[Pomp-commits] r1157 - 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 May 22 19:40:17 CEST 2015 

Author: kingaa
Date: 2015-05-22 19:40:16 +0200 (Fri, 22 May 2015)
New Revision: 1157

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/mif.R
   pkg/pomp/inst/CITATION
   pkg/pomp/inst/NEWS
   pkg/pomp/inst/NEWS.Rd
   pkg/pomp/man/mif.Rd
   pkg/pomp/tests/ou2-mif.Rout.save
   www/content/NEWS.html
   www/vignettes/pomp.pdf
Log:
- replace 'cooling.factor' with 'cooling.factor.50' in 'mif'
- update NEWS file

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/DESCRIPTION	2015-05-22 17:40:16 UTC (rev 1157)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.63-7
-Date: 2015-05-21
+Version: 0.64-1
+Date: 2015-05-22
 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.R
===================================================================
--- pkg/pomp/R/mif.R	2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/R/mif.R	2015-05-22 17:40:16 UTC (rev 1157)
@@ -13,7 +13,7 @@
            var.factor='numeric',
            ic.lag='integer',
            cooling.type='character',
-           cooling.fraction='numeric',
+           cooling.fraction.50='numeric',
            method='character',
            random.walk.sd = 'numeric',
            conv.rec = 'matrix'
@@ -57,7 +57,7 @@
          hyperbolic={
            if (fraction>=1)
              stop(
-                  "mif error: ",sQuote("cooling.fraction"),
+                  "mif error: ",sQuote("cooling.fraction.50"),
                   " must be < 1 when cooling.type = ",
                   sQuote("hyperbolic"),
                   call.=FALSE
@@ -86,7 +86,7 @@
                           particles,
                           rw.sd,
                           Np, var.factor, ic.lag,
-                          cooling.type, cooling.fraction,
+                          cooling.type, cooling.fraction.50,
                           method,
                           tol, max.fail,
                           verbose, transform, .ndone = 0L,
@@ -206,16 +206,16 @@
             )
   }
   
-  if (missing(cooling.fraction))
-    stop("mif error: ",sQuote("cooling.fraction")," must be specified",call.=FALSE)
-  cooling.fraction <- as.numeric(cooling.fraction)
-  if ((length(cooling.fraction)!=1)||(cooling.fraction<0)||(cooling.fraction>1))
-    stop("mif error: ",sQuote("cooling.fraction")," must be a number between 0 and 1",call.=FALSE)
+  if (missing(cooling.fraction.50))
+    stop("mif error: ",sQuote("cooling.fraction.50")," must be specified",call.=FALSE)
+  cooling.fraction.50 <- as.numeric(cooling.fraction.50)
+  if ((length(cooling.fraction.50)!=1)||(cooling.fraction.50<0)||(cooling.fraction.50>1))
+    stop("mif error: ",sQuote("cooling.fraction.50")," must be a number between 0 and 1",call.=FALSE)
   
   cooling <- cooling.function(
                               type=cooling.type,
                               perobs=(method=="mif2"),
-                              fraction=cooling.fraction,
+                              fraction=cooling.fraction.50,
                               ntimes=ntimes
                               )
 
@@ -370,7 +370,7 @@
       conv.rec=conv.rec,
       method=method,
       cooling.type=cooling.type,
-      cooling.fraction=cooling.fraction,
+      cooling.fraction.50=cooling.fraction.50,
       paramMatrix=if (method=="mif2") paramMatrix else array(data=numeric(0),dim=c(0,0))
       )
 }
@@ -384,7 +384,7 @@
                     particles, rw.sd,
                     Np, ic.lag, var.factor = 1,
                     cooling.type = c("geometric","hyperbolic"),
-                    cooling.fraction,
+                    cooling.fraction.50,
                     method = c("mif","unweighted","fp","mif2"),
                     tol = 1e-17, max.fail = Inf,
                     verbose = getOption("verbose"),
@@ -434,7 +434,7 @@
                          rw.sd=rw.sd,
                          Np=Np,
                          cooling.type=cooling.type,
-                         cooling.fraction=cooling.fraction,
+                         cooling.fraction.50=cooling.fraction.50,
                          var.factor=var.factor,
                          ic.lag=ic.lag,
                          method=method,
@@ -476,7 +476,7 @@
                     ivps,
                     particles, rw.sd,
                     Np, ic.lag, var.factor,
-                    cooling.type, cooling.fraction,
+                    cooling.type, cooling.fraction.50,
                     method,
                     tol,
                     transform,
@@ -490,7 +490,7 @@
             if (missing(ic.lag)) ic.lag <- object at ic.lag
             if (missing(var.factor)) var.factor <- object at var.factor
             if (missing(cooling.type)) cooling.type <- object at cooling.type
-            if (missing(cooling.fraction)) cooling.fraction <- object at cooling.fraction
+            if (missing(cooling.fraction.50)) cooling.fraction.50 <- object at cooling.fraction.50
             if (missing(method)) method <- object at method
             if (missing(transform)) transform <- object at transform
 
@@ -506,7 +506,7 @@
                 rw.sd=rw.sd,
                 Np=Np,
                 cooling.type=cooling.type,
-                cooling.fraction=cooling.fraction,
+                cooling.fraction.50=cooling.fraction.50,
                 var.factor=var.factor,
                 ic.lag=ic.lag,
                 method=method,

Modified: pkg/pomp/inst/CITATION
===================================================================
--- pkg/pomp/inst/CITATION	2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/inst/CITATION	2015-05-22 17:40:16 UTC (rev 1157)
@@ -27,7 +27,7 @@
    )		 
 
 citEntry(
-         header="The correct citation of the package itself is:",
+         header="Additionally, please cite the package itself:",
          entry="Manual",
          title="{pomp}: {S}tatistical Inference for Partially Observed {M}arkov Processes",
          author=personList(

