references.bib

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@InCollection{ballberry1987,
  Title                    = {A model predicting stomatal conductance and its contribution to the control of photosynthesis under different environmental conditions.},
  Author                   = {Ball, J. T. and Woodrow, I.E. and Berry, J. A.},
  Booktitle                = {Progress in photosynthesis research},
  Year                     = {1987},

  Address                  = {Dordrecht, the Netherlands},
  Editor                   = {Biggins, J.},
  Pages                    = {221--224}
}

@Article{barton2012,
  Title                    = {Effects of elevated atmospheric [{CO}2] on instantaneous transpiration efficiency at leaf and canopy scales in {Eucalyptus} saligna},
  Author                   = {Barton, Craig V. M. and Duursma, Remko A. and Medlyn, Belinda E. and Ellsworth, David S. and Eamus, Derek and Tissue, David T. and Adams, Mark A. and Conroy, Jann and Crous, Kristine Y. and Liberloo, Marion and L{\~{A}}{\P}w, Markus and Linder, Sune and McMurtrie, Ross E.},
  Journal                  = {Global Change Biology},
  Year                     = {2012},
  Note                     = {2},
  Pages                    = {585--595},
  Volume                   = {18},

  Doi                      = {10.1111/j.1365-2486.2011.02526.x}
}

@Article{bernacchi2001,
  Title                    = {Improved temperature response functions for models of {Rubisco}-limited photosynthesis},
  Author                   = {Bernacchi, C. J. and Singsaas, E. L. and Pimentel, C. and Portis Jr, A. R. and Long, S. P.},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {2001},
  Number                   = {2},
  Pages                    = {253--259},
  Volume                   = {24},

  Doi                      = {10.1111/j.1365-3040.2001.00668.x}
}

@Article{bonan2014,
  Title                    = {Modeling stomatal conductance in the earth system: linking leaf water-use efficiency and water transport along the soil - plant - atmosphere continuum},
  Author                   = {Bonan, G. B. and Williams, M. and Fisher, R. A. and Oleson, K. W.},
  Journal                  = {Geosci. Model Dev.},
  Year                     = {2014},
  Number                   = {5},
  Pages                    = {2193--2222},
  Volume                   = {7},

  Doi                      = {10.5194/gmd-7-2193-2014}
}

@Article{buckley2014,
  Title                    = {Is stomatal conductance optimized over both time and space in plant crowns? {A} field test in grapevine ({Vitis} vinifera)},
  Author                   = {Buckley, Thomas N. and Martorell, Sebastia and Diaz-Espejo, Antonio and Tom{\`{a}}s, Magdalena and Medrano, Hip{\'{o}}lito},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {2014},
  Number                   = {12},
  Pages                    = {2707--2712},
  Volume                   = {37},

  Copyright                = {© 2014 John Wiley \& Sons Ltd},
  Doi                      = {10.1111/pce.12343}
}

@Book{caemmerer2000,
  Title                    = {Biochemical Models of Leaf Photosynthesis},
  Author                   = {von Caemmerer, Susanne},
  Year                     = {2000}
}

@Article{caemmerer1981,
  Title                    = {Some relationships between the biochemistry of photosynthesis and the gas exchange of leaves},
  Author                   = {von Caemmerer, S. and Farquhar, GD},
  Journal                  = {Planta},
  Year                     = {1981},
  Note                     = {4},
  Pages                    = {376--387},
  Volume                   = {153}
}

@Article{collatz1991,
  Title                    = {Physiological and environmental regulation of stomatal conductance, photosynthesis and transpiration: a model that includes a laminar boundary layer},
  Author                   = {Collatz, GJ and Ball, JT and Grivet, C and Berry, JA},
  Journal                  = {Agricultural and Forest Meteorology},
  Year                     = {1991},
  Note                     = {2-4},
  Pages                    = {107--136},
  Volume                   = {54}
}

@Article{cowan1977,
  Title                    = {Stomatal function in relation to leaf metabolism and environment},
  Author                   = {Cowan, I. and Farquhar, G. D.},
  Journal                  = {Symposia of the Society for Experimental Biology},
  Year                     = {1977},
  Pages                    = {471--505},
  Volume                   = {31}
}

@Misc{dekauwefitfarquhar,
  Title                    = {FitFarquharModel. Accessed 2015-07-09.},

  Author                   = {De Kauwe, M.G.},
  HowPublished             = {\url{https://github.com/mdekauwe/FitFarquharModel}},
  Note                     = {Accessed: 2015-07-03}
}

