Package: animovement 0.6.0

Mikkel Roald-Arbøl

animovement: An R toolbox for analysing animal movement across space and time

An R toolbox for analysing animal movement across space and time.

Authors:Mikkel Roald-Arbøl [aut, cre]

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animovement.pdf |animovement.html✨
animovement/json (API)
NEWS

# Install 'animovement' in R:
install.packages('animovement', repos = c('https://roaldarbol.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/roaldarbol/animovement/issues

Pkgdown site:https://www.roald-arboel.com

On CRAN:

animal-behaviouranimal-movementneuroethologyneuroscience

4.72 score 8 stars 8 scripts 70 exports 73 dependencies

Last updated 2 months agofrom:635e69978d. Checks:1 OK, 3 ERROR, 2 FAILURE, 2 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 02 2025
R-4.5-winNOTEFeb 02 2025
R-4.5-macERRORFeb 02 2025
R-4.5-linuxERRORFeb 02 2025
R-4.4-winNOTEFeb 02 2025
R-4.4-macERRORFeb 02 2025
R-4.3-winOUTDATEDDec 07 2024
R-4.3-macOUTDATEDDec 07 2024

Exports:add_centroidalign_timeseriescalculate_kinematicscalculate_speedcalculate_statisticscalculate_straightnesscheck_confidencecheck_na_gapsizecheck_na_timingcheck_poseclassify_by_stabilityclassify_by_thresholdclassify_high_periodsclassify_low_periodsdoes_file_have_expected_headersensure_file_has_expected_headersensure_file_has_headersfilter_highpassfilter_highpass_fftfilter_kalmanfilter_kalman_irregularfilter_lowpassfilter_lowpass_fftfilter_movementfilter_na_confidencefilter_na_roifilter_na_speedfilter_rollmeanfilter_rollmedianfilter_sgolayfind_lagfind_peaksfind_troughsget_example_dataget_metadataggplot_na_gapsizegroup_everyinit_metadatamap_to_cartesianmap_to_polarplot_position_timeseriesplot_speed_timeseriesread_animaltaread_bonsairead_deeplabcutread_idtrackerread_lightningposeread_movementread_sleapread_trackballread_treadmillread_trexreplace_nareplace_na_linearreplace_na_locfreplace_na_splinereplace_na_stinereplace_na_valuerotate_coordsset_framerateset_individualset_start_datetimeset_uuidtransform_to_egocentrictranslate_coordsvalidate_animaltavalidate_deeplabcut_csvvalidate_filesvalidate_timevalidate_trackball

Dependencies:anytimeBHbitbit64bootcircularclicollapsecolorspacecommonmarkcpp11crayoncurldplyrfansifarvergenericsggplot2ggtextgluegridtextgtablehmsisobandjanitorjpeglabelinglatticelifecyclelubridatemagrittrmarkdownMASSMatrixmgcvmunsellmvtnormnlmepatchworkpillarpkgconfigpngprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloRcppParallelrhdf5rhdf5filtersRhdf5librlangrollscalessignalsnakecasestinepackstringistringrtibbletidyrtidyselecttimechangetzdbutf8vctrsviridisLitevroomwithrxfunxml2

Introduction to animovement

Rendered fromanimovement.Rmdusingknitr::rmarkdownon Feb 02 2025.

Last update: 2024-09-15
Started: 2024-09-10

Readme and manuals

Help Manual

Help pageTopics
Add Centroid to Movement Dataadd_centroid
Align a time series with a reference series using cross-correlationalign_timeseries
Calculate kinematics from position datacalculate_kinematics
Calculate Speed from Position Datacalculate_speed
Calculate summary statisticscalculate_statistics
Visualize the distribution of confidence values for each keypointcheck_confidence
Visualize the occurrence of gap sizes in the datacheck_na_gapsize
Visualize the timing of missing values in the datacheck_na_timing
Analyze the distribution of distances from keypoints to the centroidcheck_pose
Classify Movement States Based on Stability Analysisclassify_by_stability
Classify Values Into Sequences with Minimum Run Length Constraintsclassify_by_threshold
Classifies Periods of High Activity in Time Series Using Peaks and Troughsclassify_high_periods
Classifies Periods of Low Activity in Time Series Using Peaks and Troughsclassify_low_periods
Apply Butterworth Highpass Filter to Signalfilter_highpass
Apply FFT-based Highpass Filter to Signalfilter_highpass_fft
Kalman Filter for Regular Time Seriesfilter_kalman
Kalman Filter for Irregular Time Series with Optional Resamplingfilter_kalman_irregular
Apply Butterworth Lowpass Filter to Signalfilter_lowpass
Apply FFT-based Lowpass Filter to Signalfilter_lowpass_fft
Smooth Movement Datafilter_movement
Filter low-confidence values in a datasetfilter_na_confidence
Filter coordinates outside a region of interest (ROI)filter_na_roi
Filter values by speed thresholdfilter_na_speed
Apply Rolling Mean Filterfilter_rollmean
Apply Rolling Median Filterfilter_rollmedian
Apply Savitzky-Golay Filter to Movement Datafilter_sgolay
Find optimal time lag between two time series using cross-correlationfind_lag
Find Peaks in Time Series Datafind_peaks
Find Troughs in Time Series Datafind_troughs
Download example tracking dataget_example_data
Get/extract metadataget_metadata
Group every N observations togethergroup_every
Initiate movement metadatainit_metadata
Map from polar to Cartesian coordinatesmap_to_cartesian
Map from Cartesian to polar coordinatesmap_to_polar
Plot Time Series of Keypoint Positionplot_position_timeseries
Plot Time Series of Keypoint Speedplot_speed_timeseries
Read AnimalTA dataread_animalta
Read centroid tracking data from Bonsairead_bonsai
Read DeepLabCut dataread_deeplabcut
Read idtracker.ai dataread_idtracker
Read LightningPose dataread_lightningpose
Read movement dataread_movement
Read SLEAP dataread_sleap
Read trackball dataread_trackball
Read treadmill dataread_treadmill
Read TRex Movement Tracking Dataread_trex
Replace Missing Values Using Various Methodsreplace_na
Replace Missing Values Using Linear Interpolationreplace_na_linear
Replace Missing Values Using Last Observation Carried Forwardreplace_na_locf
Replace Missing Values Using Spline Interpolationreplace_na_spline
Replace Missing Values Using Stineman Interpolationreplace_na_stine
Replace Missing Values with a Constant Valuereplace_na_value
Rotate coordinates in Cartesian spacerotate_coords
Adjust time values to reflect a new framerateset_framerate
Assign a new individual identifier to all rows in a datasetset_individual
Set starting datetimeset_start_datetime
Set UUIDset_uuid
Transform coordinates to egocentric reference frametransform_to_egocentric
Translate coordinates (Cartesian)translate_coords