yaps v1.2.5

New stuff

Add support for ping_type = ‘sbi_doulbe’. Special case - needs carefull contrsuction of TOA-matrix.
More robustification of the optimizer.
More pre-flight checks to catch issues with inp.
Use separate diffusivity for Z when estimating 3D

Moved example data hald to an external package with yaps example data yapsdata. Available from github using devtools::install_github(‘baktoft/yapsdata’).
Lots of examples and tests added.

New site added to github pages intended to collect yaps-related resources, how-tos etc. (https://baktoft.github.io/yaps/)
Add first step-by-step tutorial to yaps pages
Add function to sequentially fine-tune sync model.
Add option to use speed of sound based on logged temperatur in the synchronisation process.
Add function to fine-tune sync_model based on residual threshold
Add plot to check temporal stability of sync_models. Try plotSyncModelResids(sync_model, by=‘temporal’)
Add option to impose spatial constraints (BBox only) and plot a visual of the constraint. Mainly used to constrain parameter space and increase speed and convergence.
Add various checks in checkInpSync()
Add option to use selective downsampling in getInpSync().
Add function to plot hydros from sync_model - usefull if hydros were re-positioned during getSyncModel().
Add option to estimate Z-dimension (depth) of tracks.
Add function to calucate speed of sound from water temperature, salinity and depth - tempToSs(temp, sal, depth).
Add github actions to hopefully ensure nothing breaks from now on…

Fix nasty bug in likelihood contribution of ToP-estimation when using random burst interval (ping_type = ‘rbi’)
Fix bug in getInpSync() - failed if sync_tag was only heard on own hydro
Eliminate estimation of log_sigma_hydros_xy in sync_model
Relax priors on SS in both track and sync model - consider to switch to softplus instead
Return plsd object from getSyncModel
Fix bug in getToaYaps() that allowed too short/too high BI to pass through when using ping_type=‘rbi’ and very fast transmitters
Fix bug in getToaYaps() that added to many empty pings when ping_type=‘sbi’.

Add option to use alternative optimization function (EXPERIMENTAL). Try nloptr() instead of default nlminb(), if you have issues with e.g. false convergence.
Add option to use linear correction information when running the sync model (EXPERIMENTAL).
Add option to specify all three ping types in testYaps(). PingType can be ‘sbi’ (default), ‘rbi’ or ‘pbi’
Not related to package development, but check out yaps-live https://baktoft.shinyapps.io/yapslive/ to see yaps in action.

Split cpp file into pingType, Edist and ss specifics. Make code more readable and eliminates the need for ‘diffuse priors’ on parameters.
Implement testthat functions to ensure future updates doesn’t break anything. Work in progress…
Update readMe.md

Add sync_model and known burst sequences to example data hald
Add extra plots to plotSyncModelCheck()
Improve diagnostic plots - now violins instead on boxplots
Add first version of checkInp(). More tests will be added to catch common mistakes
Added a NEWS.md file to track changes to the package
Make console output from runYaps() more user friendly - work in progress