[Pomp-commits] r467 - in pkg/inst: . doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon May 9 23:11:44 CEST 2011
Author: kingaa
Date: 2011-05-09 23:11:44 +0200 (Mon, 09 May 2011)
New Revision: 467
Added:
pkg/inst/doc/index.html
Modified:
pkg/inst/ChangeLog
pkg/inst/NEWS
pkg/inst/doc/advanced_topics_in_pomp.pdf
pkg/inst/doc/intro_to_pomp.Rnw
pkg/inst/doc/intro_to_pomp.pdf
Log:
- add a diagram to intro vignette
- add 'index.html' file for vignettes
- fix NEWS file format
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2011-05-09 20:36:38 UTC (rev 466)
+++ pkg/inst/ChangeLog 2011-05-09 21:11:44 UTC (rev 467)
@@ -1,5 +1,28 @@
2011-05-09 kingaa
+ * [r464] inst/NEWS: - update
+ * [r463] NAMESPACE, R/pomp.R, data/blowflies.rda, data/dacca.rda,
+ data/euler.sir.rda, data/gillespie.sir.rda, data/gompertz.rda,
+ data/ou2.rda, data/ricker.rda, data/rw2.rda, data/verhulst.rda,
+ inst/ChangeLog, inst/NEWS, inst/data-R/euler.sir.R,
+ inst/data-R/gompertz.R, inst/data-R/ou2.R, inst/data-R/ricker.R,
+ inst/data-R/verhulst.R, inst/doc/advanced_topics_in_pomp.Rnw,
+ inst/doc/advanced_topics_in_pomp.pdf,
+ inst/doc/gompertz-trajmatch.rda, inst/doc/intro_to_pomp.Rnw,
+ inst/doc/intro_to_pomp.pdf, inst/examples/gompertz.R,
+ inst/examples/gompertz.c, inst/examples/logistic.R,
+ inst/examples/sir.R, inst/include/pomp.h, man/pomp-class.Rd,
+ man/pomp.Rd, src/pomp.h, src/skeleton.c, tests/fhn.R,
+ tests/fhn.Rout.save, tests/logistic.R, tests/logistic.Rout.save,
+ tests/ou2-simulate.Rout.save, tests/pomppomp.R,
+ tests/pomppomp.Rout.save, tests/ricker.Rout.save, tests/rw2.R,
+ tests/rw2.Rout.save, tests/sir.R, tests/sir.Rout.save,
+ tests/skeleton.Rout.save: - the 'pomp' arguments 'skeleton.map'
+ and 'skeleton.vectorfield' are now deprecated in favor of
+ 'skeleton' and 'skeleton.type'
+ - 'pomp' is now a generic function with methods for data of type
+ 'numeric', 'matrix', 'data.frame', and 'pomp'. the latter method
+ allows for copying of 'pomp' objects with modification.
* [r462] R/pomp-methods.R: - remove printing of call slot
* [r461] src/gompertz.c: - better commenting and some cleanup
* [r460] R/pomp-fun.R: - fix bug in error-checking
Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS 2011-05-09 20:36:38 UTC (rev 466)
+++ pkg/inst/NEWS 2011-05-09 21:11:44 UTC (rev 467)
@@ -1,245 +1,223 @@
NEWS
0.37-1
- o 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"'.
+ o 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"'.
- o 'pomp' is now a method rather than a function.
- Calling it on a 'pomp' object copies the object; one can optionally modify some of the slots.
+ o 'pomp' is now a method rather than a function.
+ Calling it on a 'pomp' object copies the object; one can optionally modify some of the slots.
- o 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.
+ o 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.
- o 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 documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+ o 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 documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
-0.36-7:
+0.36-7
+ o 'trajectory' now gives a more informative error when no skeleton is present
- o 'trajectory' now gives a more informative error when no skeleton is present
+ o 'pred.mean', 'pred.var', and 'filter.mean' methods are now defined for 'pfilterd.pomp' objects (and not just 'mif' objects)
- o 'pred.mean', 'pred.var', and 'filter.mean' methods are now defined for 'pfilterd.pomp' objects (and not just 'mif' objects)
+ o A new 'data()'-loadable example is included: do '?blowflies' to read about it.
