[Pomp-commits] r901 - in www: . content vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 21 13:07:48 CET 2014
Author: kingaa
Date: 2014-03-21 13:07:47 +0100 (Fri, 21 Mar 2014)
New Revision: 901
Added:
www/content/NEWS.html
www/vignettes/pomp.pdf
Modified:
www/content/vignettes.htm
www/index.php
Log:
- link to development version of manual and NEWS
Added: www/content/NEWS.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: News for Package 'pomp'</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+
+<table width="100%" summary="page for NEWS"><tr><td>NEWS</td><td align="right">R Documentation</td></tr></table>
+
+<h2>News for Package 'pomp'</h2>
+
+<h3>Changes in pomp version 0.49-1</h3>
+
+
+<ul>
+<li><p> A new method, 'probe.match.objfun', constructs objective functions suitable for use in optimizers.
+</p>
+</li>
+<li><p> 'pomp' now depends on 'nloptr', which provides a suite of optimization algorithms.
+This package can now be used in various methods for optimization of an objective function.
+</p>
+</li>
+<li><p> New inline C functions 'to_log_barycentric' and 'from_log_barycentric' are provided in 'pomp.h' to facilitate log-barycentric transformations.
+These have proven very useful in dealing with parameters constrained to sum to one (e.g., initial conditions of compartmental models).
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.48-3</h3>
+
+
+<ul>
+<li><p> Correct a bug in 'abc' to do with parameter transformation.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.48-1</h3>
+
+
+<ul>
+<li><p> Create new 'dprior' and 'rprior' slots for 'pomp' objects.
+These will be used by the Bayesian methods (currently 'abc', 'bsmc', and 'pmcmc').
+The 'hyperparams' argument to these methods has been removed;
+hyperparameters are now treated just as any others.
+</p>
+</li>
+<li><p> 'bsmc' can now be called so that the particles are drawn from the prior distribution (as set by the 'rpior' slot).
+</p>
+</li>
+<li><p> Some of the longer tests will only be run if an environment variable is set.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.47-4</h3>
+
+
+<ul>
+<li><p> Revisit 'dacca' bug. Set negative compartments to zero along with compartments immediately downstream.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.47-3</h3>
+
+
+<ul>
+<li><p> Fix bug that arises only very occasionally in the 'dacca' cholera example.
+</p>
+</li>
+<li><p> Modify 'dacca' model so that rare positivity violations are punished in a different way.
+This modifies the formal model slightly.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.47-2</h3>
+
+
+<ul>
+<li><p> By default, 'pompBuilder' now creates all files in the temporary directory.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.47-1</h3>
+
+
+<ul>
+<li><p> 'abc' implements Approximate Bayesian Computation for pomp models.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.46-1</h3>
+
+
+<ul>
+<li><p> 'pompExample' now has an optional argument, 'envir', determining which environment the pomp object will be loaded into.
+</p>
+</li>
+<li><p> 'logmeanexp' now has an optional argument, 'se', allowing for computation of an approximate standard error.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.45-8</h3>
+
+
+<ul>
+<li><p> bug fix in 'gompertz' example.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.45-7</h3>
+
+
+<ul>
+<li><p> bug fix in 'pmcmc': Metropolis-Hastings ratio was incorrect except for flat priors!
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.45-6</h3>
+
+
+<ul>
+<li><p> a fix so that 'pompBuilder' will find 'pomp.h' header file on Windows machines. Thanks to Dave Hayman for finding the problem.
+</p>
+</li>
+<li><p> new 'logmeanexp' function.
+</p>
+</li>
+<li><p> some reorganization of the source package structure.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.45-4</h3>
+
+
+<ul>
+<li><p> changes in the way 'reulermultinom', 'deulermultinom', 'dot_product' are exported to other packages. Rather than just being exported as linkables, these are now also defined as static inline functions in the 'pomp.h' header.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.45-3</h3>
+
+
+<ul>
+<li><p> fix bug with 'continue' and method 'mif2'
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.45-2</h3>
+
+
+<ul>
+<li><p> new method to coerce 'pfilterd.pomp' objects to data-frames.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.45-1</h3>
+
+
+<ul>
+<li><p> 'profileDesign' can now handle variables of mixed type.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.44-1</h3>
+
+
+<ul>
+<li><p> New 'mif2' option for 'mif'.
