[Pomp-commits] r620 - in pkg: . inst man

[noreply at r-forge.r-project.org]

Author: kingaa
Date: 2012-03-07 23:11:07 +0100 (Wed, 07 Mar 2012)
New Revision: 620

Modified:
   pkg/DESCRIPTION
   pkg/inst/NEWS
   pkg/man/blowflies.Rd
   pkg/man/pfilter.Rd
Log:
- update documentation of 'blowflies'
- correct error in 'pfilter' documentation


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-03-06 23:50:27 UTC (rev 619)
+++ pkg/DESCRIPTION	2012-03-07 22:11:07 UTC (rev 620)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.40-7
-Date: 2012-03-06
+Date: 2012-03-07
 Revision: $Rev$
 Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
 Maintainer: Aaron A. King <kingaa at umich.edu>

Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS	2012-03-06 23:50:27 UTC (rev 619)
+++ pkg/inst/NEWS	2012-03-07 22:11:07 UTC (rev 620)
@@ -2,6 +2,11 @@
 0.40-7
      o	'parmat' now gracefully handles the case when 'params' is already a matrix.
 
+     o	Error in the documentation of 'pfilter' repaired.
+       	Thanks to Alex Smith for pointing this out.
+
+     o	Improvements in the documentation of the Nicholson blowflies data 'data(blowflies)'.
+
 0.40-6
      o	When a pomp object is updated using 'pomp', the 'params' slot will now be copied over (appropriately transformed).
      	Before, it was simply dropped.

Modified: pkg/man/blowflies.Rd
===================================================================
--- pkg/man/blowflies.Rd	2012-03-06 23:50:27 UTC (rev 619)
+++ pkg/man/blowflies.Rd	2012-03-07 22:11:07 UTC (rev 620)
@@ -5,7 +5,7 @@
 \docType{data}
 \title{Model for Nicholson's blowflies.}
 \description{
-  \code{blowfly1} and \code{blowfly2} are \code{pomp} objects encoding stochastic delay-difference models.
+  \code{blowflies1} and \code{blowflies2} are \code{pomp} objects encoding stochastic delay-difference models.
 }
 \usage{data(blowflies)}
 \examples{
@@ -13,5 +13,38 @@
 plot(blowflies1)
 plot(blowflies2)
 }
+\details{
+  The data are from "population I", a control culture in one of A. J. Nicholson's experiments with the Australian sheep-blowfly \emph{Lucilia cuprina}.
+  The experiment is described on pp. 163--4 of Nicholson (1957).
+  Unlimited quantities of larval food were provided;
+  the adult food supply (ground liver) was constant at 0.4g per day.
+  The data were taken from the table provided by Brillinger et al. (1980).
+}
 \seealso{\code{\link{pomp-class}} and the vignettes}
+\references{
+  A. J. Nicholson (1957)
+  The self-adjustment of populations to change.
+  Cold Spring Harbor Symposia on Quantitative Biology, \bold{22}, 153--173.
+  
+  Y. Xia and H. Tong (2011)
+  Feature Matching in Time Series Modeling.
+  \emph{Statistical Science} \bold{26}, 21--46.
+
+  E. L. Ionides (2011)
+  Discussion of ``Feature Matching in Time Series Modeling'' by Y. Xia and H. Tong.
+  \emph{Statistical Science} \bold{26}, 49--52.
+
+  S. N. Wood (2010)
+  Statistical inference for noisy nonlinear ecological dynamic systems.
+  \emph{Nature} \bold{466}, 1102--1104.
+ 
+  W. S. C. Gurney, S. P. Blythe, and R. M. Nisbet (1980)
+  Nicholson's blowflies revisited.
+  \emph{Nature} \bold{287}, 17--21.
+
+  D. R. Brillinger, J. Guckenheimer, P. Guttorp and G. Oster (1980)
+  Empirical modelling of population time series: The case of age and density dependent rates.
+  in G. Oster (ed.), Some Questions in Mathematical Biology, vol. 13, pp. 65--90.
+  American Mathematical Society, Providence.
+}
 \keyword{datasets}

Modified: pkg/man/pfilter.Rd
===================================================================
--- pkg/man/pfilter.Rd	2012-03-06 23:50:27 UTC (rev 619)
+++ pkg/man/pfilter.Rd	2012-03-07 22:11:07 UTC (rev 620)
@@ -43,9 +43,9 @@
     When \code{object} is of class \code{mif}, this is by default the same number of particles used in the \code{mif} iterations.
   }
   \item{tol}{
-    positive numeric scalar; particles with log likelihood below \code{tol} are considered to be \dQuote{lost}.
+    positive numeric scalar; particles with likelihood less than \code{tol} are considered to be \dQuote{lost}.
     A filtering failure occurs when, at some time point, all particles are lost.
-    When all particles are lost, the conditional log likelihood at that time point is set to be \code{log(tol)}.
+    When all particles are lost, the conditional likelihood at that time point is set to \code{tol}.
   }
   \item{max.fail}{
     integer; the maximum number of filtering failures allowed.