- o A new 'data()'-loadable example is included: do '?blowflies' to read about it.
+0.36-6
+ o 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.
-0.36-6:
+0.36-5
+ o The "intro_to_pomp" vignette has been updated. The first part of the vignette centers on a new, more transparent first example.
- o 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.
+ o 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.
-0.36-5:
+ o There is now a method for 'loglik' on 'probed.pomp' objects. This returns the synthetic likelihood.
- o The "intro_to_pomp" vignette has been updated. The first part of the vignette centers on a new, more transparent first example.
+ o The box-constrained simulated annealing optimization method 'sannbox' is now an option in 'probe.match'.
- o 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.
+ o Calling 'states' on a pomp object having no unobserved states now fails gracefully (returning NULL rather than generating an error).
- o There is now a method for 'loglik' on 'probed.pomp' objects. This returns the synthetic likelihood.
+ o 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.
- o The box-constrained simulated annealing optimization method 'sannbox' is now an option in 'probe.match'.
- o Calling 'states' on a pomp object having no unobserved states now fails gracefully (returning NULL rather than generating an error).
+0.36-1
+ o 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.
- o 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.
+ o When 'traj.match' is called, the returned 'traj.matched.pomp' object has its 'states' slot filled with the model trajectory at the fitted parameters.
+ o More optimization methods are now provided in 'traj.match'. These include the new algorithm "sannbox", an optionally box-constrained simulated annealing algorithm.
-0.36-1:
+ o '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'.
- o 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.
+ o 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.
- o When 'traj.match' is called, the returned 'traj.matched.pomp' object has its 'states' slot filled with the model trajectory at the fitted parameters.
+0.35-1
+ o 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.
- o More optimization methods are now provided in 'traj.match'. These include the new algorithm "sannbox", an optionally box-constrained simulated annealing algorithm.
+ o The synthetic likelihood is now the quantity that is maximized in 'probe.match'.
- o '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'.
+ o 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.
- o 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.
+ o Changed the way that 'probe.acf' accepts lags. Now an arbitrary set of lags can be selected.
-0.35-1:
+ o A bug in the new method 'obs' has been fixed.
- o 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.
+ o A protection-stack overflow bug in 'probe' has been fixed.
- o The synthetic likelihood is now the quantity that is maximized in 'probe.match'.
+ o The 'seed' slot in 'probed.pomp' and 'spect.pomp' objects has been removed, along with unwanted behavior to do with it.
- o 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.
-
- o Changed the way that 'probe.acf' accepts lags. Now an arbitrary set of lags can be selected.
-
- o A bug in the new method 'obs' has been fixed.
-
- o A protection-stack overflow bug in 'probe' has been fixed.
-
- o The 'seed' slot in 'probed.pomp' and 'spect.pomp' objects has been removed, along with unwanted behavior to do with it.
-
0.34-2:
- o Added a method to coerce 'probed.pomp' objects to 'data.frame' objects.
+ o Added a method to coerce 'probed.pomp' objects to 'data.frame' objects.
- o Fix bug when 'simulate' is run on objects that inherit from 'pomp' but are not themselves pomps.
+ o 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.
- o 'simulate' and 'rprocess' are accelerated somewhat through judicious use of 'memcpy'.
+ o 'simulate' and 'rprocess' are accelerated somewhat through judicious use of 'memcpy'.
-0.34-1:
+0.34-1
+ o 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.
- o 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.
+ o 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'.
- o 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'.
+ o 'simulate' has been re-implemented in C for speed.
- 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'.
- o A new method 'obs' for pomp objects returns the contents of the 'data' slot.
- It is synonymous with 'data.array'.
+ o A banner is now displayed on package attachment.
- o A banner is now displayed on package attachment.
+ o 'coef<-' now behaves like ordinary vector assignment.
- o 'coef<-' now behaves like ordinary vector assignment.
+ o 'probe' and 'spect' now take an argument 'params'.
- o 'probe' and 'spect' now take an argument 'params'.
+ o 'probe.cov' and 'probe.cor' have been removed in favor of 'probe.acf' and 'probe.ccf'.
