Streamlined panelPomp-methods documentation.
Added panelMeasles to panelPomp models documentation family.
Fixed redirected link in documentation.
Added two new datasets: twentycities and uk_measles. These data contain measles incidence data from 20 UK cities.
Added a new panelPomp model example: panelMeasles.
Added Aaron Abkemeier as a package contributor.
Added Jesse Wheeler as one of the package authors in citation file.
Changed package maintainers
Updated package governance file and website
Standardized package version numbering system to four point system.
Fixed broken links in function documentation.
Changed the default cooling.type argument in the mif2() function to be "geometric" in order to be consistent with the pomp package.
Added format argument to coef.panelPomp method, with options c("vector", "list"). This functionality makes the pparams function obsolete, so it has been removed from the package in this version.
Changed the pParams() function name to toParamList().
Modified the toVectorPparams() function so that it returns a vector instead of a data.frame object with a single row. The name of the function was also changed to toParamVec(), and is a near inverse of the toParamList() function.
Updated unit tests and documentation.
Change the generic unitlogLik to unitLogLik to match camel-case style of package. The original function is deprecated in this version and will be removed in future updates.
Changed panelPomp S4 object slot name from unit.objects to unit_objects in order to be consistent with pomp pacakge. Corresponding getter and setter methods for this slot have also been changed from unitobjects() to unit_objects().
Added generics shared(), shared()<-, specific(), and specific()<-. These generics provide convinient access to parameters of a panelPomp object, but the setter methods also allow for changing a parameter type between shared and unit-specific.
Added function runif_panel_design(), which is useful for generating design matrices for PanelPOMP models.
Minor typo fixes to package and function documentation.
Added a type check for the params arguement of the
pfilter function in order to throw more user friendly error.
A more user friendly error is thrown when the user specifies a
parameter as both shared and unit specific in the mif2 function.
Added a match.arg call in mif2.internal; this will
allow the default option for the cooling.type argument in
mif2 to no longer throw an error, and mimics the behaviour of the
mif2 function in the pomp package.
The pParams function no longer changes the order of the unit
specific parameter names; this was causing an error because the
barycentric parameter transformation requires that the parameters
are adjacent to one another in the parameter vector.
Improved documentation for panel_logmeanexp.
More robust input checking for the pfilter function with
user friendly error messages.
Improved documentation and tests.
Submitted to CRAN.
Fixed bug in fromVectorPparams() to make it a true inverse of toVectorPparams().
Homogenized documentation; added examples.
New coercion to pompList and update to list.
panelGompertzLikelihood replaces kalman_gompertz.R.
expunged panelPompExample.
Names added to plot; pfilter matches units by name.
New simulate function.
New panelRandomWalk example.
panelPompExample is now deprecated and will be removed in the
near future.
New plot method for panelPomp objects.
Additional functions implementing Kalman filtering to panels and to the Gompertz model.
Minor improvements to the interface.
Additional examples: contacts() and panelGompertz().
The minimum version of pomp supported is now 2.7.
The minimum version of pomp supported is now 2.1. While
this is likely to imply substantial changes in pomp objects (on which
panelPomp objects rely) there are only three fundamental changes that
break panelPomp's backwards compatibility:
The first argument pfilter(object, ...) changes to data.
The first argument mif2(object, ...) changes to data.
The ‘conv.rec’ method has been deprecated, replaced by the new ‘traces’ method.
Improvements to the interface.
A new conv.rec method.
Many improvements to the interface.
panelPompExamples() now allows creating panelPomp objects that come with the package.
New documentation and tests.
New documentation and tests.
New documentation and tests.
New documentation and additional tests.
New documentation and additional tests and coverage.
New tests added.
New methods.
A bug in pfilter and mif2 has been fixed (pomp's default filtering tolerance tol=1e-17 was used instead of values specified by the user). Thanks to Aaron King for finding it.
New tests added.
Eliminate need to protect rw.sd from being evaluated.
Unused variable purged.
pPfilter.internal streamlined.
Test for reproducibility of pfilter calculations added.