pathtrackr: An r package for video tracking and analysing animal movement

Abstract

Techniques for visualising and analysing animal movement patterns are widely used in behavioural studies. While commercial options exist for analysing animal movement via video, the cost of these is often prohibitive. To meet the need for an efficient and cost‐effective video tracking and analysis tool, we have developed the pathtrackr package for the open‐source programming environment r. The pathtrackr package allows for an automated and consolidated workflow, from video input to statistical output (with addition of the open‐source FFmpeg application), of an animal's movement. The software tracks a single animal at a time across a variety of visual contexts, notably heterogenous backgrounds and variable lighting, and can deal with localised background movement that does not overlap with the animal. The software does not need training like many other solutions. We also include diagnostic tools in the package for troubleshooting. Here, we provide an overview of the package and example workflow for using its various functions. Validation with simulated data shows that pathtrackr provides very accurate results, at the same time removing observer subjectivity and greatly reducing data collection times.

Are There Personality Differences between Rural vs. Urban-Living Individuals of a Specialist Ground Beetle, Carabus convexus?

“…As soon as the beetle stopped moving around, the lid was lifted, and the behavior was recorded for 90 s using a GoPro HERO6 camera (CHDHX-601-FW). Videos were analyzed using the pathtrackr package [ 46 ]. We registered the number of squares crossed by the individual (squares visit hereafter), the covered distance (in mm), and the total amount of time spent in motion (sec; motion time hereafter).…”

Using a variant of the optomotor response as a visual defect detection assay in zebrafish

“…Movement of the fish in response to each stimulus can be analyzed in three ways, described below. In general, as this method is designed to be implemented easily without costly behavioral software or time-costly coding setup, it is not well-suited to using currently available open-source computer vision tracking software such as PathtrackR [ 15 ].…”

“…Open source behavioral software may be a viable option to track the fish in this behavioral setup. Easier to use options that the authors recommend include PathtrackR [ 15 ], ZebraZoom [ 17 ]. Current open-source behavioral tracking software performs better when there is a constant background as most computer vision-based tracking is done using organism-background contrast differences.…”

A checklist for choosing between R packages in ecology and evolution

“…Furthermore, publications describing the use of packages in ecology and evolution strongly suggest that the package will be functional and potentially appropriate to your own adventure, that is, see the R package codyn on CRAN for community dynamic measures with documentation and a peer‐reviewed publication to describe it in depth (Hallett et al, ). There are many other examples also published in the journal Methods in Ecology and Evolution (Duthie et al, ; Harmer & Thomas, ; Remelgado, Wegmann, & Safi, ; Wubs et al, ). Another important attribute of packages is the frequency of use.…”

“…Methods in Ecology and Evolution(Duthie et al, 2018;Harmer & Thomas, 2019;Remelgado, Wegmann, & Safi, 2019;Wubs et al, 2019). Another important attribute of packages is the frequency of use.…”