+</p>
+</li>
+<li><p> The default behavior for 'mif' and 'pfilter' with respect to filtering failures has been changed.
+Before, the default behavior has been to stop with an error on the first filtering failure ('max.fail=0').
+Now, the default is 'max.fail=Inf', i.e., an error is never triggered.
+</p>
+</li>
+<li><p> The implementation of MIF cooling schedules has been changed to make it more general.
+The cooling schedule is now specified by a 'type' and a 'fraction'.
+Currently, supported 'cooling.type's include 'geometric' (the old behavior) and 'hyperbolic', i.e., a 1/(1+n) schedule.
+The 'cooling.fraction' argument specifies the cooling at 50 iterations.
+That is, if s is the intensity of the random-walk perturbation to parameters at the first iteration ('rw.sd'), then the intensity at iteration 50 is s*cooling.fraction.
+</p>
+</li>
+<li><p> Remove all data()-loadable pomp objects.
+To load the prebuilt example pomp objects from previous versions, use the new 'pompExample' function.
+E.g., instead of 'data(euler.sir)', do 'pompExample("euler.sir")'.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.43-4</h3>
+
+
+<ul>
+<li><p> Clean up tests.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.43-3</h3>
+
+
+<ul>
+<li><p> Fix bug in 'pompBuilder' on mac.
+</p>
+</li>
+<li><p> Fix bug in 'dmeasure' when log=TRUE. Bug located by R. Reiner.
+</p>
+</li>
+<li><p> Add 'eff.sample.size' and 'cond.logLik' methods for 'pfilterd.pomp' objects.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.43-1</h3>
+
+
+<ul>
+<li><p> Modify 'traj.match.objfun' to allow arbitrary parameters to be passed to the ODE integrator.
+</p>
+</li>
+<li><p> Add 'params' argument to 'pomp' so that parameters can be specified at the time the pomp object is created.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.42-6</h3>
+
+
+<ul>
+<li><p> Improve error checking in 'pomp'.
+</p>
+</li>
+<li><p> Add support for covariates to 'pompBuilder'.
+</p>
+</li>
+<li><p> Add native parameter transformation routines to the demos.
+</p>
+</li>
+<li><p> Change the warning behavior in 'lookup_table' so that warnings are not generated unless true extrapolation is performed (i.e., eliminate the warnings at the boundary).
+</p>
+</li>
+<li><p> Some small modifications to the 'pomp.h' header file.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.42-4</h3>
+
+
+<ul>
+<li><p> When 'trajectory' calls 'ode', there is a need to preserve information across calls to the vectorfield-evaluating function.
+The code has been modified to do this in a cleaner way.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.42-2</h3>
+
+
+<ul>
+<li><p> Several minor bugs have been fixed.
+See the ChangeLog for details.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.42-1</h3>
+
+
+<ul>
+<li><p> An EXPERIMENTAL facility for constructing pomp objects out of native C routines is now included (pompBuilder).
+This facility is being actively developed and future changes may not be backward compatible.
+</p>
+</li>
+<li><p> A new facility allowing access to the 'userdata' slot of a pomp object from compiled 'rprocess', 'rmeasure', 'dprocess', 'dmeasure', 'skeleton', and 'partrans' codes is now available.
+Calls to the new C routines 'get_pomp_userdata', 'get_pomp_userdata_int', and 'get_pomp_userdata_double' allow retrieval of these elements.
+</p>
+</li>
+<li><p> Some of the data()-loadable examples have been reworked to make use of the above facility.
+The parameterization of these examples has changed.
