From noreply at r-forge.r-project.org  Wed Jul  1 21:31:52 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  1 Jul 2015 21:31:52 +0200 (CEST)
Subject: [Pomp-commits] r1237 - in pkg/pomp: inst/examples tests
Message-ID: <20150701193152.C2939185570@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-01 21:31:52 +0200 (Wed, 01 Jul 2015)
New Revision: 1237

Modified:
   pkg/pomp/inst/examples/bbs.R
   pkg/pomp/inst/examples/euler.sir.R
   pkg/pomp/inst/examples/gillespie.sir.R
   pkg/pomp/tests/bbs-trajmatch.R
   pkg/pomp/tests/bbs-trajmatch.Rout.save
   pkg/pomp/tests/bbs.Rout.save
   pkg/pomp/tests/gillespie.R
   pkg/pomp/tests/gillespie.Rout.save
   pkg/pomp/tests/pfilter.Rout.save
Log:
- change some initial conditions to match those in code

Modified: pkg/pomp/inst/examples/bbs.R
===================================================================
--- pkg/pomp/inst/examples/bbs.R	2015-06-30 11:32:39 UTC (rev 1236)
+++ pkg/pomp/inst/examples/bbs.R	2015-07-01 19:31:52 UTC (rev 1237)
@@ -28,7 +28,7 @@
        beta.sd=0,
        pop=1400,
        rho=0.9,sigma=3.6,
-       S.0=0.999,I.0=0.001,R.0=0
+       S_0=0.999,I_0=0.001,R_0=0
        ),
      rprocess=euler.sim(
        step.fun="_sir_euler_simulator",
@@ -43,7 +43,7 @@
      paramnames=c(
        "gamma","mu","iota",
        "beta","beta.sd","pop","rho",
-       "S.0","I.0","R.0"
+       "S_0","I_0","R_0"
        ),
      zeronames=c("cases"),
      nbasis=1L,
@@ -51,7 +51,7 @@
      period=1.0,
      logvar=c(
        "beta","gamma","mu","iota","sigma","beta.sd",
-       "S.0","I.0","R.0"
+       "S_0","I_0","R_0"
        ),
      logitvar="rho",
      toEstimationScale=function (params, logvar, logitvar, ...) {

Modified: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R	2015-06-30 11:32:39 UTC (rev 1236)
+++ pkg/pomp/inst/examples/euler.sir.R	2015-07-01 19:31:52 UTC (rev 1237)
@@ -221,7 +221,7 @@
        beta.sd=1e-3,
        pop=2.1e6,
        rho=0.6,
-       S.0=26/400,I.0=0.001,R.0=1-26/400
+       S_0=26/400,I_0=0.001,R_0=1-26/400
        ),
      rprocess=euler.sim(
        step.fun="_sir_euler_simulator",
@@ -237,7 +237,7 @@
      paramnames=c(
        "gamma","mu","iota",
        "beta1","beta.sd","pop","rho",
-       "S.0","I.0","R.0"
+       "S_0","I_0","R_0"
        ),
      zeronames=c("cases"),
      fromEstimationScale="_sir_par_trans",

Modified: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R	2015-06-30 11:32:39 UTC (rev 1236)
+++ pkg/pomp/inst/examples/gillespie.sir.R	2015-07-01 19:31:52 UTC (rev 1237)
@@ -532,7 +532,7 @@
        gamma=24,mu=1/70,iota=0.1,
        beta1=330,beta2=410,beta3=490,
        rho=0.1,
-       S.0=0.05,I.0=1e-4,R.0=0.95,
+       S_0=0.05,I_0=1e-4,R_0=0.95,
        pop=1000000,
        beta.sd=0
        ),
@@ -564,11 +564,11 @@
      paramnames=c(
        "gamma","mu","iota",
        "beta1","beta.sd","pop","rho",
-       "S.0","I.0","R.0"
+       "S_0","I_0","R_0"
        ),
      zeronames=c("cases"),
      comp.names=c("S","I","R"),
-     ic.names=c("S.0","I.0","R.0"),
+     ic.names=c("S_0","I_0","R_0"),
      fromEstimationScale="_sir_par_trans",
      toEstimationScale="_sir_par_untrans",
      nbasis=3L,

Modified: pkg/pomp/tests/bbs-trajmatch.R
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.R	2015-06-30 11:32:39 UTC (rev 1236)
+++ pkg/pomp/tests/bbs-trajmatch.R	2015-07-01 19:31:52 UTC (rev 1237)
@@ -5,7 +5,7 @@
 guess <- c(
            mu=0,gamma=1/3,beta=1,beta.sd=0,iota=0,
            pop=1400,rho=0.9,sigma=3.6,
-           S.0=1390,I.0=1,R.0=0
+           S_0=1390,I_0=1,R_0=0
            )
 est <- c("beta","gamma")
 

Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-06-30 11:32:39 UTC (rev 1236)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-07-01 19:31:52 UTC (rev 1237)
@@ -1,5 +1,5 @@
 
-R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
 Copyright (C) 2015 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -25,7 +25,7 @@
 > guess <- c(
 +            mu=0,gamma=1/3,beta=1,beta.sd=0,iota=0,
 +            pop=1400,rho=0.9,sigma=3.6,
-+            S.0=1390,I.0=1,R.0=0
++            S_0=1390,I_0=1,R_0=0
 +            )
 > est <- c("beta","gamma")
 > 
@@ -81,4 +81,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.116   0.064   2.181 
+  2.527   0.055   2.564 

Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save	2015-06-30 11:32:39 UTC (rev 1236)
+++ pkg/pomp/tests/bbs.Rout.save	2015-07-01 19:31:52 UTC (rev 1237)
@@ -1,5 +1,5 @@
 
-R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
 Copyright (C) 2015 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -27,12 +27,12 @@
 > coef(bbs)
        gamma           mu         iota         beta      beta.sd          pop 
    0.3333333    0.0000000    0.0000000    1.4000000    0.0000000 1400.0000000 
-         rho        sigma          S.0          I.0          R.0 
+         rho        sigma          S_0          I_0          R_0 
    0.9000000    3.6000000    0.9990000    0.0010000    0.0000000 
 > coef(bbs,transform=TRUE)
        gamma           mu         iota         beta      beta.sd          pop 
   -1.0986123         -Inf         -Inf    0.3364722         -Inf 1400.0000000 
-         rho        sigma          S.0          I.0          R.0 
+         rho        sigma          S_0          I_0          R_0 
    2.1972246    1.2809338   -0.0010005   -6.9077553         -Inf 
 > 
 > bbs <- pomp(bbs,
@@ -48,7 +48,7 @@
 > signif(coef(fit1),3)
    gamma       mu     iota     beta  beta.sd      pop      rho    sigma 
    0.333    0.000    0.000    3.570    0.000 1400.000    0.900    1.920 
-     S.0      I.0      R.0 
+     S_0      I_0      R_0 
    0.999    0.001    0.000 
 > 
 > fit2 <- bsmc2(bbs,params=coef(bbs),Np=5000,transform=TRUE,
@@ -56,14 +56,14 @@
 > signif(coef(fit2),3)
    gamma       mu     iota     beta  beta.sd      pop      rho    sigma 
    0.333    0.000    0.000    3.670    0.000 1400.000    0.900    1.940 
-     S.0      I.0      R.0 
+     S_0      I_0      R_0 
    0.999    0.001    0.000 
 > 
 > fit3 <- traj.match(bbs,est=c("beta","sigma"),transform=TRUE)
 > signif(coef(fit3),3)
    gamma       mu     iota     beta  beta.sd      pop      rho    sigma 
    0.333    0.000    0.000    2.090    0.000 1400.000    0.900    0.474 
-     S.0      I.0      R.0 
+     S_0      I_0      R_0 
    0.999    0.001    0.000 
 > 
 > sim1 <- simulate(bbs,nsim=20,as.data.frame=TRUE,include.data=TRUE)
@@ -72,4 +72,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  5.636   0.048   5.699 
+  6.228   0.044   6.259 

Modified: pkg/pomp/tests/gillespie.R
===================================================================
--- pkg/pomp/tests/gillespie.R	2015-06-30 11:32:39 UTC (rev 1236)
+++ pkg/pomp/tests/gillespie.R	2015-07-01 19:31:52 UTC (rev 1237)
@@ -8,10 +8,10 @@
             beta3=490,
             gamma=24,
             iota=0.1,
-            S.0=0.05,
-            I.0=1e-4,
-            R.0=0.95,
-            N.0=1000000
+            S_0=0.05,
+            I_0=1e-4,
+            R_0=0.95,
+            N_0=1000000
             )
 
 seasonality <- data.frame(
@@ -65,13 +65,13 @@
               measurement.model=reports~binom(size=cases,prob=0.1),
               initializer=function(params, t0, ...){
                 comp.names <- c("S","I","R")
-                icnames <- paste(comp.names,"0",sep=".")
+                icnames <- paste(comp.names,"0",sep="_")
                 snames <- c("S","I","R","N","cases")
                 fracs <- params[icnames]
                 x0 <- numeric(length(snames))
                 names(x0) <- snames
-                x0["N"] <- params["N.0"]
-                x0[comp.names] <- round(params['N.0']*fracs/sum(fracs))
+                x0["N"] <- params["N_0"]
+                x0[comp.names] <- round(params['N_0']*fracs/sum(fracs))
                 x0
               }
               ),

Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save	2015-06-30 11:32:39 UTC (rev 1236)
+++ pkg/pomp/tests/gillespie.Rout.save	2015-07-01 19:31:52 UTC (rev 1237)
@@ -1,5 +1,5 @@
 
-R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
 Copyright (C) 2015 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -25,10 +25,10 @@
 +             beta3=490,
 +             gamma=24,
 +             iota=0.1,
-+             S.0=0.05,
-+             I.0=1e-4,
-+             R.0=0.95,
-+             N.0=1000000
++             S_0=0.05,
++             I_0=1e-4,
++             R_0=0.95,
++             N_0=1000000
 +             )
 > 
 > seasonality <- data.frame(
@@ -82,13 +82,13 @@
 +               measurement.model=reports~binom(size=cases,prob=0.1),
 +               initializer=function(params, t0, ...){
 +                 comp.names <- c("S","I","R")
-+                 icnames <- paste(comp.names,"0",sep=".")
++                 icnames <- paste(comp.names,"0",sep="_")
 +                 snames <- c("S","I","R","N","cases")
 +                 fracs <- params[icnames]
 +                 x0 <- numeric(length(snames))
 +                 names(x0) <- snames
-+                 x0["N"] <- params["N.0"]
-+                 x0[comp.names] <- round(params['N.0']*fracs/sum(fracs))
++                 x0["N"] <- params["N_0"]
++                 x0[comp.names] <- round(params['N_0']*fracs/sum(fracs))
 +                 x0
 +               }
 +               ),
@@ -130,4 +130,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.392   0.036   2.456 
+  2.508   0.040   2.529 

Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save	2015-06-30 11:32:39 UTC (rev 1236)
+++ pkg/pomp/tests/pfilter.Rout.save	2015-07-01 19:31:52 UTC (rev 1237)
@@ -1,5 +1,5 @@
 
-R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
 Copyright (C) 2015 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -50,7 +50,7 @@
 > print(coef(pf))
    gamma       mu     iota    beta1    beta2    beta3  beta.sd      pop 
 2.60e+01 2.00e-02 1.00e-02 4.00e+02 4.80e+02 3.20e+02 1.00e-03 2.10e+06 
-     rho      S.0      I.0      R.0 
+     rho      S_0      I_0      R_0 
 6.00e-01 6.50e-02 1.00e-03 9.35e-01 
 > print(pf$loglik,digits=4)
 [1] -947.4
@@ -62,7 +62,7 @@
 > print(coef(pf))
    gamma       mu     iota    beta1    beta2    beta3  beta.sd      pop 
 2.60e+01 2.00e-02 1.00e+00 4.00e+02 4.80e+02 3.20e+02 1.00e-03 2.10e+06 
-     rho      S.0      I.0      R.0 
+     rho      S_0      I_0      R_0 
 6.00e-01 6.50e-02 1.00e-03 9.35e-01 
 > print(logLik(pf),digits=4)
 [1] -945.4
@@ -76,4 +76,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  6.308   0.040   6.488 
+  8.475   0.034   8.491 


From noreply at r-forge.r-project.org  Wed Jul  1 21:31:58 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  1 Jul 2015 21:31:58 +0200 (CEST)
Subject: [Pomp-commits] r1238 - www/content
Message-ID: <20150701193158.CA11B185570@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-01 21:31:58 +0200 (Wed, 01 Jul 2015)
New Revision: 1238

