[Pomp-commits] r954 - in pkg/pomp: . R man

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

Author: kingaa
Date: 2014-05-17 16:05:42 +0200 (Sat, 17 May 2014)
New Revision: 954

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/mif-methods.R
   pkg/pomp/man/abc-methods.Rd
   pkg/pomp/man/pmcmc-methods.Rd
Log:
- minor fixes to documentation
- small change to 'conv.rec' for 'mif'


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2014-05-16 20:24:51 UTC (rev 953)
+++ pkg/pomp/DESCRIPTION	2014-05-17 14:05:42 UTC (rev 954)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.50-6
-Date: 2014-05-16
+Version: 0.50-7
+Date: 2014-05-17
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/mif-methods.R
===================================================================
--- pkg/pomp/R/mif-methods.R	2014-05-16 20:24:51 UTC (rev 953)
+++ pkg/pomp/R/mif-methods.R	2014-05-17 14:05:42 UTC (rev 954)
@@ -47,8 +47,8 @@
 ## extract the convergence record
 conv.rec.internal <- function (object, pars, transform = FALSE, ...) {
   if (transform) {
-    pars.improper <- c("loglik","nfail")
-    pars.proper <- setdiff(colnames(object at conv.rec),pars.improper)
+    pars.proper <- names(coef(object))
+    pars.improper <- setdiff(colnames(object at conv.rec),pars.proper)
     retval <- cbind(
                     t(
                       partrans(

Modified: pkg/pomp/man/abc-methods.Rd
===================================================================
--- pkg/pomp/man/abc-methods.Rd	2014-05-16 20:24:51 UTC (rev 953)
+++ pkg/pomp/man/abc-methods.Rd	2014-05-17 14:05:42 UTC (rev 954)
@@ -1,8 +1,6 @@
 \name{abc-methods}
 \docType{methods}
 \alias{abc-methods}
-\alias{dprior,abc-method}
-\alias{dprior-abc}
 \alias{conv.rec,abc-method}
 \alias{conv.rec-abc}
 \alias{plot-abc}
@@ -12,17 +10,16 @@
 \usage{
 \S4method{conv.rec}{abc}(object, pars, \dots)
 \S4method{plot}{abc}(x, y, pars, scatter = FALSE, \dots)
-\S4method{dprior}{abc}(object, params, log = FALSE, \dots)
 }
 \arguments{
   \item{object, x}{The \code{abc} object.}
   \item{pars}{Names of parameters.}
   \item{y}{Ignored.}
-  \item{scatter}{WHAT DOES THIS DO?}
-  \item{params}{
-    Named vector of parameters.
+  \item{scatter}{
+    optional logical;
+    If \code{TRUE}, draw scatterplots.
+    If \code{FALSE}, draw traceplots.
   }
-  \item{log}{if TRUE, log probabilities are returned.}
   \item{\dots}{
     Further arguments (either ignored or passed to underlying functions).
   }
@@ -30,7 +27,7 @@
 \section{Methods}{
   \describe{
     \item{conv.rec}{
-      \code{conv.rec(object, pars = NULL)} returns the columns of the convergence-record matrix corresponding to the names in \code{pars}.
+      \code{conv.rec(object, pars)} returns the columns of the convergence-record matrix corresponding to the names in \code{pars}.
       By default, all rows are returned.
     }
     \item{plot}{

Modified: pkg/pomp/man/pmcmc-methods.Rd
===================================================================
--- pkg/pomp/man/pmcmc-methods.Rd	2014-05-16 20:24:51 UTC (rev 953)
+++ pkg/pomp/man/pmcmc-methods.Rd	2014-05-17 14:05:42 UTC (rev 954)
@@ -31,7 +31,7 @@
 \section{Methods}{
   \describe{
     \item{conv.rec}{
-      \code{conv.rec(object, pars = NULL)} returns the columns of the convergence-record matrix corresponding to the names in \code{pars}.
+      \code{conv.rec(object, pars)} returns the columns of the convergence-record matrix corresponding to the names in \code{pars}.
       By default, all rows are returned.
     }
     \item{logLik}{