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 (aka. the Gillespie stochastic simulation algorithm). 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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2.2-3 by Philip Johnson, 3 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