Optimus: a general purpose adaptive optimisation engine in R

Motivation: Many calculations in computational biology necessitate a use of a probabilistic optimisation protocol to determine a set of parameters that capture the system at a desired state in the configurational space. Here, we developed a flexible optimisation engine in R that can be plugged to any, simple or complex, modelling initiative through a few lucid interfacing functions, to perform a seamless optimisation with rigorous parameter sampling. Results: Optimus features an acceptance ratio simulated annealing, acceptance ratio replica exchange, and adaptive thermoregulation, thus driving a Monte Carlo optimisation process in a flexible manner, through constrained acceptance frequency but unconstrained adaptive pseudo temperature regiments. We show the applicability of our R optimiser to a wide variety of problems spanning data analyses and computational biology tasks. Availability and Implementation: Optimus is written and implemented in R, and is freely available from the http://github.com/SahakyanLab/Optimus repository. Contact: aleksandr.sahakyan@imm.ox.ac.uk Supplementary Information: Supplementary information with more details, tutorials, and developer instructions is available. ### Competing Interest Statement The authors have declared no competing interest.