@Article{dekauwe2015,
  Title                    = {A test of an optimal stomatal conductance scheme within the {CABLE} land surface model},
  Author                   = {De Kauwe, M. G. and Kala, J. and Lin, Y.-S. and Pitman, A. J. and Medlyn, B. E. and Duursma, R. A. and Abramowitz, G. and Wang, Y.-P. and Miralles, D. G.},
  Journal                  = {Geosci. Model Dev.},
  Year                     = {2015},
  Number                   = {2},
  Pages                    = {431--452},
  Volume                   = {8},

  Doi                      = {10.5194/gmd-8-431-2015}
}

@Article{duursma2014,
  Title                    = {The peaked response of transpiration rate to vapour pressure deficit in field conditions can be explained by the temperature optimum of photosynthesis},
  Author                   = {Duursma, Remko A. and Barton, Craig V. M. and Lin, Yan-Shih and Medlyn, Belinda E. and Eamus, Derek and Tissue, David T. and Ellsworth, David S. and McMurtrie, Ross E.},
  Journal                  = {Agricultural and Forest Meteorology},
  Year                     = {2014},
  Pages                    = {2--10},
  Volume                   = {189--190},

  Doi                      = {10.1016/j.agrformet.2013.12.007}
}

@Article{duursma2012,
  Title                    = {{MAESPA}: a model to study interactions between water limitation, environmental drivers and vegetation function at tree and stand levels, with an example application to [{CO}2] $\times$ drought interactions},
  Author                   = {Duursma, R. A. and Medlyn, B. E.},
  Journal                  = {Geosci. Model Dev.},
  Year                     = {2012},
  Note                     = {4},
  Pages                    = {919--940},
  Volume                   = {5},

  Doi                      = {10.5194/gmd-5-919-2012}
}

@Article{duursma2013,
  Title                    = {Near-optimal response of instantaneous transpiration efficiency to vapour pressure deficit, temperature and [{CO}2] in cotton (Gossypium hirsutum L.)},
  Author                   = {Duursma, Remko A. and Payton, Paxton and Bange, Michael P. and Broughton, Katrina J. and Smith, Renee A. and Medlyn, Belinda E. and Tissue, David T.},
  Journal                  = {Agricultural and Forest Meteorology},
  Year                     = {2013},
  Note                     = {0},
  Pages                    = {168--176},
  Volume                   = {168},

  Doi                      = {10.1016/j.agrformet.2012.09.005}
}

@Article{ethier2004,
  Title                    = {On the need to incorporate sensitivity to {CO}2 transfer conductance into the Farquhar{\^{a}\texteuro\textquotedblleft}von Caemmerer{\^{a}\texteuro\textquotedblleft}Berry leaf photosynthesis model},
  Author                   = {Ethier, GJ and Livingston, NJ},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {2004},
  Note                     = {2},
  Pages                    = {137--153},
  Volume                   = {27}
}

@Article{Ethier2004,
  Title                    = {On the need to incorporate sensitivity to {CO}2 transfer conductance into the Farquhar - von Caemmerer - Berry leaf photosynthesis model},
  Author                   = {Ethier, GJ and Livingston, NJ},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {2004},
  Note                     = {2},
  Pages                    = {137--153},
  Volume                   = {27}
}

@Article{farquhar1982,
  Title                    = {Stomatal conductance and photosynthesis},
  Author                   = {Farquhar, G.D. and Sharkey, T.D.},
  Journal                  = {Annual Review of Plant Physiology},
  Year                     = {1982},
  Note                     = {1},
  Pages                    = {317--345},
  Volume                   = {33}
}

@Article{farquhar1980,
  Title                    = {A biochemical model of photosynthetic {CO}2 assimilation in leaves of {C}3 species},
  Author                   = {Farquhar, G. D. and Caemmerer, S. and Berry, J. A.},
  Journal                  = {Planta},
  Year                     = {1980},
  Note                     = {1},
  Pages                    = {78--90},
  Volume                   = {149},

  Doi                      = {10.1007/BF00386231}
}

@Article{flexas2008,
  Title                    = {Mesophyll conductance to {CO}2: current knowledge and future prospects},
  Author                   = {Flexas, Jaume and Ribas-Carb{\'{o}}, Miquel and Diaz-Espejo, Antonio and Galm{\'{e}}s, Jeroni and Medrano, Hip{\'{o}}lito},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {2008},
  Number                   = {5},
  Pages                    = {602--621},
  Volume                   = {31},