Modified:
   www/content/about.htm
Log:
- update "about pomp" page

Modified: www/content/about.htm
===================================================================
--- www/content/about.htm	2015-07-01 19:31:52 UTC (rev 1237)
+++ www/content/about.htm	2015-07-01 19:31:58 UTC (rev 1238)
@@ -24,7 +24,7 @@
 
 <p>Simple worked examples are provided in <a href="./index.php?nav=vignettes">vignettes</a> and in the <code>examples</code> directory of the installed package.</p>
 
-<p>Future support for a variety of other algorithms is envisioned. A working group of the <a href="http://nceas.ucsb.edu">National&nbsp;Center&nbsp;for&nbsp;Ecological&nbsp;Analysis&nbsp;and&nbsp;Synthesis&nbsp;(NCEAS)</a>, "Inference for Mechanistic Models", is currently implementing additional methods for this package.</p>
+<p>Future support for a variety of other algorithms is envisioned.</p>
 
 <p>Please let the developers know if you find <strong>pomp</strong> useful, if you publish results obtained using it, if you come up with improvements, find bugs, or have suggestions or feature requests!</p>
 


From noreply at r-forge.r-project.org  Wed Jul  1 21:32:02 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  1 Jul 2015 21:32:02 +0200 (CEST)
Subject: [Pomp-commits] r1239 - /
Message-ID: <20150701193202.7D6EA185570@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-01 21:32:02 +0200 (Wed, 01 Jul 2015)
New Revision: 1239

Added:
   README.md
Removed:
   README
Log:
- update README file

Deleted: README
===================================================================
--- README	2015-07-01 19:31:58 UTC (rev 1238)
+++ README	2015-07-01 19:32:02 UTC (rev 1239)
@@ -1,49 +0,0 @@
-			R-Forge SVN README
-
-
-(See "http://download.r-forge.r-project.org/manuals/R-Forge_Manual.pdf"
-       for detailed information on registering a new project.
-
-1. Introduction
------------------------------------------------------------------------
-R is free software distributed under a GNU-style copyleft. R-Forge is
-a service for R users and package developers providing certain tools
-for collaborative source code management.
-
-2. The directory you're in
------------------------------------------------------------------------
-This is the repository of your project. It contains two important
-pre-defined directories namely 'www' and 'pkg'. They must not be
-deleted otherwise R-Forge's core functionality will not be available
-(daily check and build of your package or project websites).
-These two directories are standardized and therefore are going to be
-described in this README. The rest of your repository can be used as
-you like.
-
-3. 'pkg' directory
------------------------------------------------------------------------
-Typically this directory contains the R package with the usual
-DESCRIPTION and R/, man/, data/ directories etc (see 'Writing R 
-Extension' for more details). In the future it will also be possible to
-have multiple packages managed by a control file, however currently
-this feature is still under development).
-
-Furthermore, this directory will be checked out daily, the package is
-checked and if it passes this procedure it is build and made available at
-http://R-Forge.R-project.org/src/contrib/ (as source tar.gz and win32
-.zip). It should be possible to install the package via
-install.packages("foo",url="R-Forge.R-project.org") within R
-then.
-
-4. 'www' directory
------------------------------------------------------------------------
-This directory contains your project homepage which is available at
-http://<projectname>.R-Forge.R-project.org. 
-Note that it will be checked out daily, so please take
-into consideration that it will not be available right after you
-commit your changes or updates. 
-
-5. Help
------------------------------------------------------------------------
-If you need help don't hesitate to contact us
-(R-Forge at R-project.org)

Added: README.md
===================================================================
--- README.md	                        (rev 0)
+++ README.md	2015-07-01 19:32:02 UTC (rev 1239)
@@ -0,0 +1,4 @@
+**pomp**, an *R* package for statistical inference using partially observed Markov processes
+
+- the `pkg` directory contains the source code for several `R` packages  
+- the `www` directory contains the `pomp` website


From noreply at r-forge.r-project.org  Wed Jul  1 21:51:05 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  1 Jul 2015 21:51:05 +0200 (CEST)
Subject: [Pomp-commits] r1240 - /
Message-ID: <20150701195105.4E70C186DDC@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-01 21:51:05 +0200 (Wed, 01 Jul 2015)
New Revision: 1240

Modified:
   README.md
Log:
- add info on official website

Modified: README.md
===================================================================
--- README.md	2015-07-01 19:32:02 UTC (rev 1239)
+++ README.md	2015-07-01 19:51:05 UTC (rev 1240)
@@ -2,3 +2,5 @@
 
 - the `pkg` directory contains the source code for several `R` packages  
 - the `www` directory contains the `pomp` website
+
+The package's official website is [pomp.r-forge.r-project.org](http://pomp.r-forge.r-project.org).


From noreply at r-forge.r-project.org  Wed Jul  1 22:10:07 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  1 Jul 2015 22:10:07 +0200 (CEST)
Subject: [Pomp-commits] r1241 - /
Message-ID: <20150701201007.9B80F1855F2@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-01 22:10:07 +0200 (Wed, 01 Jul 2015)
New Revision: 1241

Added:
   TODO.md
Removed:
   TODO
Log:
- move TODO to markdown format

Deleted: TODO
===================================================================
--- TODO	2015-07-01 19:51:05 UTC (rev 1240)
+++ TODO	2015-07-01 20:10:07 UTC (rev 1241)
@@ -1,8 +0,0 @@
-- documentation on 'mifList', 'pmcmcList', etc.
-- 'transform' argument for pmcmc?
-- 'initializer' -> 'rinit' and perhaps 'dinit'
-- documentation: "regular parameters" instead of "non-IVP"
-- add 'coef' method for 'mifList' objects
-- objective function for spectrum matching
-- one-point SCQL function for possible use in fitting initial conditions
-- save particle filtering variance?  Prediction means are optional.  Only interesting for end-user if one wants to look at residuals.

Copied: TODO.md (from rev 1240, TODO)
===================================================================
--- TODO.md	                        (rev 0)
+++ TODO.md	2015-07-01 20:10:07 UTC (rev 1241)
@@ -0,0 +1,10 @@
+### pomp to-do list
+
+- documentation on 'mifList', 'pmcmcList', etc.
+- 'transform' argument for pmcmc?
+- 'initializer' -> 'rinit' and perhaps 'dinit'
+- documentation: "regular parameters" instead of "non-IVP"
+- add 'coef' method for 'mifList' objects
+- objective function for spectrum matching
+- one-point SCQL function for possible use in fitting initial conditions
+- save particle filtering variance?  Prediction means are optional.  Only interesting for end-user if one wants to look at residuals.


From noreply at r-forge.r-project.org  Thu Jul  2 03:18:47 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  2 Jul 2015 03:18:47 +0200 (CEST)
Subject: [Pomp-commits] r1242 - pkg/pomp/inst/doc
Message-ID: <20150702011847.78FAF187B5C@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-02 03:18:46 +0200 (Thu, 02 Jul 2015)
New Revision: 1242

Modified:
   pkg/pomp/inst/doc/index.html
Log:
- remove links to out-dated docs, replace with link to package website

Modified: pkg/pomp/inst/doc/index.html
===================================================================
--- pkg/pomp/inst/doc/index.html	2015-07-01 20:10:07 UTC (rev 1241)
+++ pkg/pomp/inst/doc/index.html	2015-07-02 01:18:46 UTC (rev 1242)
@@ -8,22 +8,7 @@
 <body>
 <h2><b>pomp</b> user guides and other documentation</h2>
 
-<table>
-<tr>
-<td>Introduction to <strong>pomp</strong></td>
-<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/intro_to_pomp.pdf">(PDF)</a></td>
-<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/intro_to_pomp.R">(R code)</a></td>
-</tr>
-<tr>
-<td>Advanced topics in <strong>pomp</strong></td>
-<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/advanced_topics_in_pomp.pdf">(PDF)</a></td>
-<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/advanced_topics_in_pomp.R">(R code)</a></td>
-</tr>
-<tr>
-<td><strong>pomp</strong> package manual</td>
-<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/pomp.pdf">(PDF)</a></td>
-</tr>
-</table>
+Visit the <a href="http://pomp.r-forge.r-project.org/index.php?nav=vignettes"><b>pomp</b> website for the pomp paper, tutorials, examples, and other documentation</a> 
 
 <p><a href="../html/00Index.html">Back to <b>pomp</b> package index</a></p>
 </body>


From noreply at r-forge.r-project.org  Thu Jul  2 14:29:27 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  2 Jul 2015 14:29:27 +0200 (CEST)
Subject: [Pomp-commits] r1243 - pkg/pomp/data pkg/pomp/inst pkg/pomp/man
	www/content www/vignettes
Message-ID: <20150702122927.888BC18761B@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-02 14:29:27 +0200 (Thu, 02 Jul 2015)
New Revision: 1243

Added:
   pkg/pomp/data/ewcitmeas.rda
Modified:
   pkg/pomp/inst/NEWS.Rd
   pkg/pomp/man/measles.Rd
   www/content/NEWS.html
   www/vignettes/pomp.pdf
Log:
- add 'ewcitmeas' dataset