+These changes are not backward compatible: codes that depend on the data()-loadable examples may be broken.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.41-8</h3>
+
+
+<ul>
+<li><p> A demonstration of 'pompBuilder' has been put into the 'advanced topics' vignette.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.41-7</h3>
+
+
+<ul>
+<li><p> A bug in the 'blowflies' example has been fixed.
+Thanks to Greg Minshall for discovering it.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.41-6</h3>
+
+
+<ul>
+<li><p> The 'gompertz' example parameter transformations have been changed.
+No longer are the names of the parameter vector changed in the transformation.
+This change is not backward-compatible, but only codes using this example are affected.
+</p>
+</li>
+<li><p> The 'euler.sir' and 'gillespie.sir' examples have been changed.
+The transmission rate beta(t) is now the arithmetic sum of the seasonality basis functions.
+Before, it was the geometric sum.
+R0 is now given by the arithmetic average of the beta parameters divided by (gamma+mu).
+This change is not backward-compatible, but only codes using these examples are affected.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.41-5</h3>
+
+
+<ul>
+<li><p> An experimental facility for constructing pomp objects with native C routines is now included.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.41-4</h3>
+
+
+<ul>
+<li><p> The 'blowflies', 'euler.sir', 'gillespie.sir', 'bbs', and 'ricker' data()-loadable examples have been changed to make the parameterization simpler and more natural.
+This change is not backward-compatible, but only codes using this example are affected.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.41-3</h3>
+
+
+<ul>
+<li><p> In 'trajectory', all vectorfield and map evaluation is now done in C for speed.
+For continuous-time dynamical systems, this gives an approximately 4-fold speedup.
+</p>
+</li>
+<li><p> Demos have been created to show some examples.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.41-2</h3>
+
+
+<ul>
+<li><p> A segfault bug in 'bbs' example has been fixed.
+</p>
+</li>
+<li><p> The posterior medians (not means) are now stored in the 'params' slot of the 'bsmcd.pomp' object.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.41-1</h3>
+
+
+<ul>
+<li><p> New arguments in 'mif', 'nlf', 'bsmc', 'pmcmc', 'probe-match', and 'traj-match' allow the estimation to be done on a transformed parameter space.
+When 'transform=TRUE' in these commands ('transform.params=TRUE' for 'nlf'), estimation is performed on the transformed parameter space.
+This is described and demonstrated in the 'intro_to_pomp' vignette.
+</p>
+</li>
+<li><p> The data()-loadable examples have been re-implemented to make use of the above-mentioned facility.
+Note that this new functionality makes it unnecessary to "un-transform" model parameters within the user-specified 'rprocess', 'dprocess', 'rmeasure', 'dmeasure', 'skeleton', and 'initializer' codes.
+This change is not backward-compatible, but only codes using these data()-loadable example are affected.
+</p>
+</li>
+<li><p> The Bayesian sequential Monte Carlo command 'bsmc' now returns not a list but an object of class 'bsmcd.pomp'.
+An experimental 'plot' method for objects of this class now exists.
+Also, the parameter posterior means are now stored in the 'params' slot of the 'bsmcd.pomp' object:
+access them with the 'coef' command as usual.
+</p>
+</li>
+<li><p> A new example, using data from an influenza outbreak in a British boarding school and an SIR model, has been included.
+Do 'data(bbs)' to load it.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.40-9</h3>
+
+
+<ul>
+<li><p> Setting the new argument 'as.data.frame' to 'TRUE' in 'simulate' and 'trajectory' causes the results to be returned as a data-frame.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.40-8</h3>
+
+
+<ul>
+<li><p> A new method 'partrans' allows transformation of vectors or matrices of parameters.
+The parameter transformations have been pushed into C for speed.
+It is possible to specify native parameter transformation routines in addition to C functions, but this last facility has not yet been extensively tested.
+A new slot 'has.trans' has been introduced into the 'pomp' class, and the types of slots 'par.trans' and 'par.untrans' have changed.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.40-7</h3>
+
+
+<ul>
+<li><p> 'parmat' now gracefully handles the case when 'params' is already a matrix.
