Recent Releases of pomp
pomp - 6.0.4.0
- The new function
append_dataappends a data frame to an existing CSV file (creating the file if it does not exist). This facilitates keeping a database of parameter-space explorations. - The new function
eeulermultinomgives the expectation of an Euler-multinomial random variable.
- R
Published by github-actions[bot] about 1 year ago
pomp - 6.0.1.0
This release contains two breaking changes.
- From version 5.8.4, the manner in which extra model elements (
userdata) are supplied has changed. As of that version, use of the old method generated a warning. As of this version, an error will be generated. To supply additional elements (i.e., beyond parameters, latent-state variables, observations, and covariates) to the basic model components, provide them as a list via theuserdataargument. - In calls to
pompelementary and inference algorithms, it is now necessary to pass all arguments by name. This has always been good practice, but from this release, calls that rely on the position of arguments will typically generate errors.
See the news blog for more detail.
- R
Published by github-actions[bot] about 1 year ago
pomp - 5.9.1.0
The rprocess plugin onestep now always takes exactly one step to get from one observation time to the next, even when the interval between them is zero. That is, if P is a 'pomp' object with an rprocess built using rprocess=onestep(f), t0=timezero(P), and t=time(P), then f will be called exactly once for the interval (t0,t[1]) and once for each of the intervals (t[i-1],t[i]), i=2,...,length(t).
- R
Published by github-actions[bot] over 1 year ago
pomp - 5.9.0.0
User-visible change
As documented in the manual, basic model components have access to parameters, covariates, state variables, and in some cases, the data. To make additional elements available to the basic model components, pomp provides the "userdata" facility. From this version, such elements should be furnished to pomp functions in a list via the argument userdata. For the present, the old behavior will still work, but will generate a warning. In a future release, this will become an error.
Bug fix
A bug in covariate-table extrapolation for the case order="constant" has been fixed.
Feature enhancement
A new experimental function repair_lookup_table is provided to help eliminate unnecessary warnings about extrapolation. One can use it "repair" a covariate table that does not span the full temporal range of observations. This is simply a matter of performing the extrapolations and adding them to the lookup table. See the manual for more information and an example.
Other changes
Functions with names that include dots (.), which have been defunct since version 4.7, have now been expunged entirely.
- R
Published by github-actions[bot] over 1 year ago
pomp - 5.8.4.0
To add additional elements for use by the basic model components (i.e., "userdata"), the userdata argument should now be used. The old behavior will still work, but will generate a warning. In a future release, this will become an p error.
- R
Published by github-actions[bot] over 1 year ago
pomp -
Almost identical to version 5.7. Contains one improvement to the documentation relative to that release.
- R
Published by kingaa almost 2 years ago
pomp -
- Minor corrections to documentation.
- Changes in some C codes to avoid issues detected by rchk.
- Fixed bug in
wquantintroduced by changes inpbetawith R version 4.3.3.
- R
Published by kingaa almost 2 years ago
pomp -
- C-level functions
set_pomp_userdataandunset_pomp_userdataare no longer exported. bspline_evalis no longer exported.
- R
Published by kingaa about 2 years ago
pomp -
Changes in 'pomp' version 5.4.1:
- C-level functions
set_pomp_userdataandunset_pomp_userdataare no longer exported.
- R
Published by kingaa over 2 years ago
pomp -
Eliminate spurious warnings arising on certain platforms.
- R
Published by kingaa over 2 years ago
pomp -
Changes in pomp version 5.3.1:
stewnow returns timing information by default.
- R
Published by kingaa over 2 years ago
pomp -
Changes in pomp version 5.2.5:
- The new option
on_loadallows one to specify a C snippet that will be executed at the time the C snippet library is loaded. - Internally, the
userdataare made available via calls topompLoadrather than within each call to a pomp workhorse.
- R
Published by kingaa over 2 years ago
pomp -
- The data frames returned by
cond_logLikandeff_sample_sizewhenformat="data.frame"have been improved. In particular, they contain (as variabletime) the times (rather than the index of the time vector as before). - Changes to the report generated by
spy. - Some documentation improvements.
- R
Published by kingaa over 2 years ago
pomp -
Changes in pomp version 5.2.3:
- The manual pages have been reorganized, with improved cross-linking.
- A bug in
filter_trajetc. arising when not all state variables have names was fixed.
- R
Published by kingaa over 2 years ago
pomp -
This version adds the new basic component
dinitfor evaluating the probability density function of the initial-state distribution. There is a corresponding workhorse function,dinit().The constructor
pompnow takes the optional argumentnstatevars, which can be used to increase the dimension of the latent state-vectors created byrinit. By default,nstatevars = length(statenames), andnstatevarscan only be used to increase, not to decrease, the dimension of the latent state process. Moreover,nstatevarshas no effect if therinitbasic component is furnished as an R function.Name checking on internally-created vectors and arrays is less strict than previously. In particular, it is possible to have variables without names (i.e.,
"").
- R
Published by kingaa over 2 years ago
pomp -
Changes in pomp version 5.2.1:
reulermultinomnow returnsNArather thanNaN, in keeping with the behavior ofrbinom. Thanks to John Drake for calling attention to this issue.
