diagnosticPDF: Track an animal's movement across a series of still frames...

Description Usage Arguments Details Value

View source: R/diagnosticPDF.R

Description

diagnosticPDF contains the same function as the core pathtrackr::trackPath function but, in addition, produces a pdf with disgnostic plots for troubleshooting problematic animals and tracks. A set of six plots for each frame allow the user to view the tracking behaviour of the function on a frame by frame basis.

Usage

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diagnosticPDF(dirpath, xarena, yarena, fps = 30, box = 1,
  jitter.damp = 0.9)

Arguments

dirpath

a character string specifying a directory containing only jpeg files extracted from a video

xarena

an integer specifying the arena width in mm; this value is used for distance and velocity calculations, an incorrect value will not cause an error but will result in inaccurate calculations

yarena

an integer specifying the arena height in mm; this value is used for distance and velocity calculations, an incorrect value will not cause an error but will result in inaccurate calculations

fps

an integer specifying the frame rate at which jpegs were extracted from a video; this value is used for distance and velocity calculations, an incorrect value will not cause an error but will result in inaccurate calculations

box

an integer specifying the size of the tracking box relative to the initial animal selection box; a larger box size will help prevent the animal being lost (useful for fast moving animals) but will also increase sensitivity to background and lighting changes (default 1)

jitter.damp

a value between 0.5 and 1. Reduces noise in the animal's track, useful if the animal's track is very jittery, which may overestiamte path length. A value of 1 indicates no jitter damping, 0.5 indicates extreme damping and is unlikely to be useful

Details

See documentation for trackPath.

Value

A list containing a matrix of xy co-ordinates of the animal in each frame, a matrix of movement data including the distance, velocity and trajectories of movement between frames, summary statistics, and a diagnostic PDF.


gunpowder78/pathtrackr documentation built on Nov. 18, 2017, 1:56 p.m.