Package: yaps 1.2.5

Henrik Baktoft

yaps: Track Estimation using YAPS (Yet Another Positioning Solver)

Estimate tracks of animals tagged with acoustic transmitters. 'yaps' was introduced in 2017 as a transparent open-source tool to estimate positions of fish (and other aquatic animals) tagged with acoustic transmitters. Based on registrations of acoustic transmitters on hydrophones positioned in a fixed array, 'yaps' enables users to synchronize the collected data (i.e. correcting for drift in the internal clocks of the hydrophones/receivers) and subsequently to estimate tracks of the tagged animals. The paper introducing 'yaps' is available in open access at Baktoft, Gjelland, Økland & Thygesen (2017) <doi:10.1038/s41598-017-14278-z>. Also check out our cookbook with a completely worked through example at Baktoft, Gjelland, Økland, Rehage, Rodemann, Corujo, Viadero & Thygesen (2019) <doi:10.1101/2019.12.16.877688>. Additional tutorials will eventually make their way onto the project website at <https://baktoft.github.io/yaps/>.

Authors:Henrik Baktoft [cre, aut], Karl Gjelland [aut], Uffe H. Thygesen [aut], Finn Økland [aut]

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yaps.pdf |yaps.html✨
yaps/json (API)
NEWS

# Install 'yaps' in R:
install.packages('yaps', repos = c('https://mhpob.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/baktoft/yaps/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • dat_align - Example data for showcasing yaps function alignBurstSeq
  • ssu1 - Test data from Florida Bay

On CRAN:

4.09 score 19 stars 65 scripts 24 downloads 25 exports 46 dependencies

Last updated 1 years agofrom:ed315f92f4. Checks:OK: 1 ERROR: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-win-x86_64ERROROct 15 2024
R-4.5-linux-x86_64ERROROct 15 2024
R-4.4-win-x86_64ERRORNov 16 2024
R-4.4-mac-x86_64ERRORNov 16 2024
R-4.4-mac-aarch64ERRORNov 16 2024
R-4.3-win-x86_64ERRORNov 16 2024
R-4.3-mac-x86_64ERRORNov 16 2024
R-4.3-mac-aarch64ERRORNov 16 2024

Exports:alignBurstSeqapplySynccheckInpcheckInpSyncfineTuneSyncModelgetBboxgetInpgetInpSyncgetSyncCoveragegetSyncModelgetToaYapsplotBboxplotSyncModelCheckplotSyncModelHydrosplotSyncModelResidsplotYapsprepDetectionsrunTmbrunYapssimHydrossimTelemetryTracksimToasimTrueTracktempToSstestYaps

Dependencies:bootcircularclicolorspacecowplotdata.tablefansifarverggplot2ggrepelgluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmenloptrpillarpkgconfigplyrR6RColorBrewerRcppRcppEigenreshape2rlangscalesstringistringrtibbletictocTMButf8vctrsviridisviridisLitewithrzoo

Readme and manuals

Help Manual

Help pageTopics
Align synced data with known burst sequencealignBurstSeq
Apply sync model to toa matrix to obtain synced dataapplySync
Check consistency of 'inp' object obtained from 'getInp()'checkInp
Check consistency of 'inp_sync' object obtained from 'getInpSync()'checkInpSync
Example data for showcasing yaps function alignBurstSeq()dat_align
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.fineTuneSyncModel
Get a standard bounding box to impose spatial constraintsgetBbox
Get prepared inp-object for use in TMB-callgetInp
Get object inp for synchronizationgetInpSync
Quick overview to check if all hydros have enough data within each offset period.getSyncCoverage
Get sync model from inp_sync object obtained by 'getInpSync()'getSyncModel
Build TOA matrix from synced data.table - also do some pre-filtering of severe MP, pruning loose ends etcgetToaYaps
Graphical representation of spatial constraintsplotBbox
Plot to check how well the sync model is workingplotSyncModelCheck
Plot hydrophone positions. Especially useful if some hydro re-positioned as part of the sync model.plotSyncModelHydros
Plot residuals of sync_model to enable check of modelplotSyncModelResids
Basic plots of yaps outputplotYaps
Experimental! Prepare detections data.table from raw data - csv-files exported from vendor softwareprepDetections
Function to run TMB to estimate trackrunTmb runYaps
Sim hydrophone array configurationsimHydros
Simulate telemetry track based on known true track obtained using simTrueTracksimTelemetryTrack
Sim TOA matrix for the supplied telemetryTracksimToa
Simulate a known movement track for subsequent estimation using YAPSsimTrueTrack
Test data from Florida Bayssu1
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)tempToSs
Test YAPS core functionalitytestYaps