[Pomp-commits] r976 - in pkg/pomp: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jun 17 14:46:34 CEST 2014
Author: kingaa
Date: 2014-06-17 14:46:34 +0200 (Tue, 17 Jun 2014)
New Revision: 976
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/abc.R
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/man/abc.Rd
Log:
- remove 'transform' argument from 'abc'
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2014-06-17 12:46:29 UTC (rev 975)
+++ pkg/pomp/DESCRIPTION 2014-06-17 12:46:34 UTC (rev 976)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.51-2
-Date: 2014-06-12
+Version: 0.51-3
+Date: 2014-06-16
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/abc.R
===================================================================
--- pkg/pomp/R/abc.R 2014-06-17 12:46:29 UTC (rev 975)
+++ pkg/pomp/R/abc.R 2014-06-17 12:46:34 UTC (rev 976)
@@ -4,7 +4,6 @@
contains='pomp',
slots=c(
pars = 'character',
- transform = 'logical',
Nabc = 'integer',
probes='list',
scale = 'numeric',
@@ -18,14 +17,13 @@
start, pars,
rw.sd, probes,
epsilon, scale,
- verbose, transform,
+ verbose,
.ndone = 0L,
.getnativesymbolinfo = TRUE,
...) {
object <- as(object,'pomp')
gnsi <- as.logical(.getnativesymbolinfo)
- transform <- as.logical(transform)
Nabc <- as.integer(Nabc)
epsilon <- as.numeric(epsilon)
epssq <- epsilon*epsilon
@@ -134,17 +132,8 @@
for (n in seq_len(Nabc)) { # main loop
theta.prop <- theta
-
- if (transform)
- theta.prop <- partrans(object,params=theta.prop,dir='inverse',
- .getnativesymbolinfo=gnsi)
-
theta.prop[pars] <- rnorm(n=length(pars),mean=theta.prop[pars],sd=rw.sd)
- if (transform)
- theta.prop <- partrans(object,params=theta.prop,dir='forward',
- .getnativesymbolinfo=gnsi)
-
gnsi <- FALSE
## compute the probes for the proposed new parameter values
@@ -187,7 +176,6 @@
object,
params=theta,
pars=pars,
- transform=transform,
Nabc=Nabc,
probes=probes,
scale=scale,
@@ -205,7 +193,6 @@
start, pars, rw.sd,
probes, scale, epsilon,
verbose = getOption("verbose"),
- transform = FALSE,
...) {
if (missing(start))
@@ -239,8 +226,7 @@
scale=scale,
epsilon=epsilon,
rw.sd=rw.sd,
- verbose=verbose,
- transform=transform
+ verbose=verbose
)
}
)
@@ -250,7 +236,6 @@
signature=signature(object="probed.pomp"),
function (object, probes,
verbose = getOption("verbose"),
- transform = FALSE,
...) {
if (missing(probes)) probes <- object at probes
@@ -258,7 +243,6 @@
f(
object=object,
probes=probes,
- transform=transform,
...
)
}
@@ -271,7 +255,6 @@
start, pars, rw.sd,
probes, scale, epsilon,
verbose = getOption("verbose"),
- transform,
...) {
if (missing(Nabc)) Nabc <- object at Nabc
@@ -281,7 +264,6 @@
if (missing(probes)) probes <- object at probes
if (missing(scale)) scale <- object at scale
if (missing(epsilon)) epsilon <- object at epsilon
- if (missing(transform)) transform <- object at transform
f <- selectMethod("abc","pomp")
@@ -295,7 +277,6 @@
scale=scale,
epsilon=epsilon,
verbose=verbose,
- transform=transform,
...
)
}
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2014-06-17 12:46:29 UTC (rev 975)
+++ pkg/pomp/inst/NEWS 2014-06-17 12:46:34 UTC (rev 976)
@@ -1,5 +1,9 @@
_N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p'
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_1-_3:
+
+ • ‘transform’ argument for ‘pmcmc’ and ‘abc’ has been removed.
+
_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_1-_2:
• More informative error messages are generated when a needed
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2014-06-17 12:46:29 UTC (rev 975)
+++ pkg/pomp/inst/NEWS.Rd 2014-06-17 12:46:34 UTC (rev 976)
@@ -1,5 +1,10 @@
\name{NEWS}
\title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.51-3}{
+ \itemize{
+ \item \code{transform} argument for \code{pmcmc} and \code{abc} has been removed.
+ }
+}
\section{Changes in \pkg{pomp} version 0.51-2}{
\itemize{
\item More informative error messages are generated when a needed variable cannot be found.
Modified: pkg/pomp/man/abc.Rd
===================================================================
--- pkg/pomp/man/abc.Rd 2014-06-17 12:46:29 UTC (rev 975)
+++ pkg/pomp/man/abc.Rd 2014-06-17 12:46:34 UTC (rev 976)
@@ -18,12 +18,12 @@
\usage{
\S4method{abc}{pomp}(object, Nabc = 1, start, pars,
rw.sd, probes, scale, epsilon,
- verbose = getOption("verbose"), transform = FALSE, \dots)
+ verbose = getOption("verbose"), \dots)
\S4method{abc}{probed.pomp}(object, probes,
- verbose = getOption("verbose"), transform = FALSE, \dots)
+ verbose = getOption("verbose"), \dots)
\S4method{abc}{abc}(object, Nabc, start, pars,
rw.sd, probes, scale, epsilon,
- verbose = getOption("verbose"), transform, \dots)
+ verbose = getOption("verbose"), \dots)
\S4method{continue}{abc}(object, Nabc = 1, \dots)
}
\arguments{
@@ -62,10 +62,6 @@
\item{verbose}{
logical; if TRUE, print progress reports.
}
- \item{transform}{
- logical;
- if \code{TRUE}, optimization is performed on the transformed scale.
- }
\item{\dots}{
Additional arguments.
These are currently ignored.
@@ -75,7 +71,7 @@
An object of class \code{abc}.
This class inherits from class \code{\link[=probed.pomp-class]{probed.pomp}} and contains the following additional slots:
\describe{
- \item{pars, Nabc, dprior, hyperparams, transform, scale, epsilon}{
+ \item{pars, Nabc, dprior, hyperparams, scale, epsilon}{
These slots hold the values of the corresponding arguments of the call to \code{abc}.
}
\item{random.walk.sd}{
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