[pomp-announce] pomp version 0.34-1 released

[Aaron A. King]

There are a number of changes in pomp with this release.  Most are 
augmentations of the package's capabilities or changes in the internal 
implementations that improve speed (sometimes dramatically).

There is one change, too, to some of the defaults, which may need attention if 
you have codes that depend on pomp defaults.  Read on for details.

o  The default behaviors of 'simulate' and 'trajectory' with respect to the 
argument 'times' have changed.  In each of these functions, there is a new 
argument, 't0', which specifies the time at which the initial conditions 
obtain. The default for 't0' is 'timezero(object)'. The default for 'times' 
is now 'time(object,t0=FALSE)' (it was 'time(object,t0=TRUE)'). This change 
eliminates a persistent source of annoyance in that 'simulate' 
and 'trajectory' sometimes returned usually undesired values at the initial 
time.  You can ensure that your codes will continue to function as intended 
by specifying the values of the 'times' and 't0' arguments to these 
functions, thus removing dependence on the defaults in these functions. To 
aid you in this, a warning is now displayed whenever you make a function call 
that may be affected by the change in default behaviors. These warnings will 
be removed in the not-too-distant future. See the documentation 
("pomp?simulate", "pomp?trajectory") for a description of the new default 
behaviors.

o  The 'states' slot of a pomp object now holds values of the state process 
only at the times given in the 'times' slot. This is a change from the 
earlier behavior in which the 'states' slot sometimes (but not always) 
included the value of the state process at 't0'.

o  'simulate' has been re-implemented in C for speed.

o  A new method 'obs' for pomp objects returns the contents of the 'data' 
slot. It is synonymous with 'data.array' but is easier to type.

o  'coef<-' now behaves like ordinary vector assignment, i.e., coef(object) <- 
x does what y <- x would do, and coef(object,names) <- x does what y[names] 
<- x would do.

o  'probe' and 'spect' now take an argument 'params', which allows you to 
override the default, params = coef(object).

o  'probe.cov' and 'probe.cor' have been removed in favor of 'probe.acf' 
and 'probe.ccf', which are much faster.  Thanks to Simon Wood for the 
inspiration for these functions.

o  The functions 'euler.simulate', 'onestep.simulate', and 'onestep.density', 
deprecated since version 0.29-1, have been removed.

-- 
Aaron A. King, Ph.D.
Ecology & Evolutionary Biology
Mathematics
Center for the Study of Complex Systems
University of Michigan
GPG Public Key: 0x6E74F51B
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