  Doi                      = {10.1111/j.1365-3040.2007.01757.x}
}

@Misc{leafweb,
  Title                    = {LeafWeb. Accessed 2015-07-09},

  Author                   = {Gu, L.},
  HowPublished             = {\url{http://leafweb.ornl.gov/Pages/LeafWeb.aspx}},
  Note                     = {Accessed: 2015-07-03}
}

@Article{gu2010,
  Title                    = {Reliable estimation of biochemical parameters from {C}3 leaf photosynthesis - intercellular carbon dioxide response curves},
  Author                   = {Gu, Lianhong and Pallardy, Stephen G. and Tu, Kevin and Law, Beverly E. and Wullschleger, Stan D.},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {2010},
  Number                   = {11},
  Pages                    = {1852--1874},
  Volume                   = {33},

  Copyright                = {© 2010 Blackwell Publishing Ltd},
  Doi                      = {10.1111/j.1365-3040.2010.02192.x}
}

@Book{jones1992,
  Title                    = {Plants and microclimate: a quantitative approach to environmental plant physiology. 2nd {Edition}.},
  Author                   = {Jones, H. G.},
  Publisher                = {Cambridge University Press},
  Year                     = {1992},

  Address                  = {Cambridge},
  Edition                  = {2nd}
}

@Article{leuning1995,
  Title                    = {A critical-appraisal of a combined stomatal-photosynthesis model for C-3 plants},
  Author                   = {Leuning, R.},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {1995},
  Note                     = {4},
  Pages                    = {339--355},
  Volume                   = {18}
}

@Article{leuning1990,
  Title                    = {Modelling stomatal behaviour and photosynthesis of {Eucalyptus} grandis},
  Author                   = {Leuning, R.},
  Journal                  = {Australian Journal of Plant Physiology},
  Year                     = {1990},
  Pages                    = {159--175},
  Volume                   = {17}
}

@Article{leuning1989,
  Title                    = {Theory and practice of a portable photosynthesis instrument},
  Author                   = {Leuning, R. and Sands, P.},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {1989},
  Number                   = {6},
  Pages                    = {669--678},
  Volume                   = {12},

  Doi                      = {10.1111/j.1365-3040.1989.tb01236.x}
}

@Article{lin2015,
  Title                    = {Optimal stomatal behaviour around the world},
  Author                   = {Lin, Yan-Shih and Medlyn, Belinda E. and Duursma, Remko A. and Prentice, I. Colin and Wang, Han and Baig, Sofia and Eamus, Derek and de Dios, Victor Resco and Mitchell, Patrick and Ellsworth, David S. and de Beeck, Maarten Op and Wallin, G{\"{o}}ran and Uddling, Johan and Tarvainen, Lasse and Linderson, Maj-Lena and Cernusak, Lucas A. and Nippert, Jesse B. and Ocheltree, Troy W. and Tissue, David T. and Martin-StPaul, Nicolas K. and Rogers, Alistair and Warren, Jeff M. and De Angelis, Paolo and Hikosaka, Kouki and Han, Qingmin and Onoda, Yusuke and Gimeno, Teresa E. and Barton, Craig V. M. and Bennie, Jonathan and Bonal, Damien and Bosc, Alexandre and L{\"{o}}w, Markus and Macinins-Ng, Cate and Rey, Ana and Rowland, Lucy and Setterfield, Samantha A. and Tausz-Posch, Sabine and Zaragoza-Castells, Joana and Broadmeadow, Mark S. J. and Drake, John E. and Freeman, Michael and Ghannoum, Oula and Hutley, Lindsay B. and Kelly, Jeff W. and Kikuzawa, Kihachiro and Kolari, Pasi and Koyama, Kohei and Limousin, Jean-Marc and Meir, Patrick and Lola da Costa, Antonio C. and Mikkelsen, Teis N. and Salinas, Norma and Sun, Wei and Wingate, Lisa},
  Journal                  = {Nature Climate Change},
  Year                     = {2015},
  Number                   = {5},
  Pages                    = {459--464},
  Volume                   = {5},

  Copyright                = {© 2014 Nature Publishing Group},
  Doi                      = {10.1038/nclimate2550}
}

@Article{lin2012,
  Title                    = {Temperature responses of leaf net photosynthesis: the role of component processes},
  Author                   = {Lin, Yan-Shih and Medlyn, Belinda E. and Ellsworth, David S.},
  Journal                  = {Tree Physiology},
  Year                     = {2012},
  Note                     = {2},
  Pages                    = {219--231},
  Volume                   = {32},

