Package: tagtools 0.2.0

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]

tagtools_0.2.0.tar.gz
tagtools_0.2.0.tar.gz(r-4.5-noble)tagtools_0.2.0.tar.gz(r-4.4-noble)
tagtools_0.2.0.tgz(r-4.4-emscripten)tagtools_0.2.0.tgz(r-4.3-emscripten)
tagtools.pdf |tagtools.html✨
tagtools/json (API)
NEWS

# Installtagtools in R:

install.packages('tagtools',repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

beaked_whale - Set of sensor lists for a beaked_whale
harbor_seal - Set of sensor lists for a harbor seal

81 exports 1 stars 0.23 score 92 dependencies 199 downloads

Last updated 7 days agofrom:36cf7f72ee

Exports:a2pr absorption acc_wgs84 add_nc apply_cal block_acf block_mean block_rms body_axes buffer check_AM cline col_line3 comp_filt crop crop_all crop_to csv2struct decdc decz depth_rate depth2pressure detect_peaks dive_stats draw_axis dsf euler2rotmat extract extract_cues find_dives fir_nodelay fit_tracks fix_offset_3d fix_pressure hilbert_env hilbert_transform htrack image_irreg inclination interp_nan interp2length inv_axis julian_day lalo2llf load_nc m_dist m2h make_info make_specgram mean_absorption median_filter merge_fields metadata_editor msa njerk norm2 ocdr odba plott plott_base prh_predictor1 prh_predictor2 ptrack read_cats rotate_data rotate_vecs rotation_test rotmat2euler rough_cal_3d save_nc sens_struct smooth sound_speed spectrum_level speed_from_depth spherical_cal tag2animal tortuosity track3D undo_cal zero_crossings

Dependencies:askpass base64enc bit bit64 boot bslib cachem CircStats cli clipr colorspace cowplot cpp11 crayon crosstalk curl data.table digest dplyr evaluate fansi farver fastmap fontawesome fs generics ggplot2 glue gtable highr hms htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling later latex2exp lattice lazyeval lifecycle lubridate magrittr MASS matlab Matrix memoise mgcv mime munsell ncdf4 nlme openssl pillar pkgconfig plotly pracma prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readr rlang rmarkdown sass scales signal stringi stringr sys tibble tidyr tidyselect timechange tinytex tzdb utf8 vctrs viridisLite vroom withr xfun yaml zoo zoom

Help page	Topics
Pitch and roll from acceleration	a2pr
Calculates the absorption coefficient for sound in seawater	absorption
Calculate total acceleration	acc_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 data	apply_cal
Set of sensor lists for a beaked_whale	beaked_whale
Compute autocorrelation function	block_acf
Compute mean of sample blocks	block_mean
Compute RMS of sample blocks	block_rms
Generate the cardinal axes of an animal	body_axes
Buffers a signal vector into matrix	buffer
Compute field intensity of tag acceleration and magnetometer data.	check_AM
Add colored line segments to a plot	cline
Plot coloured line(s) in 3 dimensions with plot_ly	col_line3
Complementary filtering of a signal.	comp_filt
Interactive data cropping tool.	crop
Reduce the time span of a dataset	crop_all
Reduce the time span of data	crop_to
Read tag metadata from csv	csv2struct
Reduce the sampling rate	decdc
Decimate sampling rate recursively.	decz
Estimate the vertical velocity	depth_rate
Convert depth to pressure	depth2pressure
Detect peaks in signal vector data	detect_peaks
Compute summary statistics for dives or flights	dive_stats
Draw time axis on plott plot.	draw_axis
Estimate the dominant stroke frequency	dsf
Make a rotation (or direction cosine) matrix	euler2rotmat
Extract a sub-sample of data	extract
Extract multiple sub-samples of data	extract_cues
Find time cues for dives	find_dives
Delay-free filtering	fir_nodelay
Integrate track with reference positions	fit_tracks
Estimate the offset in each axis	fix_offset_3d
Correct a depth or altitude profile	fix_pressure
Find matching researcher in a list of known tag researchers	get_researcher
Find matching species in a list of marine mammals	get_species
Set of sensor lists for a harbor seal	harbor_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 signal	hilbert_transform
Simple horizontal dead-reckoned track	htrack
Plot an image with an irregular grid.	image_irreg
Estimate the inclination angle	inclination
Remove NAs from sensor data and return indices of (rows of) filled values	interp_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 frame	lalo2llf
Load a tag dataset from a netCDF file.	load_nc
Calculate Mahalanobis distance	m_dist
Heading from accelerometer and magnetometer data	m2h
Make an info structure with tag metadata	make_info
Plot a spectrogram with default settings	make_specgram
Calculate the mean absorption in salt water	mean_absorption
Computes the nth-order median filter	median_filter
Merge the fields of two lists	merge_fields
Edits a html file from given csv.	metadata_editor
Compute MSA	msa
Compute the norm-jerk	njerk
Compute the row-wise vector norm	norm2
Estimate the forward speed	ocdr
Compute ODBA	odba
Plot tag data time series	plott
Plot tag data time series	plott_base
Helper function for plott	plott_static_panel
Predict the tag position on a diving animal from depth and acceleration data	prh_predictor1
Predict the tag position on a diving animal from depth and acceleration data	prh_predictor2
Estimate simple dead-reckoned track	ptrack
Read a CATS data file and convert to .nc	read_cats
Read a CSV file with sensor data from a CATS tag	read_cats_csv
Rotate data.	rotate_data
Rotate triaxial vector measurements	rotate_vecs
Carry out a rotation randomization test.	rotation_test
Decompose a rotation (or direction cosine) matrix	rotmat2euler
Estimate scale factors and offsets	rough_cal_3d
Save a tag dataset to a netCDF file.	save_nc
Generate a sensor structure from a sensor data vector or matrix.	sens_struct
Low pass filter a time series	smooth
Sound speed estimation	sound_speed
Compute the spectrum level of a signal x.	spectrum_level
Estimate the forward speed of a diving animal	speed_from_depth
Deduce the calibration constants	spherical_cal
Tag-frame to animal-frame conversion	tag2animal
Measure tortuosity index	tortuosity
Reconstruct a track from pitch, heading and depth data, given a starting position	track3D
Undo calibrations steps	undo_cal
Find zero-crossings in a vector	zero_crossings

Package: tagtools 0.2.0

tagtools:Work with Data from High-Resolution Biologging Tags

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)