pomp version 1.19 is now available on CRAN. Source and binaries will soon be visible on a CRAN mirror near you.
Important note
Version 2 of pomp, with major improvements, is on its way. Because it is not fully backward-compatible, pomp version 2 is being made available temporarily as the pomp2 package. pomp2 is not available on CRAN but source and binaries can be downloaded from the pomp website. See the installation page for instructions.
pomp2 will be phased out, replaced by version 2 of pomp, around the middle of 2019. At that point, pomp versions <2 will no longer be supported.
It is recommended that users begin making the transition to version 2 now. An upgrade guide is available to help you transition your codes to the new version. In the interim period, you can have both pomp and pomp2 installed on your system simultaneously.
Release notes
pomp version 1.19 includes bug fixes and some feature enhancements.
User-visible changes
show
andprint
methods have been made very terse: they simply report on the class of the object in question. To see more detailed information about apomp
object, usespy
.- New
verbose
option intrajectory
gives diagnostic information fromdeSolve
integration routines. Of course, this is pertinent only if the model skeleton is a vectorfield. coef(object) <- NULL
, whereobject
is of classpomp
, erases any parameters stored inobject
.- The
obs
andstates
arguments ofsimulate
are deprecated and will be removed in a forthcoming release. - The old
forward
andinverse
options for thedir
argument ofpartrans
have been dispensed with. The much more descriptive optionstoEstimationScale
andfromEstimationScale
remain. - The
euler.sir
,gillespie.sir
,blowflies
,ricker
,bbs
,dacca
, andrw2
examples are all now implemented using C snippets. - The handling of
dprocess
has changed. Theonestep.dens
plugin is now deprecated and will soon be removed.dprocess
is now specified directly using either a C snippet or an R function, in much the same way that, for example,dmeasure
is specified. - A bug in
pfilter
(and hencepmcmc
) whenfilter.traj=TRUE
was discovered and fixed. In the buggy version, the filter trajectory was sampled with incorrect weights. - A bug in the display of
istate
whendeSolve::ode
errors has been fixed. - Timo Voipio contributed a pull request that traps the error resulting from
sannbox
being passed acandidate.dist
that is not a function.
API and implementation changes
- The C-level interface for
apply_probe_sims
has changed: the new argumentrho
must be the"package:pomp"
environment. - New (unexported)
solibs<-
method allows developers of packages extendingpomp
to incorporate C snippets into object that containpomp
objects. - New
hitch
function facilitates construction ofpomp.fun
objects from R functions, C snippets, and links to external libraries. - Native routines needed to access
pomp.fun
objects in C are now registered for use by other packages. - A new
pomp_defines.h
header is provided for developers of packages that depend onpomp
. - Internally,
rprocess
is no longer stored as an R function. The use of plugins is now required for the implementation of therprocess
component. Currently, there are five plugins available:onestep.sim
,discrete.time.sim
,euler.sim
,gillespie.sim
, andgillespie.hl.sim
. - The C snippet compiling facilities have been thoroughly reworked.
See the package NEWS for more details.