[Pomp-commits] r936 - in pkg/pomp: . inst/doc tests

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

Author: kingaa
Date: 2014-04-23 21:56:17 +0200 (Wed, 23 Apr 2014)
New Revision: 936

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/inst/doc/advanced_topics_in_pomp.pdf
   pkg/pomp/inst/doc/intro_to_pomp.pdf
   pkg/pomp/inst/doc/manual.pdf
   pkg/pomp/tests/ou2-nlf.R
   pkg/pomp/tests/ou2-nlf.Rout.save
Log:
- update vignettes 
- try to fix strange ou2-nlf test results


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2014-04-23 19:44:39 UTC (rev 935)
+++ pkg/pomp/DESCRIPTION	2014-04-23 19:56:17 UTC (rev 936)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.50-1
-Date: 2014-04-20
+Version: 0.50-2
+Date: 2014-04-23
 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")),
@@ -19,9 +19,11 @@
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially-observed Markov processes
 Depends: R(>= 3.0.0), stats, graphics, methods, mvtnorm, subplex, nloptr, deSolve
+Suggests: knitr
 License: GPL(>= 2)
 LazyData: true
 BuildVignettes: true
+VignetteBuilder: knitr
 MailingList: Subscribe to pomp-announce at r-forge.r-project.org for announcements by going to http://lists.r-forge.r-project.org/mailman/listinfo/pomp-announce.
 Collate: aaa.R authors.R generics.R version.R eulermultinom.R
 	 csnippet.R pomp-fun.R plugins.R 

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

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

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

Modified: pkg/pomp/tests/ou2-nlf.R
===================================================================
--- pkg/pomp/tests/ou2-nlf.R	2014-04-23 19:44:39 UTC (rev 935)
+++ pkg/pomp/tests/ou2-nlf.R	2014-04-23 19:56:17 UTC (rev 936)
@@ -15,6 +15,7 @@
           nconverge=100,
           nasymp=2000,
           trace=1,
+          method="Nelder-Mead",
           verbose=TRUE,
           eval.only=TRUE,
           seed=426094906L,
@@ -30,9 +31,9 @@
           lags=c(4,6),
           nconverge=100,
           nasymp=2000,
-          method="Nelder-Mead",
           maxit=500,
           trace=1,
+          method="Nelder-Mead",
           verbose=TRUE,
           seed=426094906L,
           lql.frac = 0.025
@@ -45,9 +46,9 @@
           lags=c(4,6),
           nconverge=100,
           nasymp=2000,
-          method="Nelder-Mead",
           maxit=500,
           trace=1,
+          method="Nelder-Mead",
           verbose=TRUE,
           eval.only=TRUE,
           seed=426094906L,
@@ -62,9 +63,9 @@
           lags=c(4,6),
           nconverge=100,
           nasymp=2000,
-          method="Nelder-Mead",
           maxit=500,
           trace=1,
+          method="Nelder-Mead",
           verbose=TRUE,
           seed=426094906L,
           lql.frac = 0.025

Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save	2014-04-23 19:44:39 UTC (rev 935)
+++ pkg/pomp/tests/ou2-nlf.Rout.save	2014-04-23 19:56:17 UTC (rev 936)
@@ -38,6 +38,7 @@
 +           nconverge=100,
 +           nasymp=2000,
 +           trace=1,
++           method="Nelder-Mead",
 +           verbose=TRUE,
 +           eval.only=TRUE,
 +           seed=426094906L,
@@ -54,9 +55,9 @@
 +           lags=c(4,6),
 +           nconverge=100,
 +           nasymp=2000,
-+           method="Nelder-Mead",
 +           maxit=500,
 +           trace=1,
++           method="Nelder-Mead",
 +           verbose=TRUE,
 +           seed=426094906L,
 +           lql.frac = 0.025
@@ -125,9 +126,9 @@
 +           lags=c(4,6),
 +           nconverge=100,
 +           nasymp=2000,
-+           method="Nelder-Mead",
 +           maxit=500,
 +           trace=1,
++           method="Nelder-Mead",
 +           verbose=TRUE,
 +           eval.only=TRUE,
 +           seed=426094906L,
@@ -142,9 +143,9 @@
 +           lags=c(4,6),
 +           nconverge=100,
 +           nasymp=2000,
-+           method="Nelder-Mead",
 +           maxit=500,
 +           trace=1,
++           method="Nelder-Mead",
 +           verbose=TRUE,
 +           seed=426094906L,
 +           lql.frac = 0.025
@@ -235,4 +236,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  6.836   0.060   6.942 
+  8.723   0.075   8.798