scorematchingad (version 0.0.67)

customll: Compile a custom log-likelihood function.

Description

Supply C++ code to specify a custom log-likelihood, much like TMB::compile() is passed C++ code that formulate models. For score matching the normalising constant of the log-likelihood can be omitted. Taping of the function currently only works with the gcc compiler, typically on Linux; taping works if customll_test() returns TRUE. Packages RcppEigen and RcppXPtrUtils must be installed.

Usage

customll(
  code,
  rebuild = FALSE,
  includes = character(),
  cacheDir = getOption("rcpp.cache.dir", tempdir()),
  showOutput = verbose,
  verbose = getOption("verbose")
)
customll_test()

Value

customll() returns an adloglikelood object (which is just an externalptr with attributes) for the compiled log-likelihood function. The returned object has an attribute fname.

customll_test() returns TRUE if taping works in your R session. Otherwise it will return FALSE and generate warnings.

Arguments

code

C++ code for a log-likelihood function (with normalising constant omitted if desired). See details for more.

rebuild

passed to Rcpp::cppFunction().

includes

passed to Rcpp::cppFunction(). For internal use.

cacheDir

passed to Rcpp::cppFunction().

showOutput

passed to Rcpp::cppFunction().

verbose

passed to Rcpp::cppFunction().

Code Argument

code must be C++ that uses only CppAD and Eigen, which makes it very similar to the requirements of the input to TMB::compile() (which also uses CppAD and Eigen).

The start of code should always be "a1type fname(const veca1 &x, const veca1 &theta){" where fname is your chosen name of the log-likelihood function, x represents a point in the data space and theta is a vector of parameters for the log-likelihood. This specifies that the function will have two vector arguments (of type veca1) and will return a single numeric value (a1type).

The type a1type is a double with special ability for being taped by CppAD. The veca1 type is a vector of a1type elements, with the vector wrapping supplied by the Eigen C++ package (that is an Eigen matrix with 1 column and dynamic number of rows).

The body of the function must use operations from Eigen and/or CppAD, prefixed by Eigen:: and CppAD:: respectively. There are no easy instructions for writing these as it is genuine C++ code, which can be very opaque to those unfamiliar with C++. I've found the quick reference pages for for Eigen useful. Limited unary and binray operations are available directly from CppAD without Eigen. For the purposes of score matching the operations should all be smooth to create a smooth log-likelihood and the normalising constant may be omitted.

Details

The function uses RcppXPtrUtils::cppXPtr() and Rcpp::cppFunction(). It is good practice to check the returned object using evalll(). The first compilation in a session can be very slow.

Examples

if (FALSE) customll_test()

myll <- customll("a1type dirichlet(const veca1 &u, const veca1 &beta) {
  size_t d  = u.size();
  a1type y(0.);  // initialize summation at 0
  for(size_t i = 0; i < d; i++)
  {   y   += beta[i] * log(u[i]);
  }
  return y;
}")
evalll(myll, rep(1/3, 3), rep(-0.5, 3))

tapes <- buildsmdtape("sim", "identity", "sim", 
 myll, rep(1/3, 3), rep(NA, 3), 
 bdryw="minsq", acut = 0.01)
evaltape(tapes$lltape, rep(1/3, 3), rep(-0.5, 3))