All functions

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()`

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

getDatTmb()

Get data for input to TMB

getInits()

Get inits for use in TMB

getInp()

Get prepared inp-object for use in TMB-call

getInpParams()

Get parameters for this specific data set

getInpSync()

Get object inp for synchronization

getParams()

Get params-list for use in TMB

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

hald

Test data from Lake Hald, Denmark

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()

Prepare detections data.table from raw data - csv-files exported from vendor software

runYaps() runTmb()

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

simTOP()

Simulate time of pings (Internal function)

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