@BOOK{Caswell01,
  author = {Caswell, H},
  year={2001},
  title={Matrix population models: construction, analysis, and interpretation},
  edition={Second edition},
  publisher={Sinauer, Sunderland}
}
@ARTICLE{Donali99,
  author = {Donali, E. and Olli, K. and Heiskanen, A.-S. and Andersen, T.},
  title = {Carbon flow patterns in the planktonic food web of the Gulf of Riga, the Baltic Sea: a reconstruction by the inverse method},
  journal = {Journal of Marine Systems},
  volume={23},
  pages={251-268},
  year = {1999}
}
@ARTICLE{Edwards02,
  author={Edwards,JS and Covert, M and Palsson, B},
  title={Metabolic Modeling of Microbes: the Flux Balance Approach},
  journal={Environmental Microbiology},
  volume={4(3)},
  pages={133-140},
  year={2002}
  }
@book{Fiacco68,
  author={AV Fiacco and GP McCormick},
  year={1968},
  title={Nonlinear programming: Sequential unconstrained minimization techniques},
  publisher= {New York: John Wiley and Sons}
}
@Manual{Haskell78,
  author={K. H. Haskell and R. J. Hanson},
  title={An algorithm for linear least squares problems with equality and nonnegativity constraints},
  note={Report SAND77-0552},
  publisher={Sandia Laboratories},
  year={1978}
}
@inproceedings{Leisch02,
  author = {Friedrich Leisch},
  title = {Sweave: Dynamic Generation of Statistical Reports Using
		  Literate Data Analysis},
  booktitle = {Compstat 2002 - Proceedings in Computational
		  Statistics},
  pages = {575-580},
  year = 2002,
  editor = {Wolfgang H{\"a}rdle and Bernd R{\"o}nz},
  publisher = {Physica Verlag, Heidelberg},
  note = {ISBN 3-7908-1517-9},
  url = {http://www.stat.uni-muenchen.de/~leisch/Sweave}
}
@Manual{lpSolve,
  title = {lpSolve: Interface to Lp\_solve v. 5.5 to solve linear or integer programs},
  author = {Michel Berkelaar and others},
  year = {2007},
  note = {R package version 5.5.8},
}
@ARTICLE{Mackey96,
  author = {Mackey, MD and Mackey, DJ and Higgins, HW and Wright, SW},
  title = {CHEMTAX - A program for estimating class abundances from chemical markers: Application to HPLC measurements of phytoplankton},
  journal = {Marine Ecology-Progress Series},
  volume={144},
  pages={265-283},
  year = {1996}
}
@Book{MASS,
    title = {Modern Applied Statistics with S},
    author = {W. N. Venables and B. D. Ripley},
    publisher = {Springer},
    edition = {Fourth},
    address = {New York},
    year = {2002},
    note = {ISBN 0-387-95457-0},
    url = {http://www.stats.ox.ac.uk/pub/MASS4},
  }
@Manual{Matrix,
    title = {Matrix: A Matrix package for R},
    author = {Douglas Bates and Martin Maechler},
    year = {2008},
    note = {R package version 0.999375-9},
  }
@ARTICLE{Meersche08,
  author= {Van den Meersche, K. and Soetaert, K. and  Middelburg, J.},
  year={2008},
  title={A Bayesian compositional estimator for microbial taxonomy based on biomarkers},
  journal={Limnology and Oceanography Methods},
  volue={6},
  pages={190-199}
  }
@Manual{BCE,
    title = {BCE: Bayesian composition estimator: estimating sample (taxonomic)
   composition from biomarker data},
    author = {Van den Meersche, K. and Soetaert, K.},
    year = {2008},
    note = {R package version 1.1},
  }
@ARTICLE{Niquil98,
  author = {Niquil, N and Jackson, GA and Legendre, L and Delesalle, B},
  title = {Inverse model analysis of the planktonic food web of Takapoto Atoll (French Polynesia).},
  journal = {Marine Ecology Progress Series},
  year = {1998},
  volume = {165},
  pages = {17-29},
}
@Manual{quadprog,
    title = {quadprog: Functions to solve Quadratic Programming Problems.S original by Berwin A. Turlach R port by Andreas Weingessel},
    author = {Andreas Weingessel},
    year = {2007},
    note = {R package version 1.4-11},
  }
@MANUAL{R2008,
  title = {\proglang{R}: A Language and Environment for Statistical Computing},
  author = {{R Development Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2008},
  note = {{ISBN} 3-900051-07-0},
  url = {http://www.R-project.org}
}
@Manual{limSolve,
    title = {limSolve: Solving linear inverse models},
    author = {Karline Soetaert and  Van den Meersche, Karel and Dick van Oevelen},
    year = {2009},
    note = {R package version 1.5},
  }
@Manual{LIM,
    title = {LIM: Linear Inverse Model examples and solution methods.},
    author = {Karline Soetaert and Dick van Oevelen},
    year = {2009},
    note = {R package version 1.4},
  }
@Manual{LIMvignette,
  title={Package LIM, implementing linear inverse models in R},
    author = {Karline Soetaert and Dick van Oevelen},
    year = {2009},
    note = {R package vignette},
}
  
