Sensitivity analysis of Repast computational ecology models with R/Repast
Authored by Garcia Antonio Prestes, Alfonso Rodriguez-Paton
Date Published: 2016
DOI: 10.1002/ece3.2580
Sponsors:
European Union
Platforms:
Repast
R
Model Documentation:
ODD
Flow charts
Pseudocode
Mathematical description
Model Code URLs:
Model code not found
Abstract
Computational ecology is an emerging interdisciplinary discipline
founded mainly on modeling and simulation methods for studying
ecological systems. Among the existing modeling formalisms, the
individual-based modeling is particularly well suited for capturing the
complex temporal and spatial dynamics as well as the nonlinearities
arising in ecosystems, communities, or populations due to individual
variability. In addition, being a bottom-up approach, it is useful for
providing new insights on the local mechanisms which are generating some
observed global dynamics. Of course, no conclusions about model results
could be taken seriously if they are based on a single model execution
and they are not analyzed carefully. Therefore, a sound methodology
should always be used for underpinning the interpretation of model
results. The sensitivity analysis is a methodology for quantitatively
assessing the effect of input uncertainty in the simulation output which
should be incorporated compulsorily to every work based on in-silico
experimental setup. In this article, we present R/Repast a GNU R package
for running and analyzing Repast Simphony models accompanied by two
worked examples on how to perform global sensitivity analysis and how to
interpret the results.
Tags
Simulation
Design
systems
Protocol
Bacterial-populations
Plasmid
Conjugation