- o 'probe.cov' and 'probe.cor' have been removed in favor of 'probe.acf' and 'probe.ccf'.
-
- o The functions 'euler.simulate', 'onestep.simulate', and 'onestep.density', deprecated since version 0.29-1, have been removed.
+ o The functions 'euler.simulate', 'onestep.simulate', and 'onestep.density', deprecated since version 0.29-1, have been removed.
-0.33-1:
+0.33-1
+ o Major improvements in speed in the probe-matching routines have been realized by coding the computationally-intensive portions of these calculations in C.
- o Major improvements in speed in the probe-matching routines have been realized by coding the computationally-intensive portions of these calculations in C.
-
- o 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.
+ o 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.
-0.32-1:
+0.32-1
+ o 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).
- o 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).
+0.31-2
+ o new "window", "timezero", and "timezero<-" methods are available for manipulating 'pomp' objects.
-0.31-2:
-
- o new "window", "timezero", and "timezero<-" methods are available for manipulating 'pomp' objects.
-
-0.31-1:
-
- o 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.
+0.31-1
+ o 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.
-0.30-1:
- o 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).
+0.30-1
+ o 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.
-0.29-5:
+0.29-5
+ o 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.
- o 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.
+0.29-1
+ o This is a major revision.
-0.29-1:
+ o Big improvements to the documentation, including worked examples in vignettes and improvements to the manual pages.
- o This is a major revision.
+ o Encoding models is now much easier through the use of "plugin" modules.
+ These are functions that write the 'rprocess' and 'dprocess' slots given minimal information on the structure of the model.
- o Big improvements to the documentation, including worked examples in vignettes and improvements to the manual pages.
+ o A plugin for continuous-time Markov process models using the Gillespie algorithm is available.
- o Encoding models is now much easier through the use of "plugin" modules.
- These are functions that write the 'rprocess' and 'dprocess' slots given minimal information on the structure of the model.
+ o A plugin for discrete-time Markov processes is now available.
- o A plugin for continuous-time Markov process models using the Gillespie algorithm is available.
+ o Several example pomps are now loadable via the data() command.
- o A plugin for discrete-time Markov processes is now available.
-
- o Several example pomps are now loadable via the data() command.
-
- o There are changes in the C interface to measurement models that are NOT BACKWARD COMPATIBLE.
+ o There are changes in the C interface to measurement models that are NOT BACKWARD COMPATIBLE.
Existing user measurement model codes will need to be modified, but these changes are minor.
All this is fully explained in the file CHANGES_0.29-1.txt.
- o The changes are documented in detail in the file CHANGES_0.29-1.txt.
+ o The changes are documented in detail in the file CHANGES_0.29-1.txt.
-0.22-1:
-
- o The nonlinear forecasting method of Kendall, Ellner, et al. is now implemented in the package. This is an "indirect inference" method using quasi-likelihood as an objective function.
+0.22-1
+ o The nonlinear forecasting method of Kendall, Ellner, et al. is now implemented in the package. This is an "indirect inference" method using quasi-likelihood as an objective function.
-0.21-4:
+0.21-4
+ o Improved documentation in "euler.Rd".
- o Improved documentation in "euler.Rd".
+0.21-3
+ o Trajectories of the deterministic skeleton can now be computed via the method "trajectory".
-0.21-3:
+ o Bug fix in stochastic Euler algorithm.
- o Trajectories of the deterministic skeleton can now be computed via the method "trajectory".
+0.20-8
+ o Better error handling in mif
- o Bug fix in stochastic Euler algorithm.
+ o Fix inaccuracy in documentation of 'pomp' arguments 'rmeasure' and 'dmeasure'
-0.20-8:
+0.20-7
+ o Bug fix in convergence record storage
- o Better error handling in mif
-
- o Fix inaccuracy in documentation of 'pomp' arguments 'rmeasure' and 'dmeasure'
-
-0.20-7:
-
- o Bug fix in convergence record storage
-
-0.20-6:
-
- o Bug fix in "intro_to_pomp" vignette
+0.20-6
+ o Bug fix in "intro_to_pomp" vignette
-0.20-5:
+0.20-5
+ o Better error handling and improved documentation for 'mif'
- o Better error handling and improved documentation for 'mif'
+ o Testing of examples in the 'examples' directory, including compilation, linking, and running of dynamically-loadable library on unix machines
- o Testing of examples in the 'examples' directory, including compilation, linking, and running of dynamically-loadable library on unix machines
+0.20-4
+ o A bug in the Euler simulator was repaired.