+</p>
+</li>
+<li><p> Error in the documentation of 'pfilter' repaired.
+Thanks to Alex Smith for pointing this out.
+</p>
+</li>
+<li><p> Improvements in the documentation of the Nicholson blowflies data 'data(blowflies)'.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.40-6</h3>
+
+
+<ul>
+<li><p> When a pomp object is updated using 'pomp', the 'params' slot will now be copied over (appropriately transformed).
+Before, it was simply dropped.
+</p>
+</li>
+<li><p> The 'gillespie.sir' example has been changed to make the reporting rate equal to 'rho'.
+Before, it was fixed at 10%.
+</p>
+</li>
+<li><p> A new error-trap has been put into 'probe' and 'probe.match' for the case nsim < nprobes.
+Thanks to Dani Jonas for finding this error.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.40-5</h3>
+
+
+<ul>
+<li><p> More informative error messages when dimension of state space or data space disagree internally.
+</p>
+</li>
+<li><p> The 'weighted' argument to 'mif' and 'continue' is now deprecated in favor of a new argument 'method'.
+The old 'weighted=T' corresponds to 'method="mif"' while the old 'weighted=F' corresponds to 'method="unweighted"'.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.40-4</h3>
+
+
+<ul>
+<li><p> New functions 'traj.match.objfun' and 'probe.match.objfun' have been added.
+These functions construct functions of one argument suitable for use as objective functions in 'optim'-like optimizers (iincluding 'subplex' and 'sannbox').
+Minimizing these functions solves the trajectory-matching problem and probe-matching problem, respectively.
+This allows the user much greater flexibility in choice of optimization algorithm than is afforded by 'traj.match' and 'probe.match'.
+</p>
+</li>
+<li><p> The 'sannbox' optimizer, which performs simulated annealing with box constraints, is now exported and available for general use.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.40-3</h3>
+
+
+<ul>
+<li><p> The 'bsmc' method has been improved, due to the contributions of Pierre Jacob.
+Specifically, 'bsmc' no longer reports a log-likelihood (which it never actually computed anyway) but a log-evidence.
+The latter computation was supplied by Pierre Jacob.
+</p>
+</li>
+<li><p> A new helper function, 'exp2geom_rate_correction' has been added to the 'pomp.h' file.
+This function computes the rate r such that if N ~ geometric(prob=1-exp(-r*dt)) and T ~ exponential(rate=R), then E[N*dt] = E[T].
+This is useful in approximating a continuous-time death process by a discrete time (Euler) process.
+In particular, in such a case, T is the waiting time to death in the former and N*dt is the waiting time to death in the latter.
+An Euler binomial or multinomial process with rate r=exp2geom_rate_correction(R,dt) will have the same mean waiting time as the exponential process with rate R.
+Thanks to Sebastien Ballesteros for suggesting this.
+</p>
+</li>
+<li><p> A new helper function, 'rgammawn' has been added, with both R and C interfaces.
+This function draws an increment of a Gamma white-noise process with a given intensity.
+Specifically, dw=rgammwn(sigma,dt) is Gamma distributed with mean dt and variance sigma^2*dt.
+In this case, mu*dw/dt is suitable for use as a random rate in an Euler-multinomial process.
+Thanks to Sebastien Ballesteros for suggesting this.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.40-2</h3>
+
+
+<ul>
+<li><p> A bug to do with computation of the number of steps needed in discrete-time simulation and trajectory computations has been fixed.
+This bug was introduced in version 0.40-1.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.40-1</h3>
+
+
+<ul>
+<li><p> It is now possible for discrete-time determistic skeletons to have a general step-size.
+Before, the stepsize was always forced to be 1.
+The new argument 'skelmap.delta.t' in 'pomp' (default value 1) sets this step-size.
+NB: in implementing this feature, a new slot has been added to the basic 'pomp' class.
+'pomp' objects created with versions <0.40-1 will not therefore work with this version and must be re-created.
