[Pomp-commits] r1116 - pkg/pomp pkg/pomp/R pkg/pomp/inst pkg/pomp/man pkg/pomp/tests www/content www/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 27 16:21:25 CET 2015
Author: kingaa
Date: 2015-02-27 16:21:25 +0100 (Fri, 27 Feb 2015)
New Revision: 1116
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/mif.R
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/man/mif.Rd
pkg/pomp/tests/ou2-mif.R
pkg/pomp/tests/ou2-mif.Rout.save
pkg/pomp/tests/ou2-mif2.R
pkg/pomp/tests/ou2-mif2.Rout.save
www/content/NEWS.html
www/vignettes/pomp.pdf
Log:
- mif's 'cooling.factor' argument, long deprecated, has been removed
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-02-27 14:13:28 UTC (rev 1115)
+++ pkg/pomp/DESCRIPTION 2015-02-27 15:21:25 UTC (rev 1116)
@@ -1,7 +1,7 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.61-4
+Version: 0.62-1
Date: 2015-02-27
Authors at R: c(person(given=c("Aaron","A."),family="King",
role=c("aut","cre"),email="kingaa at umich.edu"),
Modified: pkg/pomp/R/mif.R
===================================================================
--- pkg/pomp/R/mif.R 2015-02-27 14:13:28 UTC (rev 1115)
+++ pkg/pomp/R/mif.R 2015-02-27 15:21:25 UTC (rev 1116)
@@ -86,7 +86,7 @@
particles,
rw.sd,
Np, var.factor, ic.lag,
- cooling.type, cooling.fraction, cooling.factor,
+ cooling.type, cooling.fraction,
method,
tol, max.fail,
verbose, transform, .ndone = 0L,
@@ -206,23 +206,6 @@
)
}
- ## the following deals with the deprecated option 'cooling.factor'
- if (!missing(cooling.factor)) {
- warning(sQuote("cooling.factor")," is deprecated.\n",
- "See ",sQuote("?mif")," for instructions on specifying the cooling schedule.",
- call.=FALSE)
- cooling.factor <- as.numeric(cooling.factor)
- if ((length(cooling.factor)!=1)||(cooling.factor<0)||(cooling.factor>1))
- stop("mif error: ",sQuote("cooling.factor")," must be a number between 0 and 1",call.=FALSE)
- if (missing(cooling.fraction)) {
- cooling.fraction <- cooling.factor^50
- } else {
- warning("specification of ",sQuote("cooling.factor"),
- " is overridden by that of ",sQuote("cooling.fraction"),
- call.=FALSE)
- }
- }
-
if (missing(cooling.fraction))
stop("mif error: ",sQuote("cooling.fraction")," must be specified",call.=FALSE)
cooling.fraction <- as.numeric(cooling.fraction)
@@ -399,9 +382,9 @@
start,
ivps = character(0),
particles, rw.sd,
- Np, ic.lag, var.factor,
+ Np, ic.lag, var.factor = 1,
cooling.type = c("geometric","hyperbolic"),
- cooling.fraction, cooling.factor,
+ cooling.fraction,
method = c("mif","unweighted","fp","mif2"),
tol = 1e-17, max.fail = Inf,
verbose = getOption("verbose"),
@@ -453,7 +436,6 @@
rw.sd=rw.sd,
Np=Np,
cooling.type=cooling.type,
- cooling.factor=cooling.factor,
cooling.fraction=cooling.fraction,
var.factor=var.factor,
ic.lag=ic.lag,
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2015-02-27 14:13:28 UTC (rev 1115)
+++ pkg/pomp/inst/NEWS 2015-02-27 15:21:25 UTC (rev 1116)
@@ -1,5 +1,15 @@
_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._6_2-_1:
+
+ • ‘mif’ now has the default value ‘var.factor=1’. Since
+ ‘var.factor’ has long been a required parameter, this change
+ is backward compatible. Since ‘var.factor’ has long been a
+ required parameter, this change is backward compatible.
