Tau-Leaping Stochastic Simulation

Implements adaptive tau leaping to approximate the trajectory of a continuous-time stochastic process as described by Cao et al. (2007) The Journal of Chemical Physics . This package is based upon work supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip Johnson and NIH R01-AI049334 to Rustom Antia.


Version 2.2-1 - 19 Sept 2016

  • rework to avoid usage of C99 features not included in C++98
  • use title case for package title in DESCRIPTION
  • update maintainer email address

Version 2.2 - 19 Nov 2014

  • Add check for infinite transition rate; if found, abort with a meaningful warning message and return results generated until this point.
  • If abort due to user interrupt, now return results generated so far.

Version 2.1 - 8 May 2014

  • Remove automatic byte-code compilation of R rate functions handed to ssa.adaptivetau (previously had been using library(compile)). Previous behavior led to significant inefficiencies if ssa.adaptivetau was called multiple times with the same rate function; thanks to Sebastian Funk for raising this issue. Instead, modify documentation to recommend that users use enableJIT(1).

Version 2.0 - 24 Mar 2014

  • transition matrix ("nu") can now be specified with an alternative data structure to reduce memory usage for large sparse matrices
  • new feature: transitions may be designated as "halting", which will cause simulation to stop after executing one of these transitions
  • streamlined code for dealing with transition classification
  • call PutRNGstate before calling user-supplied rate function. While the rate function itself must not be stochastic, if a unnecessary call to Get/PutRNGState were to occur (e.g., as done by Rcpp at entry/exit to all exported functions), the adaptivetau algorithm could get scrambled. Adding this call covers this situation at relatively low cost.
  • fix vignette typo
  • bug fix: incorrect type allocation for R_NamesSymbol; thanks to Brian Ripley for catching.
  • handle case where final time ("tf" parameter) is an integer data type; thanks to Sebastian Funk for sending a patch.

Version 1.1-1 - 11 Nov 2013

  • Remove #include , which appears (?) to have been unnecessary and causes a conflict when using isnan with -std=c++11 and "using namespace std".
  • Replace "isnan" (from standard) with "ISNAN" (R macro to ensure portability)
  • also remove stray files from vignette directory

Version 1.1 - 27 July 2013

  • Fix use of "eval" by using R_EmptyEnv instead of NULL.
  • Revert memory leak prevention / error handling code due to not being part of the public R API (as pointed out by Brian Ripley, only public API is allowed in CRAN). Unfortunately interrupting execution will now almost certainly lead to memory leaking.

Version 1.0-1 - 27 Sept 2012

  • Fixed validity check that aborts on non-integer initial conditions (previously was being too permissive).
  • removed .Rhistory file accidently left under /vignettes directory

Version 1.0 - 9 Apr 2012

  • Fixed memory bug which could, under some circumstances, have lead to segmentation fault from premature garbage collection.
  • Fixed implementation of implicit tau-leaping algorithm (used when Jacobian supplied & specified by adaptive tau algorithm) and clarified corresponding documentation.
  • Fixed error handling to free memory allocated in heap upon abort
  • Added new entrypoint -- ssa.exact -- that directly runs the "exact" simulation C++ function rather than the tau-leaping algorithm.
  • Made algorithm more robust for deterministic transitions.
  • Improved error messages when passed invalid initial conditions or rate function.
  • Byte-code compile user rate functions if compiler package is available.
  • Allow ssa.maketrans to handle variable names in addition to indices.
  • Wrote vignette with three examples.

Version 0.902 - 30 Dec 2010

  • Fix Solaris compiler errors.

Version 0.901 - 12 Nov 2010

  • Fix non-portable use of LAPACK_LIBS. Thanks to Brian Ripley.

Version 0.9 - 19 Oct 2010

  • First version in CRAN

Reference manual

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2.2-1 by Philip Johnson, 2 years ago

Browse source code at https://github.com/cran/adaptivetau

Authors: Philip Johnson

Documentation:   PDF Manual  

Task views: Differential Equations

GPL (>= 3) license

Enhances compiler

Imported by DSAIDE, DSAIRM.

See at CRAN