+</p>
+</li>
+<li><p> The deterministic skeleton trajectory functions now look for variables named in 'zeronames' and treat these variables as accumulators.
+This brings the behavior of the deterministic skeleton functions into line with 'rprocess'.
+A new section of the "advanced topics" vignette discusses accumulator variables and 'zeronames'.
+</p>
+</li>
+<li><p> Include the user manual PDF among the vignettes.
+</p>
+</li>
+<li><p> The new function 'parmat' creates a suitable matrix of parameters in one line.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.39-5</h3>
+
+
+<ul>
+<li><p> Bug fix in 'bsmc' that arises when the state space is 1-D.
+Thanks to Arnab Bhattacharya for finding the bug.
+</p>
+</li>
+<li><p> Some inconsistencies in the arguments of 'bsmc' have been fixed.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.39-4</h3>
+
+
+<ul>
+<li><p> Minor corrections to the documentation for 'spect', 'probe', and 'traj.match'.
+</p>
+</li>
+<li><p> Fix infelicity in 'traj.match' and 'nlf' that arises when the 'data' slot has no rownames.
+Rownames are not strictly required for the 'data' slot.
+</p>
+</li>
+<li><p> The 'sannbox' algorithm now should work even when the objective function throws a non-finite value.
+The behavior now is to replace non-finite values with a large number.
+This behavior follows that of the 'SANN' method in 'optim.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.39-3</h3>
+
+
+<ul>
+<li><p> The help files for 'pfilter' and 'mif' have been updated to explain how to use a variable number of particles in the particle filtering algorithm.
+</p>
+</li>
+<li><p> Inside 'init.state', a check has been added to make sure that the user's initializer function returns a vector of uniform size, as per the algorithms' assumptions.
+Thanks to Micaela Martinez-Bakker for catching this.
+</p>
+</li>
+<li><p> 'mif' has been modified so as to allow estimation of initial-value parameters alone via fixed-lag smoothing.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.39-2</h3>
+
+
+<ul>
+<li><p> When 'po' is a 'pomp'-class object with covariates, 'as.data.frame(po)' and 'as(po,"data.frame")' now contain columns for the covariates.
+The latter are interpolated, if necessary, at the observation times.
+</p>
+</li>
+<li><p> Bug fix: when 'pfilter' is called with a single parameter vector supplied in the 'params' argument, these parameters are copied into the 'params' slot of the resulting 'pfilterd.pomp' object.
+Before, this failed when the 'params' slot of the 'pomp' object was empty.
+A similar bug existed in 'traj.match' and has likewise been fixed.
+</p>
+</li>
+<li><p> To eliminate warnings and confusion during package check, 'profile.design' has been replaced by 'profileDesign'.
+For parallelism, 'slice.design' and 'sobol.design' have been replaced by 'sliceDesign' and 'sobolDesign', respectively.
+The older forms are now deprecated and will be removed in a future release.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.39-1</h3>
+
+
+<ul>
+<li><p> New facilities for parameter transformation are provided.
+New optional arguments 'parameter.transform' and 'parameter.inv.transform' to 'pomp' allow the user to specify transformations between natural and internal parameter scalings.
+A new option 'transfom' to 'coef' and 'coef<-' allows the user to get and set parameters on the natural scale.
+See 'pomp?coef' and the "intro_to_pomp" vignette for details and examples.
+Similarly, the 'conv.rec' method now takes an optional 'transform' argument.
+</p>
+</li>
+<li><p> Minor improvements to the documentation.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.38-5</h3>
+
+
+<ul>
+<li><p> 'pfilter' will now give an error if ever a non-finite likelihood (dmeasure value) is returned.
+Before, errors were only generated when dmeasure returned NA.
+</p>
+</li>
+<li><p> 'spect' now returns frequencies reflective of the observation times.
+Before, the frequencies were given as fractions of the sampling frequency.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.38-4</h3>
+
+
+<ul>
+<li><p> Improvements to the documentation.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.38-3</h3>
+
+
+<ul>
+<li><p> Clarifications and minor improvements in the help pages.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.38-2</h3>
+
+
+<ul>
+<li><p> A new section describing and demonstrating nonlinear forecasting has been added to the "intro to pomp" vignette.
