respR : A package for processing and analysing respirometry data

Respirometry is perhaps the most ubiquitous practice in experimental physiology and ecology. Open, reproducible research is increasingly important to scientific outputs, and respR has been designed to be a complete workflow to assist researchers in conducting, documenting and reporting their respirometry analyses.

Visit this site to see how to get started and for vignettes (i.e. user guides) and example analyses showing how the package works.

In addition, I have an open offer to anyone struggling with their respirometry data or with how to get started with respR: get in touch and I will write you a short script showing how to import and analyse your data.

respR has also been published in Methods in Ecology and Evolution. If you use it, please cite the publication. It would be much appreciated, and be a small thank you for the many hundreds of hours we put into creating it.

We are constantly improving and updating the code, so if you have any issues or questions get in touch or better still open an issue on the package Github page. You’ll generally get an answer within a day or so!

And follow respR on Twitter for the latest news.

attackR : Predator-prey response interactions

The attackR package is associated with a study published in Proceedings of the National Academy of Sciences in which we explained how humpback whales are able to sneak up on easily-scattered anchovies, a counter-intuitive finding related to their large size and approach speeds.

Given shape, speed and size, the package can determine how any predator appears to a prey in their visual field, and allow identification of visual response thresholds. See here for more:

respfun : Respirometry utilities

The respfun package is a collection of additional functions for use with respirometry data and experiments, and it integrates nicely with respR.

Currently there are functions for calculating the effective volume of a respirometer, dividing a group metabolic rate between individuals based on their mass, and calculating a specimen density based on their buoyant mass. More functions will be added in due course. Get in touch if there is anything in particular you think I should add.

loomeR : A package for analysing escape responses using looming animations

loomeR is an R package for creating looming animations for use in behavioural and neurological experiments, and analysing responses, for example determining the Apparent Looming Threshold (ALT) of an escape response.

Looming animations are used in a range of physiological, psychological and behavioural sciences to simulate an approaching object and investigate phenomena such as perception, visual latency, escape responses, and neurological functioning.

The package has a frankly ridiculous number of options for creating and customising the animation, from use of variable expansion speeds, to using different colours, and adding frame markers to help identify when escape responses occur.

It also has functions to analyse response data and determine experimental metrics such as ALT, visual angle, and rate of change in visual angle.