Description Usage Arguments Details Value
View source: R/diagnosticPDF.R
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.
1 2 | diagnosticPDF(dirpath, xarena, yarena, fps = 30, box = 1,
jitter.damp = 0.9)
|
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 |
See documentation for trackPath
.
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.
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