[pomp-announce] pomp version 0.65-1 released

[Aaron A. King]

Dear pompateers,

pomp version 0.65-1 is now available on CRAN and coming soon to a mirror near you.

This release contains many improvements.  Highlights include:

* The documentation has been thoroughly revised.  Most of the help pages have been rewritten.  Of special interest is the help on writing Csnippets, which are now the preferred method of writing pomp objects.  Additionally, there is a new "Getting Started with 'pomp'" vignette, accessible on the package website (http://pomp.r-forge.r-project.org).

* A forthcoming Journal of Statistical Software article explains the package's motivation and structure, details many of the inference algorithms currently implemented, and presents several examples of their use.  An up-to-date version of this paper is included as a vignette, accessible via the package homepage (http://pomp.r-forge.r-project.org).

* The unfortunately named 'pomp' arguments 'parameter.transform' and 'parameter.inv.transform' have been deprecated in favor of the more mnemonic 'toEstimationScale' and 'fromEstimationScale'. Using the old arguments will result in the same behavior as previously, but a warning will be generated.

* The mif option 'cooling.fraction' has been replaced by the more descriptive 'cooling.fraction.50'. Recall that this parameter specifies the fraction of random-walk remaining after 50 mif iterations.

* The 'var.factor' argument to 'mif' now has the default value 1. Since 'var.factor' has long been a required parameter, this change is backward compatible.

* The 'mif' argument 'pars', which is redundant, is now deprecated. In a future release, this argument will be removed.

* The long-deprecated 'cooling.factor' option to 'mif' has now been removed.

* 'pmcmc' and 'abc' can now use arbitrary symmetric proposal distributions via the 'proposal' argument. In future, the requirement that proposals be symmetric should be relaxed. Two new functions, 'mvn.diag.rw' and 'mvn.rw', generate suitable proposal functions. The first generates a multivariate normal random-walk proposal with diagonal variance-covariance matrix; this duplicates the old behavior of both 'abc' and 'pmcmc'. The second, 'mvn.rw', corresponds to a multivariate normal random-walk proposal with arbitrary variance-covariance matrix.  Using these as a template, the user can easily construct alternatives.

* In 'pmcmc' and 'abc', the arguments 'pars' and 'rw.sd' are now unneeded (see above) and have been deprecated. Use of 'rw.sd' will generate a warning and result in behavior equivalent to choosing 'proposal=mvn.diag.rw(rw.sd)'. Use of 'pars' will be ignored, with a warning.

* In 'nlf', the 'transform.params' argument is now deprecated; use instead the 'transform' argument, as in the other inference methods.

* Compiler messages are now suppressed by default when Csnippets are used in construction of a pomp object. These can be enabled by setting 'options(verbose=TRUE)'.

* 'simulate' has a new argument, 'include.data', that when used in conjuncion with 'as.data.frame=TRUE' will include the actual data in the resulting data frame along with the simulations.

* The 'pompExample' function has been revamped. A search path for example directories is now stored in global option 'pomp.examples'.

* The new 'values' method extracts simulated probe values on 'probed.pomp' object.

* The 'pomp.h' header file is now better documented through comments.

* A modified version of the Liu and West (2001) algorithm is included as 'bsmc2'.

As always, please send bug reports, feature requests, and other questions to kingaa at umich.edu.

Happy pomping!

Aaron





-- 
Aaron A. King, Ph.D.
Ecology & Evolutionary Biology
Mathematics
Center for the Study of Complex Systems
University of Michigan
GPG Public Key: 0x15780975