NEWS

adaptivetau 2.3-2 (2024-10-24)

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.

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

add option to report executed transitions
explicitly use format string with "error" and "warning" functions to pass cran automatic checks.

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.

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.

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).

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.

Remove #include cmath, 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

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.

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

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.