@Manual{lbfgsb3cMF,
    title = {{lbfgsb3c}: Limited Memory BFGS Minimizer with Bounds on Parameters with
optim() 'C' Interface},
    author = {Matthew L Fidler and John C Nash and Ciyou Zhu and Richard Byrd and Jorge Nocedal and Jose Luis Morales},
    year = {2018},
    note = {R package version 2018-2.13},
    url = {https://CRAN.R-project.org/package=lbfgsb3c},
  }

@Manual{lbfgsb3JN,
    title = {{lbfgsb3}: Limited Memory BFGS Minimizer with Bounds on Parameters},
    author = {John C Nash and Ciyou Zhu and Richard Byrd and Jorge Nocedal and Jose Luis Morales},
    year = {2015},
    note = {R package version 2015-2.13},
    url = {https://CRAN.R-project.org/package=lbfgsb3},
  }


@Article{RCppDERF2011,
    title = {{Rcpp}: Seamless {R} and {C++} Integration},
    author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
    journal = {Journal of Statistical Software},
    year = {2011},
    volume = {40},
    number = {8},
    pages = {1--18},
    url = {http://www.jstatsoft.org/v40/i08/},
    doi = {10.18637/jss.v040.i08},
  }


@Book{RCppDE2013,
    title = {Seamless {R} and {C++} Integration with {Rcpp}},
    author = {Dirk Eddelbuettel},
    publisher = {Springer},
    address = {New York},
    year = {2013},
    note = {ISBN 978-1-4614-6867-7},
    doi = {10.1007/978-1-4614-6868-4},
  }

@Article{RCppDEJJB2017,
    title = {{Extending extit{R} with 	extit{C++}: A Brief Introduction to 	extit{Rcpp}}},
    author = {Dirk Eddelbuettel and James Joseph Balamuta},
    journal = {PeerJ Preprints},
    year = {2017},
    month = {aug},
    volume = {5},
    pages = {e3188v1},
    issn = {2167-9843},
    url = {https://doi.org/10.7287/peerj.preprints.3188v1},
    doi = {10.7287/peerj.preprints.3188v1},
  }

@Manual{Varadhan2015,
    title = {alabama: Constrained Nonlinear Optimization},
    author = {Ravi Varadhan},
    year = {2015},
    note = {R package version 2015.3-1},
    url = {https://CRAN.R-project.org/package=alabama},
}


@Article{DEJJB2017,
    title = {{Extending 	extit{R} with 	extit{C++}: A Brief Introduction to 	extit{Rcpp}}},
    author = {Dirk Eddelbuettel and James Joseph Balamuta},
    journal = {PeerJ Preprints},
    year = {2017},
    month = {aug},
    volume = {5},
    pages = {e3188v1},
    issn = {2167-9843},
    url = {https://doi.org/10.7287/peerj.preprints.3188v1},
    doi = {10.7287/peerj.preprints.3188v1},
}


@Manual{Fidler2018,
    title = {{lbfgsb3c}: Limited Memory BFGS Minimizer with Bounds on Parameters with
optim() 'C' Interface},
    author = {Matthew L Fidler and John C Nash and Ciyou Zhu and Richard Byrd and Jorge Nocedal and Jose Luis Morales},
    year = {2018},
    note = {R package version 2018-2.13-1},
    url = {https://CRAN.R-project.org/package=lbfgsb3c},
  }


@Manual{Coppola2014,
    title = {lbfgs: Limited-memory BFGS Optimization},
    author = {Antonio Coppola and Brandon Stewart and Naoaki Okazaki},
    year = {2014},
    note = {R package version 1.2.1},
    url = {https://CRAN.R-project.org/package=lbfgs},
}

@article{Byrd1995,
 author = {Byrd, Richard H. and Lu, Peihuang and Nocedal, Jorge and Zhu, Ciyou},
 title = {A Limited Memory Algorithm for Bound Constrained Optimization},
 journal = {SIAM J. Sci. Comput.},
 issue_date = {Sept. 1995},
 volume = {16},
 number = {5},
 month = sep,
 year = {1995},
 issn = {1064-8275},
 pages = {1190--1208},
 numpages = {19},
 url = {http://dx.doi.org/10.1137/0916069},
 doi = {10.1137/0916069},
 acmid = {210980},
 publisher = {Society for Industrial and Applied Mathematics},
 address = {Philadelphia, PA, USA}
} 

@article{Nocedal80,
  title = "Updating Quasi-Newton Matrices with Limited Storage",
  author = "Jorge Nocedal",
  year = "1980",
  month = "7",
  doi = "10.1090/S0025-5718-1980-0572855-7",
  language = "English",
  volume = "35",
  pages = "773--782",
  journal = "Mathematics of Computation"
}

@article{LiuN89,
  author    = {Dong C. Liu and 
               Jorge Nocedal},
  title     = {On the limited memory {BFGS} method for large scale optimization},
  journal   = {Math. Program.},
  volume    = {45},
  number    = {1-3},
  pages     = {503--528},
  year      = {1989},
  url       = {https://doi.org/10.1007/BF01589116},
  doi       = {10.1007/BF01589116},
  biburl    = {https://dblp.org/rec/bib/journals/mp/LiuN89},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}

@article{polak1969,
    author = {Polak, E. and Ribiere, G.},
    journal = {Revue Fran{\c{c}}aise d'Informatique et de Recherche Op{\'{e}}rationnelle},
    pages = {35--43},
    title = {{Note sur la convergence de m{\'{e}}thodes de directions conjugu{\'{e}}es}},
    volume = {16},
    year = {1969}
}

@article{Sorenson1969,
  author = {Sorenson, Harold},
  year = {1969},
  month = {12},
  pages = {421--441},
  title = {Comparison of some conjugate direction procedures for function minimization},
  volume = {288},
  journal = {Journal of The Franklin Institute - Engineering and Applied Mathematics},
  doi = {10.1016/0016-0032(69)90253-1}
}

@incollection{Beale1972, 
  author       = {Beale, E. M. L.}, 
  title        = {A Derivation of Conjugate Gradients},
  booktitle    = {Numerical Methods for Nonlinear Optimization},
  editor       = {F. A. Lootsma},
  publisher    = {Academic Press},
  address      = {London},
  pages        = {39--43},
  year         = 1972
}

@article{Gorn1960,
 author = {Gorn, S.},
 title = {Algorithms: Bisection Routine},
 journal = {Commun. ACM},
 issue_date = {March 1960},
 volume = {3},
 number = {3},
 month = mar,
 year = {1960},
 issn = {0001-0782},
 pages = {174--},
 url = {http://doi.acm.org/10.1145/367149.367173},
 doi = {10.1145/367149.367173},
 acmid = {367173},
 publisher = {ACM},
 address = {New York, NY, USA},
} 

@article{Rader1961,
 author = {Rader, Patty Jane},
 title = {Certification of Algorithm 4: Bisection Routine},
 journal = {Commun. ACM},
 issue_date = {March 1961},
 volume = {4},
 number = {3},
 month = mar,
 year = {1961},
 issn = {0001-0782},
 pages = {153--},
 url = {http://doi.acm.org/10.1145/366199.366275},
 doi = {10.1145/366199.366275},
 acmid = {366275},
 publisher = {ACM},
 address = {New York, NY, USA},
} 


@article{Muller56,
  author = {Muller, David E.},
  journal = {Mathematical Tables and Other Aids to Computation},
  note = {Later Mathematics of Computation.},
  pages = { 208--215},
  title = {A Method for Solving Algebraic Equations Using an Automatic Computer},
  volume = 10,
  year = 1956
}

@article{Ridders79,
  author = {Ridders, C.},
  journal = {Circuits and Systems, IEEE Transactions on},
  month = {11},
  number = 11,
  pages = { 979 - 980},
  title = {A new algorithm for computing a single root of a real continuous function},
  volume = 26,
  year = 1979
}



@InProceedings{Gonnet2001,
author="Gonnet, Gaston H.",
editor="Casacuberta, Carles
and Mir{\'o}-Roig, Rosa Maria
and Verdera, Joan
and Xamb{\'o}-Descamps, Sebasti{\`a}",
title="A Study of Iteration Formulas for Root Finding, Where Mathematics, Computer Algebra and Software Engineering Meet",
booktitle="European Congress of Mathematics",
year="2001",
publisher="Birkh{\"a}user Basel",
address="Basel",
pages="143--156"
}

@Misc{CoreTeam2013,
  Title                    = {{Writing \R\ Extensions}},

  Author                   = {{\R\ Core Team}},
  Year                     = {2013},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://CRAN.R-project.org/doc/manuals/R-exts.html}
}

@Misc{R-extns,
  Title                    = {{Writing \R\ Extensions}},

  Author                   = {{\R\ Core Team}},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/doc/manuals/R-exts.html}
}

@Book{acton70,
  Title                    = {Numerical Methods that Work},
  Author                   = {Forman S. Acton},
  Publisher                = {Harper and Row},
  Year                     = {1970},

  Address                  = {New York}
}

@Article{Grassmann12,
  Title                    = {{GrassmannOptim}: An {R} Package for Grassmann Manifold Optimization},
  Author                   = {Kofi P. Adragni and R. Dennis Cook and Seongho Wu},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2012},
  Number                   = {5},
  Pages                    = {1--18},
  Volume                   = {50},

  Url                      = {http://www.jstatsoft.org/v50/i05/}
}

@Article{DEoptimWilmott11,
  Title                    = {{J}ump-Diffusion Calibration using {D}ifferential {E}volution},
  Author                   = {David Ardia and Juan Ospina Arango and Norman Giraldo Gomez},
  Journal                  = {Wilmott Magazine},
  Year                     = {2011},
  Pages                    = {76--79},
  Volume                   = {55},

  Url                      = {http://www.wilmott.com/}
}

@Article{DEoptimRjournal11,
  Title                    = {{D}ifferential {E}volution with {DEoptim}: An Application to Non-Convex Portfolio Optimization},
  Author                   = {David Ardia and Kris Boudt and Peter Carl and Katharine M. Mullen and Brian G. Peterson},
  Journal                  = {The R Journal},
  Year                     = {2011},
  Number                   = {1},
  Pages                    = {27--34},
  Volume                   = {3},

  Url                      = {http://journal.r-project.org/archive/2011-1/2011-1\_index.html}
}

@Manual{DEoptim13,
  Title                    = {{DEoptim}: Differential Evolution in {R}},
  Author                   = {David Ardia and Katharine M. Mullen and Brian G. Peterson and Joshua Ulrich},
  Note                     = {version 2.2-2},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=DEoptim}
}

@Article{Barzilai88,
  Title                    = {Two-point step size gradient methods},
  Author                   = {Jonathan Barzilai and Jonathan M. Borwein},
  Journal                  = {IMA Journal of Numerical Analysis},
  Year                     = {1988},
  Number                   = {1},
  Pages                    = {141--148},
  Volume                   = {8}
}

@Manual{p-minqa,
  Title                    = {\pkg{minqa}: Derivative-Free Optimization Algorithms by Quadratic
 Approximation},
  Author                   = {Douglas Bates and Katharine M. Mullen and John C. Nash and Ravi Varadhan},
  Note                     = {R package version 1.1.13},
  Organization             = {R Foundation for Statistical Computing},
  Year                     = {2010},

  Url                      = {http://CRAN.R-project.org/package=minqa}
}

@Book{bateswatts,
  Title                    = {Nonlinear Regression Analysis and Its Applications},
  Author                   = {D. M. Bates and D. G. Watts},
  Publisher                = {Wiley},
  Year                     = {1988}
}

@Article{BatesWatts81,
  Title                    = {A Relative Off set Orthogonality Convergence Criterion for Nonlinear least Squares},
  Author                   = {Bates, Douglas M. and Watts, Donald G.},
  Journal                  = {Technometrics},
  Year                     = {1981},
  Number                   = {2},
  Pages                    = {179-183},
  Volume                   = {23}
}

@Manual{p-nlstools,
  Title                    = {nlstools: tools for nonlinear regression diagnostics},
  Author                   = {Florent Baty and Marie-Laure Delignette-Muller},
  Note                     = {R package version 0.0-15},
  Year                     = {2013}
}

@Article{Belisle1992,
  Title                    = {Convergence Theorems for a Class of Simulated Annealing Algorithms on {\$\R\^{}d\$}},
  Author                   = {C. J. P. Belisle},
  Journal                  = {Annals of Applied Probability},
  Year                     = {1992},
  Pages                    = {885--895},
  Volume                   = {29},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@Article{Belisle92,
  Title                    = {Convergence Theorems for a Class of Simulated Annealing
 Algorithms on {$\R^d$}},
  Author                   = {C. J. P. Belisle},
  Journal                  = {Annals of Applied Probability},
  Year                     = {1992},
  Pages                    = {885--895},
  Volume                   = {29}
}

@Manual{Rmalschains12,
  Title                    = {Continuous Optimization using Memetic Algorithms with Local Search Chains (MA-LS-Chains) in R},
  Author                   = {Christoph Bergmeir and Daniel Molina and Jos\'e M. Ben\'itez},
  Note                     = {R package version 0.1},
  Year                     = {2012}
}

@Manual{p-lpSolve,
  Title                    = {{lpSolve: Interface to Lp\_solve v. 5.5 to solve linear / integer programs}},
  Author                   = {Michel Berkelaar and {others}},
  Note                     = {R package version 5.6.7},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=lpSolve}
}

