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version 3.2 released

04 December 2020

pomp version 3.2 has been released to CRAN and will be available soon at a mirror near you. This release contains relatively minor improvements, primarily to the documentation.

The only significant user-visible changes concern the functions profileDesign, sliceDesign, runifDesign, and sobolDesign, which have been deprecated and will be removed in a future release. They are replaced by profile_design, slice_design, runif_design, and sobol_design, respectively.

In addition, the behavior of profile_design has changed. Previously, the same random (type="runif") or sub-random (type="sobol") sequence was used for all non-profile parameters. The new behavior is that, for each profile slice, a distinct set of points is generated.

documentation improvements in version

05 August 2020

pomp development version has just been released on the package github site. It contains a number of improvements to the package help pages. These are also available online (as the package manual).

version released

19 July 2020

pomp development version has just been released on the package github site. This release introduces the profile_design function, which is intended to replace profileDesign. The so-called profile design consists of a series of slices through a parameter space perpendicular to one or more coordinate axes. The old behavior was to generate a single set of points in one of these slices (randomly according to a uniform distribution when type="runif" and according to a sub-random (Sobol’) sequence when type="sobol") and then copy these points across all slices. Thus, in a projection perpendicular to the slices, all nprof generated points would lie atop one another. The new behavior is to generate the points in each slice independently. Thus, a projection perpendicular to the slices will display n*nprof points, where n is the number of slices.

For stylistic reasons, the other design functions, sliceDesign, runifDesign, and sobolDesign have been replaced by slice_design, runif_design, and sobol_design, respectively.

The older functions remain in place, but are deprecated and will be removed in a future release.

volunteer needed

09 July 2020

I’m looking for a volunteer who can maintain the pomp installation instructions for Mac users. Personally, I work pretty much exclusively on linux machines. I think I’m more or less able to keep up with the Windows installation instructions, but with respect to the Mac, I’m not keeping up. It seems I turned around and several things changed at once.

If there’s a Mac user out there, a veteran installer of pomp, who can edit/augment the Mac installation instructions on an ongoing basis, to keep up with advice from the R core team, probably including revising or replacing the gfortran installation instructions, it would a great service to the pomp community!

Please contact me if you’re interested.

version 3.1 released

05 July 2020

pomp version 3.1 has just been released to CRAN and is on its way to a mirror near you. From this version pomp now requires at least version 4 of R.

Significant user-visible changes

Old function    Replacement
onestep.dens   direct specification of dprocess component
onestep.sim   onestep
discrete.time.sim     discrete_time
euler.sim   euler
gillespie.sim   gillespie
gillespie.hl.sim     gillespie_hl
conv.rec   traces
values or as(x,"data.frame")

New features

Under the hood

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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.