- R
Published by kingaa over 2 years ago
pomp - version 5.0.0.3
We no longer import from plyr.
The
dimnamesattributes of various arrays that appear in pomp, including arrays of observables, state variables, parameters, covariates, and so on, have been made uniform. In particular, when a dimension of an array corresponds to variables with different names, this dimension is itself named "name". Previously, its name was sometimes "variable" and sometimes "parameter". This change is meant to streamline interaction with the tidyverse.Some minor bugfixes.
- R
Published by kingaa almost 3 years ago
pomp - Identical to version 4.7
- Functions with names.that.contain.dots that were been deprecated in version 4.5.1 are now defunct. Attempts to use such functions will generate an error with a message indicating the replacement function.
plotnow removesNA.
- R
Published by github-actions[bot] almost 3 years ago
pomp -
Changes in 'pomp' version 4.6.4:
• Better handling of ‘listie’s (lists of ‘pomp’ objects).
• New ‘concat’ function to turn lists of ‘pomp’ objects into
‘listies’.
- R
Published by kingaa about 3 years ago
pomp -
The ‘states’ and ‘obs’ methods take a new optional argument, format. Setting format="data.frame" causes the method to return the states or data in a convenient data-frame format.
- R
Published by kingaa about 3 years ago
pomp -
When melt is applied to a list, the identifier variable is now ‘.Lx’, where x denotes the level. This applies when as.data.frame is used to coerce a list of ‘pomp’ objects, and when saved_states is used to extract the particles from a list of ‘pfilterd_pomp’ objects.
- R
Published by kingaa about 3 years ago
pomp -
A new
formatargument has been added to the extractor functionscond_logLik,eff_sample_size,filter_mean,filter_traj,forecast,pred_mean,pred_var, andsaved_states. This allows the user to extract the relevant elements in data-frame format if desired.pomp no longer depends on the superseded packages reshape2 or plyr.
pomp has a new dependency on the package dplyr.
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.
- R
Published by kingaa about 3 years ago
pomp -
All
pompfunctions with names.that.contain.dots have been deprecated in favor of functions insnake_case. This is to avoid anticipated problems with CRAN checks, which (falsely) assume that certain functions with dotted.names are S3 methods. From this point, no exporedpompfunction has such a name.The
dimnamesattributes for some of the arrays computed inpfilterandpmcmccomputations have changed. In particular, whereas in previous versions, thetimedimension was given names that were character strings composed of decimal representations of the time (difficult to work with and prone to roundoff error), thetimedimension now is not given names.A bug that resulted in
gompertzgiving different simulations on Windows machines has been fixed.
- R
Published by kingaa about 3 years ago
pomp -
This release fixes a bug in trajectory computation for deterministic, discrete-time maps. Thanks to Felicia Magpantay for finding the bug and reporting it!
In addition, this release includes
- changes that allow one to extract weighted as well as unweighted particles from a
pfiltercomputation and - changes to the
wquantfunction for estimating quantiles given weighted samples.
As ever, the release can be installed by executing
install.packages("pomp",repos="https://kingaa.github.io")
in an R session.
- R
Published by kingaa about 3 years ago
pomp -
Version 4 contains a few changes that are not backward compatible. These are all to do with the elementary function ‘trajectory’, which computes trajectories of the deterministic dynamical skeleton. See below for details.
• The behavior of ‘trajectory’ now fully conforms to the behavior of other ‘pomp’ elementary functions. In particular, one can now add, remove, or modify basic model components in a call to ‘trajectory’ just as one can with ‘simulate’, ‘pfilter’, ‘probe’, etc. Before version 4, additional arguments to ‘trajectory’ (i.e., those passed via ‘...’) were passed on to the ODE integrator in the case of continuous-time deterministic skeletons (i.e., vectorfields) and ignored in the case of discrete-time skeletons (i.e., maps). As of version 4, in order to adjust ODE integrator settings it is necessary to use the ‘odecontrol’ argument of ‘trajectory’. This behavior matches that of ‘trajobjfun’.
• It is now possible to create a ‘pomp’ object from scratch using ‘trajectory’, together with a specification of the rinit and skeleton components. Prior to version 4, in order to do so, it was necessary to first create a dummy data set, then call ‘pomp’, and then pass the resulting ‘pomp’ object to ‘trajectory’. This can now be achieved in one call.
• The user now has the option, in a call to ‘trajectory’, to have the results returned as one or ‘pomp’ objects. In this regard, its behavior matches that of ‘simulate’.
- R
Published by kingaa over 4 years ago
pomp - https://github.com/kingaa/pomp/releases/tag/3.2.0.0
- R
Published by kingaa about 5 years ago
pomp -
- As promised, the default value of
tolin the particle-filtering algorithmspfilter,pmcmc,mif2, andbsmc2has been changed to zero. A warning continues to be issued iftolis set to anything other than 0. In a future release, the option to choose a nonzero tolerance will be removed entirely. - In traces and diagnostic plotting methods, the
nfailvariable (tracking numbers of filtering failures) has been dropped.
- R
Published by kingaa almost 6 years ago