup function

scoring

• log and crps!

portalcasting v0.50.0

Update prefab_model_controls.yaml

• including a nicer print_name for rendering the model texts

portalcasting v0.49.0

Added a clearing out step to fill_data

Updated download climate forecasts to check for version pre-updates

portalcasting v0.48.0

Settings updates to avoid redownloading archive

• settings overwrite is now FALSE by default to manage the version match decision making
• the directory resources portalpredictions version is updated to be the correct value ("latest"; was NULL)
• the overwrite setting is temporarily removed from the file saving functions to prevent argument name confusion
• we need to have an external location of file version to compare

Fixing jags model inits values

• Model values were not facilitating good chain mixing, updated now

More transitions from moons to newmoons to align naming

portalcasting v0.47.0

Patching error in cast metadata output for jags models

• Multiple models had the jags_logistic_covariates name being used in the metadata output when that was not correct.