+
+ • The long-deprecated ‘cooling.factor’ option to ‘mif’ has now
+ been removed.
+
_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_1-_3:
• ‘mif’'s ‘pars’ argument, which is redundant, is now
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2015-02-27 14:13:28 UTC (rev 1115)
+++ pkg/pomp/inst/NEWS.Rd 2015-02-27 15:21:25 UTC (rev 1116)
@@ -1,5 +1,13 @@
\name{NEWS}
\title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.62-1}{
+ \itemize{
+ \item \code{mif} now has the default value \code{var.factor=1}.
+ Since \code{var.factor} has long been a required parameter, this change is backward compatible.
+ Since \code{var.factor} has long been a required parameter, this change is backward compatible.
+ \item The long-deprecated \code{cooling.factor} option to \code{mif} has now been removed.
+ }
+}
\section{Changes in \pkg{pomp} version 0.61-3}{
\itemize{
\item \code{mif}'s \code{pars} argument, which is redundant, is now deprecated.
Modified: pkg/pomp/man/mif.Rd
===================================================================
--- pkg/pomp/man/mif.Rd 2015-02-27 14:13:28 UTC (rev 1115)
+++ pkg/pomp/man/mif.Rd 2015-02-27 15:21:25 UTC (rev 1116)
@@ -37,8 +37,8 @@
}
\usage{
\S4method{mif}{pomp}(object, Nmif = 1, start, ivps = character(0),
- particles, rw.sd, Np, ic.lag, var.factor,
- cooling.type, cooling.fraction, cooling.factor,
+ particles, rw.sd, Np, ic.lag, var.factor = 1,
+ cooling.type, cooling.fraction,
method = c("mif","unweighted","fp","mif2"),
tol = 1e-17, max.fail = Inf,
verbose = getOption("verbose"), transform = FALSE, \dots)
@@ -107,7 +107,7 @@
the scaling coefficient relating the width of the starting particle distribution to \code{rw.sd}.
In particular, the width of the distribution of particles at the start of the first \code{mif} iteration will be \code{random.walk.sd*var.factor}.
}
- \item{cooling.type, cooling.fraction, cooling.factor}{
+ \item{cooling.type, cooling.fraction}{
specifications for the cooling schedule, i.e., the manner in which the intensity of the parameter perturbations is reduced with successive filtering iterations.
\code{cooling.type} specifies the nature of the cooling schedule.
@@ -115,8 +115,6 @@
When \code{cooling.type="hyperbolic"}, on the n-th \code{mif} iteration, the relative perturbation intensity is \code{(s+1)/(s+n)}, where \code{(s+1)/(s+50)=cooling.fraction}.
\code{cooling.fraction} is the relative magnitude of the parameter perturbations after 50 \code{mif} iterations.
- \code{cooling.factor} is now deprecated:
- to achieve the old behavior, use \code{cooling.type="geometric"} and \preformatted{cooling.fraction=(cooling.factor)^50.}
}
\item{method}{
\code{method} sets the update rule used in the algorithm.
Modified: pkg/pomp/tests/ou2-mif.R
===================================================================
--- pkg/pomp/tests/ou2-mif.R 2015-02-27 14:13:28 UTC (rev 1115)
+++ pkg/pomp/tests/ou2-mif.R 2015-02-27 15:21:25 UTC (rev 1116)
@@ -28,7 +28,7 @@
var.factor=1,
ic.lag=10,
cooling.type="geometric",
- cooling.factor=0.95,
+ cooling.fraction=0.95^50,
max.fail=100
)
@@ -86,17 +86,6 @@
ou2,
Nmif=1,
ivps=c("x1.0","x2.0"),
- rw.sd=c(alpha.1=0.1,alpha.4=0.2,alpha.3=0),
- Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
- cooling.factor=0.95,ic.lag=10,var.factor=1
- )
- )
-
-try(
- mif(
- ou2,
- Nmif=1,
- ivps=c("x1.0","x2.0"),
rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
Np=100,ic.lag=10,var.factor=1
)
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2015-02-27 14:13:28 UTC (rev 1115)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2015-02-27 15:21:25 UTC (rev 1116)
@@ -61,13 +61,11 @@
+ var.factor=1,
+ ic.lag=10,
+ cooling.type="geometric",
-+ cooling.factor=0.95,
++ cooling.fraction=0.95^50,
+ max.fail=100
+ )
-Warning messages:
-1: mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
-2: 'cooling.factor' is deprecated.
