Function reference • MoveR

Import

Import raw data from various video tracking software into R env.

readAnimalTA(): Import AnimalTA tracking output .csv file.

readCtrax(): Import Ctrax tracking output .mat file.

readIdtracker(): Import idtracker.ai tracking output .npy file.

readPlain(): Import plain tracking output from a table.

readTrackR(): Import TrackR tracking output .csv file.

readTrex(): Import Trex tracking output .npz files.

Visualize

Visualize the tracklets of all or specified particles over time.

drawTracklets(): Display tracklets on a plot.

Manage ROI

Create or retrieve the location of ROI.

assignROI(): Assign ROI(s) identity to particle's position

circles(): Generate points located on circles contour and draw circle(s).

locROI(): Locate ROI

polygons(): Generate points located on polygon vertices and draw polygon(s).

Clean/Filter

Create custom filter to either clean/remove spurious track parts or filter/resample the dataset.

filterFunc(): Create and test a custom filter on tracklets.

filterTracklets(): Apply a custom filter on tracklets.

mergeFilters(): Merge condition tests (i.e., filterFunc outputs).

resampTracklets(): Resampling tracklets.

Evaluate

Evaluate the quantity of data removed over the cleaning/filtering process and perform sensitivity analysis between video tracking and manual detection.

detectPerf(): Compute sensitivity index for particles detection.

summary(<tracklets>): Summary statistics of the tracking data.

trackStats(): Summary statistics of the tracking data - DEPRECATED !

Basic Descriptors

Performed simple computation over each tracklet.

activity1(): Determine active or inactive states according to the speed of a particles along its trajectory.

analyseTracklets(): Perform custom computation over a tracklet list.

dist2Edge(): Compute the distance from the particle to the edge of an object (e.g., the arena) over its trajectory.

dist2Pt(): Compute euclidean distance between a particle and object(s).

distTraveled(): Compute the distance traveled by a particle over a trajectory.

sinuosity(): Compute corrected rediscretized sinuosity index for a given tracklet.

speed(): Compute particle's speed over a trajectory.

turnAngle(): Compute particle's turning angle over a trajectory.

High-Order Descriptors

Performed more advanced computation over each tracklet.

activity2(): Determine active or inactive states according to density based clustering method.

ANND(): Compute Average Nearest Neighbour Distance (ANND) among tracklets.

exploredArea(): Compute the total surface explored and display the corresponding heatmap.

DCoef(): Compute the net square displacement (population spread).

MSD(): Compute Mean Square Displacement (MSD).

Temporal Trends

Analyse temporal trends for a given computation over time by averaging the value of each track and compute a studentized 95% confidence interval (bootstrap).

temporalTrend(): Perform analysis across tracklets and time.

temporalBoot(): Compute 95% studentized CI across tracklets and time.

Identify Sequences

Identify specified sequences over tracklets according to custom pattern (e.g., displacement across area).

IdStateSeq(): Identify and extract specified patterns/sequences from tracklets.

Utilities

Some utilities functions helping to either import sample data, convert it or locate particles’ position.

convert2List(): Convert a tracklets object to list of variables.

convert2Tracklets(): Convert a list of variables to list of tracklets.

countMat(): Build count matrix in a 2 dimensional space.

DLsampleData(): Download sample data to depict the use of the MoveR package.

flipYCoords(): flip y coordinates.

getInfo(): Get information in a tracklets object.

listGet(): Get an object within a dataframe, a list or a nested list.

locPos(): Locate a particle position.

setInfo(): Set information in a tracklets object.

slidWindow(): Sliding window.

trackletsClass(): Create an object of class tracklets.