pomp version 6.1 has been released to CRAN and will soon appear on a mirror near you. This release contains breaking changes as well as some additional features.
User-visible changes
New interface for userdata becomes mandatory
Since version 5.8.4, the manner in which one provides extra elements to basic model components (i.e., beyond parameters, latent state variables, covariates, time, and observations: the so-called userdata) has changed.
During a grace period, the old method still worked, though it generated a warning.
In versions 6.X, an error will be generated.
To supply additional elements to the basic model components, pass them as elements of a named list via the userdata argument, which can be furnished to any elementary algorithm or estimation algorithm, and of course, to the pomp constructor itself.
Passing arguments by position now results in an error in most cases
In calls to pomp elementary and inference algorithms, it is now necessary to pass arguments by name and not by position. This has always been good practice, but from this release, calls that rely on the position of arguments will typically generate errors.
Feature enhancements
Initial value parameters in mif2
It is now possible to specify more than one lag in the ivp function, which is evaluated only when the mif2 perturbations are specified.
See ?mif2.
Keeping a database of explorations
In conducting an extensive exploration of a likelihood surface, it is useful to maintain a database of places visited, together with associated likelihood values.
The new function append_data assists in this.
It simply appends a given data frame to an existing CSV file (creating the file if it does not exist).
Expectation of an Euler-multinomial random variable
The new function eeulermultinom gives the expectation of an Euler-multinomial random variable.
There is also an interface to this function in the C API.
Other changes
The save.states option to pfilter has changed.
See pfilter and saved_states for details.
The deprecated options will still work for the present, but will generate a warning, with advice about how to change.
Ultimately, these options will be removed.
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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. |