Added: pkg/pomp/data/ewcitmeas.rda
===================================================================
--- pkg/pomp/data/ewcitmeas.rda	                        (rev 0)
+++ pkg/pomp/data/ewcitmeas.rda	2015-07-02 12:29:27 UTC (rev 1243)
@@ -0,0 +1,129 @@
+?7zXZ
i"?6!
?X????>?])TW"?nR?????????j='S???a _?jg????1o
+???
?j?&-??K?,?s|?2UdH???3??
??+??qD????*??????v??as]%?l ?????N???	zS?0??"T??e?z}]j?>|?-???X???????N?k??#s??tn`?\?/Q?cb~FZTr?*f??/]u????????m?E????M??A?f?7T?Qf?qJ???h?^??Q??SLC?=s??r???K??EA??\/2????q|A??
+~8Q??????????f?????;??^??0?+xq+?1??)
+??,?????l??p?\Z	1?c?TQH????D$R?2???fzz???f?W????`%O?Yhwa?<????u????sK????A/?2?-?2Y???????r??U>pa??QiC???!?[!?u??e???A?r????Y?T%???r#?????in??$??????.WDd}?0v?b?X??H??4f??	???l7?????A?y???hJ????=?>??NK?6?X"A%v?,?? ?????????!-d?B??%???S??\osbk???+!?0???+
+?n,???????T?IW?Bf????9?<.>?|.?
+S?S???C?]?k?y?/w?J?^^??ua?????i??M????k?,~t?j(???IpsVN??@????Y
??2?}??W?g??su?????ru8??kz?\?\V?5???`!8?*W??o???	<?e????K?aH#????,?X????tG?{s?O`???vhB	N3???? z?t?7?dO).?H?b)
+X?p?"K??v???H?z_?V?.?T??"?q?
+?d?????{??_	??P???j$?A6w????8d?wxYV=?{??????v?hr???????4?|f?????U??}o????E?????????,??a???*???I?XkGV?~??V??|??ii?.$\?z?u??R?{
?2ui??t?Jr	?+????n??FD?N?T?zLN??4????????G=A???P??~I0?hJ?v??V?b:, H?+6?|??-o?%m at v???.?So????)????P????5d?????L:|?l??$?Sa?A?L???z?@???v??????4?(??f?;?v{?????&???m??L???Po?R???!V`
+?K??s?_???p??=u`?\?$)pD?X?cr???'8? ?@???J?@??-??I???????????fFq????
+Z?5??dv??\????i@?<S???a??????t?`??fKF??g?R??V*Y?????SS^?????VXt??Z???????hQ9??{?OJ??~df?m????/??;D9R,0U??$y??????????E??u??~?Z^?/o?g??????EO????3?????X??L{?2?,>'?92?51z+?
+?a???
)~???[	???=?s?X~???%
+c?"???SY*???nZ2????;????R??|??	r?m?4H?.*??w?????Uo??2????3sM??.z2Vt/??@?V?s\uFN??8?,?;?????T??(K#?U8?
+?4/?vy?.?????V??n:?m??o??N?#d??=??hq%?bK?:?>?O7?C4??I?l?_J#T??? T?6?:_??7,1???	S??`Q	n?L?K??
+?????@?Y??~?g??C?GV???$	?>l????B????ILo}Z??O??C[eQ$??7X?4FY&??*?B????$?=???rNU&?j???L?tf?????X?N?7?n9??3????{?? 21??u??7?Y???p???ww%?????LAw?[?0?SHb??#?W????JK???T6????? 1?!1????^k{?5????#Q?d?\?w??&P?`?????YW?]??uS???%dr??"?~#-??D9??h?u~?|??xDU?V?S???f?= ?????<??xSP?|?WA?/> ??m???h????Q? 4??s?YH??ZQ?n??>RoKO4??	??Fw????? ?|??????v??w?G???x???????/??N???????|i??HZ\??I?t4x0?????2(???HV?J?'*
+??Z!]?m??:?7?9!?u"?????^vi
??3C5???-??y?E???,7-??"????v???>?O?W???4????Q?Ho?l????K?????	yJ?@:????r???P+????ZY3+p]u????>v?w????@M?F#???/?C?B?"?pu-??@Wu0 =5<???e)R??^????=9????N??P?D?a?&3A?11u4V????q?0????3
tl?j4w&|
+?5;
W?'h??"k"??Qy?:???y?C?9_*?2???3?(c?M?y8?
+R??W????Z?????;?????? ?+????`??U??I//?e??E?0
+Zj?N?2???M/N?O????!F|?wL?6?N\g,??M??????!???jJ??r?????Zz?_??????}H;??&???z8#?h?#??T?Jw???(4Q??????&a?i]|??????J??Y?j???I??B???YYW$??4?~d??v?J+)!?Q.??53?C
+GB?9~?H?????e?	z?~5-???e"?[:????g??????M@?t??????|?0??????H?|??!? ??"????^??4????????zd?h???kL??
+"e7???3%?um?x??^6?D?f6??X?<??=??UEjc???e
+l?Z?
????G?m'???z!?-??z??y????Q?dm?,+??H??pn??Tt???)??g??0n????B]?????M?Nt?????\??;81f&??|y]?C?????~???<???)????;?s????3?d1$?f
????C?????3?Uad???#]?C????*??<&?K?????U9????i?_	??^?????????{?yo3??%?(c?uO??*?$K?9f?|?????;?/?
A?o??3??@`?|?2 at J???h?V?-??"??k?c`?????kp??	?=G?+???g?M&??????:???7?g???gg?'??5?h7i?
+??q?$?????4N??z??J?<?ue?/????#j?,=w???|?????4????zS?sQ???`Z\*pW?????????=????H!??G!??F?
+7~f%G???TM?(?:????v??
/?t?_???rv.5
+?1.@???6X???KxP?*?c??9?J<X???8????c_9??S??t{???d??95!^`?ql????t?fnh???go?F???um?'q???Bf?Hk?J?f(5s\?kB|?,?N?B?D??k???"?@=?<K?#?
+?|?O?v??
+?PxT????x?4?	???????Y%^D??&B????37,?7?4&???v{.??;??????=????G4x???U?7?0qK?S?????H04b?`S7?fb???DC?o???g?????D????o?G????O????M???
+Aj?m??1aRg{?u.??XL?pv???H'u?=*??%?????[?,?rw???O??/o<???,??<???r??.???????P??d?W0???q;?m? k?t!???????s??r??,???4?L?????"??>j????%???? ?????????"Z?.E??C<
+?qM?qQ'?v??~q??????4gA?IZ?n?D??s??u^??18_?x;?????vT??????!2H]g?{|???=??u??1.??i??W?~?T?a q????_$x_?,M?'??`?n?#?R?SN??$Sq|'??,?m??h?????????G?*??cw??????????A???Z4 :???x??w??????2?7???q??#?8V=e~~+)?O%?o9d"?#???Z????X7???w?+???c????`??nj_oDa?????M????????l%?Ul?|a?ci?4???s??y?E?@?
 ?n#??)5AD??hL.????*??Y?
+???p;?^?UH??A?+??????
??f?'???nv[-)*????????m??)_??v??`k??q?5?6?4e?~??s??|u?4?0??@??????{qs??_?}??!?}p????
+??&H??!N???K@???"?;?2?Q^??+O?w?V+b To!??]??_J??? _?}??IY?????{g?`hh???~???:?F???y??????????z?.?F??tPc??=@??3"qS?G
i?
7???'?$???H?????@@???p???????n2?2SR?2??P??*?????<EeQ?'???h????#?
+"??c?g?Y??>??????D??Q_c?[p(?????1?U??o?_?`??&l??|?#???;??	?}5?x
+t??LB????	?????P ?}p?`??+??w6??gE?1????O??5W??)??T#&??^tV??[?N6?k?
?U?k???b~?*?G?????????o5m{'p?Q?0?X???|??L02Qc@?'z?[:?????V\?
?o? x??#?rM!cQ??E?5?$zo1l~BJs?Ip8p7????????%????g?O?x???e{.*S???X6?????Mu~?XG??}??"cQ??!