+</p>
+</li>
+<li><p> Fixed bug in 'nlf': desire for transient period (nconverge>0) was unrecognized.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.38-1</h3>
+
+
+<ul>
+<li><p> Fixed bug in 'pomp' when 'data' is of class 'pomp': userdata should be preserved.
+</p>
+</li>
+<li><p> Improved discussion of SIR model in "Intro to pomp" vignette.
+</p>
+</li>
+<li><p> In 'pfilterd.pomp' objects, 'saved.states' and 'saved.params' slots are now length-ntimes lists of arrays.
+</p>
+</li>
+<li><p> It is now possible to use variable numbers of particles in 'pfilter'.
+The 'Np' argument may be specified as a single number as before, or now as either a vector of numbers or a function.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.37-2</h3>
+
+
+<ul>
+<li><p> The "advanced topics" vignette has been much augmented and improved.
+</p>
+</li>
+<li><p> The 'euler.sir' example (load it with 'data(euler.sir)') has a different measurement model: a discretized normal distribution with the same mean and variance as before.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.37-1</h3>
+
+
+<ul>
+<li><p> The arguments 'skeleton.map' and 'skeleton.vectorfield' are now deprecated.
+Specify a discrete-time skeleton using 'skeleton.type="map"' and a continuous-time skeleton via 'skeleton.type="vectorfield"'.
+</p>
+</li>
+<li><p> 'pomp' is now a generic function.
+Calling it on a 'pomp' object copies the object; one can optionally modify some of the slots.
+</p>
+</li>
+<li><p> Two new files 'gompertz.R' and 'gompertz.c' are in the 'examples' directory.
+These contain codes needed to reproduce the Gompertz example in the 'intro_to_pomp' vignette.
+</p>
+</li>
+<li><p> The warning messages to do with the default behaviors of 'simulate' and 'trajectory' with respect to the arguments 'times' and 't0' have been removed.
+These warnings were introduced in version 0.34-1 to alert users to changes in the default behavior of 'simulate' and 'trajectory' introduced with that version.
+See the help ("pomp?simulate", "pomp?trajectory") for details.
+</p>
+</li>
+<li><p> It is now possible to save both the states and particles portions of the filtering distributions computed in 'pfilter'.
+This is accomplished by means of the logical 'save.states' and 'save.params' arguments to 'pfilter'.
+The particles are stored in rank-3 arrays in the slots 'saved.states' and 'saved.params'.
+This results in the need for a change in the structure of 'pfilterd.pomp' objects: note that 'pfilterd.pomp' objects (including 'mif' and 'pmcmc' objects) created under pre-0.37-1 version of the package will not load under versions >= 0.37-1.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.36-7</h3>
+
+
+<ul>
+<li><p> 'trajectory' now gives a more informative error when no skeleton is present
+</p>
+</li>
+<li><p> 'pred.mean', 'pred.var', and 'filter.mean' methods are now defined for 'pfilterd.pomp' objects (and not just 'mif' objects)
+</p>
+</li>
+<li><p> A new 'data()'-loadable example is included: do '?blowflies' to read about it.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.36-6</h3>
+
+
+<ul>
+<li><p> The B-spline basis construction functions 'bspline.basis' and 'periodic.bspline.basis' now take a 'names' argument that allows one to give names to the basis functions.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.36-5</h3>
+
+
+<ul>
+<li><p> The "intro_to_pomp" vignette has been updated. The first part of the vignette centers on a new, more transparent first example.
+</p>
+</li>
+<li><p> A bug in 'pfilter' has been fixed. This bug was introduced in version 0.32-6 (SVN revision 315). Upon filtering failure, state variables were left un-updated. Thanks to Karim Khader for reporting circumstances that led to the identification of this bug.
