NEWS.md

In GillespieSSA2: Gillespie's Stochastic Simulation Algorithm for Impatient People

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 for compile_reactions().

GillespieSSA2 0.2.7 (14-07-2020)

• BUG FIX: Renamed autoplot.ssa() to plot_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() to ssa_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 and propensity_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 to ssa_btl, ssa_etl and ode_em.

GillespieSSA2 0.2.2 (12-07-2019)

• MINOR CHANGE: Renamed ssa_em() to ode_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 matrix nu 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.

GillespieSSA2 documentation built on Jan. 24, 2023, 1:10 a.m.