@Manual{p-quadprog,
  Title                    = {quadprog: Functions to solve Quadratic Programming Problems.},
  Author                   = {S original by Berwin A. Turlach R port by Andreas Weingessel},
  Note                     = {R package version 1.5-5},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=quadprog}
}

@PhdThesis{Bhat2011,
  Title                    = {Some aspects of mathematical programming in statistics},
  Author                   = {Bhat, K. A.},
  School                   = {Post Graduate Deptartment of Statistics, Univ. of Kashmir},
  Year                     = {2011},

  Address                  = {Srinagar, India},
  Note                     = {Ph. D. Dissertation}
}

@Article{Birgin2000,
  Title                    = {Nonmonotone Spectral Projected Gradient Methods on
 Convex Sets},
  Author                   = {Ernesto G. Birgin and Jos{\'e} Mario Mart{\'\i}nez and
 Marcos Raydan},
  Journal                  = {SIAM J Optimization},
  Year                     = {2000},

  Month                    = {June--July},
  Number                   = {4},
  Pages                    = {1196--1211},
  Volume                   = {10},

  Url                      = {http://epubs.siam.org/sam-bin/dbq/article/33096}
}

@Article{Birgin2000a,
  Title                    = {Nonmonotone Spectral Projected Gradient Methods on Convex Sets},
  Author                   = {Ernesto G. Birgin and Jos{\'e} Mario Mart{\'\i}nez and Marcos Raydan},
  Journal                  = {SIAM J Optimization},
  Year                     = {2000},

  Month                    = jun,
  Number                   = {4},
  Pages                    = {1196--1211},
  Volume                   = {10},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://epubs.siam.org/sam-bin/dbq/article/33096}
}

@Article{Birgin01spg,
  Title                    = {SPG: Software for convex-constrained optimization},
  Author                   = {Ernesto G. Birgin and Mart'inez Marcos Raydan},
  Journal                  = {ACM Transactions on Mathematical Software},
  Year                     = {2001},
  Pages                    = {340--349},
  Volume                   = {27}
}

@Book{AIMMS06,
  Title                    = {{AIMMS optimization modeling}},
  Author                   = {Bisschop, Johannes and Roelofs, Marcel},
  Publisher                = {Paragon Decision Technology},
  Year                     = {2006},

  ISBN                     = {1847539122}
}

@Article{Bjork:1967,
  Title                    = {Solving Least Squares Problems by {Gram--Schmidt} Orthogonalization},
  Author                   = {A. Bjork},
  Journal                  = {BIT},
  Year                     = {1967},
  Pages                    = {1--21},
  Volume                   = {7}
}

@Article{Boer02atutorial,
  Title                    = {A Tutorial on the Cross-Entropy Method},
  Author                   = {P. T. De Boer and D.P. Kroese and S. Mannor and R.Y. Rubinstein},
  Journal                  = {Annals of Operations Research},
  Year                     = {2002},
  Volume                   = {134}
}

@Manual{p-R2admb,
  Title                    = {R2admb: ADMB to R interface functions},
  Author                   = {Ben Bolker and Hans Skaug and Jeff Laake},
  Note                     = {R package version 0.7.10},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=R2admb}
}

@Manual{p-bbmle,
  Title                    = {bbmle: Tools for general maximum likelihood estimation},
  Author                   = {Ben Bolker and R Development Core Team},
  Note                     = {R package version 1.0.13},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=bbmle}
}

@Manual{Borchers-pracma,
  Title                    = {pracma: Practical Numerical Math Functions},
  Author                   = {Hans Werner Borchers},
  Note                     = {R package version 2.0.7},
  Year                     = {2017},

  Url                      = {https://CRAN.R-project.org/package=pracma}
}

@Manual{p-adagio,
  Title                    = {adagio: Discrete and Global Optimization Routines},
  Author                   = {Hans Werner Borchers},
  Note                     = {R package version 0.5.9},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=adagio}
}

@Manual{p-nloptwrap,
  Title                    = {nloptwrap: Wrapper for Package nloptr},
  Author                   = {Hans W Borchers},
  Note                     = {R package version 0.5-1},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=nloptwrap}
}

@Manual{p-pracma,
  Title                    = {pracma: Practical Numerical Math Functions},
  Author                   = {Hans W Borchers},
  Note                     = {R package version 1.5.0},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=pracma}
}

@Manual{p-trustOptim,
  Title                    = {trustOptim: Trust region nonlinear optimization, efficient for sparse
 Hessians},
  Author                   = {Michael Braun},
  Note                     = {R package version 0.8.1},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=trustOptim}
}

@Article{Bremmerman70,
  Title                    = {A method for unconstrained global optimization},
  Author                   = {Hans Bremmerman},
  Journal                  = {Math. Biosci.},
  Year                     = {1970},
  Pages                    = {1--15},
  Volume                   = {9}
}

@Book{Brent1973,
  Title                    = {Algorithms for Minimization without Derivatives},
  Author                   = {Brent, R.},
  Publisher                = {Prentice-Hall},
  Year                     = {1973},

  Address                  = {Englewood Cliffs, NJ},

  Owner                    = {john},
  Timestamp                = {2018.08.29}
}

@Article{Broyden70,
  Title                    = {The convergence of a class of double-rank minimization algorithms},
  Author                   = {Broyden, C. G.},
  Journal                  = {Journal of the Institute of Mathematics and Its Applications},
  Year                     = {1970},
  Pages                    = {76-–90},
  Volume                   = {6}
}

@Article{Byrd95,
  Title                    = {A Limited Memory Algorithm for Bound Constrained Optimization},
  Author                   = {Richard H. Byrd and Peihuang Lu and Jorge Nocedal and Ci You Zhu},
  Journal                  = {SIAM Journal on Scientific Computing},
  Year                     = {1995},

  Month                    = sep,
  Number                   = {5},
  Pages                    = {1190--1208},
  Volume                   = {16},

  Acknowledgement          = {#ack-nhfb#},
  Bibdate                  = {Fri Dec 4 16:17:35 MST 1998},
  Coden                    = {SJOCE3},
  ISSN                     = {1064-8275 (print), 1095-7197 (electronic)},
  Mrclass                  = {90C30 (65K05)},
  Mrnumber                 = {96e:90039},
  Mrreviewer               = {Henry Wolkowicz}
}

@Article{Davidon91,
  Title                    = {Variable Metric Method for Minimization},
  Author                   = {C. Davidon, William},
  Journal                  = {SIAM J. Optimization},
  Year                     = {1991},

  Month                    = {02},
  Pages                    = {1 - 17},
  Volume                   = {1},

  Doi                      = {10.1137/0801001}
}

@Article{Cauchy1848,
  Title                    = {Méthode générale pour la resolution des systémes d’équations simultanées},
  Author                   = {Cauchy, A.},
  Journal                  = {C. R. Acad. Sci.},
  Year                     = {1848},
  Pages                    = {536-8},
  Volume                   = {27},

  Address                  = {Paris}
}

@Article{Cauchy1848a,
  Title                    = {M\'{e}thode g\'{e}n\'{e}rale pour la resolution des syst\'{e}mes d'\'{e}quations simultan\'{e}es},
  Author                   = {Cauchy, A.},
  Journal                  = {C. R. Acad. Sci.},
  Year                     = {1848},
  Pages                    = {536--8},
  Volume                   = {27},

  __markedentry            = {[john:6]},
  Address                  = {Paris},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@Article{Chan:1983,
  Title                    = {Algorithms for Computing the Sample Variance: Analysis and Recommendations},
  Author                   = {T. F. C. Chan and G. H. Golub and R. J. LeVeque},
  Journal                  = {The American Statistician},
  Year                     = {1983},
  Number                   = {3},
  Pages                    = {242--247},
  Volume                   = {37}
}

@Manual{Colombi2012,
  Title                    = {smco: A simple Monte Carlo optimizer using adaptive coordinate
sampling},
  Author                   = {Prof. Juan David Velasquez H. Universidad Nacional de Colombia},
  Note                     = {R package version 0.1},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=smco}
}

@Manual{smco12,
  Title                    = {smco: A simple Monte Carlo optimizer using adaptive coordinate sampling},
  Author                   = {Prof. Juan David Velasquez H. Universidad Nacional de Colombia},
  Note                     = {R package version 0.1},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=smco}
}

@Book{Conn09,
  Title                    = {Introduction to Derivative-Free Optimization},
  Author                   = {A. R. Conn and K. Scheinberg and L.N.Vicente},
  Publisher                = {SIAM},
  Year                     = {2009},

  Address                  = {Philadelphia},

  __markedentry            = {[john:6]},
  ISBN                     = {0898716683, 9780898716689},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@Book{Conn2009,
  Title                    = {Introduction to Derivative-Free Optimization},
  Author                   = {Conn, Andrew R. and Scheinberg, Katya and Vicente, Luis N.},
  Publisher                = {Society for Industrial and Applied Mathematics},
  Year                     = {2009},

  Address                  = {Philadelphia, PA, USA},

  ISBN                     = {0898716683, 9780898716689}
}

@Article{Cruz2006,
  Title                    = {Spectral residual method without gradient information for solving large-scale nonlinear systems: Theory and experiments},
  Author                   = {William La Cruz and Jos\'{e} Mario Mart\'{\i}nez and Marcos Raydan},
  Journal                  = {Mathematics of Computation},
  Year                     = {2006},
  Pages                    = {1429--1448},
  Volume                   = {75},

  __markedentry            = {[john:6]},
  Institution              = {unknown},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@Article{Cruz06spectralresidual,
  Title                    = {Spectral residual method without gradient information for solving large-scale nonlinear systems: Theory and experiments},
  Author                   = {William La Cruz and José Mario Martínez and Marcos Raydan},
  Journal                  = {Mathematics of Computation},
  Year                     = {2006},
  Pages                    = {1429--1448},
  Volume                   = {75}
}

@TechReport{Cruz04spectralresidual,
  Title                    = {Spectral residual method without gradient information for solving large-scale nonlinear systems: Theory and experiments},
  Author                   = {William La Cruz and José Mario Martínez and Marcos Raydan},
  Institution              = {unknown},
  Year                     = {2004}
}

@Article{Dai01,
  Title                    = {An Efficient Hybrid Conjugate Gradient Method for Unconstrained
 Optimization},
  Author                   = {Y. H. Dai and Y. Yuan},
  Journal                  = {Annals of Operations Research},
  Year                     = {2001},
  Number                   = {1-4},
  Pages                    = {33-47},
  Volume                   = {103},

  Bibsource                = {DBLP, http://dblp.uni-trier.de},
  Ee                       = {http://dx.doi.org/10.1023/A:1012930416777}
}

@Article{Dai99,
  Title                    = {A Nonlinear Conjugate Gradient Method with a Strong Global Convergence Property},
  Author                   = {Y. H. Dai and Y. Yuan},
  Journal                  = {SIAM Journal on Optimization},
  Year                     = {1999},
  Pages                    = {177--182},
  Volume                   = {10}
}

@Article{Davidon59,
  Title                    = {Variable metric method for minimization},
  Author                   = {Davidon, W.C.},
  Year                     = {1959},

  Month                    = {11},

  Doi                      = {10.2172/4222000},
  Place                    = {United States}
}

@InProceedings{Dekker69,
  Title                    = {Finding a zero by means of successive linear interpolation},
  Author                   = {Dekker, T. J.},
  Booktitle                = {Constructive Aspects of the Fundamental Theorem of Algebra},
  Year                     = {1969},
  Editor                   = {Dejon, B. and Henrici, P.},
  Publisher                = {Wiley-Interscience},

  Location                 = {London},
  Owner                    = {john},
  Timestamp                = {2018.08.29}
}

@Manual{p-fitdistrplus,
  Title                    = {fitdistrplus: help to fit of a parametric distribution to non-censored or censored data },
  Author                   = {Marie Laure Delignette-Muller and Regis Pouillot and Jean-Baptiste Denis and Christophe Dutang},
  Note                     = {R package version 1.0-1},
  Year                     = {2013}
}

@InProceedings{Deng06,
  Title                    = {{Adaptation of the UOBYQA Algorithm for Noisy Functions}},
  Author                   = {Deng, Geng and Ferris, Michael C.},
  Booktitle                = {{WSC '06: Proceedings of the 38th Winter Simulation Conference}},
  Year                     = {2006},

  Address                  = {Monterey, California},
  Pages                    = {312--319},
  Publisher                = {Winter Simulation Conference},

  ISBN                     = {1-4244-0501-7}
}

@Book{DennisSchnabel96,
  Title                    = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations},
  Author                   = {Dennis, J. and Schnabel, R.},
  Publisher                = {Society for Industrial and Applied Mathematics},
  Year                     = {1996},

  Address                  = {Englewood Cliffs, NJ},

  Doi                      = {10.1137/1.9781611971200},
  Eprint                   = {http://epubs.siam.org/doi/pdf/10.1137/1.9781611971200},
  Url                      = {http://epubs.siam.org/doi/abs/10.1137/1.9781611971200}
}

@Book{DenSchnab83,
  Title                    = {Numerical Methods for Unconstrained Optimization and Nonlinear Equations},
  Author                   = {Dennis, J. E. and Schnabel, R. B.},
  Publisher                = {Prentice-Hall},
  Year                     = {1983},

  Address                  = {Englewood Cliffs, NJ}
}

@Book{dixon1972nonlinear,
  Title                    = {Nonlinear optimisation},
  Author                   = {Dixon, L.C.W.},
  Publisher                = {The English Universities Press Ltd.},
  Year                     = {1972},