-See '?mif' for instructions on specifying the cooling schedule.
+Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
>
> mif2 <- mif(ou2,Nmif=30,start=guess2,
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
@@ -135,18 +133,6 @@
+ ou2,
+ Nmif=1,
+ ivps=c("x1.0","x2.0"),
-+ rw.sd=c(alpha.1=0.1,alpha.4=0.2,alpha.3=0),
-+ Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
-+ cooling.factor=0.95,ic.lag=10,var.factor=1
-+ )
-+ )
-Error : mif error: 'pars' and 'ivps' must be mutually disjoint subsets of 'names(start)' and must have a positive random-walk SDs specified in 'rw.sd'
->
-> try(
-+ mif(
-+ ou2,
-+ Nmif=1,
-+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
+ Np=100,ic.lag=10,var.factor=1
+ )
@@ -293,4 +279,4 @@
>
> proc.time()
user system elapsed
- 15.048 0.037 15.088
+ 15.232 0.060 15.274
Modified: pkg/pomp/tests/ou2-mif2.R
===================================================================
--- pkg/pomp/tests/ou2-mif2.R 2015-02-27 14:13:28 UTC (rev 1115)
+++ pkg/pomp/tests/ou2-mif2.R 2015-02-27 15:21:25 UTC (rev 1116)
@@ -70,7 +70,7 @@
ic.lag=10,
cooling.whatsit=200,
cooling.type="geometric",
- cooling.factor=0.95,
+ cooling.fraction=0.95^50,
max.fail=100,
method="mif"
)
Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save 2015-02-27 14:13:28 UTC (rev 1115)
+++ pkg/pomp/tests/ou2-mif2.Rout.save 2015-02-27 15:21:25 UTC (rev 1116)
@@ -97,14 +97,12 @@
+ ic.lag=10,
+ cooling.whatsit=200,
+ cooling.type="geometric",
-+ cooling.factor=0.95,
++ cooling.fraction=0.95^50,
+ max.fail=100,
+ method="mif"
+ )
-Warning messages:
-1: mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
-2: 'cooling.factor' is deprecated.
-See '?mif' for instructions on specifying the cooling schedule.
+Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
> mif2b <- continue(mif2b,Nmif=50)
>
> mif2c <- mif(ou2,Nmif=50,start=guess1,
@@ -144,4 +142,4 @@
>
> proc.time()
user system elapsed
- 66.333 0.037 66.430
+ 66.324 0.058 66.448
Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html 2015-02-27 14:13:28 UTC (rev 1115)
+++ www/content/NEWS.html 2015-02-27 15:21:25 UTC (rev 1116)
@@ -8,6 +8,21 @@
<h2>News for package ‘pomp’</h2>
+<h3>Changes in <span class="pkg">pomp</span> version 0.62-1</h3>
+
+
+<ul>
+<li> <p><code>mif</code> now has the default value <code>var.factor=1</code>.
+Since <code>var.factor</code> has long been a required parameter, this change is backward compatible.
+Since <code>var.factor</code> has long been a required parameter, this change is backward compatible.
+</p>
+</li>
+<li><p> The long-deprecated <code>cooling.factor</code> option to <code>mif</code> has now been removed.
+</p>
+</li></ul>
+
+
+
<h3>Changes in <span class="pkg">pomp</span> version 0.61-3</h3>
Modified: www/vignettes/pomp.pdf
===================================================================
(Binary files differ)
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