[Pomp-commits] r661 - pkg/inst/doc

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

Author: kingaa
Date: 2012-04-15 18:07:02 +0200 (Sun, 15 Apr 2012)
New Revision: 661

Modified:
   pkg/inst/doc/advanced_topics_in_pomp.Rnw
   pkg/inst/doc/advanced_topics_in_pomp.pdf
   pkg/inst/doc/intro_to_pomp.Rnw
   pkg/inst/doc/intro_to_pomp.pdf
Log:
- update vignettes


Modified: pkg/inst/doc/advanced_topics_in_pomp.Rnw
===================================================================
--- pkg/inst/doc/advanced_topics_in_pomp.Rnw	2012-04-15 15:43:19 UTC (rev 660)
+++ pkg/inst/doc/advanced_topics_in_pomp.Rnw	2012-04-15 16:07:02 UTC (rev 661)
@@ -388,7 +388,7 @@
      statenames=c("S","I","R","cases","W"),
      ## the order of the parameters assumed in the native routines:
      paramnames=c(
-       "gamma","mu","iota","logbeta1","beta.sd",
+       "gamma","mu","iota","beta1","beta.sd",
        "pop","rho","nbasis","degree","period"
        ), 
      ## designate 'cases' as an accumulator variable
@@ -438,11 +438,11 @@
 <<sir-sim>>=
 params <- c(
             gamma=26,mu=0.02,iota=0.01,
-            logbeta1=log(1200),logbeta2=log(1800),logbeta3=log(600),
+            beta1=400,beta2=480,beta3=320,
             beta.sd=1e-3,                      
             pop=2.1e6,
             rho=0.6,
-            S.0=26/1200,I.0=0.001,R.0=1-0.001-26/1200
+            S.0=26/400,I.0=0.001,R.0=1-0.001-26/400
             )                                                     
 
 sir <- simulate(sir,params=c(params,nbasis=3,degree=3,period=1),seed=3493885L)

Modified: pkg/inst/doc/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)

Modified: pkg/inst/doc/intro_to_pomp.Rnw
===================================================================
--- pkg/inst/doc/intro_to_pomp.Rnw	2012-04-15 15:43:19 UTC (rev 660)
+++ pkg/inst/doc/intro_to_pomp.Rnw	2012-04-15 16:07:02 UTC (rev 661)
@@ -1705,7 +1705,7 @@
 B-splines are useful in this regard and \pkg{pomp} provides some simple facilities for using these.
 If $s_{i}(t)$, $i=1,\dots,k$ is a periodic B-spline basis, as in Fig.~\ref{fig:seas-basis-plot}, then we can for example define
 \begin{equation*}
-  \log\beta(t)=\sum_{i}\!b_{i}\,s_{i}(t)
+  \beta(t)=\sum_{i}\!b_{i}\,s_{i}(t)
 \end{equation*}
 and, by varying the coefficients $b_{i}$, we can obtain a wide variety of shapes for $\beta(t)$.
 In \pkg{pomp}, we can define a set of periodic B-spline basis functions by doing:

Modified: pkg/inst/doc/intro_to_pomp.pdf
===================================================================
(Binary files differ)