Nonlinear Parameter Optimization Using R Tools

Appendix A

R packages used in examples

The following R packages were used in the examples in this book. Sources for those not on CRAN (Comprehensive R Archive Network) are noted.

• adagio: Discrete and global optimization routines
• alabama: Constrained nonlinear optimization
• BB: Solving and optimizing large-scale nonlinear systems
• bbmle: Tools for general maximum likelihood estimation
• compiler: This is now provided as a standard package in the base distribution.
• DEoptim: Global optimization by differential evolution
• deSolve: General solvers for initial value problems of ordinary differential equations (ODE), partial differential equations (PDE), differential algebraic equations (DAE), and delay differential equations (DDE)
• expm: Matrix exponential
• GA: Genetic algorithms
• gaoptim: Genetic algorithm optimization for real-based and permutation-based problems
• GenSA: R functions for generalized Simulated Annealing
• gnm: Generalized nonlinear models
• grofit: The package was developed to fit many growth curves obtained under different conditions
• linprog: Linear programming/optimization
• MASS: Functions and data sets to support Venables and Ripley, ‘Modern Applied Statistics with S’ (4th edition, 2002). This recommended package generally is installed with the base distribution.
• maxLik: Maximum likelihood estimation
• microbenchmark: Submicrosecond accurate timing functions
• minpack.lm: R interface to the Levenberg–Marquardt nonlinear least squares algorithm found in MINPACK, plus support for ...