News blog
new document defining the pomp C API
27 July 2019
pomp provides C entry points to a number of facilities for model specification. The new C API document describes these.
In particular, pomp provides C-level access to several different probability distributions of use in modeling, facilities for working with splines, and parameter transformations.
The final section of the document describes the prototypes for the basic model components. Users wishing to write libraries to hold basic model components must furnish functions of these prototypes that perform the basic model component computations.
pomp version 2.2 released to CRAN
24 June 2019
pomp version 2.2 has been released to CRAN and is on its way to a mirror near you.
This release adds one new feature: it is now possible to create diagnostic plots by calling plot directly on the objective functions created by probe_objfun and spect_objfun.
In addition, a small but annoying bug in profileDesign, when the new option type="runif" is used, has been fixed.
pomp version 2.1 released to CRAN
01 June 2019
I have just released pomp version 2.1 to CRAN. For the last six months, this has been available on the pomp website as the package pomp2.
Because it is not fully backward-compatible, pomp version 2 is being made available temporarily as the pomp2 package. Hopefully, most of you will have been using pomp2 for some time now, but if you find yourself needing to update old codes and workflows for the new version, have a look at the upgrade guide, which summarizes all the changes in version 2.
If you have pomp2 on your system, you should now remove it entirely, and replace all references to pomp2 in your codes with references to pomp.
As always, please don’t hesitate to bring questions, conundrums, puzzles, paradoxes, bugs, and feature requests, to my attention via by raising an Issue.
Upgrade Guide updates
23 December 2018
The pomp Version 2 Upgrade Guide has been revised. It now includes before-and-after examples of codes rewritten for pomp version 2. This is meant to help you revise pomp version <2 codes to take advantage of the new features.
As a reminder, an alpha-release preview of pomp version 2 is available as pomp2 on the pomp website. Do
install.packages("pomp2",repos="https://kingaa.github.io")
to install it. It is possible to have both pomp (version <2) and pomp2 installed simultaneously during workflow migration.
Around the middle of 2019, pomp2 will be renamed pomp and uploaded to CRAN as version 2.1. From that point forward, there will be no support for older versions of pomp.
Getting Started with pomp2
22 December 2018
The “Getting Started with pomp” vignette has been completely rewritten for pomp version 2. If you are new to pomp, or want to get up to speed on the changes coming in pomp version 2, have a look! The vignette is available here.
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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. |