Package: tagtools 0.3.0

Stacy DeRuiter

tagtools: Work with Data from High-Resolution Biologging Tags

High-resolution movement-sensor tags typically include accelerometers to measure body posture and sudden movements or changes in speed, magnetometers to measure direction of travel, and pressure sensors to measure dive depth in aquatic or marine animals. The sensors in these tags usually sample many times per second. Some tags include sensors for speed, turning rate (gyroscopes), and sound. This package provides software tools to facilitate calibration, processing, and analysis of such data. Tools are provided for: data import/export; calibration (from raw data to calibrated data in scientific units); visualization (for example, multi-panel time-series plots); data processing (such as event detection, calculation of derived metrics like jerk and dynamic acceleration, dive detection, and dive parameter calculation); and statistical analysis (for example, track reconstruction, a rotation test, and Mahalanobis distance analysis).

Authors:Stacy DeRuiter [aut, cre, cph], Mark Johnson [aut, cph], David Sweeney [aut], Ye Joo McNamara-Oh [aut], Samuel Fynewever [aut], Racheal Tejevbo [aut], Tiago Marques [aut], Yuqian Wang [aut], Su Ogedegbe [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tagtools/json (API)

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

Bug tracker:https://github.com/animaltags/tagtools_r/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

Conda:

openblascppopenmp

5.90 score 10 stars 44 scripts 382 downloads 108 exports 17 dependencies

Last updated from:9b7bda5c05. Checks:12 OK, 3 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK141
linux-devel-x86_64OK225
source / vignettesOK199
linux-release-arm64OK124
linux-release-x86_64OK171
macos-release-arm64OK214
macos-release-x86_64OK450
macos-oldrel-arm64WARNING255
macos-oldrel-x86_64WARNING387
windows-devel-arm64OK374
windows-devel-x86_64OK198
windows-release-arm64OK361
windows-release-x86_64OK104
windows-oldrel-x86_64WARNING150
wasm-releaseOK113

Exports:a2prabsorptionacc_wgs84add_ncapply_calauto_cal_accblock_acfblock_meanblock_rmsblock_stdbody_axesbuffercheck_AMclinecol_line3comp_filtconv_cppcropcrop_allcrop_tocsv2structdecdcdeczdeglitchdepth_ratedepth2pressuredetect_peaksdive_statsdo_caldraw_axisdsfeuler2rotmatextractextract_cuesfind_divesfir_nodelayfit_tracksfix_offset_3dfix_offset_pressurefix_pressureget_brhilbert_envhilbert_transformhtrackimage_irreginclinationinterp_naninterp2lengthinv_axisjulian_daylalo2llfload_nclssolve3m_distm2hmake_infomake_specgrammean_absorptionmedian_filtermerge_fieldsmetadata_editormsanjerknorm2ocdrodbaplottplott_baseprh_predictor1prh_predictor2ptrackread_catsread_cats_csvread_smrtread_smrt_archiveread_smrt_gpsread_smrt_smremove_nanrotate_datarotate_vecsrotation_testrotmat2eulerrough_cal_3dsave_ncsens_spectrumsens_structsm_assemble_swvsm_ch_subsetsm_channelssm_cuetabsm_dir_checksm_fnamessm_get_calsm_get_configsm_parse_swvsm_xml_devidsmoothsound_archivesound_speedspectrum_levelspeed_from_depthspherical_calspherical_lstag2animaltortuositytrack3Dundo_calzero_crossings

Dependencies:clicpp11genericsgluegsignallifecyclelubridatemagrittrncdf4pracmaRcppRcppArmadillorlangstringistringrtimechangevctrs