  Address                  = {London}
}

@Article{Domini02,
  Title                    = {On the Use of Generalized Additive Models in Time-Series Studies of Air Pollution and Health.},
  Author                   = {F. Dominici},
  Journal                  = {American Journal of Epidemiology},
  Year                     = {2002},
  Number                   = {3},
  Pages                    = {193--202},
  Volume                   = {156},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@Article{Dominici2002,
  Title                    = {On the Use of Generalized Additive Models in Time-Series 
 Studies of Air Pollution and Health.},
  Author                   = {F. Dominici},
  Journal                  = {American Journal of Epidemiology},
  Year                     = {2002},
  Number                   = {3},
  Pages                    = {193-202},
  Volume                   = {156}
}

@Article{linbench03,
  Title                    = {The {LINPACK} Benchmark: Past, Present, and Future},
  Author                   = {J. J. Dongarra and P. Luszczek and A. Petitet},
  Journal                  = {Concurrency and Computation: Practice and Experience},
  Year                     = {2003},

  Month                    = {August},
  Number                   = {9},
  Pages                    = {803--820},
  Volume                   = {15}
}

@Article{Dugg84,
  Title                    = {Regression Analysis of Nonlinear {Arrhenius} Plots: An Empirical Model and a Computer Program.},
  Author                   = {Duggleby, R G},
  Journal                  = {Computers in Biology and Medicine},
  Year                     = {1984},
  Number                   = {4},
  Pages                    = {447--55},
  Volume                   = {14},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@Article{Duggleby1984,
  Title                    = {Regression Analysis of Nonlinear {Arrhenius} Plots: An Empirical Model and 
 a Computer Program.},
  Author                   = {Duggleby, R G},
  Journal                  = {Computers in Biology and Medicine},
  Year                     = {1984},
  Number                   = {4},
  Pages                    = {447-55},
  Volume                   = {14}
}

@Manual{RcppDE12,
  Title                    = {RcppDE: Global optimization by differential evolution in C++},
  Author                   = {Dirk Eddelbuettel},
  Note                     = {R package version 0.1.1. Extends DEoptim which itself is based on DE-Engine (by Rainer Storn)},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=RcppDE}
}

@Manual{minpacklm12,
  Title                    = {minpack.lm: R interface to the Levenberg-Marquardt nonlinear least-squares
algorithm found in MINPACK, plus support for bounds},
  Author                   = {Timur V. Elzhov and Katharine M. Mullen and Andrej-Nikolai Spiess and Ben Bolker},
  Note                     = {R package version 1.1-6},
  Organization             = {R Project for Statistical Computing},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=minpack.lm}
}

@Article{Eugster2012,
  Title                    = {Domain-Based Benchmark Experiments: Exploratory and
 Inferential Analysis},
  Author                   = {Manuel J. A. Eugster and Torsten Hothorn and
 Friedrich Leisch},
  Journal                  = {Austrian Journal of Statistics},
  Year                     = {2012},
  Number                   = {1},
  Pages                    = {5--26},
  Volume                   = {41},

  Url                      = {http://www.stat.tugraz.at/AJS/ausg121/121Leisch.pdf}
}

@Article{Eugster2012a,
  Title                    = {Domain-Based Benchmark Experiments: Exploratory and Inferential Analysis},
  Author                   = {Manuel J. A. Eugster and Torsten Hothorn and Friedrich Leisch},
  Journal                  = {Austrian Journal of Statistics},
  Year                     = {2012},
  Number                   = {1},
  Pages                    = {5--26},
  Volume                   = {41},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://www.stat.tugraz.at/AJS/ausg121/121Leisch.pdf}
}

@Article{Eugster2011,
  Title                    = {Exploratory Analysis of Benchmark Experiments -- An
 Interactive Approach},
  Author                   = {Manuel J. A. Eugster and Friedrich Leisch},
  Journal                  = {Computational Statistics},
  Year                     = {2011},
  Number                   = {4},
  Pages                    = {699--710},
  Volume                   = {26},

  Doi                      = {10.1007/s00180-010-0227-z},
  Preprinturl              = {http://epub.ub.uni-muenchen.de/10604/}
}

@Article{Eugster2011a,
  Title                    = {Exploratory Analysis of Benchmark Experiments -- An Interactive Approach},
  Author                   = {Manuel J. A. Eugster and Friedrich Leisch},
  Journal                  = {Computational Statistics},
  Year                     = {2011},
  Number                   = {4},
  Pages                    = {699--710},
  Volume                   = {26},

  __markedentry            = {[john:6]},
  Doi                      = {10.1007/s00180-010-0227-z},
  Owner                    = {john},
  Preprinturl              = {http://epub.ub.uni-muenchen.de/10604/},
  Timestamp                = {2018.11.16}
}

@Article{Feldman91,
  Title                    = {Availability of f2c - a Fortran to C converter},
  Author                   = {Feldman, S. I. and Gay, D. M. and Maimone, M. W. and Schryer, N. L.},
  Journal                  = {SIGPLAN Fortran Forum},
  Year                     = {1991},

  Month                    = jul,
  Number                   = {2},
  Pages                    = {14--15},
  Volume                   = {10},

  Address                  = {New York, NY, USA},
  Issue_date               = {July 1991},
  Numpages                 = {2},
  Publisher                = {ACM}
}

@Article{Fletcher70,
  Title                    = {A New Approach to Variable Metric Algorithms},
  Author                   = {R. Fletcher},
  Journal                  = {Computer Journal},
  Year                     = {1970},
  Number                   = {3},
  Pages                    = {317-322},
  Volume                   = {13},

  Bibsource                = {DBLP, http://dblp.uni-trier.de}
}

@Article{FletReeves64,
  Title                    = {Function minimization by conjugate gradients},
  Author                   = {Fletcher, R. and Reeves, C. M.},
  Journal                  = {The Computer Journal},
  Year                     = {1964},
  Number                   = {2},
  Pages                    = {149-154},
  Volume                   = {7}
}

@Book{Forsythe77,
  Title                    = {Computer Methods for Mathematical Computations},
  Author                   = {Forsythe, George E. and Malcolm, Michael A. and Moler, Cleve B.},
  Publisher                = {Prentice Hall Professional Technical Reference},
  Year                     = {1977},

  ISBN                     = {0131653326},
  Owner                    = {john},
  Timestamp                = {2018.08.29}
}

@Misc{Fox2006,
  Title                    = {{TEACHER'S CORNER} Structural Equation Modeling With the sem Package in {R}},

  Author                   = {John Fox},
  Year                     = {2006},

  __markedentry            = {[john:6]},
  Journal                  = {STRUCTURAL EQUATION MODELING},
  Numeber                  = {3},
  Owner                    = {john},
  Pages                    = {465–-486},
  Timestamp                = {2018.11.16},
  Volume                   = {13}
}

@Misc{Fox-sem,
  Title                    = {{TEACHER’S CORNER} Structural Equation Modeling With the sem Package in {R}},

  Author                   = {John Fox},
  Year                     = {2006},

  Journal                  = {STRUCTURAL EQUATION MODELING},
  Numeber                  = {3},
  Pages                    = {465–-486},
  Volume                   = {13}
}

@Manual{p-sem,
  Title                    = {sem: Structural Equation Models},
  Author                   = {John Fox and Zhenghua Nie and Jarrett Byrnes},
  Note                     = {R package version 3.1-301},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=sem}
}

@Misc{Fox1997,
  Title                    = {The {Port Mathematical Subroutine Library}, Version 3},

  Author                   = {Phyllis Fox},
  Year                     = {1997},

  __markedentry            = {[john:6]},
  Address                  = {Murray Hill, NJ},
  Owner                    = {john},
  Publisher                = {AT\&T Bell Laboratories},
  Timestamp                = {2018.11.16},
  Url                      = {http://www.bell-labs.com/project/PORT/}
}

@Misc{PORTlib,
  Title                    = {The {Port Mathematical Subroutine Library}, Version 3},

  Author                   = {Phyllis Fox},
  Year                     = {1997},

  Address                  = {Murray Hill, NJ},
  Publisher                = {AT\&T Bell Laboratories},
  Url                      = {http://www.bell-labs.com/project/PORT/}
}

@Article{Fox1978PORT,
  Title                    = {The {PORT} Mathematical Subroutine Library},
  Author                   = {P. A. Fox and A. D. Hall and N. L. Schryer},
  Journal                  = {ACM Transactions on Mathematical Software (TOMS)},
  Year                     = {1978},

  Month                    = jun,
  Number                   = {2},
  Pages                    = {104--126},
  Volume                   = {4}
}

@Book{Gentle:1998,
  Title                    = {Numerical Linear Algebra for Applications in Statistics},
  Author                   = {James E. Gentle},
  Publisher                = {Springer},
  Year                     = {1998}
}

@Article{Bioc04,
  Title                    = {Bioconductor: Open Software Development for Computational Biology and 
 Bioinformatics},
  Author                   = {Robert C Gentleman and Vincent J. Carey and Douglas M. Bates and {others}},
  Journal                  = {Genome Biology},
  Year                     = {2004},
  Pages                    = {R80},
  Volume                   = {5},

  Url                      = {http://genomebiology.com/2004/5/10/R80}
}

@Article{Geradin71,
  Title                    = {The computational efficiency of a new minimization algorithm for eigenvalue analysis},
  Author                   = {Geradin, M.},
  Journal                  = {J. Sound Vib.},
  Year                     = {1971},
  Pages                    = {319--331},
  Volume                   = {19}
}

@Manual{p-trust,
  Title                    = {trust: Trust Region Optimization},
  Author                   = {Charles J. Geyer},
  Note                     = {R package version 0.1-4},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=trust}
}

@InProceedings{Geyer91,
  Title                    = {Markov chain Monte Carlo maximum likelihood},
  Author                   = {C. J. Geyer},
  Booktitle                = {{Computing Science and Statistics, Proceedings of the 23rd Symposium on the Interface}},
  Year                     = {1991},
  Pages                    = {n.a.},
  Publisher                = {American Statistical Association, New York}
}

@Manual{Ghalanos2012,
  Title                    = {Rsolnp: General Non-linear Optimization Using Augmented Lagrange Multiplier Method},
  Author                   = {Alexios Ghalanos and Stefan Theussl},
  Note                     = {R package version 1.14},
  Year                     = {2012},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://CRAN.R-project.org/package=Rsolnp}
}

@Manual{p-Rsolnp,
  Title                    = {Rsolnp: General
 Non-linear Optimization Using Augmented Lagrange Multiplier Method},
  Author                   = {Alexios Ghalanos and Stefan Theussl},
  Note                     = {R package version 1.14},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=Rsolnp}
}

@Manual{p-numDeriv,
  Title                    = {\pkg{numDeriv}: Accurate Numerical Derivatives},
  Author                   = {Paul Gilbert},
  Note                     = {R package version 2009.2-1},
  Organization             = {R Foundation for Statistical Computing},
  Year                     = {2009},

  Url                      = {http://www.bank-banque-canada.ca/pgilbert}
}

@Book{gillmurraywright,
  Title                    = {Practical Optimization},
  Author                   = {P. E.~Gill and W.~Murray and M. H.~Wright},
  Publisher                = {Academic Press},
  Year                     = {1981}
}

@Misc{Gil93,
  Title                    = {p2c},

  Author                   = {Dave Gillespie},
  Year                     = {1993},

  __markedentry            = {[john:6]},
  Address                  = {Boston, MA},
  Owner                    = {john},
  Publisher                = {Free Software Foundation},
  Timestamp                = {2018.11.16},
  Url                      = {http://directory.fsf.org/project/p2c/}
}

@Misc{Gillespie1993,
  Title                    = {p2c},

  Author                   = {Dave Gillespie},
  Year                     = {1993},

  Address                  = {Boston, MA},
  Publisher                = {Free Software Foundation},
  Url                      = {http://directory.fsf.org/project/p2c/}
}

@Article{Glover89,
  Title                    = {Tabu Search - Part 1},
  Author                   = {Fred Glover},
  Journal                  = {ORSA Journal on Computing},
  Year                     = {1989},
  Number                   = {2},
  Pages                    = {190--206},
  Volume                   = {1}
}

@Article{Goldberg:1991,
  Title                    = {What Every Computer Scientist Should Know About Floating-Point Arithmetic},
  Author                   = {David Goldberg},
  Journal                  = {ACM Computing Surveys},
  Year                     = {1991},
  Pages                    = {5--48},

  Colume                   = {23},
  Lnumber                  = {1},
  Url                      = {http://www.validlab.com/goldberg/paper.pdf}
}

@Article{Goldfarb70,
  Title                    = {A Family of Variable Metric Updates Derived by Variational Means},
  Author                   = {Goldfarb, D.},
  Journal                  = {Mathematics of Computation},
  Year                     = {1970},
  Number                   = {109},
  Pages                    = {23--26},
  Volume                   = {24}
}

@InProceedings{Golub1979,
  Title                    = {Extensions and Uses of the Variable Projection Algorithm for Solving Nonlinear Least Squares Problems},
  Author                   = {Gene H. Golub and Randall J. LeVeque},
  Booktitle                = {Proceedings of the Army Numerical Analysis and Computing Conference},
  Year                     = {1979},
  Pages                    = {1--12},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@InProceedings{GolubLeveque79,
  Title                    = {Extensions and Uses of the Variable Projection
 Algorithm for Solving Nonlinear Least Squares
 Problems},
  Author                   = {Gene H. Golub and Randall J. LeVeque},
  Booktitle                = {Proceedings of the Army Numerical Analysis and Computing Conference},
  Year                     = {1979},
  Pages                    = {1--12}
}

