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TODO

  • DONE Upgrade to recent cppad, to get the abs/sign bugfix of version 2013-11-27.
  • DONE Eliminate Wall warnings.
  • Make instructions how to disable Wall compiler flag, and more generally how to locate global Makeconf and create local Makevars.
  • Roxygen documentation:
    • The use of dyn.load is confusing (add 'seealso' to ?compile)
    • The summary method of sdreport is undocumented.
  • DONE Make it work on common platforms (Linux, Windows, Mac OS X).
  • Clean up R-code: newton, options, MakeADFun: class(output).
  • MakeADFun: Call dyn.load if DLL not loaded (?)
  • parList: use last.par.best as default (?)
  • DONE parallel_start.hpp does not yet have parallel Hessian member.
  • DONE Metis symbolic analysis with 3d example.
  • Move methods, such as "parList", out of the object.
  • DONE Rinterface should remember to set DLL="..."
  • DONE sdreport() on R-side to get sd of ADREPORT().
  • DONE solveSubset to get sd's of all random effects.
  • Make importence sampler work in high dim - need a GMRFsample.
  • Compile and testing workflow:
    • DONE Eliminate need to restart R.
    • DONE Give better message if PARAMETER(name) evaluates to NULL.
    • DONE Improve compile times by either precompiling or allow incomplete compilations.
    • DONE Array bounds checking option
  • DONE template() should never overwrite existing file.
  • DONE Review kaspers class extensions of Eigen classes, in particular array, matrix and vector
    • DONE Consistency between matrix and array fastest running dimensions.
    • DONE Desired behaviour of overloaded operations e.g. pointwise multiply vs matrix multiply.
    • Automatic cast from array to vector.
  • Make simple example of how to include "adjoint code". pexp(x,lambda) is a good example (cum. dist. function exp. distr)
  • Think about general features for calculating residuals, along the line of Kasper's ideas.
  • New feature 'exportRpackage()' to wrap user template into a self contained R-package, optionally as standalone (independent of TMB package). By default linking to the TMB installation for smaller package size.
  • DONE Implement atomic AD operators of entire Rmath special function library. Example: D_x(psigamma(x,n))=psigamma(x,n+1)
  • DONE Implement atomic AD operators of certain matrix operations (linking to BLAS) to e.g. better handle templates using multivariate normal distribution with dense covariance matrices.
  • DONE Implement atomic AD operator of matrix exponential.
  • Package should pass "make check"/"R CMD check" without warnings.
  • Make unary functions work on arrays and preserve dimension.
  • Disable array methods that give unexpected results (e.g. .Block() ).
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