-0.20-4:
+ o The Euler simulator no longer calls GetRNGState() and PutRNGState().
+ When a native routine is used for the Euler step, it must contain these calls.
- o A bug in the Euler simulator was repaired.
+ o A potential bug in the Euler-multinomial simulator was repaired.
- o The Euler simulator no longer calls GetRNGState() and PutRNGState().
- When a native routine is used for the Euler step, it must contain these calls.
-
- o A potential bug in the Euler-multinomial simulator was repaired.
-
-0.20-2:
-
- o The lookup_table (see file 'include/pomp.h') interface for C codes has been streamlined.
+0.20-2
+ o The lookup_table (see file 'include/pomp.h') interface for C codes has been streamlined.
It is now slightly more straightforward to set up a 'struct lookup_table'.
See the examples ('include/examples').
- o Added 'logistic.R' to the 'tests' directory.
+ o Added 'logistic.R' to the 'tests' directory.
This is a one-variable stochastic differential equation simulated using Euler-Maruyama.
- o The SIR example ('examples/sir.R') now includes two pomps: one with native routines implementing rprocess, dprocess, and skeleton, the other using R files.
+ o The SIR example ('examples/sir.R') now includes two pomps: one with native routines implementing rprocess, dprocess, and skeleton, the other using R files.
The comparison may be instructive.
- o Several bugs fixed.
+ o Several bugs fixed.
0.20-1
+ o This is a major revision.
- o This is a major revision.
-
- o The basic structure of the 'pomp' class has been changed to better support the use of native routines as well as R functions.
+ o The basic structure of the 'pomp' class has been changed to better support the use of native routines as well as R functions.
In particular, the 'rmeasure', 'dmeasure', and 'skeleton' methods can now be specified either as R functions or as native routines.
Native routines are specified by name; an optional 'PACKAGE' argument is provided to narrow the search.
The search is done not at the time of the call to 'pomp' but at the time the function is used.
- o Support has been added for covariates, in the form of lookup tables.
+ o Support has been added for covariates, in the form of lookup tables.
This has been accomplished through the addition of slots 'tcovar', 'covar', and 'covarnames' to the 'pomp' class.
'rmeasure', 'dmeasure', 'skeleton', and 'init.state' now perform lookup when covariates exist and pass this information to the user-defined function.
'rprocess' and 'dprocess' receive the full lookup table ('tcovar' plus 'covar').
- o 'rmeasure', 'dmeasure', and 'skeleton' are now specified by a function (or native routine) that does the computation for ONE state vector and ONE parameter vector.
+ o 'rmeasure', 'dmeasure', and 'skeleton' are now specified by a function (or native routine) that does the computation for ONE state vector and ONE parameter vector.
This is analogous to the way that 'init.state' has operated from the beginning.
It greatly simplifies model specification from the user's point of view without changing the low-level methods interfaces (pomp methods 'rmeasure', 'dmeasure', 'skeleton', 'init.states').
However, THIS CHANGE IS NOT BACKWARD-COMPATIBLE: users will need to rewrite code for the 'rmeasure', 'dmeasure', and 'skeleton' slots.
In practice, this should not be difficult.
It involves removing loops over 'times' and columns of 'params' and (if covariates are used in the measurement model or deterministic skeleton) making use of the 'covars' argument passed to the user function.
- o The interface to the 'euler.simulate' and 'euler.density' facilities have changed to make them consistent with the new pomp class.
+ o The interface to the 'euler.simulate' and 'euler.density' facilities have changed to make them consistent with the new pomp class.
- o The header files have been reorganized: 'include/euler.h' and 'include/lookup_table.h' have been replaced with a single 'include/pomp.h'.
