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tagtools

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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

187

Version

0.2.0

License

GPL (>= 3)

Homepage

<https://animaltags.org>

Maintainer

Stacy DeRuiter

Last Published

June 28th, 2024

Functions in tagtools (0.2.0)

Estimate the dominant stroke frequency

Decimate sampling rate recursively.

Convert depth to pressure

Estimate the vertical velocity

Detect peaks in signal vector data

Estimate the offset in each axis

Find matching researcher in a list of known tag researchers

Integrate track with reference positions

Correct a depth or altitude profile

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_transform

Return the Hilbert transform of a signal

Extract a sub-sample of data

Extract multiple sub-samples of data

Find matching species in a list of marine mammals

Set of sensor lists for a harbor seal

Heading from accelerometer and magnetometer data

Draw time axis on plott plot.

Delay-free filtering

Reduce the sampling rate

Find time cues for dives

Compute summary statistics for dives or flights

Make a rotation (or direction cosine) matrix

Load a tag dataset from a netCDF file.

Compute the norm-jerk

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

Convert between dates and Julian day numbers.

Convert latitude-longitude track points into a local level frame

Compute the row-wise vector norm

Identify invariant axis in triaxial movement measurements.

Calculate Mahalanobis distance

Make an info structure with tag metadata

Simple horizontal dead-reckoned track

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

Estimate the inclination angle

Computes the nth-order median filter

Read a CATS data file and convert to .nc

Read a CSV file with sensor data from a CATS tag

metadata_editor

Edits a html file from given csv.

plott_static_panel

Helper function for plott

Low pass filter a time series

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

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

Decompose a rotation (or direction cosine) matrix

Carry out a rotation randomization test.

Rotate triaxial vector measurements

mean_absorption

Calculate the mean absorption in salt water

Estimate the forward speed

Save a tag dataset to a netCDF file.

Plot tag data time series

Plot a spectrogram with default settings

Plot an image with an irregular grid.

Estimate scale factors and offsets

Plot tag data time series

Merge the fields of two lists

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

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

Undo calibrations steps

Tag-frame to animal-frame conversion

Estimate simple dead-reckoned track

Deduce the calibration constants

speed_from_depth

Estimate the forward speed of a diving animal

Sound speed estimation

Measure tortuosity index

Compute the spectrum level of a signal x.

Find zero-crossings in a vector

Calculates the absorption coefficient for sound in seawater

Pitch and roll from acceleration

Implement a calibration on tag sensor data

Compute autocorrelation function

Calculate total acceleration

Compute RMS of sample blocks

Set of sensor lists for a beaked_whale

Generate the cardinal axes of an animal

Compute mean of sample blocks

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

Interactive data cropping tool.

Compute field intensity of tag acceleration and magnetometer data.

Reduce the time span of data

Reduce the time span of a dataset

Add colored line segments to a plot

Complementary filtering of a signal.

Read tag metadata from csv

Buffers a signal vector into matrix

Plot coloured line(s) in 3 dimensions with plot_ly