@Article{Golub1973,
  Title                    = {The Differentiation of Pseudo-Inverses and Nonlinear Least Squares Problems Whose Variables Separate},
  Author                   = {G. H. Golub and V. Pereyra},
  Journal                  = {SIAM Journal of Numerical Analysis},
  Year                     = {1973},

  Month                    = apr,
  Number                   = {2},
  Pages                    = {413--432},
  Volume                   = {10},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@Article{GolubPereyra73,
  Title                    = {The Differentiation of Pseudo-Inverses and Nonlinear
 Least Squares Problems Whose Variables Separate},
  Author                   = {G. H. Golub and V. Pereyra},
  Journal                  = {SIAM Journal of Numerical Analysis},
  Year                     = {1973},

  Month                    = apr,
  Number                   = {2},
  Pages                    = {413--432},
  Volume                   = {10}
}

@Article{Hager2006b,
  Title                    = {A Survey of Nonlinear Conjugate Gradient Methods},
  Author                   = {William W. Hager and Hongchao Zhang},
  Journal                  = {Pacific Journal of Optimization},
  Year                     = {2006},
  Pages                    = {35--58},
  Volume                   = {2}
}

@Article{Hager2005,
  Title                    = {A new conjugate gradient method with 
                              guaranteed descent and an efficient line search},
  Author                   = {William W. Hager and Hongchao Zhang},
  Journal                  = {SIAM J. Optim.},
  Year                     = {2005},
  Number                   = {1},
  Pages                    = {170--192},
  Volume                   = {16}
}

@Article{Hager2006a,
  Title                    = {{Algorithm 851}: {CG\_DESCENT}, a conjugate gradient
 method with guaranteed descent},
  Author                   = {William W. Hager and Hongchao Zhang},
  Journal                  = {ACM Transactions on Mathematical Software},
  Year                     = {2006},
  Month                    = mar,
  Number                   = {1},
  Pages                    = {113--137},
  Volume                   = {32}
}

@Book{HansenWalster2004,
  Title                    = {Global Optimization Using Interval Analysis},
  Author                   = {E. R. Hansen and G. W. Walster},
  Publisher                = {MIT Press},
  Year                     = {2004},

  Address                  = {Cambridge, Massachusetts}
}

@Manual{p-Rsymphony,
  Title                    = {Rsymphony: Symphony in R},
  Author                   = {Reinhard Harter and Kurt Hornik and Stefan Theussl},
  Note                     = {R package version 0.1-16},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=Rsymphony}
}

@Article{Hartley61,
  Title                    = {The Modified Gauss-Newton Method for the Fitting of Non-linear Regression Functions by Least Squares},
  Author                   = {Hartley, H. O.},
  Journal                  = {Technometrics},
  Year                     = {1961},
  Pages                    = {269-–280},
  Volume                   = {3}
}

@Manual{p-nleqslv,
  Title                    = {nleqslv: Solve systems of non linear equations},
  Author                   = {Berend Hasselman},
  Note                     = {R package version 2.0},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=nleqslv}
}

@Manual{HHpackage:2015,
  Title                    = {HH: Statistical Analysis and Data Display: Heiberger and Holland.},
  Author                   = {Richard M. Heiberger},
  Note                     = {R package version 3.1-15},
  Year                     = {2015},

  Url                      = {http://CRAN.R-project.org/package=HH}
}

@Book{Heiberger:1989,
  Title                    = {Computation for the Analysis of Designed Experiments},
  Author                   = {Richard M. Heiberger},
  Publisher                = {Wiley},
  Year                     = {1989}
}

@Book{HH2,
  Title                    = {Statistical Analysis and Data Display: An Intermediate Course with Examples in R},
  Author                   = {Richard M. Heiberger and Burt Holland},
  Publisher                = {Springer-Verlag, New York},
  Year                     = {2015},
  Edition                  = {Second},

  Url                      = {http://www.springer.com/978-1-4939-2121-8}
}

@Book{RthroughExcelbook:2009pub,
  Title                    = {R through Excel: A Spreadsheet Interface for Statistics, Data Analysis, and Graphics},
  Author                   = {Richard M. Heiberger and Erich Neuwirth},
  Publisher                = {Springer},
  Year                     = {2009},

  Url                      = {http://www.springer.com/978-1-4419-0051-7}
}

@Manual{p-linprog,
  Title                    = {{linprog: Linear Programming / Optimization}},
  Author                   = {Arne Henningsen},
  Note                     = {R package version 0.9-2},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=linprog}
}

@Article{p-systemfit,
  Title                    = {systemfit: A Package for Estimating Systems of Simultaneous Equations in R},
  Author                   = {Arne Henningsen and Jeff D. Hamann},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2007},
  Number                   = {4},
  Pages                    = {1--40},
  Volume                   = {23},

  Url                      = {http://www.jstatsoft.org/v23/i04/}
}

@Article{Hestenes1952,
  Title                    = {Methods of conjugate gradients for solving linear systems},
  Author                   = {Hestenes, M. R. and Stiefel, E.},
  Journal                  = {Journal of research of the National Bureau of Standards},
  Year                     = {1952},
  Pages                    = {409--436},
  Volume                   = {49}
}

@Book{holland75,
  Title                    = {{Adaptation in Natural and Artificial Systems}},
  Author                   = {Holland, J. H.},
  Publisher                = {University of Michigan Press},
  Year                     = {1975},

  Address                  = {Ann Arbor, MI, USA}
}

@Article{Hooke61,
  Title                    = {``Direct Search'' Solution of Numerical and Statistical
 Problems},
  Author                   = {Robert Hooke and
 T. A. Jeeves},
  Journal                  = {J. ACM},
  Year                     = {1961},
  Number                   = {2},
  Pages                    = {212-229},
  Volume                   = {8},

  Bibsource                = {DBLP, http://dblp.uni-trier.de},
  Ee                       = {http://doi.acm.org/10.1145/321062.321069}
}

@Manual{p-ROI,
  Title                    = {ROI: R Optimization Infrastructure},
  Author                   = {Kurt Hornik and David Meyer and Stefan Theussl},
  Note                     = {R package version 0.0-7},
  Year                     = {2011},

  Url                      = {http://CRAN.R-project.org/package=ROI}
}

@Book{Huet1996,
  Title                    = {Statistical tools for nonlinear regression: a practical guide with {S-PLUS} examples},
  Author                   = {S. (Sylvie) Huet and others},
  Publisher                = {Springer-Verlag},
  Year                     = {1996},

  Address                  = {Berlin \& New York},
  Series                   = {Springer series in statistics},

  __markedentry            = {[john:6]},
  Acknowledgement          = {\#ack-nhfb\#},
  Bibdate                  = {Tue Sep 22 08:25:09 MDT 1998},
  ISBN                     = {0-387-94727-2},
  Isbn-13                  = {978-0-387-94727-3},
  Keywords                 = {Regression analysis; Nonlinear theories; Parameter estimation.},
  Lccn                     = {QA278.2.S73 1996},
  Owner                    = {john},
  Pages                    = {ix + 154},
  Timestamp                = {2018.11.16}
}

@Book{Huet1996a,
  Title                    = {Statistical tools for nonlinear regression: a
 practical guide with {S-PLUS} examples},
  Author                   = {S. (Sylvie) Huet and others},
  Publisher                = {Springer-Verlag},
  Year                     = {1996},

  Address                  = {Berlin \& New York},
  Series                   = {Springer series in statistics},

  Acknowledgement          = {#ack-nhfb#},
  Bibdate                  = {Tue Sep 22 08:25:09 MDT 1998},
  ISBN                     = {0-387-94727-2},
  Isbn-13                  = {978-0-387-94727-3},
  Keywords                 = {Regression analysis; Nonlinear theories; Parameter
 estimation.},
  Lccn                     = {QA278.2.S73 1996},
  Pages                    = {ix + 154}
}

@Manual{soma11,
  Title                    = {soma: General-purpose optimisation with the Self-Organising Migrating
Algorithm},
  Author                   = {Jon Clayden; based on the work of Ivan Zelinka},
  Note                     = {R package version 1.1.0},
  Year                     = {2011},

  Url                      = {http://CRAN.R-project.org/package=soma}
}

@Article{Jacobi1846,
  Title                    = {{\"U}ber ein leichtes Verfahren die in der Theorie der S{\"a}cul{\"a}rst{\"o}rungen vorkommenden Gleichungen numerisch aufzul{\"o}sen},
  Author                   = {C. G. J. Jacobi},
  Journal                  = {Crelle},
  Year                     = {1846},
  Pages                    = {51--94},
  Volume                   = {30}
}

@Article{JoeNash,
  Title                    = {Numerical Optimization and Surface Estimation with Imprecise Function Evaluations},
  Author                   = {Joe, Harry and Nash, John C.},
  Journal                  = {Statistics and Computing},
  Year                     = {2003},
  Number                   = {3},
  Pages                    = {277--286},
  Volume                   = {13},

  Address                  = {Hingham, MA, USA},
  Doi                      = {http://dx.doi.org/10.1023/A:1024226918553},
  ISSN                     = {0960-3174},
  Publisher                = {Kluwer Academic Publishers}
}

@Article{Joh03,
  Title                    = {Mineralization of Aged Atrazine, Terbuthylazine, 2,4-D, and Mecoprop in Soil and Aquifer Sediment},
  Author                   = {H. Johannesen and J. Aamand},
  Journal                  = {Environmental Toxicology and Chemistry},
  Year                     = {2003},
  Pages                    = {722--729},
  Volume                   = {22},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@Article{Johannesen2003,
  Title                    = {Mineralization of Aged Atrazine, Terbuthylazine, 2,4-D, and Mecoprop 
 in Soil and Aquifer Sediment},
  Author                   = {H. Johannesen and J. Aamand},
  Journal                  = {Environmental Toxicology and Chemistry},
  Year                     = {2003},
  Pages                    = {722--729},
  Volume                   = {22}
}

@Misc{Johnson2008,
  Title                    = {{The NLopt nonlinear-optimization package}},

  Author                   = {Steven G. Johnson},
  Year                     = {2008},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://ab-initio.mit.edu/nlopt}
}

@Misc{NLoptSJ,
  Title                    = {{The NLopt nonlinear-optimization package}},

  Author                   = {Steven G. Johnson},
  Year                     = {2008},

  Url                      = {http://ab-initio.mit.edu/nlopt}
}

@Article{Jones70,
  Title                    = {Spiral -- a new algorithm for non-linear parameter estimation using least squares},
  Author                   = {Jones, A},
  Journal                  = {Computer Journal},
  Year                     = {1970},
  Number                   = {3},
  Pages                    = {301--308},
  Volume                   = {13}
}

@Book{Kahaner89,
  Title                    = {Numerical Methods and Software},
  Author                   = {Kahaner, David and Moler, Cleve and Nash, Stephen},
  Publisher                = {Prentice-Hall, Inc.},
  Year                     = {1989},

  Address                  = {Upper Saddle River, NJ, USA},

  ISBN                     = {0-13-627258-4}
}

@Article{grofit10,
  Title                    = {{grofit}: Fitting Biological Growth Curves with {R}},
  Author                   = {Matthias Kahm and Guido Hasenbrink and Hella Lichtenberg-Frat\'{e} and Jost Ludwig and Maik Kschischo},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2010},
  Number                   = {7},
  Pages                    = {1--21},
  Volume                   = {33},

  Url                      = {http://www.jstatsoft.org/v33/i07/}
}

@Article{p-kernlab,
  Title                    = {kernlab -- An {S4} Package for Kernel Methods in {R}},
  Author                   = {Alexandros Karatzoglou and Alex Smola and Kurt Hornik and Achim Zeileis},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2004},
  Number                   = {9},
  Pages                    = {1--20},
  Volume                   = {11},

  Url                      = {http://www.jstatsoft.org/v11/i09/}
}

@MastersThesis{Karush39,
  Title                    = {Minima of Functions of Several Variables with Inequalities as Side Constraints},
  Author                   = {W. Karush},
  School                   = {Dept. of Mathematics, Univ. of Chicago},
  Year                     = {1939},

  Address                  = {Chicago, Illinois},
  Note                     = {M.Sc. Dissertation}
}

@Book{kelley1987iterative,
  Title                    = {Iterative Methods for Optimization},
  Author                   = {Kelley, C.T.},
  Publisher                = {Society for Industrial and Applied Mathematics},
  Year                     = {1987},
  Series                   = {Frontiers in Applied Mathematics},

  ISBN                     = {9780898714333},
  Lccn                     = {lc99011141},
  Url                      = {http://books.google.ca/books?id=Bq6VcmzOe1IC}
}

@Article{Kelley97,
  Title                    = {Detection and Remediation of Stagnation in the Nelder-Mead Algorithm Using a Sufficient Decrease Condition},
  Author                   = {C. T. Kelley},
  Journal                  = {SIAM Journal on Optimization},
  Year                     = {1997},
  Pages                    = {43--55},
  Volume                   = {10}
}

@InProceedings{Kennedy95PSO,
  Title                    = {Particle swarm optimization},
  Author                   = {Kennedy, J. and Eberhart, R.},
  Booktitle                = {Neural Networks, 1995. Proceedings., IEEE International Conference on},
  Year                     = {1995},
  Pages                    = {1942-1948},
  Volume                   = {4}
}