  Doi                      = {10.1093/treephys/tpr141}
}

@Article{long2003,
  Title                    = {Gas exchange measurements, what can they tell us about the underlying limitations to photosynthesis? {Procedures} and sources of error},
  Author                   = {Long, S. P. and Bernacchi, C. J.},
  Journal                  = {Journal of Experimental Botany},
  Year                     = {2003},
  Number                   = {392},
  Pages                    = {2393--2401},
  Volume                   = {54},

  Doi                      = {10.1093/jxb/erg262},
  Pmid                     = {14512377}
}

@Article{mcdermitt1989,
  Title                    = {{CO}2 response curves can be measured with a field-portable closed-loop photosynthesis system},
  Author                   = {McDermitt, D. K. and Norman, J. M. and Davis, J. T. and Ball, T. M. and Arkebauer, T. J. and Welles, J. M. and Roerner, S. R.},
  Journal                  = {Annales des Sciences Forestieres},
  Year                     = {1989},
  Number                   = {Supplement},
  Pages                    = {416s--420s},
  Volume                   = {46},

  Doi                      = {10.1051/forest:19890593}
}

@Article{medlyn2011,
  Title                    = {Reconciling the optimal and empirical approaches to modelling stomatal conductance},
  Author                   = {Medlyn, B.E. and Duursma, R.A. and Eamus, D and Ellsworth, D.S. and Prentice, I.C. and Barton, C.V.M. and Crous, K.Y. and De Angelis, P and Freeman, M and Wingate, L.},
  Journal                  = {Global Change Biology},
  Year                     = {2011},
  Note                     = {6},
  Pages                    = {2134--2144},
  Volume                   = {17},

  Doi                      = {10.1111/j.1365-2486.2010.02375.x}
}

@Misc{medlynfigshare,
  Title                    = {Tumbarumba Gas Exchange.},

  Author                   = {Medlyn, Belinda and Pepper, David and Keith, Heather},

  Doi                      = {10.6084/m9.figshare.1538079}
}

@Article{medlyn2002,
  Title                    = {Temperature response of parameters of a biochemically based model of photosynthesis. {II}. A review of experimental data},
  Author                   = {Medlyn, B. E. and Dreyer, E. and Ellsworth, D. and Forstreuter, M. and Harley, P. C. and Kirschbaum, M. U. F. and Le Roux, X. and Montpied, P. and Strassemeyer, J. and Walcroft, A. and Wang, K. and Loustau, D.},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {2002},
  Note                     = {9},
  Pages                    = {1167--1179},
  Volume                   = {25}
}

@Article{medlyn2013,
  Title                    = {The optimal stomatal response to atmospheric {CO}2 concentration: {Alternative} solutions, alternative interpretations},
  Author                   = {Medlyn, Belinda E. and Duursma, Remko A. and De Kauwe, Martin G. and Prentice, I. Colin},
  Journal                  = {Agricultural and Forest Meteorology},
  Year                     = {2013},
  Pages                    = {200--203},
  Volume                   = {182-183},

  Doi                      = {10.1016/j.agrformet.2013.04.019}
}

@Article{medlyn2007,
  Title                    = {Linking leaf and tree water use with an individual-tree model},
  Author                   = {Medlyn, B. E. and Pepper, D. A. and O'Grady, A. P. and Keith, H.},
  Journal                  = {Tree Physiology},
  Year                     = {2007},
  Note                     = {12},
  Pages                    = {1687--1699},
  Volume                   = {27}
}

@Book{pearcey1989,
  Title                    = {Plant {Physiological Ecology}: {Field} methods and instrumentation},
  Author                   = {Pearcey, R. and Mooney, H. A. and Rundel, Philip},
  Year                     = {1989}
}

@Article{peltoniemi2012,
  Title                    = {Co-optimal distribution of leaf nitrogen and hydraulic conductance in plant canopies},
  Author                   = {Peltoniemi, Mikko S. and Duursma, Remko A. and Medlyn, Belinda E.},
  Journal                  = {Tree Physiology},
  Year                     = {2012},
  Note                     = {5},
  Pages                    = {510--519},
  Volume                   = {32},

  Doi                      = {10.1093/treephys/tps023}
}

@Manual{rfoundation,
  Title                    = {R: A Language and Environment for Statistical Computing},

  Address                  = {Vienna, Austria},
  Author                   = {{R Core Team}},
  Organization             = {R Foundation for Statistical Computing},
  Year                     = {2015}
}

@Book{ritz2008,
  Title                    = {Nonlinear regression with {R}},
  Author                   = {Ritz, Christian and Streibig, Jens Carl},
  Year                     = {2008}
}