+ o The header files have been reorganized: 'include/euler.h' and 'include/lookup_table.h' have been replaced with a single 'include/pomp.h'.
Significant additions have been made to support the new structure of the pomp class.
Specifically, new prototypes have been defined for native routines to implement the measurement model, the process model, and the deterministic skeleton.
Modified: pkg/inst/doc/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)
Added: pkg/inst/doc/index.html
===================================================================
--- pkg/inst/doc/index.html (rev 0)
+++ pkg/inst/doc/index.html 2011-05-09 21:11:44 UTC (rev 467)
@@ -0,0 +1,17 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+<title>pomp vignettes</title>
+<link rel="stylesheet" type="text/css" href="../../R.css">
+</head>
+<body>
+<h2>Vignettes of package pomp</h2>
+<dl>
+<dt><a href="intro_to_pomp.pdf">intro_to_pomp.pdf</a>:</dt>
+<dd>Introduction to <b>pomp</b></dd>
+<dt><a href=
+"advanced_topics_in_pomp.pdf">advanced_topics_in_pomp.pdf</a>:</dt>
+<dd>Advanced topics in <b>pomp</b></dd>
+</dl>
+</body>
+</html>
Modified: pkg/inst/doc/intro_to_pomp.Rnw
===================================================================
--- pkg/inst/doc/intro_to_pomp.Rnw 2011-05-09 20:36:38 UTC (rev 466)
+++ pkg/inst/doc/intro_to_pomp.Rnw 2011-05-09 21:11:44 UTC (rev 467)
@@ -1057,6 +1057,52 @@
\clearpage
\section{A more complex example: a seasonal epidemic model}
+\begin{figure}
+ \begin{center}
+ \resizebox{0.8\textwidth}{!}{
+ \Large
+ \setlength{\unitlength}{5pt}
+ \begin{picture}(44,20)(-5,-4)
+ \thicklines
+ \put(0,0){\framebox(6,6){$S$}}
+ \put(16,0){\framebox(6,6){$I$}}
+ \put(32,0){\framebox(6,6){$R$}}
+ \put(-4,3){\vector(1,0){4}}
+ \put(-3.7,3.9){$\mu$}
+ \put(6,3){\vector(1,0){10}}
+ \put(9,3.9){$\lambda(t)$}
+ \put(3,-0.2){\vector(0,-1){4}}
+ \put(4,-3){$\mu$}
+ \put(19,-0.2){\vector(0,-1){4}}
+ \put(20,-3){$\mu$}
+ \put(22,3){\vector(1,0){10}}
+ \put(26,1){$\gamma$}
+ \put(27,4){\vector(0,1){5}}
+ \put(27.7,6){$\rho$}
+ \put(27,11.5){\circle{5}}
+ \put(26,10.7){{$C$}}
+ \put(35,-0.2){\vector(0,-1){4}}
+ \put(36,-3){$\mu$}
+ \end{picture}
+ }
+ \end{center}
+ \label{fig:SIR}
+ \caption{
+ Diagram of the SIR model.
+ The host population is divided into three classes according to their infection status:
+ S, susceptible hosts;
+ I, infected (and infectious) hosts;
+ R, recovered and immune hosts.
+ Births result in new susceptibles and all individuals have a common death rate $\mu$.
+ Since the birth rate equals the death rate, the expected population size, $N=S+I+R$, remains constant.
+ The S$\to$I rate, $\lambda$, called the \emph{force of infection}, depends on the number of infectious individuals according to $\lambda(t)={\beta(t)\,\xi(t)\,I}/{N}$,
+ where $\beta(t)$ is the seasonal (periodic) contact rate and $\xi(t)$ is a white noise.
+ The I$\to$R, or recovery, rate is $\gamma$.
+ The case reports, $C$, count infected individuals with probability $\rho$.
+ Since diagnosed cases are treated with bed-rest and hence removed, infections are counted upon transition to R.
+ }
+\end{figure}
+
The SIR model is a mainstay of theoretical epidemiology.
It has the deterministic skeleton
\begin{equation*}
Modified: pkg/inst/doc/intro_to_pomp.pdf
===================================================================
(Binary files differ)
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