@Article{Kirkpatrick83,
  Title                    = {Optimization by Simulated Annealing},
  Author                   = {S. Kirkpatrick and C. D. Gelatt Jr. and M. P. Vecchi},
  Journal                  = {Science},
  Year                     = {1983},

  Month                    = {May},
  Number                   = {4598},
  Pages                    = {671--680},
  Volume                   = {220}
}

@Manual{quantreg13,
  Title                    = {quantreg: Quantile Regression},
  Author                   = {Roger Koenker},
  Note                     = {R package version 5.05},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=quantreg}
}

@Book{Koenker2005,
  Title                    = {Quantile regression},
  Author                   = {Koenker, R.},
  Publisher                = {Cambridge University Press},
  Year                     = {2005},

  Address                  = {Cambridge},

  Doi                      = {10.1017/CBO9780511754098}
}

@Book{Koenker2005a,
  Title                    = {Quantile regression},
  Author                   = {Koenker, R.},
  Publisher                = {Cambridge University Press},
  Year                     = {2005},

  Address                  = {Cambridge},

  Doi                      = {10.1017/CBO9780511754098}
}

@Article{Kovalchik12,
  Title                    = {A general binomial regression model to estimate standardized risk differences from binary response data},
  Author                   = {Kovalchik, Stephanie A. and Varadhan, Ravi and Fetterman, Barbara and Poitras, Nancy E. and Wacholder, Sholom and Katki, Hormuzd A.},
  Journal                  = {Statistics in Medicine},
  Year                     = {2013},
  Number                   = {5},
  Pages                    = {808--821},
  Volume                   = {32},

  Publisher                = {John Wiley \& Sons, Ltd}
}

@InProceedings{KuhnTucker51,
  Title                    = {Nonlinear programming},
  Author                   = {Kuhn, H. W. and Tucker, A. W.},
  Booktitle                = {{Proceedings of 2nd Berkeley Symposium}},
  Year                     = {1951},

  Address                  = {{Berkeley, USA}},
  Pages                    = {481 -– 492},

  Institution              = {{University of California Press}}
}

@Article{Kulkarni2011PCA,
  Title                    = {A probability collectives approach with a feasibility-based rule for constrained optimization},
  Author                   = {Kulkarni, Anand J. and Tai, K.},
  Journal                  = {Appl. Comp. Intell. Soft Comput.},
  Year                     = {2011},

  Month                    = jan,
  Pages                    = {12:12--12:12},
  Volume                   = {2011},

  Acmid                    = {2208425},
  Address                  = {New York, NY, United States},
  Articleno                = {12},
  Doi                      = {10.1155/2011/980216},
  ISSN                     = {1687-9724},
  Issue_date               = {January 2011},
  Numpages                 = {1},
  Publisher                = {Hindawi Publishing Corp.},
  Url                      = {http://dx.doi.org/10.1155/2011/980216}
}

@Manual{rbenchmark12,
  Title                    = {rbenchmark: Benchmarking routine for R},
  Author                   = {Wacek Kusnierczyk},
  Note                     = {R package version 1.0.0},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=rbenchmark}
}

@Book{Lanczos1956,
  Title                    = {Applied Analysis},
  Author                   = {Cornelius Lanczos},
  Publisher                = {Prentice-Hall},
  Year                     = {1956},

  Address                  = {Englewood Cliffs, NJ},
  Note                     = {Reprinted by Dover, New York,
 1988.},

  Pages                    = {xx + 539}
}

@Book{Lange:1999,
  Title                    = {Numerical Analysis for Statisticians},
  Author                   = {Kenneth Lange},
  Publisher                = {Springer},
  Year                     = {1999}
}

@Article{Levenberg44,
  Title                    = {A Method for the Solution of Certain Non-Linear Problems in Least Squares},
  Author                   = {Kenneth Levenberg},
  Journal                  = {Quarterly of Applied Mathematics},
  Year                     = {1944},
  Pages                    = {164-–168},
  Volume                   = {2}
}

@Article{Lu94limitedmemory,
  Title                    = {A Limited-Memory Algorithm for Bound Constrained Optimization},
  Author                   = {Peihuang Lu and Jorge Nocedal and Ciyou Zhu and Richard H. Byrd},
  Journal                  = {SIAM Journal on Scientific Computing},
  Year                     = {1994},
  Pages                    = {1190--1208},
  Volume                   = {16}
}

@Article{BUGS09,
  Title                    = {The BUGS project: Evolution, critique and future directions},
  Author                   = {Lunn, David and Spiegelhalter, David and Thomas, Andrew and Best, Nicky},
  Journal                  = {Statistics in Medicine},
  Year                     = {2009},
  Number                   = {25},
  Pages                    = {3049--3067},
  Volume                   = {28},

  Publisher                = {John Wiley \& Sons, Ltd.}
}

@Article{Lyness1971,
  Title                    = {Algorithm 413: ENTCAF and ENTCRE: evaluation of normalized Taylor coefficients of an analytic function},
  Author                   = {Lyness, J. N. and Sande, G.},
  Journal                  = {Communications of the ACM},
  Year                     = {1971},

  Month                    = oct,
  Number                   = {10},
  Pages                    = {669--675},
  Volume                   = {14},

  Issue_date               = {Oct. 1971}
}

@Article{MSB91,
  Title                    = {{The Parallel Genetic Algorithm as Function Optimizer}},
  Author                   = {H. M\"{u}hlenbein and D. Schomisch and J. Born},
  Journal                  = {{Parallel Computing}},
  Year                     = {1991},
  Number                   = {6-7},
  Pages                    = {619-632},
  Volume                   = {17}
}

@Manual{p-Rmpfr,
  Title                    = {Rmpfr: R MPFR - Multiple Precision Floating-Point Reliable},
  Author                   = {Martin Maechler},
  Note                     = {R package version 0.5-3},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=Rmpfr}
}

@Article{Marq63,
  Title                    = {{An Algorithm for Least-Squares Estimation of Nonlinear Parameters}},
  Author                   = {Marquardt, Donald W.},
  Journal                  = {SIAM Journal on Applied Mathematics},
  Year                     = {1963},
  Number                   = {2},
  Pages                    = {431--441},
  Volume                   = {11},

  Publisher                = {SIAM}
}

@Article{martins03,
  Title                    = {The complex-step derivative approximation},
  Author                   = {Martins, Joaquim R. R. A. and Sturdza, Peter and Alonso, Juan J.},
  Journal                  = {ACM Transactions on Mathematical Software},
  Year                     = {2003},
  Number                   = {3},
  Pages                    = {245--262},
  Volume                   = {29},

  Timestamp                = {2010-11-14T22:23:38.000+0100},
  Url                      = {http://dx.doi.org/10.1145/838250.838251}
}

@InProceedings{McCarthy1988,
  Title                    = {The use of mathematical programming for designing dual frame surveys},
  Author                   = {William F. McCarthy and David V. Bateman},
  Booktitle                = {Proceedings of the Survey Research Methods Section, 1988},
  Year                     = {1988},
  Pages                    = {652--653},
  Publisher                = {American Statistical Association, Alexandria, VA},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@InProceedings{McCarthy88,
  Title                    = {The use of mathematical programming for designing dual
 frame surveys},
  Author                   = {William F. McCarthy and David V. Bateman},
  Booktitle                = {Proceedings of the Survey Research Methods Section, 1988},
  Year                     = {1988},
  Pages                    = {652--653},
  Publisher                = {American Statistical Association, Alexandria, VA}
}

@Book{mccullagh1989generalized,
  Title                    = {Generalized Linear Models, Second Edition},
  Author                   = {McCullagh, P. and Nelder, J.A.},
  Publisher                = {Chapman and Hall},
  Year                     = {1989},
  Series                   = {Monographs on statistics and applied probability},

  ISBN                     = {9780412317606},
  Lccn                     = {99013896},
  Url                      = {http://books.google.ca/books?id=h9kFH2\_FfBkC}
}

@InCollection{bdm04,
  Title                    = {Some Details of Nonlinear Estimation},
  Author                   = {McCullough, B. D.},
  Booktitle                = {Numerical Issues in Statistical Computing for the Social Scientist},
  Publisher                = {John Wiley \& Sons, Inc.},
  Year                     = {2004},
  Chapter                  = {8},
  Editor                   = {Altman, Micah and Gill, Jeff and McDonald, Michael P.},
  Pages                    = {199--218}
}

@Article{mccren00,
  Title                    = {Some Numerical Aspects of Nonlinear Estimation},
  Author                   = {B. D. McCullough and Charles G. Renfro},
  Journal                  = {Journal of Economic and Social Measurement},
  Year                     = {2000},
  Number                   = {1},
  Pages                    = {63--77},
  Volume                   = {26}
}

@Article{rgenoud11,
  Title                    = {Genetic Optimization Using Derivatives: The {rgenoud} Package for {R}},
  Author                   = {Walter R. {Mebane, Jr.} and Jasjeet S. Sekhon},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2011},
  Number                   = {11},
  Pages                    = {1--26},
  Volume                   = {42},

  Url                      = {http://www.jstatsoft.org/v42/i11/}
}

@Manual{Melville17,
  Title                    = {mize: Unconstrained Numerical Optimization Algorithms},
  Author                   = {James Melville},
  Note                     = {R package version 0.1.1},
  Year                     = {2017},

  Url                      = {https://CRAN.R-project.org/package=mize}
}

@Manual{microbench13,
  Title                    = {microbenchmark: Sub microsecond accurate timing functions.},
  Author                   = {Olaf Mersmann},
  Note                     = {R package version 1.3-0},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=microbenchmark}
}

@Misc{Mittelm2008,
  Title                    = {Decision Tree for Optimization Software},

  Author                   = {H. Mittelman},
  Year                     = {2008},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://plato.asu.edu/guide.html}
}

@Misc{plato,
  Title                    = {Decision Tree for Optimization Software},

  Author                   = {H. Mittelman},
  Year                     = {2008},

  Url                      = {http://plato.asu.edu/guide.html}
}

@Article{moler2003ndw,
  Title                    = {Nineteen Dubious Ways to Compute the Exponential of a Matrix, Twenty-Five Years Later},
  Author                   = {Moler, Cleve and Loan, Charles Van},
  Journal                  = {SIAM Review},
  Year                     = {2003},
  Number                   = {1},
  Pages                    = {3-49},
  Volume                   = {45},

  Publisher                = {SIAM}
}

@Manual{Molga2005,
  Title                    = {Test functions for optimization needs},
  Author                   = {Molga, M. and Smutnicki, C.},
  Year                     = {2005},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://www.zsd.ict.pwr.wroc.pl/files/docs/functions.pdf}
}

@Manual{Molga2005a,
  Title                    = { Test functions for optimization needs},
  Author                   = { Molga, M. and Smutnicki, C. },
  Year                     = {2005},

  Url                      = {http://www.zsd.ict.pwr.wroc.pl/files/docs/functions.pdf}
}

@Book{Maple10,
  Title                    = {Maple~10 Programming Guide},
  Author                   = {Michael B.~Monagan and Keith O.~Geddes and K.~Michael Heal
and George Labahn and Stefan M.~Vorkoetter and James McCarron and Paul DeMarco},
  Publisher                = {Maplesoft},
  Year                     = {2005},

  Address                  = {Waterloo ON, Canada}
}

@TechReport{more80,
  Title                    = {{ANL-80-74}, {User Guide for MINPACK-1}},
  Author                   = {Mor\'{e}, J. J. and Garbow, B. S. and Hillstrom, K. E.},
  Institution              = {Argonne National Laboratory},
  Year                     = {1980},

  Keywords                 = {algorithm, fittiookeng, optimization},
  Url                      = {http://www.mcs.anl.gov/\~{}more/ANL8074a.pdf}
}

@Article{Morales2011,
  Title                    = {Remark on {Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound constrained optimization}},
  Author                   = {Morales, Jos{\'e} Luis and Nocedal, Jorge},
  Journal                  = {ACM Trans. Math. Softw.},
  Year                     = {2011},

  Month                    = {Dec},
  Number                   = {1},
  Pages                    = {7:1--7:4},
  Volume                   = {38},

  Address                  = {New York, NY, USA},
  Articleno                = {7},
  Issue_date               = {November 2011},
  Numpages                 = {4},
  Publisher                = {ACM},
  Url                      = {http://doi.acm.org/10.1145/2049662.2049669}
}

@Article{More92linesearch,
  Title                    = {Line Search Algorithms With Guaranteed Sufficient Decrease},
  Author                   = {Jorge J. More and David J. Thuente and Preprint Mcs-p},
  Journal                  = {ACM Trans. Math. Software},
  Year                     = {1992},
  Pages                    = {286--307},
  Volume                   = {20}
}

@Article{DEoptimJSS11,
  Title                    = {{DEoptim}: An {R} Package for Global Optimization by Differential Evolution},
  Author                   = {Katharine Mullen and David Ardia and David Gil and Donald Windover and James Cline},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2011},
  Number                   = {6},
  Pages                    = {1--26},
  Volume                   = {40},

  Url                      = {http://www.jstatsoft.org/v40/i06/}
}

@Manual{minpack.lm,
  Title                    = {minpack.lm: R interface to the Levenberg-Marquardt nonlinear least-squares
algorithm found in MINPACK, plus support for bounds},
  Author                   = {Katharine M. Mullen and Timur V. Elzhov and Ben Bolker},
  Note                     = {R package version 1.1-6},
  Year                     = {2012}
}