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/inst/NEWS	2015-05-22 17:40:16 UTC (rev 1157)
@@ -1,5 +1,21 @@
 _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_4-_1:
+
+        • The ‘mif’ option ‘cooling.fraction’ has been replaced by the
+          more descriptive ‘cooling.fraction.50’.  Recall that this
+          parameter specifies the fraction of random-walk remaining
+          after 50 ‘mif’ iterations.
+
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_3-_6:
+
+        • Fixed bug arising when using ‘pomp’ with ‘Csnippets’ under
+          windows.  Thanks to Hamish McCallum for reporting it.
+
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_3-_3:
+
+        • Improvements to documentation.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_3-_1:
 
         • The optimization packages ‘nloptr’ and ‘subplex’ are no

Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd	2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/inst/NEWS.Rd	2015-05-22 17:40:16 UTC (rev 1157)
@@ -1,5 +1,22 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.64-1}{
+  \itemize{
+    \item The \code{mif} option \code{cooling.fraction} has been replaced by the more descriptive \code{cooling.fraction.50}.
+    Recall that this parameter specifies the fraction of random-walk remaining after 50 \code{mif} iterations.
+  }
+}
+\section{Changes in \pkg{pomp} version 0.63-6}{
+  \itemize{
+    \item Fixed bug arising when using \code{pomp} with \code{Csnippets} under windows.
+    Thanks to Hamish McCallum for reporting it.
+  }
+}
+\section{Changes in \pkg{pomp} version 0.63-3}{
+  \itemize{
+    \item Improvements to documentation.
+  }
+}
 \section{Changes in \pkg{pomp} version 0.63-1}{
   \itemize{
     \item The optimization packages \pkg{nloptr} and \pkg{subplex} are no longer dependencies of \pkg{pomp} that will be loaded at the time \pkg{pomp} is.

Modified: pkg/pomp/man/mif.Rd
===================================================================
--- pkg/pomp/man/mif.Rd	2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/man/mif.Rd	2015-05-22 17:40:16 UTC (rev 1157)
@@ -38,14 +38,14 @@
 \usage{
 \S4method{mif}{pomp}(object, Nmif = 1, start, ivps = character(0),
     particles, rw.sd, Np, ic.lag, var.factor = 1,
-    cooling.type, cooling.fraction,
+    cooling.type, cooling.fraction.50,
     method = c("mif","unweighted","fp","mif2"),
     tol = 1e-17, max.fail = Inf,
     verbose = getOption("verbose"), transform = FALSE, \dots)
 \S4method{mif}{pfilterd.pomp}(object, Nmif = 1, Np, tol, \dots)
 \S4method{mif}{mif}(object, Nmif, start, ivps,
     particles, rw.sd, Np, ic.lag, var.factor,
-    cooling.type, cooling.fraction,
+    cooling.type, cooling.fraction.50,
     method, tol, transform, \dots)
 \S4method{continue}{mif}(object, Nmif = 1, \dots)
 \S4method{logLik}{mif}(object, \dots)
@@ -107,14 +107,14 @@
     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}{
+  \item{cooling.type, cooling.fraction.50}{
     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.
 
-    When \code{cooling.type="geometric"}, on the n-th \code{mif} iteration, the relative perturbation intensity is \code{cooling.fraction^(n/50)}.
+    When \code{cooling.type="geometric"}, on the n-th \code{mif} iteration, the relative perturbation intensity is \code{cooling.fraction.50^(n/50)}.
 
-    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.
+    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.50}.
+    \code{cooling.fraction.50} is the relative magnitude of the parameter perturbations after 50 \code{mif} iterations.
   }
   \item{method}{
     \code{method} sets the update rule used in the algorithm.

Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save	2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/tests/ou2-mif.Rout.save	2015-05-22 17:40:16 UTC (rev 1157)
@@ -1,6 +1,6 @@
 
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,8 +16,6 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
 > 
 > pompExample(ou2)
 newly created object(s):
@@ -137,7 +135,7 @@
 +         Np=100,ic.lag=10,var.factor=1
 +         )
 +     )
-Error : mif error: 'cooling.fraction' must be specified
+Error : mif error: 'cooling.fraction.50' must be specified
 > 
 > try(
 +     mif(
@@ -279,4 +277,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 15.232   0.060  15.274 
+ 11.468   0.028  11.712 

Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html	2015-05-22 16:38:43 UTC (rev 1156)
+++ www/content/NEWS.html	2015-05-22 17:40:16 UTC (rev 1157)
@@ -7,6 +7,38 @@
 
 <h2>News for package ‘pomp’</h2>
 
+<h3>Changes in <span class="pkg">pomp</span> version 0.64-1</h3>
+
+
+<ul>
+<li><p> The <code>mif</code> option <code>cooling.fraction</code> has been replaced by the more descriptive <code>cooling.fraction.50</code>.
+Recall that this parameter specifies the fraction of random-walk remaining after 50 <code>mif</code> iterations.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in <span class="pkg">pomp</span> version 0.63-6</h3>
+
+
+<ul>
+<li><p> Fixed bug arising when using <code>pomp</code> with <code>Csnippets</code> under windows.
+Thanks to Hamish McCallum for reporting it.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in <span class="pkg">pomp</span> version 0.63-3</h3>
+
+
+<ul>
+<li><p> Improvements to documentation.
+</p>
+</li></ul>
+
+
+
 <h3>Changes in <span class="pkg">pomp</span> version 0.63-1</h3>
 
 

Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf	2015-05-22 16:38:43 UTC (rev 1156)
+++ www/vignettes/pomp.pdf	2015-05-22 17:40:16 UTC (rev 1157)
@@ -1,305 +1,340 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1157

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