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tagtools

This repository contains an R package with the R version of the animaltag tool kit. 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).

Installation

You can install the current CRAN version of tagtools with:

install.packages("tagtools")

You can install the development version of tagtools from GitHub with:

# install.packages("devtools")
devtools::install_github("animaltags/tagtools_r")

Further background

Documentation and vignettes are available at: https://animaltags.github.io/tagtools_r/

This material is based upon research supported by the United States Office of Naval Research under Award Number N00014-16-1-3089.

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Version

Install

install.packages('tagtools')

Monthly Downloads

175

Version

0.3.0

License

GPL (>= 3)

Homepage

https://animaltags.org

Maintainer

Stacy DeRuiter

Last Published

December 18th, 2025

Functions in tagtools (0.3.0)

Convolution (in C++)

Complementary filtering of a signal.

Make a rotation (or direction cosine) matrix

Delay-free filtering

Detect peaks in signal vector data

Compute summary statistics for dives or flights

hilbert_transform

Return the Hilbert transform of a signal

Find matching researcher in a list of known tag researchers

Find matching species in a list of marine mammals

Plot coloured line(s) in 3 dimensions with plot_ly

Reduce the sampling rate

Decimate sampling rate recursively.

Extract a sub-sample of data

Simple horizontal dead-reckoned track

Integrate track with reference positions

Identify invariant axis in triaxial movement measurements.

Convert between dates and Julian day numbers.

Buffers a signal vector into matrix

Load a tag dataset from a netCDF file.

Set of sensor lists for a 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.

Convert latitude-longitude track points into a local level frame

Interactive data cropping tool.

Make an info structure with tag metadata

Compute the row-wise vector norm

Plot a spectrogram with default settings

Predict the tag position on a diving animal from depth and acceleration data

Compute field intensity of tag acceleration and magnetometer data.

Extract multiple sub-samples of data

Find time cues for dives

Estimate the vertical velocity

Convert depth to pressure

Estimate scale factors and offsets

Decompose a rotation (or direction cosine) matrix

Predict the tag position on a diving animal from depth and acceleration data

Plot an image with an irregular grid.

Compute tortuosity index

Estimate the forward speed

tagtools-package

Undo calibrations steps

Read a CSV file with sensor data from a CATS tag

Reconstruct a track from pitch, heading and depth data, given a starting position

Draw time axis on plott plot.

Reduce the time span of a dataset

mean_absorption

Calculate the mean absorption in salt water

Computes the nth-order median filter

Low pass filter a time series

Sound speed estimation

Deduce the calibration constants

Heading from accelerometer and magnetometer data

Estimate the inclination angle

Estimate the offset in each axis

Correct a depth or altitude profile

Interpolate regularly sampled data to increase its sampling rate and match its length to another variable.

Estimate the dominant stroke frequency

Estimate simple dead-reckoned track

Compute the norm-jerk

Save a tag dataset to a netCDF file.

Read CATS csv data file(s) and convert to .nc

Tag-frame to animal-frame conversion

Generate a sensor structure from a sensor data vector or matrix.

speed_from_depth

Estimate the forward speed of a diving animal

Compute the spectrum level of a signal x.

plott_static_panel

Helper function for plott

Plot tag data time series

Calculate Mahalanobis distance

Remove NAs from sensor data and return indices of (rows of) filled values

Carry out a rotation randomization test.

Rotate triaxial vector measurements

Find zero-crossings in a vector

metadata_editor

Edits a html file from given csv.

Merge the fields of two lists

Plot tag data time series

Compute autocorrelation function

Compute RMS of sample blocks

Implement a calibration on tag sensor data

Pitch and roll from acceleration

Calculates the absorption coefficient for sound in seawater

Save an item to a NetCDF or add one tag sensor or metadata variable to a NetCDF archive file.

Set of sensor lists for a beaked_whale

Calculate total acceleration

Generate the cardinal axes of an animal

Compute mean of sample blocks

Reduce the time span of data

Add colored line segments to a plot

Read tag metadata from csv