@Manual{p-nnls,
  Title                    = {{nnls:} The Lawson-Hanson algorithm for non-negative least squares {(NNLS)}},
  Author                   = {Katharine M. Mullen and Ivo H. M. van Stokkum},
  Note                     = {R package version 1.4},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=nnls}
}

@Article{Mullen2007,
  Title                    = {Algorithms for separable nonlinear least squares with application to modelling time-resolved spectra},
  Author                   = {Mullen, Katharine M. and Vengris, Mikas and Stokkum, Ivo H.},
  Journal                  = {J. of Global Optimization},
  Year                     = {2007},

  Month                    = jun,
  Number                   = {2},
  Pages                    = {201--213},
  Volume                   = {38},

  ISSN                     = {0925-5001},
  Issue_date               = {June 2007},
  Numpages                 = {13}
}

@Manual{LMurphy12,
  Title                    = {likelihood: Methods for maximum likelihood estimation},
  Author                   = {Lora Murphy},
  Note                     = {R package version 1.5},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=likelihood}
}

@Manual{p-likelihood,
  Title                    = {likelihood: Methods for maximum likelihood estimation},
  Author                   = {Lora Murphy},
  Note                     = {R package version 1.5},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=likelihood}
}

@InProceedings{jn1987termin,
  Title                    = {Termination strategies for nonlinear parameter determination},
  Author                   = {John C. Nash},
  Booktitle                = {Proceedings of the Australian Society for Operations Research Annual Conference},
  Year                     = {1987},

  Address                  = {Melbourne, Australia},
  Editor                   = {Santosh Kumar},
  Month                    = {October},
  Pages                    = {322 -- 334}
}

@InProceedings{jnCTAC87,
  Title                    = {Function minimization on small or special computers},
  Author                   = {John C. Nash},
  Booktitle                = {Computational Techniques and Applications: CTAC-87},
  Year                     = {1988},

  Address                  = {Amsterdam},
  Editor                   = {Noye, J. and Fletcher, C.},
  Pages                    = {509--516},
  Publisher                = {Elsevier Science Publishers}
}

@Book{jncnm79,
  Title                    = { Compact numerical methods for computers : linear algebra
 and function minimisation},
  Author                   = {Nash, J. C.},
  Publisher                = { Hilger, Bristol : },
  Year                     = {1979 },

  Catalogue-url            = { http://nla.gov.au/nla.cat-vn1060620 },
  ISBN                     = { 0852743300 },
  Language                 = { English },
  Life-dates               = { 1979 - },
  Pages                    = { ix, 227 p. : },
  Subjects                 = { Numerical analysis - Data processing. },
  Type                     = { Book }
}

@Manual{rootoned18,
  Title                    = {rootoned: Roots of one-dimensional functions in R-only code},
  Author                   = {John C Nash},
  Note                     = {R package version 2018-7.30},
  Year                     = {2018},

  Owner                    = {john},
  Timestamp                = {2018.08.29},
  Url                      = {https://r-forge.r-project.org/R/?group_id=395}
}

@Manual{Nash-snewton,
  Title                    = {snewton: Safeguarded Newton and General Gradient Approach for Function Minimization},
  Author                   = {John C. Nash},
  Note                     = {R package version 2017-4.20/r1516},
  Year                     = {2017},

  Url                      = {https://R-Forge.R-project.org/projects/optimizer/}
}

@Manual{optimr16,
  Title                    = {{optimr}: A Replacement and Extension of the 'optim' Function},
  Author                   = {John C Nash},
  Year                     = {2016},

  Url                      = {http://CRAN.R-project.org/package=optimr}
}

@Article{NashBest14,
  Title                    = {On Best Practice Optimization Methods in {R}},
  Author                   = {John C. Nash},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2014},
  Number                   = {2},
  Pages                    = {1--14},
  Volume                   = {60},

  Url                      = {http://www.jstatsoft.org/v60/i02/}
}

@Book{nlpor14,
  Title                    = {{Nonlinear Parameter Optimization Using R Tools}},
  Author                   = {Nash, John C.},
  Publisher                = {John Wiley \& Sons: Chichester},
  Year                     = {2014},
  Month                    = may,
  Note                     = {Companion website (see http://www.wiley.com//legacy/wileychi/nash/). JNfile: 14nlpor.pdf},

  ISBN                     = {978-1-118-56928-3},
  Language                 = {English},
  Pages                    = {304 p.},
  Type                     = {Book},
  Url                      = {http://www.wiley.com//legacy/wileychi/nash/}
}

@Article{jnsign12,
  Title                    = {{Letter: Weigh less in tonnes?}},
  Author                   = {Nash, John C.},
  Journal                  = {Significance},
  Year                     = {2012},

  Month                    = {December},
  Number                   = {6},
  Pages                    = {45},
  Volume                   = {9},

  Institution              = {{Royal Statistical Society}}
}

@Manual{p-Rcgmin,
  Title                    = {{\pkg{Rcgmin}}: Conjugate Gradient Minimization of Nonlinear Functions with Box Constraints},
  Author                   = {John C. Nash},
  Note                     = {R package version 2011-2.10},
  Organization             = {Nash Information Services Inc.},
  Year                     = {2011}
}

@Manual{p-Rvmmin,
  Title                    = {{\pkg{Rvmmin}}: Variable Metric Nonlinear Function Minimization with Bounds Constraints},
  Author                   = {John C. Nash},
  Note                     = {R package version 2011-2.25},
  Organization             = {Nash Information Services Inc.},
  Year                     = {2011}
}

@Article{nash2000toptenDantzig,
  Title                    = {The {Dantzig} Simplex Method for Linear Programming},
  Author                   = {Nash, John C.},
  Journal                  = {Computing in Science and Engineering},
  Year                     = {2000},

  Month                    = {January},
  Number                   = {1},
  Pages                    = {29-31},
  Volume                   = {2},

  Address                  = {Piscataway, NJ, USA},
  Publisher                = {IEEE Educational Activities Department}
}

@Article{nashderive95,
  Title                    = {Computer algebra systems: DERIVE},
  Author                   = {Nash, John C.},
  Journal                  = {The American Statistician},
  Year                     = {1995},

  Month                    = {February},
  Note                     = {JNFile: ??},
  Number                   = {1},
  Pages                    = {93-99},
  Volume                   = {49}
}

@Book{cnm79,
  Title                    = {Compact Numerical Methods for Computers: Linear Algebra and Function 
 Minimisation},
  Author                   = {John C. Nash},
  Publisher                = {Adam Hilger},
  Year                     = {1979},

  Address                  = {Bristol},
  Note                     = {Second Edition, 1990, Bristol: Institute of Physics Publications.}
}

@Book{Nash1979b,
  Title                    = {Compact numerical methods for computers : linear algebra and function minimisation},
  Author                   = {Nash, J. C.},
  Publisher                = {Hilger, Bristol :},
  Year                     = {1979},

  Address                  = {Bristol},
  Note                     = {Second Edition, 1990, Bristol: Institute of Physics Publications.},

  __markedentry            = {[john:6]},
  Catalogue-url            = {http://nla.gov.au/nla.cat-vn1060620},
  ISBN                     = {852743300},
  Language                 = {English},
  Life-dates               = {1979 -},
  Owner                    = {john},
  Pages                    = {ix, 227 p. :},
  Subjects                 = {Numerical analysis - Data processing.},
  Timestamp                = {2018.11.16},
  Type                     = {Book}
}

@InProceedings{jnkp79tsl,
  Title                    = {Fitting two straight lines},
  Author                   = {Nash, John C. and Kevin Price},
  Booktitle                = {Proceedings of Computer Science and Statistics: 
 12th annual Symposium on the Interface : May 10 \& 11, 1979, University of Waterloo, 
 Waterloo, Ontario, Canada,
 Jane Gentleman (ed.)},
  Year                     = {1979},
  Month                    = {May},
  Note                     = {JNFile: 78Fitting2StraightLines.pdf. Page numbers may be in error. 
 Also Engineering and Statistical Research Institute, Agriculture
 Canada, Contribution No. I-99, 1978},
  Pages                    = { 363--367 },
  Publisher                = {University of Waterloo, Ontario, Canada}
}

@Article{JNRV11,
  Title                    = {Unifying Optimization Algorithms to Aid Software System Users: {optimx} for {R}},
  Author                   = {John C. Nash and Ravi Varadhan},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2011},

  Month                    = {8},
  Number                   = {9},
  Pages                    = {1--14},
  Volume                   = {43},

  Accepted                 = {2011-08-05},
  Bibdate                  = {2011-08-05},
  Coden                    = {JSSOBK},
  Day                      = {24},
  ISSN                     = {1548-7660},
  Submitted                = {2010-08-12},
  Url                      = {http://www.jstatsoft.org/v43/i09/}
}

@Article{jnrv2011JSSOBKv43i09,
  Title                    = {Unifying Optimization Algorithms to Aid Software System Users: optimx for {R}},
  Author                   = {John C. Nash and Ravi Varadhan},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2011},

  Month                    = {8},
  Number                   = {9},
  Pages                    = {1--14},
  Volume                   = {43},

  Accepted                 = {2011-08-05},
  Bibdate                  = {2011-08-05},
  Coden                    = {JSSOBK},
  Day                      = {24},
  ISSN                     = {1548-7660},
  Submitted                = {2010-08-12},
  Url                      = {http://www.jstatsoft.org/v43/i09}
}

@Manual{p-optimx,
  Title                    = {\pkg{optimx}: A Replacement and Extension of the {optim()} function},
  Author                   = {John C Nash and Ravi Varadhan},
  Note                     = {R package version 2011-3.5},
  Organization             = {Nash Information Services Inc. and Johns Hopkins University},
  Year                     = {2011}
}

@Book{jnmws87,
  Title                    = {{Nonlinear Parameter Estimation: An Integrated System in BASIC}},
  Author                   = {John C. Nash and Mary Walker-Smith},
  Publisher                = {Marcel Dekker},
  Year                     = {1987},

  Address                  = {New York},
  Note                     = {See \url{http://www.nashinfo.com/nlpe.htm} for an expanded downloadable version.}
}

@InBook{SGN83,
  Author                   = {Stephen G. Nash},
  Chapter                  = {Truncated-Newton Methods for Large-Scale Minimization},
  Editor                   = {H. E. Rauch},
  Pages                    = {91--100},

  Booktitle                = {Applications of Nonlinear Programming to Optimization and Control}
}

@Article{NashTN2000,
  Title                    = {A survey of truncated-{Newton} methods},
  Author                   = {Stephen G. Nash},
  Journal                  = {Journal of Computational and Applied Mathematics},
  Year                     = {2000},
  Pages                    = {45--59},
  Volume                   = {124}
}

@Article{NelderMead65,
  Title                    = {A Simplex Method for Function Minimization},
  Author                   = {J. A. Nelder and R. Mead},
  Journal                  = {Computer Journal},
  Year                     = {1965},

  Month                    = {January},
  Number                   = {4},
  Pages                    = {308--313},
  Volume                   = {7}
}

@Misc{RExcel:2014,
  Title                    = {{RExcel}},

  Author                   = {Erich Neuwirth},
  Year                     = {2014},

  Url                      = {http://rcom.univie.ac.at}
}

@TechReport{Nielsen2000,
  Title                    = {{UCMINF} - an Algorithm for Unconstrained, Nonlinear Optimization},
  Author                   = {H. B. Nielsen},
  Institution              = {{ Department of Mathematical Modelling, Technical University of Denmark.}},
  Year                     = {2000},
  Month                    = {dec},
  Note                     = {Report IMM-REP-2000-18},

  Pages                    = {24},
  Url                      = {http://www2.imm.dtu.dk/~hbn/publ/TR0019.ps}
}

@Manual{p-ucminf,
  Title                    = {ucminf: General-purpose unconstrained non-linear optimization},
  Author                   = {Hans Bruun Nielsen and Stig Bousgaard Mortensen},
  Note                     = {R package version 1.1-3},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=ucminf}
}

@Article{OlearyRust13,
  Title                    = {Variable projection for nonlinear least squares problems},
  Author                   = {O'Leary, Dianne P. and Rust, Bert W.},
  Journal                  = {Computational Optimization and Applications},
  Year                     = {2013},
  Number                   = {3},
  Pages                    = {579-593},
  Volume                   = {54},

  ISSN                     = {0926-6003},
  Publisher                = {Springer US}
}

@Article{Pachon2009,
  Title                    = {{Barycentric-Remez algorithms for best polynomial approximation in the chebfun system}},
  Author                   = {Pach\'{o}n, R. and Trefethen, L. N.},
  Journal                  = {BIT Numerical Mathematics},
  Year                     = {2009},
  Number                   = {4},
  Pages                    = {721--741},
  Volume                   = {49},

  Doi                      = {10.1007/s10543-009-0240-1},
  Url                      = {http://www.springerlink.com/index/10.1007/s10543-009-0240-1}
}

@Misc{genstat,
  Title                    = {GenStat for Windows (12th Edition) Introduction},

  Author                   = {R.W. Payne and D.A. Murray and S.A. Harding and D.B. Baird and D.M. Soutar},
  Year                     = {2009},

  __markedentry            = {[john:6]},
  Address                  = {Hemel Hempstead},
  Owner                    = {john},
  Publisher                = {VSN International},
  Timestamp                = {2018.11.16}
}