@Manual{limecoli,
    title = {Escherichia coli Core Metabolism Model in LIM.},
    author = {Karline Soetaert},
    year = {2009},
    note = {LIM package vignette},
  }
@Article{oevelen09,
    title = {Quantifying Food Web Flows Using Linear Inverse Models.},
    author = {Dick van Oevelen and Karel van den Meersche and Filip Meysman and Karline Soetaert and Jack J Middelburg and Alain F Vezina},
    journal = {Ecosystems},
    year = {2009},
    doi = {10.1007/s10021-009-9297-6},
    url = {http://www.springerlink.com/content/4q6h4011511731m5/fulltext.pdf},
    keywords = {Food web, Inverse models, mass balance, optimization, likelihood, stable isotopes, stoichiometry, flux balance analysis},
  }
@Manual{diagram,
    title = {diagram: Functions for visualising simple graphs (networks), plotting flow diagrams},
    author = {Karline Soetaert},
    year = {2008},
    note = {R package version 1.4},
  }
@Manual{ecolMod,
    title = {ecolMod: "A practical guide to ecological modelling - using R as a simulation platform"},
    author = {Karline Soetaert and Peter MJ Herman},
    year = {2008},
    note = {R package version 1.1},
  }
@Manual{shape,
    title = {shape: Functions for plotting graphical shapes, colors},
    author = {Karline Soetaert},
    year = {2008},
    note = {R package version 1.2.2},
  }
@article{Leguerrier03,
 author={Leguerrier, D. and Niquil, N. and Boileau, N. and Rzeznik, J. and Sauriau, P.G.
 and  Le Moine, O. and Bacher, C.},
 year={2003},
 title={Numerical analysis of the food web of an intertidal mudflat ecosystem on
 the Atlantic coast of France},
 journal ={Marine Ecology Progress Series},
 volume={ 246},
 pages={17-37}
}
@article{Eldridge93,
 author={Eldridge, P.M. and Jackson, G.A.},
 year={1993},
 title={Benthic trophic dynamics in California coastal basin and
   continental slope communities inferred using inverse analysis},
 journal={Marine Ecology Progress Series},
 volume={99},
 pages={115-135}
}
@article{diffendorfer01,
 author={Diffendorfer, J.E. and Richards, P.M. and Dalrymple, G.H. and DeAngelis, D.L.},
 year={2001},
 title={Applying Linear Programming to estimate fluxes in ecosystems or food webs:
an example from the herpetological assemblage of the freshwater Everglades},
 journal= {Ecological Modelling},
 volume={144},
 pages={99-120}
 }
 @article{oevelen06,
 author={Van Oevelen, D and Soetaert, K. and Middelburg, J.J. and Herman, P.M.J. and
  Moodley, L. and Hamels, I. and Moens, T. and Heip, C.H.R.},
 year={2006},
 title={Carbon flows through a benthic food web: Integrating biomass, isotope and tracer data},
 journal={Journal of Marine Research},
 volume ={64},
 pages={1-30}
}

@book{Vanderbei00,
 author={Vanderbei, R.J},
 year ={2000},
 title={Linear programming, Foundations and extensions},
 publisher={Kluwer Academic Publishers},
 city={Boston}
}

@Manual{NetIndices,
    title = {NetIndices: Estimating network indices, including trophic structure of foodwebs in R},
    author = {Karline Soetaert and Julius Kipyegon Kones},
    year = {2008},
    note = {R package version 1.2},
}
@Article{NetIndicesArt,
    title = {Are network indices robust indicators of food web functioning? a Monte Carlo approach.},
    author = {Julius Kipyegon Kones and Karline Soetaert and Dick van Oevelen and John Owino},
    journal = {Ecological Modelling},
    volume = {220},
    pages = {370-382},
    year = {2009},
    doi = {http://dx.doi.org/10.1016/j.ecolmodel.2008.10.012},
    keywords = {Food web, Inverse models, Network indices, Minimum norm solution,
              Monte Carlo average solution.},
  }
@Article{xsample,
   author       = {Van den Meersche, Karel and Karline Soetaert and
                   Van Oevelen, Dick },
   title                = {\code{xsample()}: An \proglang{R} Function
for
                   Sampling Linear Inverse Problems},
   journal      = {Journal of Statistical Software, Code Snippets},
   year         = {2009},
   volume       = {30},
   number       = {1},
   pages                = {1--15},
   url          = {http://www.jstatsoft.org/v30/c01/}
}

@article{ToxLim,
    author = {Frederik de Laender and Dick van Oevelen and Jack J.J. Middelburg and Karline Soetaert},
    year = {2009},
    title = {Incorporating Ecological Data and Associated Uncertainty in
  Bioaccumulation Modeling: Methodology Development and Case Study},
    journal = {Environmental Science and Technology},
    volume = {43 No. 7},
    pages = {2620-2626},
  }
