If you are interested in finding the best decisions over time to save or eradicate the cutest species, then you are probably interested in using Stochastic Dynamic Programming (SDP) or its mathematical model Markov Decision Process (MDP). If you have a burning problem ready to be solved but not sure how to, then good news we have released the MDPToolbox (ver. 4) in R, Matlab, Octave and Scilab. Please spread the word, the toolbox is free! Thanks to Ecography, you can now support our efforts by citing our paper:
To download the toolbox: http://www7.inra.fr/mia/T/MDPtoolbox/
If you are still unsure about SDP, try: Marescot, L., G. Chapron, I. Chadès, P. Fackler, C. Duchamp, E. Marboutin, and O. Gimenez. 2013. Complex decisions made simple: a primer on stochastic dynamic programming. Methods in Ecology and Evolution 4:872-884.