+c????.? ?Z.c6??Z@:???<?F?_?????????)???z??@X???8=??UJ?&tn{#?a?-???s??,?q?[F?q?3??d#??-?x?<y?,?????q3????F?R??{?}?l??????????-\J??????7?:~?<7q??????????S?>?>@4U????????I??,??o?J?24?
H?x?<t?c??a???^*2?=_?fX?(??v??\x?:??? p!N?=??n??b}?????????N9??MF??=v??|?lr?
+'e??U6?;+????????????X?<+?j??d?m???]???G?PS???y!????s|[~X??]_N?0?z????LW?5
+_??j'?f)?q???o?t???
+????D????I2??)i?uG?<,???m???#)??5p5p?AoC?^?Mr8p??F9*?5C\???J??m?"??1y@?T?#=??P??3?G`??Eh?6??G=??ZL=kX???[??????tg?b???R?????=??cw.?(?^?HuO?G??{?0?j??|???GqD??3???&!?2?????C??`???+	??gX??[~??-????s??"???m?B5e=???>o G?
???????V?x%??%?Kt%|E'?o???+??+?y????6 ??jg?t7??d???*]?_??Zf??????b?V????#8*1$?(????????j??????Q???3???)?$???hl?$a=?X????t??qWw?qG?N??q?W???B?,????"~???L'??UW&?`X at 4N6?+'? 
G??3??6????~????.>??X??|?????	??I??q??????C???I?C??:??xy*|~??^?
+??l*???e??4????~?????]UD????	??{?~?>0?? K?[????a0???-?zdLx??SI?)|`oq??/8X???????D?*?KwB?@?u??t?m$?m2c????.?|Yj?%?qHp??K?OJ?7k?(?????(???BoU5?9?X4w??p??W????q?CSu???w??`? ?ol?X+H!??v:ms??N)	z?O])??d?oZ>?P+4BuD;x`??k1??Z?}???6r?]????ck???!?Ca?;?K?0??????s????7^??????&_?????%??@)%@?'
+`?	?r??"/???n]Ik:?T"??g??V?d\Xa?b;f?????ba??k???L?????.?>?x?`+????;???[?????#Gx?\???????1?e;????{?J??d5Vk
??{}?????
+???'v?=$??0W?X??VW?h??????"??=??<?/?}???????7;??X????<?>??bp??:??*_??%nO???<?i?pm??S2C:`???)_4s??h??T?@??????9?>???<?\f`?w??Xv@??
??? R&h?Hcd?/#?????p????vb??3???{?r??A?M?d?.???I?^?`?pc<?????
+??-w<?!aD*????x??????
+??\?>??tt?Mzg<?)??W?????&??[	?????~7u?)???x??+??b?B??!)g?2\u@?#??yI??l5???????#?????Hw??s???-{??s ??	uP\??k?>?o?]??\????98~?-\??Y
+?<????TG?(???CF??di?ur'J????o???.Wy.??I#?0??H?%???4?Riz?(oJ?5?O?dF??4??W ???
#??P??2?t??6?/??/?&?f?z?9?l-?6X?)?????U?^?3????2?0[/?
+130?Q????
s{(o?YM??F???hZ??,?1?
??L?+?=??"3?.?nG??????2Y>?@??N?????????M??D8?q????HU???^??e?c?pc`l??|??er???????I???P_KB(F????????_1???#??????c??{???38M?:?V4>?????}?p???
+N5%???}?o????X?Gh???F8-?????__?L????y??aq???|/2?????XG`??:|J?p?????????<??????`?p??0?z???R`(?????
+??????F?rs?????P?yN????U5>sQ??U??$??\?????6i2L?X???????????
+?GZ?(??????|?????yV?Zc?CU??[ Zq??Q?HY?GG+?M??:t?Ci???????-???kK??#D-?"?o??n????X0?'J??.??m?fc9???,?u?[m?r?OS??A>?NnY????R???Q??EZ[\]U??`?)X]????<'B?;?eS?9o?|u?3g???X@??vPZ?X+????a??Wl?
+<?d??]Z?????t37??WP?0G???%?S]?vrubZetG?cZ???|?S^;???v??@?|?e????a?}
+???S????e
+kS^?y?s????K|?x?qw??????.xFU???<?z??
+-?????e?(ie???xt???r?k???&??)?_???aR??.l?k??:<?????Lm??A?0)???u????x^?'b?r,???????=<Z7???????o]????wP?????@{??Yy???????/???wv????Co?]???;ym&o????K???3?J
+?%??{??Ct?N?,.?z?,!?J4?????g_??%(Z?o?1K??/z?E??KY????_?Y?]?<??4?bQ??!???[*_M?????T
+???m?????P^??vVPY????i?v???g?J|6?tv??T`?`?-a???????IX
+???h??C/??h5??????%??0F? ???????p?p???Z??kE?e?15[?q??
+??&????????b?lM?8??X???0??I? ??*??
+???}?G??Z?oNFS??[?6i?????Iu??%??.????4K?x3???j?~?$Fx????%?\/	Q??0{??1?Y??R???4??-?LN??Mu??????>??C?B???\p>7??N}Tt??n?WN?A?????$????C?o??????I>?N???????,??????#J??p?w?????;?=?????<??????Q??t????55?"
+Oc???Q???8?,9?C#J?L???@??8?8????DQTK????t!??0"d/Gt.???v?w?]?N
+[:???#?t0??m??T??6?b%?n?u??n?????8 h?
+s"G,d?<???R?C?????"S?a??2??I_???"???_??\??T7o-???*$tZ'>???q??#?*????q<??$?????]???`????????j
+?@EyrPI??So???kR
?c	??{:z;57????}G<?'}2?|?L???????>2b?????<pI??u?	9??????V????-?????jiF??mp
+?F?????->??
+??>5?????
?????%V9hmJ???x
+???U???
+????!H?zF???u??r??????@???t|??
+??0?????	Y?h?f(q????@?b??	????<???H??k8p?]???B?&?>q?????V??@R??+??????X???r????/C?e???X?s??s??????_?7?&)8??1	?4&??W???X??,Qq???B? I???mz7???T??G?E?)????\??@~?wb??p???#?
+???3?}q?$@?
;?Io???V??4???J\???$?N????x???d6??!Vm???????????G?x??C??}?Ze???&?B?u:!??"??
???*??p1!???'s?Ja??&??I?:??B?#?7bjV?
???-?'???R???>}_?J??v?&????dUt?/.??V?N?=?1M}<F?tCVy???v??A$?~???_??~?VO?4?#????c?:?n?3?)!???5w???7?l???H??????U?GpK1?'o???B?'???n?????:?c?)?}??Y?(????`n??TI????{????????!g*??M?????*??>9[???r?DX?K?+{??s49??2W?c??????^???;???.y??c??N2~?>??P???=NN	!U??E??tPw??????9?????WjH?<|????a????????
+b????@?=???
+Z=V??X???M???.????4??C? ?Rk?8
+E???,|O???O??|???&6geAR??SiB>2s??Z??"D??^?$?????}??????2?q?????2???_???I?l	??D?-,S?$????Cg??
+1??Vo?????P$??}H??];Y?`v???M?*#r5n?2}r??^??.(??????V?(Y?PF(????)f7?|??ab?<tk??9=?>RgD+????g???a?k??x?D???X?@	????@?z)??|??b??I<?:p1PIh
????:u"\+1?E8??(?H#???\?????? ?'??e??? ?
+??xs?GTG@?????W???r?	[_1?fG????6????K?????/R?5c??<r?3?#????C)?h??rE???LS*?0l?Kb2?????S??P`?ss?n?P?b?P?Q?l<)k~,?????k?2?????? ??U?
+}|*?ZL??=W??P??Ap;?,??0^???a)U?XU????7W?%7?T????JuGE?T"?@??;??5?V at h????\?S?~???6
?.?M??Ng??-N?9?/??$??F?????U???4???clk??????G?+[|`?x??2J?????????=?u,]?!?e?cO????b??h????)V"??#?C<???P?4?pc?Y??????????bm??b???
o?4??|?b??2L'Y???V=b???p??Q??&??	
+wr?|?U?#?R????:???]q?$ )??dp?Nm2Af?H??4-m?U???q?f
+-R?6??????WZe?/?
+???L?:??h??o??W
+????(???|d_Z?QRv??
???U????c??????\????????VI??G??-T??j??~??T>??l<???m??????+0????8:??C????y???5?V???C?:38S?yC???1+????)u?$???u3????X@ P?"????q?m???p?????Ci??l??d??cQ?1?=??????n/???W??%????;!!??N???????q?;??~,????o:?)2]???"?[?[?????Y????i3)jX??m}??Z$??
??Jh??\?K1?A????/_?'? B3N#m??h??u??MY???]????}>?=??3????UP.?5???4v??J?&??7"6????\????????
+???J??? :?mL??????????`Oi??????????:??1?=??c[?h]??yK?????'{?r=?^q???	J??#/?!??95??=,??p[v?1c???/??\j?E*???S???	?nByiss?
+x?(???T?i ?.??ya!/??k???O,?8? ???g[??fV)???????.(?????>??????+b?????
z??&/???(`4??+??	?\?c??Z???bi)>?%???L?????c???2?#?????u?A?&jv?????0s?8?im??S?M?[FP1?
+???#??	[%N3+?????2?u??+?m???{??;?N???k
????|?|?F?=?b??????f{??']Y??Y??}UA\Bxe???o?X?,???JoT??yan:j???s?k??z?#?5$=U??r.!?N???'??`??l
:?*??E???d?z"?x??N????l?k?E)0??`*?)???I]3?????Z?;?i?2?F#
+???x<??)d?P??????}$????6xD????-~m??????][? G??WX??<??%?O?G8?	?$e?
? ?i??f?		x??
+??0???????c??P?gHz????h:?Q?}?*???x?????$MS??<Bk?5|??)?)?6?T?????`????)15?.?)?3??Ls?z?n??D??_?f??dl??I??(	?h?~?x#Bh]?n
+?4?w?3Sou??)????^???R??+???H?z???nt??a1E%U?r?????K? \s??W?_?Bi?Gh?u_?-??P???k???zk???l?
+??)?i???U??8???\?"@????????1?ts?j?j??3?????
+D??:?O??h<u???owP?Z?|??ts???R??????}?i%??"?*?7?0xhQ!???<?U?????????8?????S???????b)?m??????????W???p?????"??
+-????Z??Zu???b?u?%?????/]??"????????V???ux?????B???0??k?????f]??@?;?5'?m6??PRPX6al???~???7g?D%!8?j?m????e7w
+?GA?(
+;???8,???s=?????5w3?b?&h92b??\?R??v-?7_??ft,?+/?????!%?]????K?\?m??????9??6
Y!5???G?P?;in???????f??G????XO%?i_??B??3)???h???W??2y?k?N?.,o???rn????"?nS?H?G@:_/???j??4?'?%%&??	??U?eH??Ij?Y?F????FZ??:?j??bO???<nwm?M?f;a=e~??DL??(?G????=O??6?q?%??+?5???\?
+Xi37????:???5?kC?B]??????CC??lOl?Hk??hQ???????I<H???|????
??3???{7?	?zgb??-??,?}??$|????n??3}?o?6???g}????/?vd???vc??'??"<??I?o??F??9?:??T?2=??w8??a?k?I???
+????
+?[?^??^?:'`6D?eA?=W?j????y???????	,&?D+?S??
+M&??i???n{?????6?1?H???u??????a??a?to?{-???3?B????'?g??7:,??|??}m?	?
?&?hJX????????X?c??P8??l,.
+???-l+g???_??-:'?????l4c??f5??5 ???{?z2?f?J?4-??X??SV??????	?fA?8T??X?(?????????????@?rS3??)j??0
+??,?<?$T???^????I?4??????
+[??p????w?-?????i?=?????~??T?8??f?????"h?)?D`)??H?5???b??J
+:??q??40P ?~?&????
+??T%?Y?wO}????J[??,t?N?'???)G|6??????6????a??bl3W?~%?"h?G???;???
+?o$?b??'?b???9v??R??????~??Q??^?G?Ca?td???t+?e?????*?x<??]k.uM??{????????>???????(5:*?d???*F?~H!????K?csT??b?k???????19??f?`?n?J?j???L7?Z???(]?t|??+|;oQ?q???_?? ????}W?l??????)]H???K?v??"?Yx_?nI???=???4????q>D?9Wa??5???3?J\?G?"?p??????=	?_????3,1]???
+?O+?;?/6/???&?Yt8????W???_1?Wh?(U????QdV?'c?.?x ??%b&
+Tu????P?V???6?d]??c?/r???4??Y??
+?????c:????????-??4?OfV???2?p8???t7??/????e???+?????7?.GP(?$?z?+?R
+??f)???????????T??????
+?HDi%???799ck?%?
+?>g?L??
+?????????%?
`?-?>?????%A?)`Z?R?Z????9)??v??~&????k8?`3?!????g?L???9X???d?2?^m-??;??JR???\?????3"+|??????n?.??]
?NB???"?
+?P????x??;cg???,??@??eSTH[?q????????vG??f?/?????8&??????c?.?`???"??????????xU{????(U??w?!`??S???I??qI???]+*;??.?:??4r?!????9?gV?t?T?W?M?????l??!????kb??r%:?DltQ2L?l?WT???PI-?H6?zgX??.??2?K?a???'?=??????}?-#????+n????!???[?\????RP*?m?????????'w
+??xh?4	?W?tX4??m
+B????n????m??eZO~??L?(%?q???O??S/?M?77 V?5?<o??????0L??G?i"U?`???{??@??5=?????Fj??$J???z?*g\??f4+P?]T??:?B??U?4M?'??:??H??g?? ???r?G'b?m???E^??/?g\H?{????Q???L-4??????=?
/Z*p?s?7?}?f?N???y?tX??cA|??~??Y?qe?!^???'????e?Za?L??????r?n 74?a*'}?l6);O?J@N?	Y9???????R ?I?Nk~|T??
+4M?\@?0 at M??F????T(????5??^???m??5?Fh/?m?>?rS??????@U/1?W?
+???]L??3|3?o??V????.????:Paq?6???5}?vV?}~??2? ??w????i
??H???SR???GQ\?????q=?_)?7T??*?;Yg??
+J??r??2??D?O&???[?/,??????4??w?w?I??-??vj1?? ?N?!?E4P???S5??????an??el???v????M??
Y??l?|?K?T?z;????o?[g?F??|>V??????A?A?c?>???Iw??vF???yI??yn8m????!7??=V?6VA???w????OuY9cs???0.}?N?/?Zf
+??y????I??Z??`?lIM??|?&?Gc
+??KZ???1?AM??[=??????	~?bc????4?N???*/??-??Ctdod??Q?c?Y?_?E??
+_&???a???z??d?6??a5?m0?S`?f??R?O??xM?L8?r???J????+?y????EH?Lv??[???*/??S?{??H-?:\?h?$>3j?G??B"`s??M???w??
s}???Q???P??`???mU:???Ux?
+Z ?D??0???W3?E??.?dUH1????lR?????#UXK?????Tb??8???\???^?j?"??*K????q?'?c????!X??zG	????;???=??g???#?^??2_?l??,^?pq??c???o?%?]V?<???d???N??1???f????kr1??my??NtE???KE"??dv6D?h:???b??"???to??pyV??=t?tP?/???????:e???m?Z
+\???%??^Z?:y???n)?(?W????YNM*_??]?yXXK?+~>?????K??p?qg|\c
+?????\E??fQ?B;
+_
???@@?N???)??V??}&`!???
?`_?g?[|?aB?K????q??l???]???'?z???(0l,7c??]^?9?H??Kj??.+?Y????_??
?6J?_??I?X? ??X?oc4hi-"}n?}?1????Sv??(???UY????>?X??w!??m/V?K?km?_???>???F???????n|3?hh?P?y?8?9?<??'ZGo)?????????&%?U4?0?$??????I?z(??KZYxY??M&9n^??f-?n?V????	??F7?l???m?Nue????+??@?zA*??
#? B4u?{
+=3mMM?
?x??pVU???i?????r!b4??t??7~?V???jJ\zi???^??CK??U#R0I?0??\??9?
GF????1?????rL????pL7ut?^}??A?X,?t???r???Bt??k?6_????e??1S'? ??vG?
+j??M??????r?X51?
+??^C
+???:?wP?1??w)?3E?E??O?k$T=?I?.?[U?W?D?'????Q|???a???e?-C?o5?KP'zMa??u???a?1F??7??????????1$???$un?IxG?l??h??????????d??? ??]$\?'_?j+
+?????6
+?Gi??3c\??K
+l??j/683?????
+??vT??s??D?"vF[?s??_R~?c,O??%????????Q?????}W??=???^f????????`?z?B????7?Rc?	???xC?L??)x?,X?5?9?S?&??????B$?O[K}{??>~i????@?Q??[????????TM>3k??Q*?z??aoT?]????p>????????<^?&w?Y,?????a?#U???m$??5?>Z?|V,{8?V??u?"A9??h????N???L?e??~<???!XD]?R?.8}^?????f??4A<????KE???i??
+??+\^????k??{?????w`?????8????-_?????T7??"
???dJ???'????x?e1???g>w??`??f?w???7,???u????(!?<1?S?`???V???Ge????MZbi???????	3cd??h|??`?b???????u?????G???3???}9?F????PG???r?
+?ptNo??d1W???6g+`?X??u???a?t?0T?-xbe???k%????
???`\_c?U???in?z????z?73?k_.?4???'h???@?Ec??
[????????0?????a?ujO?s??{????Uh??f#??G/?Su??f?%/i??oD???0????,?????{?(G?_?????v???ut??!????ET???&???o?????????c?????????4????z??p???????????????8??oVq?
+g???-Zn?K?8d??g??
+`?????m???
?}??t1|?>0
+?
YZ
\ No newline at end of file

Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd	2015-07-02 01:18:46 UTC (rev 1242)
+++ pkg/pomp/inst/NEWS.Rd	2015-07-02 12:29:27 UTC (rev 1243)
@@ -1,5 +1,10 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.69-2}{
+  \itemize{
+    \item Measles data from England and Wales, kindly provided by Ben Bolker, are now included as \code{ewmeas} and \code{ewcitmeas}.
+  }
+}
 \section{Changes in \pkg{pomp} version 0.68-2}{
   \itemize{
     \item When using \code{Csnippet}s, by default, the C codes and shared-object files are stored in the R session's temporary directory.

Modified: pkg/pomp/man/measles.Rd
===================================================================
--- pkg/pomp/man/measles.Rd	2015-07-02 01:18:46 UTC (rev 1242)
+++ pkg/pomp/man/measles.Rd	2015-07-02 12:29:27 UTC (rev 1243)
@@ -1,19 +1,23 @@
 \name{Childhood disease incidence data}
 \alias{LondonYorke}
 \alias{ewmeas}
+\alias{ewcitmeas}
 \docType{data}
 \title{Historical childhood disease incidence data}
 \description{
-  \code{LondonYorke} is a data-frame containing the monthly number of reported cases of chickenpox, measles, and mumps from two American cities (Baltimore and New York) in the mid-20th century (1928--1972).
+  \code{LondonYorke} is a data frame containing the monthly number of reported cases of chickenpox, measles, and mumps from two American cities (Baltimore and New York) in the mid-20th century (1928--1972).
 