@Misc{Payne2009,
  Title                    = {GenStat for Windows (12th Edition) Introduction},

  Author                   = {R.W. Payne and D.A. Murray and S.A. Harding and
 D.B. Baird and D.M. Soutar},
  Year                     = {2009},

  Address                  = {Hemel Hempstead},
  Publisher                = {VSN International}
}

@Book{Pereyra10,
  Title                    = {Exponential Data Fitting and its Applications},
  Author                   = {Pereyra, Victor and Scherer, Godela},
  Publisher                = {Bentham Science Publishers},
  Year                     = {2010},

  Address                  = {Sharjah}
}

@Manual{p-nlme,
  Title                    = {nlme: Linear and Nonlinear Mixed Effects Models},
  Author                   = {Jose Pinheiro and Douglas Bates and Saikat DebRoy and Deepayan Sarkar and {R Core Team}},
  Note                     = {R package version 3.1-111},
  Year                     = {2013}
}

@Misc{Powell,
  Title                    = {Direct search algorithms for optimization calculations},

  Author                   = {Powell,M. J. D.},

  __markedentry            = {[john:6]},
  Doi                      = {10.1017/S0962492900002841},
  Eprint                   = {http://journals.cambridge.org/article\_S0962492900002841},
  ISSN                     = {1474-0508},
  Journal                  = {Acta Numerica},
  Numpages                 = {50},
  Owner                    = {john},
  Pages                    = {287--336},
  Timestamp                = {2018.11.16},
  Url                      = {http://dx.doi.org/10.1017/S0962492900002841},
  Volume                   = {7}
}

@Misc{Powell98,
  Title                    = {Direct search algorithms for optimization calculations},

  Author                   = {Powell,M. J. D.},

  Doi                      = {10.1017/S0962492900002841},
  Eprint                   = {http://journals.cambridge.org/article\_S0962492900002841},
  ISSN                     = {1474-0508},
  Journal                  = {Acta Numerica},
  Numpages                 = {50},
  Pages                    = {287--336},
  Url                      = {http://dx.doi.org/10.1017/S0962492900002841},
  Volume                   = {7}
}

@Misc{Powell09,
  Title                    = {{The BOBYQA algorithm for bound constrained optimization without derivatives}},

  Author                   = {Powell, M. J. D.},
  Month                    = aug,
  Year                     = {2009},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://www.damtp.cam.ac.uk/user/na/NA\_papers/NA2009\_06.pdf}
}

@Misc{Powell2009,
  Title                    = {{The BOBYQA algorithm for bound constrained optimization without derivatives}},

  Author                   = {Powell, M. J. D.},
  Month                    = aug,
  Year                     = {2009},

  Url                      = {http://www.damtp.cam.ac.uk/user/na/NA\_papers/NA2009\_06.pdf}
}

@Article{Powell07,
  Title                    = {{Developments of NEWUOA for Minimization Without Derivatives}},
  Author                   = {Powell, M. J. D.},
  Journal                  = {IMA Journal of Numerical Analysis},
  Year                     = {2008},
  Number                   = {4},
  Pages                    = {649-664},
  Volume                   = {28}
}

@Article{Powell06,
  Title                    = {The {NEWUOA} software for unconstrained optimization without derivatives},
  Author                   = {M. J. D. Powell},
  Journal                  = {Large Scale Nonlinear Optimization},
  Year                     = {2006},
  Pages                    = {255--297},

  Date-added               = {2008-11-26 00:45:42 +0100},
  Date-modified            = {2008-11-26 00:52:47 +0100}
}

@Article{Powell02,
  Title                    = {UOBYQA: unconstrained optimization by quadratic approximation},
  Author                   = {M. J. D. Powell},
  Journal                  = {Mathematical Programming},
  Year                     = {2002},

  Month                    = {May},
  Number                   = {3},
  Pages                    = {555--582},
  Volume                   = {92},

  ISSN                     = {0025-5610},
  Keywords                 = {approximation},
  Posted-at                = {2010-08-31 04:22:15},
  Priority                 = {2},
  Publisher                = {Springer Berlin / Heidelberg},
  Url                      = {http://dx.doi.org/10.1007/s101070100290}
}

@Book{DEbook6,
  Title                    = {{D}ifferential {E}volution - A Practical Approach to Global Optimization},
  Author                   = {Kenneth V. Price and Rainer M. Storn and Jouni A. Lampinen},
  Publisher                = {Springer-Verlag},
  Year                     = {2006},

  Address                  = {New York},
  Month                    = jan,
  Note                     = {ISBN 540209506},
  Series                   = {Natural Computing},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@Book{Price2006,
  Title                    = {{D}ifferential {E}volution - A Practical Approach to Global Optimization},
  Author                   = {Kenneth V. Price and Rainer M. Storn and Jouni A. Lampinen},
  Publisher                = {Springer-Verlag},
  Year                     = {2006},
  Month                    = {January},
  Note                     = {ISBN 540209506},
  Series                   = {Natural Computing}
}

@Book{Price05,
  Title                    = {Differential Evolution - A Practical Approach to Global Optimization},
  Author                   = {K. V. Price and R. M. Storn and J. A. Lampinen},
  Publisher                = {Springer},
  Year                     = {2005},

  Address                  = {New York}
}

@Article{Price77,
  Title                    = {A Controlled Random Search Procedure for Global Optimisation},
  Author                   = {Wyn L. Price},
  Journal                  = {Computer Journal},
  Year                     = {1977},
  Number                   = {4},
  Pages                    = {367-370},
  Volume                   = {20},

  Bibsource                = {DBLP, http://dblp.uni-trier.de}
}

@Misc{FAQ731,
  Author                   = {{R Core Team}},
  Year                     = {2017},

  Address                  = {Vienna, Austria},
  Organization             = {R Foundation for Statistical Computing},
  Url                      = {https://cran.r-project.org/doc/FAQ/R-FAQ.html\#Why-doesn\_0027t-R-think-these-numbers-are-equal\_003f}
}

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

  Address                  = {Vienna, Austria},
  Author                   = {{R Core Team}},
  Organization             = {R Foundation for Statistical Computing},
  Year                     = {2013},

  Url                      = {http://www.R-project.org/}
}

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

  Address                  = {Vienna, Austria},
  Author                   = {{R Development Core Team}},
  Note                     = {{ISBN} 3-900051-07-0},
  Organization             = {R Foundation for Statistical Computing},
  Year                     = {2008},

  Url                      = {http://www.R-project.org}
}

@Article{FletPow63,
  Title                    = {A rapidly convergent descent method for minimization},
  Author                   = { R. Fletcher, R. and Powell, M. J. D.},
  Journal                  = {Computer Journal},
  Year                     = {1963},
  Pages                    = {163--168},
  Volume                   = {6},

  Doi                      = {10.2172/4222000},
  Place                    = {United States}
}

@InProceedings{Rajnarayan2006,
  Title                    = {Optimization Under Uncertainty Using Probability Collectives},
  Author                   = {Rajnarayan, D. and Wolpert, D.H. and Kroo, I.},
  Booktitle                = {{Proceedings of 11th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conference, Portsmouth, VA}},
  Year                     = {2006},
  Note                     = {{AIAA-2006-7033}}
}

@Book{Ratkowsky83,
  Title                    = {Nonlinear Regression Modeling: A Unified Practical Approach},
  Author                   = {David A. Ratkowsky},
  Publisher                = {Marcel Dekker Inc.},
  Year                     = {1983},

  Address                  = {New York and Basel}
}

@Article{Swendsen86,
  Title                    = {Replica Monte Carlo simulation of spin glasses},
  Author                   = {Swendsen RH and Wang JS},
  Journal                  = { Physical Review Letters},
  Year                     = {1986},
  Pages                    = {2607--2609},
  Volume                   = {57}
}

@Book{RitzStreibig2008,
  Title                    = {Nonlinear Regression with R},
  Author                   = {C. Ritz and J. C. Streibig},
  Publisher                = {Springer},
  Year                     = {2008},

  Address                  = {New York}
}

@Article{Rosenbrock60,
  Title                    = {An automatic method for finding the greatest or least value of a function},
  Author                   = {Rosenbrock, H. H.},
  Journal                  = {The Computer Journal},
  Year                     = {1960},
  Pages                    = {175–184},
  Volume                   = {3}
}

@Book{Ross90,
  Title                    = {Nonlinear estimation.},
  Author                   = {Ross, Gavin J.S.},
  Publisher                = {New York etc.: Springer-Verlag},
  Year                     = {1990},

  ISBN                     = {3-540-97278-1},
  Pages                    = {viii, 189 p.}
}

@Article{Schnabel1985,
  Title                    = {A modular system of algorithms for unconstrained minimization},
  Author                   = {Schnabel, Robert B. and Koonatz, John E. and Weiss, Barry E.},
  Journal                  = {ACM Trans. Math. Softw.},
  Year                     = {1985},

  Month                    = dec,
  Note                     = {Original report CU-CS-480-82 from 1982, revised. The UNCMIN Manual.},
  Number                   = {4},
  Pages                    = {419--440},
  Volume                   = {11},

  __markedentry            = {[john:6]},
  Acmid                    = {6192},
  Address                  = {New York, NY, USA},
  Doi                      = {10.1145/6187.6192},
  ISSN                     = {0098-3500},
  Issue_date               = {Dec. 1985},
  Numpages                 = {22},
  Owner                    = {john},
  Publisher                = {ACM},
  Timestamp                = {2018.11.16},
  Url                      = {http://doi.acm.org/10.1145/6187.6192}
}

@Article{Schnabel85,
  Title                    = {A Modular System of Algorithms for Unconstrained Minimization},
  Author                   = {Robert B. Schnabel and John E. Koontz and Barry E. Weiss},
  Journal                  = {ACM Transactions on Mathematical Software},
  Year                     = {1985},

  Month                    = dec,
  Number                   = {4},
  Pages                    = {419--440},
  Volume                   = {11}
}

@Manual{p-PBSadmb,
  Title                    = {PBSadmb: ADMB for R Using Scripts or GUI},
  Author                   = {Jon T. Schnute and Rowan Haigh and Alex Couture-Beil},
  Note                     = {R package version 0.66.87},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=PBSadmb}
}

@Article{p-GA,
  Title                    = {{GA}: A Package for Genetic Algorithms in {R}},
  Author                   = {Luca Scrucca},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2013},
  Number                   = {4},
  Pages                    = {1--37},
  Volume                   = {53},

  Url                      = {http://www.jstatsoft.org/v53/i04/}
}

@Book{Seber89Wild,
  Title                    = {{Nonlinear regression}},
  Author                   = {Seber, G. A. F. and Wild, C. J.},
  Publisher                = {Wiley},
  Year                     = {1989},

  Address                  = {New York}
}

@Article{rgenoudpolitical,
  Title                    = {Genetic Optimization Using Derivatives: Theory and Application to Nonlinear Models},
  Author                   = {Jasjeet S. Sekhon and Walter R. {Mebane, Jr.}},
  Journal                  = {Political Analysis},
  Year                     = {1998},
  Pages                    = {189--213},
  Volume                   = {7}
}

@Article{Shanno70A,
  Title                    = {Conditioning of quasi-Newton methods for function minimization},
  Author                   = {Shanno, David F.},
  Journal                  = {Mathematics of Computation},
  Year                     = {1970},
  Number                   = {111},
  Pages                    = {647--656},
  Volume                   = {24}
}

@Article{Shanno70B,
  Title                    = {Optimal conditioning of quasi-Newton methods},
  Author                   = {Shanno, David F. and Kettler, Paul C.},
  Journal                  = {Mathematics of Computation},
  Year                     = {1970},

  Month                    = jul,
  Number                   = {111},
  Pages                    = {657--664},
  Volume                   = {24}
}

@Article{Shrager85RRR,
  Title                    = {A Rapid Robust Rootfinder},
  Author                   = {Richard I. Shrager},
  Journal                  = {Mathematics of Computation},
  Year                     = {1985},

  Month                    = jan,
  Number                   = {169},
  Pages                    = {151--165},
  Volume                   = {44}
}

@Manual{Soetaert-rootSolve,
  Title                    = {rootSolve: Nonlinear root finding, equilibrium and steady-state analysis of ordinary differential equations
},
  Author                   = {Karline Soetaert},
  Note                     = {R package 1.6},
  Year                     = {2009},

  Owner                    = {john},
  Timestamp                = {2018.08.29}
}

@Book{Soetaert2009,
  Title                    = {A Practical Guide to Ecological Modelling. Using R as a Simulation Platform},
  Author                   = {Karline Soetaert and Peter M.J. Herman},
  Publisher                = {Springer},
  Year                     = {2009},
  Note                     = {ISBN 978-1-4020-8623-6},

  Owner                    = {john},
  Pages                    = {372},
  Timestamp                = {2018.08.29}
}

@Article{Squire98,
  Title                    = {Using Complex Variables to Estimate Derivatives of Real Functions},
  Author                   = {Squire, William and Trapp, George},
  Journal                  = {SIAM Review},
  Year                     = {1998},

  Month                    = mar,
  Number                   = {1},
  Pages                    = {110--112},
  Volume                   = {40},

  Issue_date               = {March 1998}
}

@Misc{stata,
  Title                    = {Stata Statistical Software: Release 11},

  Author                   = {StataCorp},
  Year                     = {2009},

  __markedentry            = {[john:6]},
  Address                  = {College Station, TX},
  Owner                    = {john},
  Publisher                = {StataCorp LP},
  Timestamp                = {2018.11.16}
}

