Code

On this page are links to some of my public packages, or visit my Github profile

In this era of open, reproducible research, respR has been designed to be a complete workflow to assist researchers in conducting, documenting and reporting their aquatic respirometry analyses.

 

Visit this site to see how to get started and to view a range of vignettes (i.e. guides): 

https://januarharianto.github.io/respR/articles/respR.html

The package has also been published in Methods in Ecology and Evolution (link). If you use it, a citation would be much appreciated. 

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. 

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.  

respr_sticker.png

The attackR package is associated with a study featured recently on the cover of Proceedings of the National Academy of Sciences in which we examined 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: 

https://nicholascarey.github.io/attackR/articles/main.html

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

 

Looming animations are used in a range of physiological, psychological and behavioural sciences to simulate an approaching threat 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 analyses response data and determine experimental metrics such as ALT, visual angle and rate of change in visual angle.

© 2019.  Site Updated May 2019