+</p>
+</li>
+<li><p> There is now a method for 'loglik' on 'probed.pomp' objects. This returns the synthetic likelihood.
+</p>
+</li>
+<li><p> The box-constrained simulated annealing optimization method 'sannbox' is now an option in 'probe.match'.
+</p>
+</li>
+<li><p> Calling 'states' on a pomp object having no unobserved states now fails gracefully (returning NULL rather than generating an error).
+</p>
+</li>
+<li><p> The rprocess plugin 'discrete.time.sim' now takes an optional 'delta.t' argument to allow for arbitrary (but still necessarily regular) spacing of observations. By default, delta.t=1.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.36-1</h3>
+
+
+<ul>
+<li><p> There are two new classes: 'traj.matched.pomp' and 'pfilterd.pomp' to hold the results of 'traj.match' and 'pfilter' computations, respectively. The old classes 'mif' and 'pmcmc' now inherit from 'pfilterd.pomp' in a natural way.
+</p>
+</li>
+<li><p> When 'traj.match' is called, the returned 'traj.matched.pomp' object has its 'states' slot filled with the model trajectory at the fitted parameters.
+</p>
+</li>
+<li><p> More optimization methods are now provided in 'traj.match'. These include the new algorithm "sannbox", an optionally box-constrained simulated annealing algorithm.
+</p>
+</li>
+<li><p> 'probe.match' is now an S4 method (like 'pfilter', 'mif', 'pmcmc', and 'traj.match') with methods for classes 'pomp', 'probed.pomp', and 'probe.matched.pomp'.
+</p>
+</li>
+<li><p> There is a change to the interface to 'pfilter' in that 'save.states' results in the filling of the 'last.states' slot. Before version 0.36-1, the 'pfilter' returned a list. The element 'states' of that list corresponds to the slot 'last.states' in version 0.36-1. It was necessary to make this name-change in order to avoid a conflict with the 'states' slot inherited from the 'pomp' class.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.35-1</h3>
+
+
+<ul>
+<li><p> Added a facility for computation of "synthetic likelihood" (Wood 2010) using a robust estimate of the covariance. A new slot in objects of class 'probed.pomp' holds this value.
+</p>
+</li>
+<li><p> The synthetic likelihood is now the quantity that is maximized in 'probe.match'.
+</p>
+</li>
+<li><p> Added the argument 'type' to 'probe.ccf' so that either cross-covariance or cross-correlation can be returned. 'probe.ccf' and 'probe.acf' now have comparable interfaces.
+</p>
+</li>
+<li><p> Changed the way that 'probe.acf' accepts lags. Now an arbitrary set of lags can be selected.
+</p>
+</li>
+<li><p> A bug in the new method 'obs' has been fixed.
+</p>
+</li>
+<li><p> A protection-stack overflow bug in 'probe' has been fixed.
+</p>
+</li>
+<li><p> The 'seed' slot in 'probed.pomp' and 'spect.pomp' objects has been removed, along with unwanted behavior to do with it.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.34-2</h3>
+
+
+<ul>
+<li><p> Added a method to coerce 'probed.pomp' objects to 'data.frame' objects.
+</p>
+</li>
+<li><p> Fix bug when 'simulate' is run on objects that inherit from 'pomp' but are not themselves pomps.
+'simulate' should return 'pomp' objects when obs=F and states=F, regardless of what class 'object' is.
+</p>
+</li>
+<li><p> 'simulate' and 'rprocess' are accelerated somewhat through judicious use of 'memcpy'.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.34-1</h3>
+
+
+<ul>
+<li><p> The default behaviors of 'simulate' and 'trajectory' with respect to the argument 'times' has changed.
+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 an infelicity in which 'simulate' and 'trajectory' returned undesired values at the initial time.
+Users can ensure that their 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.
+To aid users in modifying their codes, a warning is now displayed whenever a potentially affected call is made.
+These warnings will be removed in a future release.
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+</p>
+</li>
+<li><p> The 'states' slot 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 included the value of the state process at 't0'.