-  \code{ewmeas} is a data-frame containing weekly reported cases of measles in England and Wales 1948--1966.
+  \code{ewmeas} and \code{ewcitmeas} are data frames containing weekly reported cases of measles in England and Wales.
+  \code{ewmeas} records the total measles reports for the whole country, 1948--1966.
+  One questionable data point has been replaced with an NA.
+  \code{ewcitmeas} records the incidence in seven English cities 1948--1987.
   These data were kindly provided by Ben Bolker, who writes:
   \dQuote{Most of these data have been manually entered from published records by various people, and are prone to errors at several levels. All data are provided as is; use at your own risk.}
-  One questionable data point has been replaced with an NA.
 }
 \usage{
 LondonYorke
 ewmeas
+ewcitmeas
 }
 \examples{
 plot(cases~time,data=LondonYorke,subset=disease=="measles",type='n',main="measles",bty='l')
@@ -38,6 +42,8 @@
     )
 
 plot(reports~time,data=ewmeas,type='l')
+
+plot(reports~date,data=ewcitmeas,subset=city=="Liverpool",type='l')
 }
 \references{
   W. P. London and J. A. Yorke,

Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html	2015-07-02 01:18:46 UTC (rev 1242)
+++ www/content/NEWS.html	2015-07-02 12:29:27 UTC (rev 1243)
@@ -7,6 +7,16 @@
 
 <h2>News for package &lsquo;pomp&rsquo;</h2>
 
+<h3>Changes in <span class="pkg">pomp</span> version 0.69-2</h3>
+
+
+<ul>
+<li><p> Measles data from England and Wales, kindly provided by Ben Bolker, are now included as <code>ewmeas</code> and <code>ewcitmeas</code>.
+</p>
+</li></ul>
+
+
+
 <h3>Changes in <span class="pkg">pomp</span> version 0.68-2</h3>
 
 

Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf	2015-07-02 01:18:46 UTC (rev 1242)
+++ www/vignettes/pomp.pdf	2015-07-02 12:29:27 UTC (rev 1243)
@@ -1,43 +1,58 @@
 %PDF-1.5
 %????
 1 0 obj
-<< /Type /ObjStm /Length 3961 /Filter /FlateDecode /N 97 /First 822 >>
+<< /Type /ObjStm /Length 4552 /Filter /FlateDecode /N 97 /First 820 >>
 stream
-x??\ks???_?o?????
-t:???:q????I:?M?%?W!W??_?s? ??Z&%?I;??{qq?b???f?Y?4??0?B?eBy?Z??0h
-L???5A??`??"???x?Im4a??
-?0??Y&?D???????R??0e1????)???d?t?R?]???n??u
-??`0???h??????Z?x??%??9gQ??0???F]3?08?
??? ?Y9&
????*?M????C(T5??
-???t???|`BD4?.,?!?y??"??
e)p????t????PH"$R?I5?,???X*?(??? l?J?/n
-?0?J{HE???**??e? gkH?P??????N?d?
-???`??&N??:(
-B?#301T??8?l1?#?r'??
<???CPKM?>=(????????F??l,$???x
-?M??<([
?dt??<?U=????Hh
-P????P;?F
	?l????@O??
-?dd????
?X????????????S???????t2kp?X1:EE????.????=e_I<?7?n???F]??:???4$M?!?????????9??xtq??4&????'?{???=?7x??O?7g??[???????6??j?MA??l?????Yr?^?:=<9Y??k?\L????}??N?Z??L????[e???I???|_?k??r?,a	?I??Z?jz??"^UnV??4??????B%?^?KcJ?o;??y.?E??R?U??R??YT??0W3??R?k?g9<?k~,?GY??Ld?????\?YlYQ??.,???.3????V??:Q??	m?u)?by??????2=??!
-g?dl?u????????4???6????Rr?l??f??#UE??C1?b;?4?b?ri???d??,??ev?X?,?U??T-??PV??R??PV?r??Z??P?K)?u??e](?BY??P???)??(R}???f!B???6'????#?J?i
-t@??I?s?-?v?,???? ]??c?????	???!?SUeh????M????Ch??????_????C8?/:?f???]\?c5?=jD5?????O?QW?HXZ??f??)??????f?q;C?E{~q?b4~V?l?Y?[?_??Y???P?b?RLQ?)J1E)?(e??Vi?J;V?i??kig??=cYh?-co??;S????S+?I
-???P??????????n??l?q???s?n?y_?)?g*?D?.???@??????????+?????}???d?l$?u?r4:?R?o:?w)#??e???`????????6&u?%:?dY?m^wbi8???Q?????<???(3?"G?????????7???p7ZI? ?h?} 	?
?{??K???~T???)?M??:????rN?V5?????6?^??7??B?N?|??? ?M???tc?<U????&M?hw????q????B{Q?>z??|?E.?Lf???4?D+E{??a????:fp?)?v~>?2???S??z???eSz?F,??M?????????????q{??
-O?????l??Lf?,?@???g?9??c??q????*?p<v??V?&>Da'??fr???8(?v?????~???.M?'c?c???
-E?VTfc??t-eK[\p\??<u??f??!??4???HG?'?@g
-"???/i0???????|?^[d"O??^Z?b???i_???frzFUh??HV?????????????o?#??????~?_?W?{????#???????3?=????H?7???9??M??????G?S~??~?8kf|?????)?6???3??v??~A?4m?u?4??.???=???_.??????Z?|??P]L>??wg?????-?????#????????wb?%pW??9???]4?????"???
k?	????p2m?Ao?y6:o???G?h:???"??
!??>?!?(?5??i???.=O??diDu[?????'??6F>nN/??\??????^'F????_???/???,????)?&g????G}e\r???G.??K???JLs)~G??K?????????B,?
-&$\?<??$??|???{????{\???q??/?M??W#?Lz?(D??Ds??B?+??;?8#?s`???P??#?dt_?f'|?
V????????????t??s99?&?????h???z????/???(M.??^{3??'?????9|"??q?YP??`???tYX?*??AP?E??i?
?|?f???$?u???!hZ??ys?!??>,??5????
~%?^???+?	?Y??b??????O??????z%?Z???????;{??3???"?{
-??]aj?`e?v???n???????\?????????lI?c
-???h????Do6Qh1?L?????<?????A??s?? ??????ZT?I?YFG?f??o??????R?.???:??K{aH5kc?>????5,?S[|
-????M r?M}??|
-O???'???? ?`b)Je?mB?e???2????????Va???(,?BU??a??$?;e??????I????%OFV^???i?????????t4??E''z??7?w;??????@?4???O-W4?o(t\?20F?9X\?Ia?f?%??-d??;Dv?zJ??8?)L?t(?K????`????>??? ????@?W??&???p%l???w
-W??V????G?_??yx9?m%j0????b???? ??B?{0~W"+???C_?????qO1?2t?%?
-????	 <?????O??J5????OE???u????g?????U??\\??r?+p???????f;_$?T	???k????'?<}?b?\???8?????!?\?0U???????s?????%nJ?Z????7rn#??7??C?+7?R?:??^?'????l?,?w?k???1@??K???W?b??>?,i?r???l??O?(?+?YnX????? kUkiw??3???v??????|?'???g~???|???J??>?????O>aR???s"?????????y?C???cB\?\????%?k@??????TR??????;*????R???QaUWt WYgf????
??l/????f?,???q?+DL?`	?e??`?!???\i)+'?&WJ?JC?????X	??v}????Cr5p???I?O6??)`kYPt???<?????<?m?(?????<Ao??u?E?he*
-??????`\?
I
Dk???jJREXq9`?mp???AFs???????t??RjE???M?J?y ?????N?
-+?pP?-????4?;????+9?.f?5?dd-eC???
-D???yHY?m?,?a!?M???E??2B???:h????)??#??$????>?X?-?????Jx-8TP=}Q?`??aP??C
-Y?Pi at rBCIG?+??Ic??aW?="?$G??????
-@%:z?????:?????;???O?S??????Ds??e?????w????7??Q?0Xx?:???j!{??8??
-g?i?8`????????0v??????2v????-??d???	J ?%W.`m
-???f?i?Zq%k?+?~\?^?p???{???M:S?c???0?M???9??*??H\ B?o??L?O}?S??Z?B-?n!q?8l??{??????
? L?
-??p?r??G?
-?WC????&??sJ????$??`?~<}??\?7???(4SrO1???%?;?I???6Up)??XP?C?1)?pN??vo??R?????!yR&???O??3SR??vL???%?E???L!\??????-bq#'??$??6x?g?B,?a??
$?=
-?ke???????v?2r????$??????????f???????U??	~qf?C?????`
?dtVzu???J????/18B???[??????O,?Bendstream
+x??\ks?6??~?m\)???J?m???/Er??V??X????f?????_O?????DIc??-Y"A?????
ZU!cU?]x?Sp?ua??/\??????
+??{#
+????4t???j4)?
+m
+a=??Bx???
+)???J?B?C?x!?#.
+????????h?u??"????^??h?v?????qEYV????J?%Ea?T?????3U8tX???3S8?Q?/?	Wx?q????9?[	4Tk%?/_iII???r???<?P(???0?\??+z?9???enQA?2??e?+UhP??J7
+c???iC?j?G??4??I?? /
+??{?	?
+??8???-??0F?
+?6$"Nu4?b5???B????!??
+3???aAY{tjA?`??l?0lA??
+?
+?FcP?
+F??ec0???
+??q9?4???e[A??
+?([^Y??n?P?xH???DH????([? ??<8O7^?(??eAx??I7]xE?
+]?4r?IHU??A??J4n??????`????x??@I`A{s??M??
+????ST,????.???-N?~$?,??z???M?u???_E?
??????KU??A??X?L.?????i=??W???Z?/??G5?>?Y<;[??????b]?????v???????b?Z????????|M3?^L?W???Pi,:??q?.???c?V<^e.?xUU*??qZ"
+(_??T??TK?k?Q?fZ?r?.x?$?-/?
+W?^?T?,???$??????tM?m"?xU?if)
+<MN*?4?x?&??cW2q*?2?(Uj?cg2?$m?<??t?7??+	?Jd|dY??>VSiJ???T???????*??L???IB?>?%6????^?J?????.???_??uI-|???X??lU????>??k?VY????i?M??,????+?oE?:)?R???"S????e???r???1?)?LYf?2S??????R????Ucd????U??2e?)+?g??b????DhP?`w<?<^|????Z`?o4?K??0wP???#??d??????5A?'?x
+?T?	$????z
+?l?)$ZY???????H?&?t?\??8?r?"???R??zET???????FUJZ??(}1????????w2?G?<??????????w????gi`i@:
+!#Z??P6Op?B?Y(:Eg??,?d??]I??-?q'?l;cLn3?????
+cy?[??[1??OR???????umv?}??QmT??(Z9???
+?i???[}O0;b???????(;??v7??6???a??)?#??F??eD?P:??w??n?i??????l?5mNQ??m?v???6??;?O?xX?_?????(v???;[?/??-?????byZ?z?\??>Z?(>?/?????8? ?P@\H?TF?f)
??V???%bLJC?~$j^~Z.^N??7??{2?C??w?B?????L??Wp????!??+L{??X//?\{?[n2Y??C????~????????`q?z?_>?1?B??????y	'????dY??/\??"?Mnvp?B|3???????O??g??
+???dp????Ke??3?<]???)j??j1cl??{?0???W???s??????@??i???pe??@e???k???????]????6`H??&???o???????e7.~???gT??H?????G?1{?????){?~b??K???f?????????g?????l1????	;f5Y??h69g'?d??kvk`?????yqV???????flV?V?????-?5?`dF??d????E??.???????o?]|?d+?????j?????lY?l???d?????'?7?w?\<qF?????`Og?SJ%}??!????c????-?~:?????-?????????'?????)?
+?1]?`c?????u}???p?Z???4?!?H?i??????/??uz>?O/???????Yw???x{??Ms?MA??),)?M??m?1??n???"xm?;??Ix?7??l?,????6????\??6??{??y?1!?B?9?'r?K&??3_?oq?????3?????m%Bmb;????V?-??s}-z???H????|`?$?s??j2?f?5`????l?:c????????}4?.?/f??r@??????????(?2.?R??^????i>2??O41m??W??D?:?4kn6??Bl=j???bV'?;??o?.N?6?]??0????:???
+??"???????
+?"?]Ac??????>?=????_??}+?F??Z7?'U?Z????
?[?2??????C??{1??9+???????U??x??:???^,???s?$???F?z4jcQF??]ZM?G????y?_Og?5n?<W?D???lyEW?O??_??????6]?.W?u"$?v?n?!?|????[??DoaI?)????$?$C??E???????$<?xGiN???y?J>X[?-??B?(??JS?<?Yl?C?
+Uj?gNc??UW?$?3??Zb???D?1????\???n??R%????(i?O
+J?{????O??????|???S?s??gU???o??^??K7?5?3?vnSr6??hn??o_??????????-?%???bH??W6?cxx
#?ZoGvW?5j?????????.?.?R????wrp~~???????????A?????????n???t?<76iC??G
?-?Xl?~?L?8??6??	:??C??L\W&W???b?g1TW?????????????p???:??9?A3F?Uu3?????+????Jp~[`???s}?.???A/D?U?D?1?????h??
+O???6\5?S??kT???o????g(????b?vJ?M???v(??{????/????????????N?
+ ??Z?
+??6~8??3???S??l?W0?????W?/??PtxU??D-:?J??-?(???t?$)IJ?q?t?$%II?1?t?$!???T:`???(??
?t?!???!?U????b?tO?w???????[:??DI?%?'??+?wf???????8"???J.l!?+]U???M;?,?y??C;??t??kZO>8w%?*4?????9?#?rC??%??p%?(??\U*???^)(M?y)
????N??x?J???5L??t??*??sj?<?>OB?????????YfFaB FihW???q%??&t???"S?R???c?W???v??C?]????I??@?VGK?;^Z???>
?6W0x?e?+?mh???z?v?%
???~?^?X\?&XQ??????$
+o??09$J#=?
+?e??a
+??'?%???n?????E
+y? ?HL2}3 !g1L???|S????E??/MLI?(,????1????(??"&?[????K?[&?_???p???W??c%m??9?mbKr`;???m???6;???p?I&????????7??HC_Tm?????~?]?a???\????p?????Z??<????;??V??9SR??????8?<???tM?? ?
+?Mg????b??a?~`GTo?A?b???C>=?v<gg???$?wi???????b5E????.?;?qMZ?l???)Z7i??%b4??????????m8]N?o?d???VL????0??<?vl?????????m"?{??D?$??zc?-??????3"?i:?<??[nm??n??????o\????h??<K2?f?S?????n???s?UGn????mL`/??3?????:??QB???q8????????_????L???`e?z'??t???y?Wo???????i_D?=???0c?K\[k?o~;Z.??P?^?l4?F+??????I?$???x???@9??=??q???ZKh[?:Zf?h?z???a?`???V??.?z??ww???=W9.???
+???X_?M}???
+,??WpE`f??@@R?????D
+?+??CM??Z??F?^c??Kj\????L?cwY???"?/=<???W???	??V????????2oWs?
+???)??h?????.??%}[??F??Cr??_%L)v????!pk???'????Cf?JE?A^??)?p?????c????-??????_F{/??I'?n?J,6?r>?_??6???bt<?u?
+z?8?G>?
+?
+???V?R|Q?=?l??7???? ???
+???ok9;?,?(-?!?T???UI??kJ?V??d?6?????"????R??Pr?S?~???%?K|?n?!N??=zf
+?GI????[)?h=?:Tw????)X?DWXKA??
???i?F?^?^???lI?	A??Q%?????R??TX;??? mEU???`?T?v??.????????@[Y????U?h?C?C??%}?%)??Y?J?_rM??7=9?O?f??BX?????G??????.ty?;"'
+v2??l????????9??s??A?s???s??O???,??K?~???dG??y?"?`iS/&_?&?J??1?J	?$k4???{%72?b??PZ%N*I.%m?Y???b\endstream
 endobj
 99 0 obj
 << /Subtype /XML /Type /Metadata /Length 1340 >>
@@ -46,12 +61,12 @@
 <?adobe-xap-filters esc="CRLF"?>
 <x:xmpmeta xmlns:x='adobe:ns:meta/' x:xmptk='XMP toolkit 2.9.1-13, framework 1.6'>
 <rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:iX='http://ns.adobe.com/iX/1.0/'>
-<rdf:Description rdf:about='uuid:64564ed9-5350-11f0-0000-fdb422cbc960' xmlns:pdf='http://ns.adobe.com/pdf/1.3/' pdf:Producer='GPL Ghostscript 9.05'/>
-<rdf:Description rdf:about='uuid:64564ed9-5350-11f0-0000-fdb422cbc960' xmlns:xmp='http://ns.adobe.com/xap/1.0/'><xmp:ModifyDate>2015-06-25T08:15:18-04:00</xmp:ModifyDate>
-<xmp:CreateDate>2015-06-25T08:15:18-04:00</xmp:CreateDate>
+<rdf:Description rdf:about='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e' xmlns:pdf='http://ns.adobe.com/pdf/1.3/' pdf:Producer='GPL Ghostscript 9.05'/>
+<rdf:Description rdf:about='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e' xmlns:xmp='http://ns.adobe.com/xap/1.0/'><xmp:ModifyDate>2015-06-26T08:28:16-04:00</xmp:ModifyDate>
+<xmp:CreateDate>2015-06-26T08:28:16-04:00</xmp:CreateDate>
 <xmp:CreatorTool>Raph Levien</xmp:CreatorTool></rdf:Description>
-<rdf:Description rdf:about='uuid:64564ed9-5350-11f0-0000-fdb422cbc960' xmlns:xapMM='http://ns.adobe.com/xap/1.0/mm/' xapMM:DocumentID='uuid:64564ed9-5350-11f0-0000-fdb422cbc960'/>
-<rdf:Description rdf:about='uuid:64564ed9-5350-11f0-0000-fdb422cbc960' xmlns:dc='http://purl.org/dc/elements/1.1/' dc:format='application/pdf'><dc:title><rdf:Alt><rdf:li xml:lang='x-default'>Inconsolata</rdf:li></rdf:Alt></dc:title></rdf:Description>
+<rdf:Description rdf:about='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e' xmlns:xapMM='http://ns.adobe.com/xap/1.0/mm/' xapMM:DocumentID='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e'/>
+<rdf:Description rdf:about='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e' xmlns:dc='http://purl.org/dc/elements/1.1/' dc:format='application/pdf'><dc:title><rdf:Alt><rdf:li xml:lang='x-default'>Inconsolata</rdf:li></rdf:Alt></dc:title></rdf:Description>
 </rdf:RDF>
 </x:xmpmeta>
                                                                         
