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Papers we might reproduce

Ye, H., Beamish, R.J., Glaser, S.M., Grant, S.C.H., Hsieh, C., Richards, L.J., Schnute, J.T. & Sugihara, G. (2015) Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling. Proceedings of the National Academy of Sciences, 201417063. Data and some code on github.

[Tina Toni, David Welch, Natalja Strelkowa, Andreas Ipsen, Michael P.H. Stumpf (2009) Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of the Royal Society Interface, 6, 187-202.] (http://rsif.royalsocietypublishing.org/content/6/31/187) Propose to reproduce ABC on Lotka Volterra equations. No data needed

[Yampolsky, Lev Y., Tobias M. M. Schaer, and Dieter Ebert. “Adaptive Phenotypic Plasticity and Local Adaptation for Temperature Tolerance in Freshwater Zooplankton.” Proceedings of the Royal Society of London B: Biological Sciences 281, no. 1776 (February 7, 2014): 20132744.] (http://rspb.royalsocietypublishing.org/content/281/1776/20132744) Data available on Dryad.

[Hooper DU, Adair EC, Cardinale BJ, Byrnes JEK, Hungate BA, et al. 2012. A global synthesis reveals biodiversity loss as a major driver of ecosystem change. Nature 486:105–8] (http://jarrettbyrnes.info/pdfs/Hooper_et_al_2012_Nature.pdf). Database is available at the National Center for Ecological Analysis and Synthesis: (http://knb.ecoinformatics.org/knb/metacat/nceas.984/nceas).

[Hekstra, D.R. & Leibler, S. (2012) Contingency and statistical laws in replicate microbial closed ecosystems. Cell, 149, 1164–1173.] (http://www.sciencedirect.com/science/article/pii/S0092867412005156). Data available by request, but cannot be put in public domain.

[Scheffer, M., Carpenter, S., Foley, J. a, Folke, C. & Walker, B. (2001) Catastrophic shifts in ecosystems. Nature, 413, 591–6.] (http://www.nature.com/nature/journal/v413/n6856/full/413591a0.html) At least reproduce / use the minimal mathematical model in Box 1, to recreate something like figure 3.

Papers with reproduction underway

Lagrue, C., Poulin, R. & Cohen, J.E. (2014) Parasitism alters three power laws of scaling in a metazoan community: Taylor’s law, density-mass allometry, and variance-mass allometry. Proceedings of the National Academy of Sciences of the United States of America, 112, 1791–1796.

Ward, E.J., Holmes, E.E., Thorson, J.T. & Collen, B. (2014) Complexity is costly: A meta-analysis of parametric and non-parametric methods for short-term population forecasting. Oikos, 123, 652–661.

Ignacio Morales-Castilla, Miguel G. Matias, Dominique Gravel, and Miguel B. Araujo (2015) Inferring biotic interactions from proxies. TREE xx 1-10 TMM: Would be interesting to reproduce this study to get an idea about the removed interactions (the forbidden ones) - and the ones that are still in, but false. Maybe one could also apply this to a smaller food web and test for the accuracy of this approach. Because the authors do not provide any test for accuracy... :( Food webs available, checking for trait data.

Papers without appropriate data

Graham, N.A.J., Jennings, S., MacNeil, M.A., Mouillot, D. & Wilson, S.K. (2015) Predicting climate-driven regime shifts versus rebound potential in coral reefs. Nature, 518, 94–97. Authors contacted. Data available on request, but could not be made public, so reproduction here not possible.

[Schmitz, O. (1997) Press pertubations and the predictability of ecological interactions in a food web. Ecology, 78, 55–69.] (http://www.esajournals.org/doi/abs/10.1890/0012-9658(1997)078%5B0055:PPATPO%5D2.0.CO;2) Data not available.

Papers below are at least mostly done.

Benincà, E., Huisman, J., Heerkloss, R., Jöhnk, K.D., Branco, P., Nes, E.H. Van, Scheffer, M. & Ellner, S.P. (1989) Chaos in a long-term experiment with a plankton community. , 1–35.. Reproduction published [here] (http://opetchey.github.io/RREEBES/Beninca_2008_Nature/report.html).

Hiltunen, T., Hairston, N.G., Hooker, G., Jones, L.E. & Ellner, S.P. (2014) A newly discovered role of evolution in previously published consumer-resource dynamics. Ecology letters, 17, 915–23. Data is available and Jason Griffiths has a reproduction already.