# Work with Data from High-Resolution Biologging Tags

## Documentation for package ‘tagtools’ version 0.3.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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.
conv_cpp | Convolution (in C++)
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 CATS csv data file(s) 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 | Compute 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