@@ -59,297 +74,293 @@
 <?xpacket end='w'?>endstream
 endobj
 100 0 obj
-<< /Type /ObjStm /Length 3028 /Filter /FlateDecode /N 97 /First 897 >>
+<< /Type /ObjStm /Length 2279 /Filter /FlateDecode /N 97 /First 876 >>
 stream
-x??[ko?F???b???b?y?E?$N? ?vZ'[?#3?Y?J?6?_????$?M?^2??px??s???;VR1???L???a?{?-s???X0x&=KJ?Lu<??L??P??z4???tE??CE?z	o*e????eZ???c?DTT?Do???(D?=p(????d:
-?Pp????H`Sx??G??B?1c??=
-??f?7??KT91?n$???2
-|Y?3VF`6?Ym?`???o?P@?
-w???V`??1e"?7????oY???c?2I3d(?C?c?O???? !?H??B?s??!E??X?$L?????)!F???Q??
-r?bS???-??,??V`IB~?E????K??-&?+?P ?t???/y???,e??????t?=?D?L#?R? O1?(A4??=???$???Er?J?"XbDQ	]P????a?Yz?H%?2? ;EJQ?Qeni"
-1*??H??D?H<?$)?%??5r???? ?k???D#??Hf???v????b!}??)zK"`&a??'O?#?ID(???w?1?h2?V?k&?d???????oL<?N?r?ZD?7???bT<?~????? A??b???~Y?????|P.}?????????l+??3??
-&_??????B????o?O??{?????e??tS?NF?
9???M?`?m ;YCv?r?	??????d_???>?]?0?????	???A?J????	rP????
?MX?/XiV???d??H??>7?"6??
-9bc?14??%y?S?V????:L???~??-?L71????E9o??p//??5?)?}?/%??(??????z<??????%9
-??[?6&p??	?;???xv???8^?&????w1!??	?QS??16r2????K?b?1?]L^{?0(?0!???lcT??????" ?E?;??7\???`i???B69U?????S??',?!,?????@?8"?!?n????$?$??l9gL?|?|UaP?????7????S???j??G?????|?;p\~????c????@???K????6jp?4?????'?NM)???w?|?1??@?e?h??S8U7_?S????S??V??0???;?j:??0?P??=?????q?*uyJ?W?(?BD? <eH\??pK???f?t_:?0iv?G?^??,4?A\i?????R?W?v??1y?3?&?8M)?t??D{x]?W??1?????5??7l???dT???H+??7?
-?g???9?l?5?;?????-b???t?LNS~g-?i???b?l?s???2?:(??#???`O????y????
-???&<?4?k???????^?????p?57z??=?i?s??:"Txk?|???P?mP?p?bQf?????o??????W???j'???hr???C?/?'?bq?z??|4????R?k?,??\?
??q?f??d??K?^???j???jHl??/?0??s??r^s?>`
-??E*?????M?
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1243

From noreply at r-forge.r-project.org  Thu Jul  2 14:30:01 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  2 Jul 2015 14:30:01 +0200 (CEST)
Subject: [Pomp-commits] r1244 - pkg/pomp
Message-ID: <20150702123001.B0E2E18761B@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-02 14:30:01 +0200 (Thu, 02 Jul 2015)
New Revision: 1244

Modified:
   pkg/pomp/DESCRIPTION
Log:
- update

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-07-02 12:29:27 UTC (rev 1243)
+++ pkg/pomp/DESCRIPTION	2015-07-02 12:30:01 UTC (rev 1244)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
 Version: 0.69-2
-Date: 2015-06-30
+Date: 2015-07-02
 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")),


From noreply at r-forge.r-project.org  Thu Jul  2 17:02:12 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  2 Jul 2015 17:02:12 +0200 (CEST)
Subject: [Pomp-commits] r1245 - pkg/pomp pkg/pomp/inst www/vignettes
Message-ID: <20150702150213.13D19183FA6@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-02 17:02:12 +0200 (Thu, 02 Jul 2015)
New Revision: 1245

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/inst/NEWS
   www/vignettes/getting_started.html
   www/vignettes/mif2.html
   www/vignettes/pomp.pdf
Log:
- add SystemRequirements for Windows users
- update vignettes

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-07-02 12:30:01 UTC (rev 1244)
+++ pkg/pomp/DESCRIPTION	2015-07-02 15:02:12 UTC (rev 1245)
@@ -1,7 +1,7 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.69-2
+Version: 0.69-3
 Date: 2015-07-02
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
@@ -20,6 +20,7 @@
 Description: Tools for working with partially observed Markov processes (POMPs, AKA stochastic dynamical systems, state-space models).  'pomp' provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods.  It is also a platform for the implementation of new inference methods.
 Depends: R(>= 3.0.0), methods
 Imports: stats, graphics, mvtnorm, deSolve, coda, subplex, nloptr
+SystemRequirements: for Windows users, Rtools (see http://cran.r-project.org/bin/windows/Rtools/)
 License: GPL(>= 2)
 LazyData: true
 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.

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2015-07-02 12:30:01 UTC (rev 1244)
+++ pkg/pomp/inst/NEWS	2015-07-02 15:02:12 UTC (rev 1245)
@@ -1,5 +1,10 @@
 _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_9-_2:
+
+        ??? Measles data from England and Wales, kindly provided by Ben
+          Bolker, are now included as ???ewmeas??? and ???ewcitmeas???.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_8-_2:
 
         ??? When using ???Csnippet???s, by default, the C codes and

Modified: www/vignettes/getting_started.html
===================================================================
--- www/vignettes/getting_started.html	2015-07-02 12:30:01 UTC (rev 1244)
+++ www/vignettes/getting_started.html	2015-07-02 15:02:12 UTC (rev 1245)
@@ -90,7 +90,7 @@
 </div>
 
 <p>Licensed under the <a href="http://creativecommons.org/licenses/by-nc/3.0">Creative Commons attribution-noncommercial license</a>. Please share and remix noncommercially, mentioning its origin.<br /><img src="data:image/png;base64,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" alt="CC-BY_NC" /></p>
-<p>This document was produced using <code>pomp</code> version 0.68.4.</p>
+<p>This document was produced using <code>pomp</code> version 0.69.3.</p>
 <div id="introduction" class="section level2">
 <h2>Introduction</h2>
 <p>This tutorial aims to help you get started using <code>pomp</code> as a suite of tools for analysis of time series data based on dynamical systems models. First, we give some conceptual background regarding the class of models???partially observed Markov processes???that <code>pomp</code> handles. We then discuss some preliminaries: installing the package and so on. Next, using a basic question about ecological population regulation as an example, we load some data and implement some models as <code>R</code> objects of class <code>pomp</code>. Finally, we illustrate some of the package???s capabilities by using its algorithms to fit and compare the models using various inference methods.</p>

Modified: www/vignettes/mif2.html
===================================================================
--- www/vignettes/mif2.html	2015-07-02 12:30:01 UTC (rev 1244)
+++ www/vignettes/mif2.html	2015-07-02 15:02:12 UTC (rev 1245)
@@ -67,7 +67,7 @@
 
 
 <p>Licensed under the <a href="http://creativecommons.org/licenses/by-nc/3.0">Creative Commons attribution-noncommercial license</a>. Please share and remix noncommercially, mentioning its origin.<br /><img src="data:image/png;base64,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" alt="CC-BY_NC" /></p>
-<p>This document was produced using <code>pomp</code> version 0.66.6.</p>
+<p>This document was produced using <code>pomp</code> version 0.69.3.</p>
 <p>Iterated filtering is a technique for maximizing the likelihood obtained by filtering. In <code>pomp</code>, it is the particle filter that is iterated. The iterated filtering of <span class="citation">Ionides et al. (2006)</span> is implemented in the <code>mif</code> function. <span class="citation">Ionides et al. (2015)</span> describe an improvement on the original <span class="citation">(Ionides et al. 2006)</span> algorithm. This ???IF2??? algorithm is implemented in the <code>mif2</code> function.</p>
 <p>The following constructs the Gompertz example that is provided with <code>pomp</code> (see <code>?gompertz</code>) and extracts the parameters at which the data were generated.</p>
 <pre class="r"><code>require(pomp)

Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf	2015-07-02 12:30:01 UTC (rev 1244)
+++ www/vignettes/pomp.pdf	2015-07-02 15:02:12 UTC (rev 1245)
@@ -1,58 +1,52 @@
 %PDF-1.5
 %????
 1 0 obj
-<< /Type /ObjStm /Length 4552 /Filter /FlateDecode /N 97 /First 820 >>
+<< /Type /ObjStm /Length 4410 /Filter /FlateDecode /N 97 /First 820 >>
 stream
-x??\ks?6??~?m\)???J?m???/Er??V??X????f?????_O?????DIc??-Y"A?????
ZU!cU?]x?Sp?ua??/\??????
-??{#
-????4t???j4)?
-m
-a=??Bx???
-)???J?B?C?x!?#.
-????????h?u??"????^??h?v?????qEYV????J?%Ea?T?????3U8tX???3S8?Q?/?	Wx?q????9?[	4Tk%?/_iII???r???<?P(???0?\??+z?9???enQA?2??e?+UhP??J7
-c???iC?j?G??4??I?? /
-??{?	?
-??8???-??0F?
-?6$"Nu4?b5???B????!??
-3???aAY{tjA?`??l?0lA??
-?
-?FcP?
-F??ec0???
-??q9?4???e[A??
-?([^Y??n?P?xH???DH????([? ??<8O7^?(??eAx??I7]xE?
-]?4r?IHU??A??J4n??????`????x??@I`A{s??M??
-????ST,????.???-N?~$?,??z???M?u???_E?
??????KU??A??X?L.?????i=??W???Z?/??G5?>?Y<;[??????b]?????v???????b?Z????????|M3?^L?W???Pi,:??q?.???c?V<^e.?xUU*??qZ"
-(_??T??TK?k?Q?fZ?r?.x?$?-/?
-W?^?T?,???$??????tM?m"?xU?if)
-<MN*?4?x?&??cW2q*?2?(Uj?cg2?$m?<??t?7??+	?Jd|dY??>VSiJ???T???????*??L???IB?>?%6????^?J?????.???_??uI-|???X??lU????>??k?VY????i?M??,????+?oE?:)?R???"S????e???r???1?)?LYf?2S??????R????Ucd????U??2e?)+?g??b????DhP?`w<?<^|????Z`?o4?K??0wP???#??d??????5A?'?x
-?T?	$????z
-?l?)$ZY???????H?&?t?\??8?r?"???R??zET???????FUJZ??(}1????????w2?G?<??????????w????gi`i@:
-!#Z??P6Op?B?Y(:Eg??,?d??]I??-?q'?l;cLn3?????
-cy?[??[1??OR???????umv?}??QmT??(Z9???
-?i???[}O0;b???????(;??v7??6???a??)?#??F??eD?P:??w??n?i??????l?5mNQ??m?v???6??;?O?xX?_?????(v???;[?/??-?????byZ?z?\??>Z?(>?/?????8? ?P@\H?TF?f)
??V???%bLJC?~$j^~Z.^N??7??{2?C??w?B?????L??Wp????!??+L{??X//?\{?[n2Y??C????~????????`q?z?_>?1?B??????y	'????dY??/\??"?Mnvp?B|3???????O??g??
-???dp????Ke??3?<]???)j??j1cl??{?0???W???s??????@??i???pe??@e???k???????]????6`H??&???o???????e7.~???gT??H?????G?1{?????){?~b??K???f?????????g?????l1????	;f5Y??h69g'?d??kvk`?????yqV???????flV?V?????-?5?`dF??d????E??.???????o?]|?d+?????j?????lY?l???d?????'?7?w?\<qF?????`Og?SJ%}??!????c????-?~:?????-?????????'?????)?
-?1]?`c?????u}???p?Z???4?!?H?i??????/??uz>?O/???????Yw???x{??Ms?MA??),)?M??m?1??n???"xm?;??Ix?7??l?,????6????\??6??{??y?1!?B?9?'r?K&??3_?oq?????3?????m%Bmb;????V?-??s}-z???H????|`?$?s??j2?f?5`????l?:c????????}4?.?/f??r@??????????(?2.?R??^????i>2??O41m??W??D?:?4kn6??Bl=j???bV'?;??o?.N?6?]??0????:???
-??"???????
-?"?]Ac??????>?=????_??}+?F??Z7?'U?Z????
?[?2??????C??{1??9+???????U??x??:???^,???s?$???F?z4jcQF??]ZM?G????y?_Og?5n?<W?D???lyEW?O??_??????6]?.W?u"$?v?n?!?|????[??DoaI?)????$?$C??E???????$<?xGiN???y?J>X[?-??B?(??JS?<?Yl?C?
-Uj?gNc??UW?$?3??Zb???D?1????\???n??R%????(i?O
-J?{????O??????|???S?s??gU???o??^??K7?5?3?vnSr6??hn??o_??????????-?%???bH??W6?cxx
#?ZoGvW?5j?????????.?.?R????wrp~~???????????A?????????n???t?<76iC??G
?-?Xl?~?L?8??6??	:??C??L\W&W???b?g1TW?????????????p???:??9?A3F?Uu3?????+????Jp~[`???s}?.???A/D?U?D?1?????h??
-O???6\5?S??kT???o????g(????b?vJ?M???v(??{????/????????????N?
- ??Z?
-??6~8??3???S??l?W0?????W?/??PtxU??D-:?J??-?(???t?$)IJ?q?t?$%II?1?t?$!???T:`???(??
?t?!???!?U????b?tO?w???????[:??DI?%?'??+?wf???????8"???J.l!?+]U???M;?,?y??C;??t??kZO>8w%?*4?????9?#?rC??%??p%?(??\U*???^)(M?y)
????N??x?J???5L??t??*??sj?<?>OB?????????YfFaB FihW???q%??&t???"S?R???c?W???v??C?]????I??@?VGK?;^Z???>
?6W0x?e?+?mh???z?v?%
???~?^?X\?&XQ??????$
-o??09$J#=?
-?e??a
-??'?%???n?????E
+y? ?HL2}3 !g1L???|S????E??/MLI?(,????1????(??"&?[????K?[&?_???p???W??c%m??9?mbKr`;???m???6;???p?I&????????7??HC_Tm?????~?]?a???\????p?????Z??<????;??V??9SR??????8?<???tM?? ?
-?Mg????b??a?~`GTo?A?b???C>=?v<gg???$?wi???????b5E????.?;?qMZ?l???)Z7i??%b4??????????m8]N?o?d???VL????0??<?vl?????????m"?{??D?$??zc?-??????3"?i:?<??[nm??n??????o\????h??<K2?f?S?????n???s?UGn????mL`/??3?????:??QB???q8????????_????L???`e?z'??t???y?Wo???????i_D?=???0c?K\[k?o~;Z.??P?^?l4?F+??????I?$???x???@9??=??q???ZKh[?:Zf?h?z???a?`???V??.?z??ww???=W9.???
-???X_?M}???
-,??WpE`f??@@R?????D
-?+??CM??Z??F?^c??Kj\????L?cwY???"?/=<???W???	??V????????2oWs?
-???)??h?????.??%}[??F??Cr??_%L)v????!pk???'????Cf?JE?A^??)?p?????c????-??????_F{/??I'?n?J,6?r>?_??6???bt<?u?
-z?8?G>?
-?
-???V?R|Q?=?l??7???? ???
-???ok9;?,?(-?!?T???UI??kJ?V??d?6?????"????R??Pr?S?~???%?K|?n?!N??=zf
-?GI????[)?h=?:Tw????)X?DWXKA??
???i?F?^?^???lI?	A??Q%?????R??TX;??? mEU???`?T?v??.????????@[Y????U?h?C?C??%}?%)??Y?J?_rM??7=9?O?f??BX?????G??????.ty?;"'
-v2??l????????9??s??A?s???s??O???,??K?~???dG??y?"?`iS/&_?&?J??1?J	?$k4???{%72?b??PZ%N*I.%m?Y???b\endstream
+x??\?s?6????m3?????L7i?8???<z?sG?i[YR%9??_?i[??vw??I???y?<???*dal?
+!t??]a
+.?*,.???????F??*??????
+?,?c
+!+UpRZ\??7???l!??8WH????/?~E?y!?C[??e!?P??P](]
?)?7?Z{?]!	8V
??*?D???R[??????m??[???pS8?????H9??????W??z+?T???J-%p?+Q(??2????
+Z?*??p?q??rIO@
+??	?
+?h@?O4Q??@=
d?Ab
+??
l??p?@/?T??,???rf
?R`??????a???y
+q??Z?:?5n?1Sc4IP?.@?4??=Hm
?T`??t?ua
?@2 at e?q ; ?eBhph 7F??$F????OH?(???T8?l??U?A???#??v?l+?+????#	????X9O7??'??l$?V
?d??G??"?
?Z??'?????Ty at v$???????/?~???V??{h?a?~?\M??z	?	???*6??>???'??????g?z???{?U]|??7Qqx% e???J?????(??-?oG???u?e\O?xvr???????????????jy??W?/+?
o??	 ???????=j??]NWDq?j|?,??????E??.??8?+??W?,^]z???V???5?O?x?_???*?e????+d?#P?D?&?t?No?	??V'h???l??:]#?<????????w?8X%?U?????O??d????H?H??l_??W?^???\z[B5?QV	???u"??|j?~?????"B??&???J?u????5RFf6TiX?????????l"t0
+???]????ao??_?RE=KB?d:??HX??77@?~?P?M ??I??ot?1?&C???e???f????W?U=??1?0???????+??'???????c?9?????1?Kk???????,?G|?s?f???>?W?????b???~?]?x]???f???????c?GK?d7????5??}??FT???a.????dBxCo?Nf???,d2>?????|t??<?1RUIg??$I?$?GR??
+I???'YO&,???C\????L?G??????d?????????; ????E??????
+?F?NV??????d}??A1P?A?????W???m??=?2;B??f{/6[?v?!???????{???)??6wikh??,?#<????v??S??w?????t?c??????.????-???.*?v???Q?;?Q?????N?`???????1t??7????o??S.??g5???????D?Q??t?8A?WR???Ujb0??K???rT???%?Z?J????O??????s??G]1?]??x?C?????><???b4A\}?B??????????o?SF?:?????????}3??t?<?]?????iM??8?d<=+2?????|?(D??m?n'??8?aGx?&2??3:????'?s"??&q?n?2???V??????^-?u7?f????Z??Pn?|o?Z?k??
+?=<m?#BY??5??#^H@??^?????b?t??}?o?!??H?R????/?C?
yf?F????95?=?#I?7?	{???=?={?^??K????7???#???????l?>?cv<????{q1b'?f
 ??OF??????K?N?
+??????????????g6a?z?dl?fl6????I?&??*?-?y??N?o???????.?.??-?/??e+?:_?5[?s?.??O???????U/f?Bt(?XT?9?QV*????????>????|<?)??[!???E}?V?\?&??'?3Ds??x???e2??V??;??????i?C???+????{_???x?a}v????:^????6?3??????:?]Vr.$?$?6	?U?M???v?/??#?????T???7??t?4????6????\??:??}????6!???sZO?(??T>?g?6???:???g????T??r???y!X?M?a!.m????Z??#{?,?O?!???"?GX??T|9????
+f?????r2Z??O??????>*???9?M&???]???z/?]?&Fi??????E?>?i??a?n?OD???????D3u?i????q??Q?d+&u2p??????$???)???lQ_g?????a?????M??r?????mk?8????7~Oy????m%??V/[???I?7{????
?7?y
+??P??R?W??A?b[3????m?e??=W?}??\?u~[?{????/I?hD????Q?eK?~?
+-????????"??????????d??j??):?xEWZ??;
+&hzy?	???n????h>?\f??,Q?]??
+)??0?mK?U????-?b?B?K<?4$n?????}m??cO??hO?(
+??$E???R?yb?#7??T?`??S#[?????F???}I?P??'?s?)r??)???J???????D&???sq??5RR?C???Le;?s*???^*_?T??H??A2??d
+?e?A&?D9??B??'s-2QP&k+S,e?8??i????????????K???JK???sE?%????t?w?J?.i?????V???J-???1???[	?z{=??????????d4]?????os???(#WSZ??e\???'????????P???3'?)FX???:"?m?Nn???lm??e~????G?z2???~?M???U74??/U]??J?????????W?Z?v???n??*}u+?N??[ ????l?5w?4????C?E%1?KU%n???z???a?m???:??9??h[it5?o?????
?????????????<?t??]??	U?d
+bf??{;Z????f??????`N	????X?&G?9cy??m??q????????E?w??[???
+}?Q??FJ??O???T??7F?]l?'8???????3??t?(7:t*UI?????R[???eix?4??\?P-O????{???-%??J??4?b
??1??????`?<B?'?qd?L?*:???
+1?v?????HE?Nd??l????Z?'??I9[?!?M?????J(Y???Sk?V%?
+??2?J?+?U?A?rC????=
+H??k"?,?H?C`U????(%??
+???7X?
+#+??JC??$?&V?C??+??_>??+?(??b????-ZyWV?A?JpP??????M?JiQ:?V??????G?>??	1j???@M?s??????c?7????u>?<????:??b?????F??p?G{}GwRk?????"?Pt???	?[??S??h*?9
??u?*Cn:5?EN??????
+?
??IYm????+|i??????j?P???sl6N0e?s?<U?&?s8??j????'h???/???9|???Fv?v??r???k?av??]?w%??????????R.??????[)????u?s+??q]??]+????_??
/8??D????J???l??dw????_O??:W?Y?j??????_?5??n
+G4pb??T????G?5*???t?Kz??g?P??
+??~
%]W0?sM??3??d?!T???E????~?v?*T??q9????Q?b????????????W??_??N?L?????>(?W??f?L?kK????????54??0??E??HE?Vdy?0?????0?*RkM)?????f??N????!??<??6]?>??I??"?:??????????????.+?????q????
+s??fI?xEj*9:I?AJf?F!j??oj?N?)6?z?]6o?q????"m???b???y?????r?;??e???C|?`?????????r]Z??XT??U??tn?q@??ub&iJ?h6?^kJ??T/
+}??8@??????-?-=??g??9|
+F}?hh?h??U?)f????????7?-9??F?/???eKR????W@?7E?n?hw???(??m(???????C??
+J
+
??E?????U??U??!??
?L?????-B????k
+?????*
+B MQi?mM???T????M???R?Y??&I???b?H???8Q?Fd??????[	??r??uK??>[?????P???n?al?!?b???2?8??_???W??M??Q%?y?R??\?}
+*?????MR?LB?p*
+I??J?????J2???????p?h?C?;??%}?
+!)???c??(A?uM?7>=???)?j???k?<?.?D?N?t??U?%?m}fz?/b?????@~??y?>+?G?
+R?9
+?#??=???#p?8)?"?\?0??E?l??R???01?ZP?H??Q?????{-b|?(q?D????W]|???m?p?)?endstream
 endobj
 99 0 obj
 << /Subtype /XML /Type /Metadata /Length 1340 >>
@@ -61,12 +55,12 @@
 <?adobe-xap-filters esc="CRLF"?>
 <x:xmpmeta xmlns:x='adobe:ns:meta/' x:xmptk='XMP toolkit 2.9.1-13, framework 1.6'>
 <rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' xmlns:iX='http://ns.adobe.com/iX/1.0/'>
-<rdf:Description rdf:about='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e' xmlns:pdf='http://ns.adobe.com/pdf/1.3/' pdf:Producer='GPL Ghostscript 9.05'/>
-<rdf:Description rdf:about='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e' xmlns:xmp='http://ns.adobe.com/xap/1.0/'><xmp:ModifyDate>2015-06-26T08:28:16-04:00</xmp:ModifyDate>
-<xmp:CreateDate>2015-06-26T08:28:16-04:00</xmp:CreateDate>
+<rdf:Description rdf:about='uuid:48b9064d-58e4-11f0-0000-47d6bebdb8a1' xmlns:pdf='http://ns.adobe.com/pdf/1.3/' pdf:Producer='GPL Ghostscript 9.05'/>
+<rdf:Description rdf:about='uuid:48b9064d-58e4-11f0-0000-47d6bebdb8a1' xmlns:xmp='http://ns.adobe.com/xap/1.0/'><xmp:ModifyDate>2015-07-02T10:36:33-04:00</xmp:ModifyDate>
+<xmp:CreateDate>2015-07-02T10:36:33-04:00</xmp:CreateDate>
 <xmp:CreatorTool>Raph Levien</xmp:CreatorTool></rdf:Description>
-<rdf:Description rdf:about='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e' xmlns:xapMM='http://ns.adobe.com/xap/1.0/mm/' xapMM:DocumentID='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e'/>
-<rdf:Description rdf:about='uuid:5e797340-541b-11f0-0000-5dee1bc85d4e' xmlns:dc='http://purl.org/dc/elements/1.1/' dc:format='application/pdf'><dc:title><rdf:Alt><rdf:li xml:lang='x-default'>Inconsolata</rdf:li></rdf:Alt></dc:title></rdf:Description>
+<rdf:Description rdf:about='uuid:48b9064d-58e4-11f0-0000-47d6bebdb8a1' xmlns:xapMM='http://ns.adobe.com/xap/1.0/mm/' xapMM:DocumentID='uuid:48b9064d-58e4-11f0-0000-47d6bebdb8a1'/>
+<rdf:Description rdf:about='uuid:48b9064d-58e4-11f0-0000-47d6bebdb8a1' xmlns:dc='http://purl.org/dc/elements/1.1/' dc:format='application/pdf'><dc:title><rdf:Alt><rdf:li xml:lang='x-default'>Inconsolata</rdf:li></rdf:Alt></dc:title></rdf:Description>
 </rdf:RDF>
 </x:xmpmeta>
                                                                         