Readme and manuals

Help Manual

Help pageTopics
Pitch and roll from accelerationa2pr
Calculates the absorption coefficient for sound in seawaterabsorption
Calculate total accelerationacc_wgs84
Save an item to a NetCDF or add one tag sensor or metadata variable to a NetCDF archive file.add_nc
Implement a calibration on tag sensor dataapply_cal do_cal
Data-driven calibration of triaxial accelerometer dataauto_cal_acc
Set of sensor lists for a beaked_whalebeaked_whale
Compute autocorrelation functionblock_acf
Compute mean of sample blocksblock_mean
Compute RMS of sample blocksblock_rms
Compute standard deviation of sample blocksblock_std
Generate the cardinal axes of an animalbody_axes
Buffers a signal vector into matrixbuffer
Compute field intensity of tag acceleration and magnetometer data.check_AM
Add colored line segments to a plotcline
Plot coloured line(s) in 3 dimensions with plot_lycol_line3
Complementary filtering of a signal.comp_filt
Convolution (in C++)conv_cpp
Interactive data cropping tool.crop
Reduce the time span of a datasetcrop_all
Reduce the time span of datacrop_to
Read tag metadata from csvcsv2struct
Reduce the sampling ratedecdc
Decimate sampling rate recursively.decz
Remove single-sample outliers from sensor data vectordeglitch
Estimate the vertical velocitydepth_rate
Convert depth to pressuredepth2pressure
Detect peaks in signal vector datadetect_peaks
Compute summary statistics for dives or flightsdive_stats
Draw time axis on plott plot.draw_axis
Estimate the dominant stroke frequencydsf
Make a rotation (or direction cosine) matrixeuler2rotmat
Extract a sub-sample of dataextract
Extract multiple sub-samples of dataextract_cues
Find time cues for divesfind_dives
Delay-free filteringfir_nodelay
Integrate track with reference positionsfit_tracks
Estimate the offset in each axisfix_offset_3d
Correct a depth or altitude profile for offsets caused by miscalibration and sensor drift.fix_offset_pressure
Correct a depth or altitude profilefix_pressure
Use magnetometer data to estimate the body rotations from cyclic locomotion movements.get_br
Find matching researcher in a list of known tag researchersget_researcher
Find matching species in a list of marine mammalsget_species
Set of sensor lists for a harbor sealharbor_seal
Compute the envelope of X using Hilbert transform. Compute the envelope of the signal matrix X using the Hilbert transform. To avoid long transforms, this function uses the overlap and add method.hilbert_env
Return the Hilbert transform of a signalhilbert_transform
Simple horizontal dead-reckoned trackhtrack
Plot an image with an irregular grid.image_irreg
Estimate the inclination angleinclination
Remove NAs from sensor data and return indices of (rows of) filled valuesinterp_nan
Interpolate regularly sampled data to increase its sampling rate and match its length to another variable.interp2length
Identify invariant axis in triaxial movement measurements.inv_axis
Convert between dates and Julian day numbers.julian_day
Convert latitude-longitude track points into a local level framelalo2llf
Load a tag dataset from a netCDF file.load_nc
Least-squares solver for 3-dimensional data-driven calibration of field sensors.lssolve3
Calculate Mahalanobis distancem_dist
Heading from accelerometer and magnetometer datam2h
Make an info structure with tag metadatamake_info
Plot a spectrogram with default settingsmake_specgram
Calculate the mean absorption in salt watermean_absorption
Computes the nth-order median filtermedian_filter
Merge the fields of two listsmerge_fields
Edits a html file from given csv.metadata_editor
Compute MSAmsa
Compute the norm-jerknjerk
Compute the row-wise vector normnorm2
Estimate the forward speedocdr
Compute ODBAodba
Plot tag data time seriesplott
Plot tag data time seriesplott_base
Helper function for plottplott_static_panel
Predict the tag position on a diving animal from depth and acceleration dataprh_predictor1
Predict the tag position on a diving animal from depth and acceleration dataprh_predictor2
Estimate simple dead-reckoned trackptrack
Read CATS csv data file(s) and convert to .ncread_cats
Read a CSV file with sensor data from a CATS tagread_cats_csv
Read SMRT tag data file(s) and convert to .ncread_smrt
Read SMRT tag data from Wildlife Computers board (Archive file) and return list of sensor data listsread_smrt_archive
Read SMRT tag GPS data file and return list of sensor data listsread_smrt_gps
Read SMRT tag data from SM board (.swv and .csv files) and return list of sensor data listsread_smrt_sm
Remove missing valuesremove_nan
Rotate data.rotate_data
Rotate triaxial vector measurementsrotate_vecs
Carry out a rotation randomization test.rotation_test
Decompose a rotation (or direction cosine) matrixrotmat2euler
Estimate scale factors and offsetsrough_cal_3d
Save a tag dataset to a netCDF file.save_nc
Spectrum level of a sensor time series, i.e., the amount of power per 1 Hz band.sens_spectrum
Generate a sensor structure from a sensor data vector or matrix.sens_struct
Assemble data from a series of swv files into sensor data listssm_assemble_swv
Subset sensor_defs data.frame to include only sensor channels in chsm_ch_subset
Get metadata about SM board / DTAG3 / DTAG4 sensor channelssm_channels
Get "cue tab" (information about file timing) for SM board wav or swv data filessm_cuetab
Check sm_dir input for formattingsm_dir_check
Get SMRT SM data file names, given a directory to search and a deployment IDsm_fnames
Get SMRT SM board sensor calibration info from xml file(s)sm_get_cal
Get SMRT SM board configuration info from xml file(s)sm_get_config
Read in one swv file from a SMRT tag's SM board, and integrate information about file timing and gapssm_parse_swv
Get SMRT tag device ID from xml file(s)sm_xml_devid
Low pass filter a time seriessmooth
Create a "sound archive" (SA) list for SMRT wav filessound_archive
Sound speed estimationsound_speed
Compute the spectrum level of a signal x.spectrum_level
Estimate the forward speed of a diving animalspeed_from_depth
Deduce the calibration constantsspherical_cal
Deduce the calibration constantsspherical_ls
Tag-frame to animal-frame conversiontag2animal
Compute tortuosity indextortuosity
Reconstruct a track from pitch, heading and depth data, given a starting positiontrack3D
Undo calibrations stepsundo_cal
Find zero-crossings in a vectorzero_crossings