Changelog

Source: NEWS.md

yaps v1.2.2

New stuff

  • 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…

Bug fixes

  • 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’.

yaps v1.2.0.9111

New stuff

  • 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 to see yaps in action.

Minor new stuff

  • 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

Bug fixes

  • Fix bug in prepDetections(). Thanks to Hugh Pederson for reporting it.

yaps v1.2.0.9110

New stuff

  • Add support for using pressure sensor data as z-values in track estimation
  • Add function alignBurstSeq() - aligns detection data with known burst sequence
  • Add option to use stationary ref tags as beacons/sync tags without hydro
  • Add testYaps() - function to test that everything is running as expected

Minor new stuff

  • 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

Bug fixes

  • Fixed bug in getToaYaps() when is.na(eposync) == TRUE
  • Add option to ignore extreme values when plotting plotSyncModelCheck()
  • Fix issue with sync_model extrapolating eposync beyond period
  • Relax initial ss and put gentle constraint on rest ss
  • Fix bug in on Attach()