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 bounds
• NISTnls: Nonlinear least squares examples from NIST
• nleqslv: Solve systems of nonlinear equations
• nlmrt: Functions for nonlinear least squares solutions
• nloptr: R interface to NLopt
• nloptwrap: Wrapper for package nloptr
• nls2: Nonlinear regression with brute force
• nnls: The Lawson–Hanson algorithm for nonnegative least squares (NNLS)
• numDeriv: Accurate numerical derivatives
• optextras: A set of tools to support optimization methods (function minimization with at most bounds and masks), https://r-forge.r-project.org/R/?group_id=395
• optimx: A replacement and extension of the optim() function
• pander: An R pandoc writer
• polynom: A collection of functions to implement a class for univariate polynomial manipulations
• pracma: Practical numerical math functions
• profr: An alternative display for profiling information
• quantreg: Quantile regression
• rbenchmark: Benchmarking routine for R
• Rcgmin: Conjugate gradient minimization of nonlinear functions with box constraints
• RcppDE: Global optimization by differential evolution in C++
• reportr: A general message and error reporting system
• rgenoud: R version of genetic optimization using derivatives
• Rmalschains: Continuous optimization using memetic algorithms with local search chains (MA-LS-Chains) in R
• Rmpfr: R MPFR—multiple precision floating-point reliable
• rootoned: Roots of one-dimensional functions in Ronly code https://r-forge.r-project.org/R/?group_id=395
• Rsolnp: General nonlinear optimization
• Rvmmin: Variable metric nonlinear function minimization with bounds constraints
• setRNG: Set (normal) random number generator and seed
• smco: A simple Monte-Carlo optimizer using adaptive coordinate sampling
• soma: General-purpose optimization with the self-organizing migrating algorithm
• stats4: Statistical functions using S4 classes. This collection of materials is part of the base distribution but appears to need loading via require().
• trust: Trust region optimization.