NEWS (original) (raw)

GillespieSSA2 0.3.0

• MINOR CHANGE: Add debug parameter to print out propensity functions before compiling.
• MINOR CHANGE: Add spaces between terms in the reaction propensity C++ code to avoid pasting together important key words (e.g. if and else).

GillespieSSA2 0.2.10

• MINOR CHANGE: Turn array of propensity functions into vector of propensity functions.

GillespieSSA2 0.2.9

• MINOR CHANGE: Update RcppExports.

GillespieSSA2 0.2.8

• BUG FIX: RNG now uses RNGScope to properly get and put the RNG state before calling RNG functions (fixes #8, thanks @bbolker!).
• DOCUMENTATION: Added example forcompile_reactions().

GillespieSSA2 0.2.7 (14-07-2020)

• BUG FIX: Renamed autoplot.ssa() toplot_ssa() for compatibility with R 4.0.

GillespieSSA2 0.2.6 (14-03-2020)

• BUG FIX: Zap small negative propensity and state values.
• FEATURE autoplot.ssa(): Allow plotting the firings.
• DEBUG FEATURE ssa(): Allow returning the GillespieSSA2 instead of running it.

GillespieSSA2 0.2.5 (21-08-2019)

• BUG FIX: Use fabs() instead of abs() to calculate the absolute value of a floating point value.
• BUG FIX: Precompiling returns a list of compiled function pointers, instead of a single function pointer that is secretly an array of function pointers.

GillespieSSA2 0.2.4 (05-08-2019)

GillespieSSA2 is now on CRAN!

• MAJOR CHANGE: Split up Rcpp code to make separate parts easier to test.
• TESTING: Write unit tests for many of the functions.
• MINOR CHANGE: Renamed ssa_direct() tossa_exact().
• MINOR CHANGE: Store firings, buffer and propensity objects only if requested.
• BUG FIX: limiting variable in ssa_btl()should be an integer, not a double.
• MINOR CHANGE: Timer now has millisecond accuracy, instead of second.

GillespieSSA2 0.2.3 (17-07-2019)

• MAJOR CHANGE: Remove nu andpropensity_functions from ssa(), instead expect a list of reaction() objects. This function provides a much more natural interface to specifying the effect and propensity of a reaction.
• MINOR CHANGE: Apply small allocation optimisations tossa_btl, ssa_etl andode_em.

GillespieSSA2 0.2.2 (12-07-2019)

• MINOR CHANGE: Renamed ssa_em() toode_em().

GillespieSSA2 0.2.1 (04-07-2019)

• BUG FIX: Fix isinf scope issue for Windows users.
• MINOR CHANGE: Move ggplot2 to Suggests.

GillespieSSA2 0.2.0 (21-06-2019)

Complete rewrite of the package:

• The main SSA function and all SSA methods have been implemented in Rcpp.
• User-defined propensity functions get compiled to Rcpp at runtime.
• All SSA methods now assume the state-change matrixnu to be sparse.

GillespieSSA2 0.1.1 (05-01-2018)

• MINOR CHANGE: Added automated testing by travis.
• MINOR CHANGE: Fixes to documentation.
• MINOR CHANGE: Also output propensities.

GillespieSSA2 0.1.0 (31-08-2017)

Initial beta release of GillespieSSA2:

• Major restructuring of GillespieSSA code.
• Optimise main algorithm code (e.g. do not save state variables directly to the global environment…).
• Implement SSA methods in Rcpp.
• Added ode_em(), an Euler-Marumaya ODE method.