---------------------------- Version 2.3-2 - 24 Oct 2024 ---------------------------- - fix PROTECT stack imbalance caused if variable names are not provided (thanks to Nicholas Davies for identifying; github issue #1). - update to use latest R API to eliminate CRAN NOTEs. ---------------------------- Version 2.3-1 - 17 Apr 2024 ---------------------------- - previously, the maxtau argument only constrained tau-leaping steps. Now modified to also constrain exact steps and the jump to the final time that occurs if all transition rates are 0; these changes allow for rate functions that are strongly time-dependent. - clarify description of maxtau argument in help page - eliminate use of Rinternal #defines that strip the Rf_ prefix ---------------------------- Version 2.3 - 28 Nov 2023 ---------------------------- - add option to report executed transitions - explicitly use format string with "error" and "warning" functions to pass cran automatic checks. ---------------------------- Version 2.2-3 - 19 March 2019 ---------------------------- - fix clang compiler error ---------------------------- Version 2.2-2 - 4 March 2019 ---------------------------- - add "Gillespie stochastic simulation algorithm" keyword phrase to DESCRIPTION to aid people searching for a package such as this one. - fix two PROTECT errors (thanks to Tomas Kalibera's tool for identifying) - refactor C++ convenience functions to avoid false warnings about PROTECT errors from above tool. - update R/C interface code to use R's automatic registration of exported symbols - remove from help pages the "see also" mention of GillespieSSA package, which has been orphaned for many years now. ---------------------------- 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