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pomp: statistical inference for partially-observed Markov processes

Version 4.6 of pomp is now on CRAN and coming soon to a mirror near you. This release contains some changes to the user interface.

Changes in function names

The biggest change from the user standpoint is that all pomp functions with names.that.contain.dots have been deprecated in favor of functions in snake_case. That is, every function that had a dot (.) in its name has been replaced by a function where every dot is replaced by an underscore (_).

This is unfortunately necessary to avoid problems with CRAN checks, which (falsely) assume that certain functions with dotted names are S3 methods. The old function names will continue to work, with a warning. In a future release, the deprecated functions will be removed.

To help you adapt your code to the new naming convention, you can download and run the to_snake_case.R script. Its usage is straightforward:

1. Make a directory and copy all files that you wish to edit into it.
2. In an R session, source this script.
3. Call the to_snake_case() function with the path to your new directory as its sole argument
4. Examine the differences between the files for correctness.
5. Move the new files back into place.

Other user-visible changes

• The extractor functions cond_logLik, eff_sample_size, filter_mean, filter_traj, forecast, pred_mean, pred_var, and saved_states now allow you to retrieve their output in a handy data-frame format, and not just in the (somewhat unwieldy) list or array formats as before. This is accomplished via the new format argument in each of these functions.

• The logmeanexp function now computes the effective sample size when the option ess=TRUE is selected. The effective sample size can be useful in determining the reliability of the logmeanexp estimate. Additionally, logmeanexp now returns a fully-named vector when either se=TRUE or ess=TRUE.

• pomp no longer depends on the superseded package reshape2. Accordingly, the melt function—useful for converting arrays and nested lists into data frames—is no longer re-exported from reshape2. pomp now contains a somewhat stricter and more limited version of this useful function.

• The magrittr pipe, %>%, is no longer re-exported by pomp: use the native R pipe, |>, instead.

• The package now requires R version 4.1 at least.

Low-level changes

• The dimnames attributes for the arrays computed in pfilter and pmcmc computations have changed. In particular, whereas in previous versions, the time dimension was given names that were character strings composed of decimal representations of the time (difficult to work with and prone to roundoff error), the time dimension now is not given names. That is, the time dimension in these arrays can be accessed by position, not by name. If you want to match these result to the observation time, use the format=data.frame option in the corresponding extractor function.

Bug fixes

• A bug that resulted in the gompertz example differing on Windows systems has been fixed.

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