@Misc{StataCorp2009,
  Title                    = {Stata Statistical Software: Release 11},

  Author                   = {StataCorp},
  Year                     = {2009},

  Address                  = {College Station, TX},
  Publisher                = {StataCorp LP}
}

@Article{TZ89,
  Title                    = {{Global Optimization}},
  Author                   = {A. T\"{o}rn and A. Zilinskas},
  Journal                  = {{Lecture Notes in Computer Science}},
  Year                     = {1989},
  Volume                   = {350},

  Address                  = {New York, NY, USA},
  Publisher                = {{Springer-Verlag}}
}

@Manual{p-gaoptim,
  Title                    = {gaoptim: Genetic Algorithm optimization for real-based and
permutation-based problems},
  Author                   = {Fernando Tenorio},
  Note                     = {R package version 1.1},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=gaoptim}
}

@Article{Thacher1960,
  Title                    = {Remark on Algorithm 2: Rootfinder},
  Author                   = {Thacher,Jr., Henry D.},
  Journal                  = {Commun. ACM},
  Year                     = {1960},

  Month                    = aug,
  Number                   = {8},
  Pages                    = {475--},
  Volume                   = {3},

  Acmid                    = {367385},
  Address                  = {New York, NY, USA},
  Doi                      = {10.1145/367368.367385},
  ISSN                     = {0001-0782},
  Issue_date               = {Aug. 1960},
  Owner                    = {john},
  Publisher                = {ACM},
  Timestamp                = {2018.08.29},
  Url                      = {http://doi.acm.org/10.1145/367368.367385}
}

@Manual{p-Rglpk,
  Title                    = {Rglpk: R/GNU Linear Programming Kit Interface},
  Author                   = {Stefan Theussl and Kurt Hornik},
  Note                     = {R package version 0.5-1},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=Rglpk}
}

@Article{TienEarn10,
  Title                    = {Multiple transmission pathways and disease dynamics in a waterborne pathogen model},
  Author                   = {J H Tien and D J D Earn},
  Journal                  = {Bulletin of Mathematical Biology},
  Year                     = {2010},
  Number                   = {6},
  Pages                    = {1506--1533},
  Volume                   = {72}
}

@Article{Toomet2008,
  Title                    = {Sample Selection Models in R: Package sampleSelection},
  Author                   = {Ott Toomet and Arne Henningsen},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2008},

  Month                    = {7},
  Number                   = {7},
  Pages                    = {1--23},
  Volume                   = {27},

  Day                      = {29}
}

@Article{Torczon95patternsearch,
  Title                    = {Pattern Search Methods for Nonlinear Optimization},
  Author                   = {Virginia Torczon},
  Journal                  = {SIAG/OPT Views and News},
  Year                     = {1995},
  Pages                    = {7--11},
  Volume                   = {6}
}

@Manual{p-gnm,
  Title                    = {Generalized nonlinear models in R: An overview of the gnm package},
  Author                   = {Heather Turner and David Firth},
  Note                     = {R package version 1.0-6},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=gnm}
}

@Manual{p-alabama,
  Title                    = {alabama: Constrained nonlinear optimization},
  Author                   = {Ravi Varadhan},
  Note                     = {R package version 2011.9-1},
  Year                     = {2012},

  Url                      = {http://CRAN.R-project.org/package=alabama}
}

@Manual{p-dfoptim,
  Title                    = {dfoptim: Derivative-free Optimization},
  Author                   = {Ravi Varadhan and Hans W. Borchers},
  Note                     = {R package version 2011.12-9},
  Organization             = {Johns Hopkins University and 
 ABB Corporate Research.},
  Year                     = {2011},

  Url                      = {http://CRAN.R-project.org/package=dfoptim}
}

@Article{p-BB,
  Title                    = {{\pkg{BB}}: An {\R} Package for Solving a Large System of Nonlinear Equations and for Optimizing a High-Dimensional Nonlinear Objective Function},
  Author                   = {Ravi Varadhan and Paul Gilbert},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2009},
  Number                   = {4},
  Pages                    = {1--26},
  Volume                   = {32},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://www.jstatsoft.org/v32/i04/}
}

@Article{Vara09,
  Title                    = {{BB}: An {\R} Package for Solving a Large System of 
 Nonlinear Equations and for Optimizing a High-Dimensional Nonlinear Objective Function},
  Author                   = {Ravi Varadhan and Paul Gilbert},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2009},
  Number                   = {4},
  Pages                    = {1--26},
  Volume                   = {32},

  Url                      = {http://www.jstatsoft.org/v32/i04/}
}

@Article{Varadhan2009,
  Title                    = {{\pkg{BB}}: An {\R} Package for Solving a Large System of 
 Nonlinear Equations and for Optimizing a High-Dimensional 
 Nonlinear Objective Function},
  Author                   = {Ravi Varadhan and Paul Gilbert},
  Journal                  = {Journal of Statistical Software},
  Year                     = {2009},
  Number                   = {4},
  Pages                    = {1--26},
  Volume                   = {32},

  Url                      = {http://www.jstatsoft.org/v32/i04/}
}

@Book{SAS,
  Title                    = {SAS},
  Author                   = {various},
  Publisher                = {SAS Institute Inc.},

  Address                  = {Cary, NC}
}

@Book{various,
  Title                    = {SAS},
  Author                   = {various},
  Publisher                = {SAS Institute Inc.},

  Address                  = {Cary, NC}
}

@Book{VenRip1994,
  Title                    = {Modern Applied Statistics with {S-PLUS}},
  Author                   = {William N. Venables and Brian D. Ripley},
  Publisher                = {Springer-Verlag},
  Year                     = {1994},

  Address                  = {Berlin, Germany~/ London, UK},

  Pages                    = {xii + 462}
}

@Article{WatsonHompack97,
  Title                    = {Algorithm 777: HOMPACK90: a suite of Fortran 90 codes for globally convergent homotopy algorithms},
  Author                   = {Watson, Layne T. and Sosonkina, Maria and Melville, Robert C. and Morgan, Alexander P. and Walker, Homer F.},
  Journal                  = {ACM Trans. Math. Softw.},
  Year                     = {1997},

  Month                    = dec,
  Number                   = {4},
  Pages                    = {514--549},
  Volume                   = {23},

  Address                  = {New York, NY, USA},
  ISSN                     = {0098-3500},
  Issue_date               = {Dec. 1997},
  Numpages                 = {36},
  Publisher                = {ACM}
}

@Article{Wegstein1960,
  Title                    = {Certification: Rootfinder},
  Author                   = {Wegstein, J. and Thacher,Jr., Henry C.},
  Journal                  = {Commun. ACM},
  Year                     = {1960},

  Month                    = jun,
  Number                   = {6},
  Pages                    = {354--},
  Volume                   = {3},

  Acmid                    = {367337},
  Address                  = {New York, NY, USA},
  Doi                      = {10.1145/367297.367337},
  ISSN                     = {0001-0782},
  Issue_date               = {June 1960},
  Owner                    = {john},
  Publisher                = {ACM},
  Timestamp                = {2018.08.29},
  Url                      = {http://doi.acm.org/10.1145/367297.367337}
}

@Article{Wenzel99,
  Title                    = {Stochastic Tunneling Approach for Global Minimization of Complex Potential Energy Landscapes},
  Author                   = {Wenzel, W. and Hamacher, K.},
  Journal                  = {Phys. Rev. Lett.},
  Year                     = {1999},

  Month                    = {Apr},
  Pages                    = {3003--3007},
  Volume                   = {82},

  Doi                      = {10.1103/PhysRevLett.82.3003},
  Issue                    = {15},
  Publisher                = {American Physical Society},
  Url                      = {http://link.aps.org/doi/10.1103/PhysRevLett.82.3003}
}

@Article{Wilkinson1961,
  Title                    = {Remarks on Algorithms 2 and 3},
  Author                   = {Wilkinson, J. H.},
  Journal                  = {Commun. ACM},
  Year                     = {1961},

  Month                    = mar,
  Number                   = {3},
  Pages                    = {153--},
  Volume                   = {4},

  Acmid                    = {366273},
  Address                  = {New York, NY, USA},
  Doi                      = {10.1145/366199.366273},
  ISSN                     = {0001-0782},
  Issue_date               = {March 1961},
  Owner                    = {john},
  Publisher                = {ACM},
  Timestamp                = {2018.08.29}
}

@Book{WilkinsonReinsch1971,
  Title                    = {Handbook for Automatic Computation: Linear Algebra (Grundlehren Der Mathematischen Wissenschaften, Vol 186)},
  Author                   = {Wilkinson, J. H. and Reinsch, C. and Bauer, F. L.},
  Publisher                = {SpringerVerlag},
  Year                     = {1986},

  ISBN                     = {387054146}
}

@Book{Mathematica4,
  Title                    = {The Mathematica Book},
  Author                   = {Stephen Wolfram},
  Publisher                = {Wolfram Research Inc.},
  Year                     = {2000}
}

@Article{GenSA13,
  Title                    = { Generalized Simulated Annealing for Global Optimization: the GenSA Package for R },
  Author                   = { Yang Xiang and Sylvain Gubian and Brian Suomela and Julia Hoeng },
  Journal                  = { The R Journal },
  Year                     = { 2013 },

  Month                    = jun,
  Number                   = { 1 },
  Pages                    = { 13--29 },
  Volume                   = { 5 },

  Url                      = { http://journal.r-project.org/archive/2013-1/xiang-gubian-suomela-etal.pdf }
}

@Article{Xiang2013,
  Title                    = {Generalized Simulated Annealing for Global Optimization: the GenSA Package for R},
  Author                   = {Yang Xiang and Sylvain Gubian and Brian Suomela and Julia Hoeng},
  Journal                  = {The R Journal},
  Year                     = {2013},

  Month                    = jun,
  Number                   = {1},
  Pages                    = {13--29},
  Volume                   = {5},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16},
  Url                      = {http://journal.r-project.org/archive/2013-1/xiang-gubian-suomela-etal.pdf}
}

@InCollection{Xie-reproducible,
  Title                    = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  Author                   = {Yihui Xie},
  Booktitle                = {Implementing Reproducible Computational Research},
  Publisher                = {Chapman and Hall/CRC},
  Year                     = {2014},
  Editor                   = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  Note                     = {ISBN 978-1466561595},

  Url                      = {http://www.crcpress.com/product/isbn/9781466561595}
}

@Manual{Xie-knitr,
  Title                    = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  Author                   = {Yihui Xie},
  Note                     = {R package version 1.20},
  Year                     = {2018},

  Url                      = {https://yihui.name/knitr/}
}

@Book{Xie-Dynamic,
  Title                    = {Dynamic Documents with {R} and knitr},
  Author                   = {Yihui Xie},
  Publisher                = {Chapman and Hall/CRC},
  Year                     = {2015},

  Address                  = {Boca Raton, Florida},
  Edition                  = {2nd},
  Note                     = {ISBN 978-1498716963},

  Url                      = {https://yihui.name/knitr/}
}

@PhdThesis{Ye1987,
  Title                    = {Interior Algorithms for Linear, Quadratic, and Linearly Constrained Non-Linear Programming},
  Author                   = {Yinyu Ye},
  School                   = {Department of EES, Stanford University},
  Year                     = {1987},

  Address                  = {Palo Alto, California},
  Note                     = {Ph. D. Dissertation},

  __markedentry            = {[john:6]},
  Owner                    = {john},
  Timestamp                = {2018.11.16}
}

@PhdThesis{Ye1987a,
  Title                    = {Interior Algorithms for Linear, Quadratic, and
 Linearly Constrained Non-Linear Programming},
  Author                   = {Yinyu Ye},
  School                   = {Department of EES, Stanford University},
  Year                     = {1987},

  Address                  = {Palo Alto, California},
  Note                     = {Ph. D. Dissertation}
}

@Manual{p-nloptr,
  Title                    = {nloptr: \R\ interface to {NLopt}},
  Author                   = {Jelmer Ypma},
  Note                     = {R package version 0.9.3},
  Year                     = {2013},

  Url                      = {http://CRAN.R-project.org/package=nloptr}
}

@Article{Zhu1997LBFGS,
  Title                    = {Algorithm 778: {L-BFGS-B}: Fortran subroutines for large-scale bound-constrained optimization},
  Author                   = {Zhu, Ciyou and Byrd, Richard H. and Lu, Peihuang and Nocedal, Jorge},
  Journal                  = {ACM Trans. Math. Softw.},
  Year                     = {1997},

  Month                    = dec,
  Number                   = {4},
  Pages                    = {550--560},
  Volume                   = {23},

  Acmid                    = {279236},
  Address                  = {New York, NY, USA},
  Doi                      = {10.1145/279232.279236},
  ISSN                     = {0098-3500},
  Issue_date               = {Dec. 1997},
  Keywords                 = {large-scale optimization, limited-memory method, nonlinear optimization, variable metric method},
  Numpages                 = {11},
  Publisher                = {ACM},
  Url                      = {http://doi.acm.org/10.1145/279232.279236}
}

@Book{Rauch83,
  Title                    = {Applications of Nonlinear Programming to Optimization and Control},
  Editor                   = {H. E. Rauch},
  Publisher                = {Pergamon Press},
  Year                     = {1983},

  Address                  = {Oxford},

  Booktitle                = {Applications of Nonlinear Programming to Optimization and Control}
}