+</p>
+</li>
+<li><p> 'simulate' has been re-implemented in C for speed.
+</p>
+</li>
+<li><p> A new method 'obs' for pomp objects returns the contents of the 'data' slot.
+It is synonymous with 'data.array'.
+</p>
+</li>
+<li><p> A banner is now displayed on package attachment.
+</p>
+</li>
+<li><p> 'coef<-' now behaves like ordinary vector assignment.
+</p>
+</li>
+<li><p> 'probe' and 'spect' now take an argument 'params'.
+</p>
+</li>
+<li><p> 'probe.cov' and 'probe.cor' have been removed in favor of 'probe.acf' and 'probe.ccf'.
+</p>
+</li>
+<li><p> The functions 'euler.simulate', 'onestep.simulate', and 'onestep.density', deprecated since version 0.29-1, have been removed.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.33-1</h3>
+
+
+<ul>
+<li><p> Major improvements in speed in the probe-matching routines have been realized by coding the computationally-intensive portions of these calculations in C.
+</p>
+</li>
+<li><p> New probes recommended by Simon Wood (Nature 466:1102-1104, 2010) have been implemented.
+In particular, the new function 'probe.marginal' regresses the marginal distributions of actual and simulated data against a reference distribution, returning as probes the regression coefficients.
+'probe.marginal' and 'probe.acf' have been coded in C for speed.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.32-1</h3>
+
+
+<ul>
+<li><p> pomp now includes parameter estimation methods based on probe-matching and power-spectrum-matching as explained in papers by Kendall et al. (B. E. Kendall, C. J. Briggs, W. M. Murdoch, P. Turchin, S. P. Ellner, E. McCauley, R. M. Nisbet, S. N. Wood (1999) Why do populations cycle? A synthesis of statistical and mechanistic modeling approaches. Ecology, 80:1789–1805) and Reuman et al. (D.C. Reuman, R.A. Desharnais, R.F. Costantino, O. Ahmad, J.E. Cohen (2006) Power spectra reveal the influence of stochasticity on nonlinear population dynamics. Proc. Nat'l. Acad. Sci., U.S.A.} 103:18860–18865).
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.31-2</h3>
+
+
+<ul>
+<li><p> new "window", "timezero", and "timezero<-" methods are available for manipulating 'pomp' objects.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.31-1</h3>
+
+
+<ul>
+<li><p> pomp now includes an implementation of the particle Markov chain Monte Carlo algorithm of Andrieu et al. (Andrieu, C., Doucet, A., & Holenstein, R. (2010) Particle Markov chain Monte Carlo methods. J. R. Stat. Soc. B 72:1–33).
+This algorithm is implemented in the method 'pmcmc': see 'help(pmcmc)' for details.
+Implementation primarily due to Ed Ionides.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.30-1</h3>
+
+
+<ul>
+<li><p> pomp now includes an implementation of the approximate Bayesian Sequential Monte Carlo algorithm of Liu & West (Liu, J. & West, M. (2001) Combining Parameter and State Estimation in Simulation-Based Filtering. In Doucet, A.; de Freitas, N. & Gordon, N. J. (eds.) Sequential Monte Carlo Methods in Practice, Springer, New York, pp. 197–224).
+This algorithm is implemented in the method 'bsmc': see 'help(bsmc)' for details.
+Thanks to Matt Ferrari and Michael Lavine for the implementation.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.29-5</h3>
+
+
+<ul>
+<li><p> The cholera transmission model from King, A. A., Ionides, E. L., Pascual, M., and Bouma, M. J. (2008) Inapparent infections and cholera dynamics, Nature 454:877–880 together with data from the Dacca district of historic Bengal are now included.
+See 'help(dacca)' for details.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in pomp version 0.29-1</h3>
+
+
+<ul>
+<li><p> This is a major revision.
+</p>
+</li>
+<li><p> Big improvements to the documentation, including worked examples in vignettes and improvements to the manual pages.
+</p>
+</li>
[TRUNCATED]
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