Work with Data from High-Resolution Biologging Tags

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Documentation for package ‘tagtools’ version 0.2.0

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a2pr Pitch and roll from acceleration
absorption Calculates the absorption coefficient for sound in seawater
acc_wgs84 Calculate total acceleration
add_nc Save an item to a NetCDF or add one tag sensor or metadata variable to a NetCDF archive file.
apply_cal Implement a calibration on tag sensor data
beaked_whale Set of sensor lists for a beaked_whale
block_acf Compute autocorrelation function
block_mean Compute mean of sample blocks
block_rms Compute RMS of sample blocks
body_axes Generate the cardinal axes of an animal
buffer Buffers a signal vector into matrix
check_AM Compute field intensity of tag acceleration and magnetometer data.
cline Add colored line segments to a plot
col_line3 Plot coloured line(s) in 3 dimensions with plot_ly
comp_filt Complementary filtering of a signal.
crop Interactive data cropping tool.
crop_all Reduce the time span of a dataset
crop_to Reduce the time span of data
csv2struct Read tag metadata from csv
decdc Reduce the sampling rate
decz Decimate sampling rate recursively.
depth2pressure Convert depth to pressure
depth_rate Estimate the vertical velocity
detect_peaks Detect peaks in signal vector data
dive_stats Compute summary statistics for dives or flights
draw_axis Draw time axis on plott plot.
dsf Estimate the dominant stroke frequency
euler2rotmat Make a rotation (or direction cosine) matrix
extract Extract a sub-sample of data
extract_cues Extract multiple sub-samples of data
find_dives Find time cues for dives
fir_nodelay Delay-free filtering
fit_tracks Integrate track with reference positions
fix_offset_3d Estimate the offset in each axis
fix_pressure Correct a depth or altitude profile
get_researcher Find matching researcher in a list of known tag researchers
get_species Find matching species in a list of marine mammals
harbor_seal Set of sensor lists for a harbor seal
hilbert_env 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
htrack Simple horizontal dead-reckoned track
image_irreg Plot an image with an irregular grid.
inclination Estimate the inclination angle
interp2length Interpolate regularly sampled data to increase its sampling rate and match its length to another variable.
interp_nan Remove NAs from sensor data and return indices of (rows of) filled values
inv_axis Identify invariant axis in triaxial movement measurements.
julian_day Convert between dates and Julian day numbers.
lalo2llf Convert latitude-longitude track points into a local level frame
load_nc Load a tag dataset from a netCDF file.
m2h Heading from accelerometer and magnetometer data
make_info Make an info structure with tag metadata
make_specgram Plot a spectrogram with default settings
mean_absorption Calculate the mean absorption in salt water
median_filter Computes the nth-order median filter
merge_fields Merge the fields of two lists
metadata_editor Edits a html file from given csv.
msa Compute MSA
m_dist Calculate Mahalanobis distance
njerk Compute the norm-jerk
norm2 Compute the row-wise vector norm
ocdr Estimate the forward speed
odba Compute ODBA
plott Plot tag data time series
plott_base Plot tag data time series
plott_static_panel Helper function for plott
prh_predictor1 Predict the tag position on a diving animal from depth and acceleration data
prh_predictor2 Predict the tag position on a diving animal from depth and acceleration data
ptrack Estimate simple dead-reckoned track
read_cats Read a CATS data file and convert to .nc
read_cats_csv Read a CSV file with sensor data from a CATS tag
rotate_data Rotate data.
rotate_vecs Rotate triaxial vector measurements
rotation_test Carry out a rotation randomization test.
rotmat2euler Decompose a rotation (or direction cosine) matrix
rough_cal_3d Estimate scale factors and offsets
save_nc Save a tag dataset to a netCDF file.
sens_struct Generate a sensor structure from a sensor data vector or matrix.
smooth Low pass filter a time series
sound_speed Sound speed estimation
spectrum_level Compute the spectrum level of a signal x.
speed_from_depth Estimate the forward speed of a diving animal
spherical_cal Deduce the calibration constants
tag2animal Tag-frame to animal-frame conversion
tortuosity Measure tortuosity index
track3D Reconstruct a track from pitch, heading and depth data, given a starting position
undo_cal Undo calibrations steps
zero_crossings Find zero-crossings in a vector