[Pomp-commits] r1186 - 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 Jun 5 15:19:40 CEST 2015 

Author: kingaa
Date: 2015-06-05 15:19:40 +0200 (Fri, 05 Jun 2015)
New Revision: 1186

Modified:
   pkg/pomp/man/mif2.Rd
   pkg/pomp/tests/getting_started.R
   pkg/pomp/tests/getting_started.Rout.save
   www/content/NEWS.html
   www/vignettes/pomp.pdf
Log:
- fix problems in documentation
- update getting_started test

Modified: pkg/pomp/man/mif2.Rd
===================================================================
--- pkg/pomp/man/mif2.Rd	2015-06-05 13:18:39 UTC (rev 1185)
+++ pkg/pomp/man/mif2.Rd	2015-06-05 13:19:40 UTC (rev 1186)
@@ -124,9 +124,8 @@
           b=rep(0.2,length(time)),
           c=ivp(0.2),
           d=ifelse(time==time[13],0.2,0),
-	  e=ivp(0.2,lag=13),
-	  f=ifelse(time<23,0.02,0)
-	}
+          e=ivp(0.2,lag=13),
+          f=ifelse(time<23,0.02,0))}
   results in perturbations of parameter \code{a} with s.d. 0.05 at every time step, while parameters \code{b} and \code{c} both get perturbations of s.d. 0.2 only before the first observation.
   Parameters \code{d} and \code{e}, by contrast, get perturbations of s.d. 0.2 only before the thirteenth observation.
   Finally, parameter \code{f} gets a random perturbation of size 0.02 before every observation falling before \eqn{t=23}.

Modified: pkg/pomp/tests/getting_started.R
===================================================================
--- pkg/pomp/tests/getting_started.R	2015-06-05 13:18:39 UTC (rev 1185)
+++ pkg/pomp/tests/getting_started.R	2015-06-05 13:19:40 UTC (rev 1186)
@@ -153,9 +153,9 @@
 sim1 <- simulate(tm,nsim=10,as.data.frame=TRUE,include.data=TRUE)
 
 ## ----parus-mif,cache=TRUE------------------------------------------------
-mf <- mif(parus,Nmif=50,Np=1000,method="mif2",cooling.fraction=0.8,
-          rw.sd=c(r=0.02,K=0.02,phi=0.02,sigma=0.02),transform=TRUE)
-mf <- mif(mf)
+mf <- mif2(parus,Nmif=50,Np=1000,cooling.fraction=0.8,
+           rw.sd=rw.sd(r=0.02,K=0.02,phi=0.02,sigma=0.02),transform=TRUE)
+mf <- mif2(mf)
 mle <- coef(mf); mle
 logmeanexp(replicate(5,logLik(pfilter(mf))),se=TRUE)
 sim2 <- simulate(mf,nsim=10,as.data.frame=TRUE,include.data=TRUE)

Modified: pkg/pomp/tests/getting_started.Rout.save
===================================================================
--- pkg/pomp/tests/getting_started.Rout.save	2015-06-05 13:18:39 UTC (rev 1185)
+++ pkg/pomp/tests/getting_started.Rout.save	2015-06-05 13:19:40 UTC (rev 1186)
@@ -175,17 +175,17 @@
 > sim1 <- simulate(tm,nsim=10,as.data.frame=TRUE,include.data=TRUE)
 > 
 > ## ----parus-mif,cache=TRUE------------------------------------------------
-> mf <- mif(parus,Nmif=50,Np=1000,method="mif2",cooling.fraction=0.8,
-+           rw.sd=c(r=0.02,K=0.02,phi=0.02,sigma=0.02),transform=TRUE)
-> mf <- mif(mf)
+> mf <- mif2(parus,Nmif=50,Np=1000,cooling.fraction=0.8,
++            rw.sd=rw.sd(r=0.02,K=0.02,phi=0.02,sigma=0.02),transform=TRUE)
+> mf <- mif2(mf)
 > mle <- coef(mf); mle
           r           K         phi         N.0       sigma 
-  2.8031511 421.5119871   0.5228287 200.0000000   0.5627677 
+  4.3268371 219.8355772   1.0220978 200.0000000   0.6898461 
 > logmeanexp(replicate(5,logLik(pfilter(mf))),se=TRUE)
-                       se 
--143.9107637    0.2511397 
+                     se 
+-144.743699    0.301315 
 > sim2 <- simulate(mf,nsim=10,as.data.frame=TRUE,include.data=TRUE)
 > 
 > proc.time()
    user  system elapsed 
- 77.484   0.432  79.814 
+ 77.812   0.492  80.066 

Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html	2015-06-05 13:18:39 UTC (rev 1185)
+++ www/content/NEWS.html	2015-06-05 13:19:40 UTC (rev 1186)
@@ -1,10 +1,9 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>R: News for package 'pomp'</title>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-<link rel="stylesheet" type="text/css" href="R.css">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: News for package 'pomp'</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<link rel="stylesheet" type="text/css" href="R.css" />
 </head><body>
 
-<table width="100%" summary="page for NEWS"><tr><td>NEWS</td><td align="right">R Documentation</td></tr></table>
+<table width="100%" summary="page for NEWS"><tr><td>NEWS</td><td style="text-align: right;">R Documentation</td></tr></table>
 
 <h2>News for package ‘pomp’</h2>
 
@@ -1558,7 +1557,7 @@
 <li> <p><code>rmeasure</code>, <code>dmeasure</code>, and <code>skeleton</code> are now specified by a function (or native routine) that does the computation for ONE state vector and ONE parameter vector.
 This is analogous to the way that <code>init.state</code> has operated from the beginning.
 It greatly simplifies model specification from the user's point of view without changing the low-level methods interfaces (pomp methods <code>rmeasure</code>, <code>dmeasure</code>, <code>skeleton</code>, <code>init.states</code>).
-However, <STRONG>this change is not backward-compatible</STRONG>: users will need to rewrite code for the <code>rmeasure</code>, <code>dmeasure</code>, and <code>skeleton</code> slots.
+However, <strong>this change is not backward-compatible</strong>: users will need to rewrite code for the <code>rmeasure</code>, <code>dmeasure</code>, and <code>skeleton</code> slots.
 In practice, this should not be difficult.
 It involves removing loops over <code>times</code> and columns of <code>params</code> and (if covariates are used in the measurement model or deterministic skeleton) making use of the <code>covars</code> argument passed to the user function.
 </p>

Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf	2015-06-05 13:18:39 UTC (rev 1185)
+++ www/vignettes/pomp.pdf	2015-06-05 13:19:40 UTC (rev 1186)
@@ -1,7 +1,7 @@
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