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  1. Abstract Summary

    Biological models contain many parameters whose values are difficult to measure directly via experimentation and therefore require calibration against experimental data. Markov chain Monte Carlo (MCMC) methods are suitable to estimate multivariate posterior model parameter distributions, but these methods may exhibit slow or premature convergence in high-dimensional search spaces. Here, we present PyDREAM, a Python implementation of the (Multiple-Try) Differential Evolution Adaptive Metropolis [DREAM(ZS)] algorithm developed by Vrugt and ter Braak (2008) and Laloy and Vrugt (2012). PyDREAM achieves excellent performance for complex, parameter-rich models and takes full advantage of distributed computing resources, facilitating parameter inference and uncertainty estimation of CPU-intensive biological models.

    Availability and implementation

    PyDREAM is freely available under the GNU GPLv3 license from the Lopez lab GitHub repository at http://github.com/LoLab-VU/PyDREAM.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
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  2. Abstract

    The daunting complexity of ecosystems has led ecologists to use mathematical modelling to gain understanding of ecological relationships, processes and dynamics. In pursuit of mathematical tractability, these models use simplified descriptions of key patterns, processes and relationships observed in nature. In contrast, ecological data are often complex, scale‐dependent, space‐time correlated, and governed by nonlinear relations between organisms and their environment. This disparity in complexity between ecosystem models and data has created a large gap in ecology between model and data‐driven approaches. Here, we explore data assimilation (DA) with the Ensemble Kalman filter to fuse a two‐predator‐two‐prey model with abundance data from a 2600+ day experiment of a plankton community. We analyse how frequently we must assimilate measured abundances to predict accurately population dynamics, and benchmark our population model's forecast horizon against a simple null model. Results demonstrate that DA enhances the predictability and forecast horizon of complex community dynamics.

     
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