News blog

version 4 is on the way

10 September 2021

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.

The behavior of trajectory now fully conforms to the behavior of other pomp elementary functions. In particular, one can now add, remove, or modify basic model components in a call to trajectory just as one can with simulate, pfilter, probe, etc. Before version 4, additional arguments to trajectory (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 the ode_control argument of trajectory. This behavior matches that of traj_objfun.
It is now possible to create a pomp object from scratch using trajectory, 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 call pomp, and then pass the resulting pomp object to trajectory. 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 or pomp objects. In this regard, its behavior matches that of simulate.

version 3.6 released

05 September 2021

pomp version 3.6 has been released to CRAN and will be available soon at a mirror near you. This release features improvements in the package manual, a few bug fixes, and some feature upgrades.

Highlights include:

Improvements to the package manual, including more examples, richer cross-linking, and better organization.
When simulate is called with format="data.frame" and include.data=TRUE, the interpolated covariates are now included in the data frame that is returned.
Stateful objective functions created by traj_objfun, nlf_objfun, probe_objfun, and spect_objfun now have default arguments. In particular, the default is argument is a zero-length numeric vector. Calling such a function with no arguments is valid if and only if the objective function was created with no variables to estimate (empty est).
The stateful objective function created by traj_objfun has been refactored so that it is independent of trajectory. This change is invisible to the user, but lays the groundwork for future changes in trajectory.
The workhorse function flow now has default arguments.
The states and obs methods now work for lists of pomp objects (listies).
A bug in rprior arising with integer-valued return vectors has been fixed.

version 3.5 released

30 July 2021

pomp version 3.5 has been released to CRAN and will be available soon at a mirror near you. The main feature upgrade concerns the reproducibility functions bake and stew, which cache calculation results. In previous versions, if the calculation was modified, or if any of its dependencies changed, it was necessary to manually delete the cache file to force recomputation. In the new release, these functions now now silently cache information about the calculation and its dependencies. If these are modified, recomputation is triggered. In addition, the user now has more control over the information that is returned. See the package manual for more details.

This release also fixes a bug in bsmc2 and upgrades the partrans function to make it easier to use with objective functions.

See the package NEWS for full details.

new versions of 'bake' and 'stew'

19 July 2021

The latest development version (3.4.5.0) is available for download on the pomp website. This release includes a major overhaul of the two reproducibility functions, bake and stew. These functions are used for caching the results of expensive calculations. In the past, if the cached calculation was modified, or if any of its dependencies changed, it was necessary to manually delete the cache file. As of version 3.4.5.0, pomp now silently caches information about the calculation and its dependencies. If these are modified, recomputation is triggered. See the package manual for more details.

To install from the package repository, do

install.packages("pomp",repos="https://kingaa.github.io/")

devtools::install_github("kingaa/pomp@3.4.5.0")

version 3.4 released

15 May 2021

pomp version 3.4 has been released to CRAN and will be available soon at a mirror near you. This release contains a bug fix and some documentation improvements. In addition, some deprecated functions have been removed. See the package NEWS for details.

Blog archive
Subscribe to this newsfeed

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.

Top