nlmrt (version 2016.3.2)

model2ssfun: Generate a sum of squares objective function from a nonlinear model expression and a vector of named parameters.

Description

Given a nonlinear model expressed as an expression of the form lhs ~ formula_for_rhs and a start vector where parameters used in the model formula are named, attempts to build the the R function for the residual sum of squares. As a side effect, a text file with the program code is generated.

Usage

model2ssfun(modelformula, pvec, funname="myss", filename=NULL)

Arguments

modelformula

This is a modeling formula of the form (as in nls) lhsvar ~ rhsexpression for example, y ~ b1/(1+b2*exp(-b3*tt)) You may also give this as a string.

pvec

A named parameter vector. For our example, we could use start=c(b1=1, b2=2.345, b3=0.123) WARNING: the parameters in the output function will be used in the order presented in this vector. Names are NOT respected in the output function.

funname

The (optional) name for the function that is generated in the file named in the next argument. The default name is 'myss'.

filename

The (optional) name of a file that is written containing the (text) program code for the function. If NULL, no file is written.

Value

An R function object that computes the sum of squares of the residuals of the nonlinear model at a set of parameters.

Details

None.

References

Nash, J. C. (1979, 1990) _Compact Numerical Methods for Computers. Linear Algebra and Function Minimisation._ Adam Hilger./Institute of Physics Publications

See Also

Function nls(), packages optim and optimx.

Examples

  # a test
  y <- c(5.308, 7.24, 9.638, 12.866, 17.069, 23.192, 31.443, 38.558, 
      50.156, 62.948, 75.995, 91.972)  # for testing
  tt <- seq_along(y)  # for testing
  f <- y ~ b1/(1 + b2 * exp(-1 * b3 * tt))
  p <- c(b1 = 1, b2 = 1, b3 = 1)
  myfn <- model2ssfun(f, p)
  cat("myfn: \n")
  print(myfn) # list the function
  cat("Compute the function at several points\n")
  ans <- myfn(p, tt = tt, y = y)
  print(ans) # should be  23520.58
  bnew <- c(b1 = 200, b2 = 50, b3 = 0.3)
  anew <- myfn(prm = bnew, tt = tt, y = y)
  print(anew)# should be  158.2324
  
  cat("Test with vector of un-named parameters \n")
  bthree <- c(100, 40, 0.1)
  athree <- try(myfn(prm = bthree, tt = tt, y = y))
  print(athree) # should be 19536.65