We have a large camera trap database of multiple carnivores species (from long-term camera trap data). We want to to examine the activity patterns to examine potential temporal aspects of co-occurrence and want to find a solid R-package that can help in that effort.
I've used the overlap package: http://www.mikemeredith.net/blog/2018/overlap_sunTime.htm
Camera trapping is a widely applied method to study and analyze wildlife diversity and their activity pattern. The data trapped need to be managed in an efficient way. For this analysis the R-package 'camt r apR' , which is a new toolbox for flexible and efficient management of data generated in camera trap based wildlife studies can be used.
Hey Jason,
A lot of people have already commented on useful packages above. I would also recommend you check out this paper, which employs some of these packages. It has a great methodology for looking at daily activity rhythms and interspecific relationships using camera trap data. Hope all is well, maybe see you at ASM in 2021!
Caravaggi, A., Gatta, M., Vallely, M. C., Hogg, K., Freeman, M., Fadaei, E., ... & Tosh, D. G. (2018). Seasonal and predator-prey effects on circadian activity of free-ranging mammals revealed by camera traps. PeerJ, 6, e5827.
- Victor
In addition to "Overlap" package, I recommend "behaviouR" package (https://bookdown.org/djc426/behaviouR-R-package-tutorials/computer-lab-6-analyzing-camera-trap-data-.html#part-2-analyze-your-serengeti-camera-trap-data). Here you can produce very nice density activity curve. I also suggest clock24.plot function in package "plotrix" (http://cran.r-project.org/web/packages/plotrix/index.html). It produces radial plot of activity pattern of animals based on hourly counts of events.
The activity package ( https://cran.r-project.org/web/packages/activity/ ) fits circular kernel density functions to animal activity data from camera-traps, as presented here: Article Quantifying levels of animal activity using camera-trap data
Not sure if outputs would be compatible with e.g. overlap.
I would suggest camtrapR to organise the dataset; it has also useful function to adjust time/date of pictures in case of a malfunctioning of the camera-trap (you can also rely on ExifTool for this).
For analyses, as already said overlap package works very fine.
You can use overlap (Meredith and Ridout 2014) --> https://cran.r-project.org/web/packages/overlap/vignettes/overlap.pdf
It will depend upon the research question you are going to abswer. Overlap and behavior R package might help
The package "activity" mentioned by Eric was quite useful for me.
https://cran.r-project.org/web/packages/activity/index.html
You can consider the circular package for analysis and the plotrix package for the plots . This article by Ross et al 2013 gives some pointers
I used to use the "Overlap" package, try this one as recommended by many researchers.
