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| 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 |