Version 4.0.0.0 of pomp is now available on the the package github repo.
This release contains a few backwardly incompatible changes, which are explained here.
All of these have to do with the elementary function trajectory, which computes trajectories of the deterministic dynamical skeleton.
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The behavior of
trajectorynow fully conforms to the behavior of otherpompelementary functions. In particular, one can now add, remove, or modify basic model components in a call totrajectoryjust as one can withsimulate,pfilter,probe, etc. Before version 4, additional arguments totrajectory(i.e., those passed via...) were passed on to the ODE integrator in the case of continuous-time deterministic skeletons (i.e., vectorfields) and ignored in the case of discrete-time skeletons (i.e., maps). As of version 4, in order to adjust ODE integrator settings it is necessary to use theode_controlargument oftrajectory. This behavior matches that oftraj_objfun. -
It is now possible to create a
pompobject from scratch usingtrajectory, together with a specification of the rinit and skeleton components. Prior to version 4, in order to do so, it was necessary to somewhat awkwardly first create a dummy data set, then callpomp, and then pass the resultingpompobject totrajectory. This can now be achieved in one call. -
The user now has the option, in a call to
trajectory, to have the results returned as one orpompobjects. In this regard, its behavior matches that ofsimulate.
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This software has been made possible by support from the U.S. National Science Foundation (Grants #EF-0545276, #EF-0430120), by the “Inference for Mechanistic Models” Working Group supported by the National Center for Ecological Analysis and Synthesis (a Center funded by N.S.F. (Grant #DEB-0553768), the University of California, Santa Barbara, and the State of California), and by the RAPIDD program of the Science & Technology Directorate, Department of Homeland Security and the Fogarty International Center, U.S. National Institutes of Health. |