pomp version 1.8 is now available on CRAN. This release introduces one new feature and fixes several bugs.
New feature
- The new
shlib.args
option topomp
, allows one to specify arbitrary options to be passed to the compiler when C snippets are used.
User-visible changes
- In Sobol’ sequence generation (i.e.,
sobolDesign
,profileDesign
), we now use the suggestion of Joe & Kuo (2003) to choose a better sequence start point. - The demos have been revised to show off current best practices.
Under the hood
- The generation of Sobol’ sequences (
sobolDesign
,profileDesign
) is now performed using the routines written in C (from the NLopt library) instead of the original TOMS 659 FORTRAN codes. The copyright notices are located in the source code. - The stochastic simulation algorithms underlying the Gillespie and K-leap methods (
gillespie.sim
,kleap.sim
) have been refactored in C. In addition, errors due to accumulation of round-off error have been repaired. The result will be more accurate, but somewhat slower when there are a very large number of reactions. - The
rw.sd
facility for specifying random-walk perturbations inmif2
has been refactored for greater stability. - There have been many improvements to the test suite. The code coverage is now 100%.
Bug fixes
- A bug in
plot
onpomp
objects with more than 10 variables to plot has been fixed. - A bug in
gillespie.sim
andkleap.sim
due to accumulation of round-off error has been repaired.
Please see the package NEWS for more details.