Function reference • tagtools

All functions

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

m_dist(): Calculate Mahalanobis distance

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

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