@Article{sellers1997,
  Title                    = {Modeling the {Exchanges} of {Energy}, {Water}, and {Carbon Between Continents} and the {Atmosphere}},
  Author                   = {Sellers, P. J. and Dickinson, R. E. and Randall, D. A. and Betts, A. K. and Hall, F. G. and Berry, J. A. and Collatz, G. J. and Denning, A. S. and Mooney, H. A. and Nobre, C. A. and Sato, N. and Field, C. B. and Henderson-Sellers, A.},
  Journal                  = {Science},
  Year                     = {1997},
  Number                   = {5299},
  Pages                    = {502--509},
  Volume                   = {275},

  Doi                      = {10.1126/science.275.5299.502},
  Pmid                     = {8999789}
}

@Article{sharkey1982,
  Title                    = {A direct confirmation of the standard method of estimating intercellular partial pressure of {CO}2},
  Author                   = {Sharkey, T.D. and Imai, K. and Farquhar, G. D. and Cowan, I.R.},
  Journal                  = {Plant physiology},
  Year                     = {1982},
  Pages                    = {657--659},
  Volume                   = {69}
}

@Article{sharkey2007,
  Title                    = {Fitting photosynthetic carbon dioxide response curves for {C}3 leaves},
  Author                   = {Sharkey, Thomas D. and Bernacchi, Carl J. and Farquhar, Graham D. and Singsaas, Eric L.},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {2007},
  Number                   = {9},
  Pages                    = {1035--1040},
  Volume                   = {30},

  Doi                      = {10.1111/j.1365-3040.2007.01710.x}
}

@Article{tholen2012,
  Title                    = {Variable mesophyll conductance revisited: theoretical background and experimental implications},
  Author                   = {Tholen, Danny and Ethier, Gilbert and Genty, Bernard and Pepin, Steeve and Zhu, Xin-Guang},
  Journal                  = {Plant, Cell \& Environment},
  Year                     = {2012},
  Number                   = {12},
  Pages                    = {2087--2103},
  Volume                   = {35},

  Copyright                = {© 2012 Blackwell Publishing Ltd},
  Doi                      = {10.1111/j.1365-3040.2012.02538.x}
}

@Misc{landfluxtools,
  Title                    = {LandFlux Tools. Accessed 2015-07-09.},

  Author                   = {Tu, K.P., Fisher, J.B.},
  HowPublished             = {\url{http://landflux.org/Tools.php}},
  Note                     = {Accessed: 2015-07-03}
}

@Article{wang1998,
  Title                    = {A two-leaf model for canopy conductance, photosynthesis and partitioning of available energy {I}: {Model} description and comparison with a multi-layered model},
  Author                   = {Wang, Y. P. and Leuning, R.},
  Journal                  = {Agricultural and Forest Meteorology},
  Year                     = {1998},
  Note                     = {1-2},
  Pages                    = {89--111},
  Volume                   = {91}
}

@Article{wright2004,
  Title                    = {The worldwide leaf economics spectrum},
  Author                   = {Wright, I. J. and Reich, P. B. and Westoby, M. and Ackerly, D. D. and Baruch, Z. and Bongers, F. and Cavender-Bares, J. and Chapin, T. and Cornelissen, J. H. C. and Diemer, M. and Flexas, J. and Garnier, E. and Groom, P. K. and Gulias, J. and Hikosaka, K. and Lamont, B. B. and Lee, T. and Lee, W. and Lusk, C. and Midgley, J. J. and Navas, M. L. and Niinemets, U. and Oleksyn, J. and Osada, N. and Poorter, H. and Poot, P. and Prior, L. and Pyankov, V. I. and Roumet, C. and Thomas, S. C. and Tjoelker, M. G. and Veneklaas, E. J. and Villar, R.},
  Journal                  = {Nature},
  Year                     = {2004},
  Note                     = {6985},
  Pages                    = {821--827},
  Volume                   = {428},

  Doi                      = {10.1038/nature02403}
}

@Article{wullschleger1993,
  Title                    = {Biochemical {Limitations} to {Carbon Assimilation} in {C}3 {Plants}---{A Retrospective Analysis} of the {A/Ci Curves} from 109 {Species}},
  Author                   = {Wullschleger, Stan D.},
  Journal                  = {Journal of Experimental Botany},
  Year                     = {1993},
  Note                     = {5},
  Pages                    = {907--920},
  Volume                   = {44},

  Doi                      = {10.1093/jxb/44.5.907}
}

@Misc{,
  Title                    = {A/Ci curve fitting},
  HowPublished             = {\url{http://landflux.org/Tools.php}},
  Note                     = {Accessed: 2015-07-03}
}