# Track Estimation using YAPS (Yet Another Positioning Solver)

## Documentation for package ‘yaps’ version 1.2.5

- DESCRIPTION file.

## Help Pages

alignBurstSeq | Align synced data with known burst sequence
applySync | Apply sync model to toa matrix to obtain synced data
checkInp | Check consistency of 'inp' object obtained from 'getInp()'
checkInpSync | Check consistency of 'inp_sync' object obtained from 'getInpSync()'
dat_align | Example data for showcasing yaps function alignBurstSeq()
fineTuneSyncModel | Fine-tune an already fitted sync_model Wrapper function to re-run getSyncModel() using the same data, but excluding outliers. Note dimensions of data might change if eps_threshold results in empty rows in the TOA-matrix.
getBbox | Get a standard bounding box to impose spatial constraints
getInp | Get prepared inp-object for use in TMB-call
getInpSync | Get object inp for synchronization
getSyncCoverage | Quick overview to check if all hydros have enough data within each offset period.
getSyncModel | Get sync model from inp_sync object obtained by 'getInpSync()'
getToaYaps | Build TOA matrix from synced data.table - also do some pre-filtering of severe MP, pruning loose ends etc
plotBbox | Graphical representation of spatial constraints
plotSyncModelCheck | Plot to check how well the sync model is working
plotSyncModelHydros | Plot hydrophone positions. Especially useful if some hydro re-positioned as part of the sync model.
plotSyncModelResids | Plot residuals of sync_model to enable check of model
plotYaps | Basic plots of yaps output
prepDetections | Experimental! Prepare detections data.table from raw data - csv-files exported from vendor software
runTmb | Function to run TMB to estimate track
runYaps | Function to run TMB to estimate track
simHydros | Sim hydrophone array configuration
simTelemetryTrack | Simulate telemetry track based on known true track obtained using simTrueTrack
simToa | Sim TOA matrix for the supplied telemetryTrack
simTrueTrack | Simulate a known movement track for subsequent estimation using YAPS
ssu1 | Test data from Florida Bay
tempToSs | Calculate speed of sound from water temperature, salinity and depth Based on H. Medwin (1975) Speed of sound in water: A simple equation for realistic parameters. (https://doi.org/10.1121/1.380790)
testYaps | Test YAPS core functionality