@@ -74,537 +68,604 @@
 <?xpacket end='w'?>endstream
 endobj
 100 0 obj
-<< /Type /ObjStm /Length 2279 /Filter /FlateDecode /N 97 /First 876 >>
+<< /Type /ObjStm /Length 2585 /Filter /FlateDecode /N 97 /First 893 >>
 stream
-x??Zko???_1@?$(4???G???5???6M?????"???s?K?k?0)?l? ????????w?????)??^y?q
-J,??bf???????64??
KX?C?h??\?c?W??1A9[??V??r?;`7=g?RS?+>*????a?E?{4????????`Q>??hd?J?'????9sLQ?x<?FG??????????M???S!??-&?TgE40?q?eA??	?PH$?'F?N?J6?????G^?'???d%?????GIE??????^T?????X4?H??DBIP??M"*n*Q%?XI*?hd?$szQ)s4h????T_PR>?**?
-?(*???
-O????-bF?`?R<????hX?K?[$???b?(?1??$k?lq?8??Y?8??Q08U??l????*?Xt?P?2V?HCIu0V?DXe??(???!????Rh?ZDjb???(?b?g?????)?3??y??o)W?0!???}????l?P??bi?Y??????[5x>?.?)FY?o^7????L4?E?"
	??1V????f1??????f?|X??|9\6U????X??{????F?????x??7?X??????M??/t+?mX?/X?+??E?X??!??d?	r?@GB??tkz?*??C?~5??R?w@?=ANv2??Qrj]_?|V8???t`????.??????r$?'X??"?H?hc_?\????y?????k??r??r????W?K ??H?????W,?L???K?????????????LJ????f??6???????????j??????C????4????B:???8?@?#?o?-+??????*?EU???&h??,o?v?1x????k&>?D?=??E??uA<?1??4d??????\t??z)????R?????Z?}f?????J1nE??t at p?',?V?^???`??K?P'1??i?w???Y??X9?t??V3???o?@?R?b???????j???W?
??x6]???j????`p3????????e???|???~[5{??!OPv-r!mj>???x\?? :?=E?,Q?+??wj??????m? ???????=mOn???6?r_?8??S?s?J?TZ3???!w???%??i??
-?]??????X?Tp?*4S?`?fl??F????J}?r??!V????P?X@????Z????@q??$???E?8r?/kJ\???(?
{??????9
Y??GZ?:?/?r2,0	???o?NZr/aO'sgA?7a???Y#8?V?? ??,?'h??/??J:???)?nV"?I????CE?k
-?!AT?b+?0?@?<??j?0?]??W%$t*!?!????bt??;??K?????d??~?5lP?1?8?p?T?
-~??o????????_?
g????xzY???z???W?9????<??o??y=	??~?cxs??w?k?~????2?B????????(?n?p1?%
??o???/??]?J???k???o??????p>?Oo???z<???bR?9q??r2?\@3+I????>K?.?v???x?x??V???us??????xt:??4????b
)????/??????[???\???`?6?R???r???G????i????4Hv?z???|???A#rSYt??I?#Du*?P?#m?????|?k[??]?\?W?Y:?\yH%?RV?M?F ?haZ??E?=?r at A.y
-?4??]D???c??S??w{+??1?]`_?s???	???ErO2???i?|???hp=??'???d?Lx???	?f???????|??????yu?[{a??#O?2j?g??b?Q?????b?u?;c???J]??X???????????8??3?]??3??91?91???k???	rl??'??
-E?h?0?~?RHb	?N|??~Ps??	x7r???????6??h?d???BS?/n????7?????pS?6?2?	Hq????~O?>????`????a?a?%???<%?=?H??3?X??~?|??
???^@???????[#?????;?J???L??.?e? A??gX??
??
-?a9???C`}Y'???l???3]_???$?0???%?j??k~???W???c???c?
-'?E.?4??????2??&6?@?}81??y?a????????????"I?Tr?????????????
-r&
$??????"???????C???56?a??
4??endstream
+x??[]?\G}?W?#<??U??(?DAH E? 
Q?3?@???k??{????Y;?^??
+Yr?;so????S?+IB
+?4?FVy??+?=?????O?$~????=Hu?????E?&??xA?D,?9^????x??|?????A?????H?ah
+?
+~7?????ub#L???????????W?
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1245

From noreply at r-forge.r-project.org  Thu Jul  2 20:02:45 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  2 Jul 2015 20:02:45 +0200 (CEST)
Subject: [Pomp-commits] r1246 - pkg/pomp
Message-ID: <20150702180245.B0298187A6B@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-02 20:02:45 +0200 (Thu, 02 Jul 2015)
New Revision: 1246

Modified:
   pkg/pomp/NAMESPACE
Log:
- update imports per Kurt Hornik's message of 2015-07-02

Modified: pkg/pomp/NAMESPACE
===================================================================
--- pkg/pomp/NAMESPACE	2015-07-02 15:02:12 UTC (rev 1245)
+++ pkg/pomp/NAMESPACE	2015-07-02 18:02:45 UTC (rev 1246)
@@ -34,8 +34,14 @@
           )
 
 import(methods)
-importFrom(graphics,plot)		
-importFrom(stats,simulate,time,coef,logLik,window)
+importFrom(graphics,plot,par,abline,pairs,matplot,box,axis,mtext,
+           points,polygon,lines,plot.default,legend,hist,rect,text)		
+importFrom(grDevices,rgb,dev.interactive)
+importFrom(stats,simulate,time,coef,logLik,window,
+           lm,residuals,fitted,sd,
+           dnorm,cov,runif,median,density,
+           spec.pgram,rnorm,weighted.mean,optim,.lm.fit,
+           setNames,cor,kernel,quantile)
 importFrom(mvtnorm,dmvnorm,rmvnorm)
 importFrom(subplex,subplex)
 importFrom(deSolve,ode)


From noreply at r-forge.r-project.org  Thu Jul  2 20:02:50 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  2 Jul 2015 20:02:50 +0200 (CEST)
Subject: [Pomp-commits] r1247 - pkg/pomp
Message-ID: <20150702180250.2ADE3187A6B@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-02 20:02:49 +0200 (Thu, 02 Jul 2015)
New Revision: 1247

Modified:
   pkg/pomp/DESCRIPTION
Log:
- increment version number

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-07-02 18:02:45 UTC (rev 1246)
+++ pkg/pomp/DESCRIPTION	2015-07-02 18:02:49 UTC (rev 1247)
@@ -1,7 +1,7 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.69-3
+Version: 0.69-4
 Date: 2015-07-02
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),


From noreply at r-forge.r-project.org  Thu Jul  2 20:02:54 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  2 Jul 2015 20:02:54 +0200 (CEST)
Subject: [Pomp-commits] r1248 - in pkg/pomp: . R
Message-ID: <20150702180254.E2ABC187A6B@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-02 20:02:54 +0200 (Thu, 02 Jul 2015)
New Revision: 1248

Modified:
   pkg/pomp/NAMESPACE
   pkg/pomp/R/nlf-guts.R
Log:
- remove need for direct call to 'lm' in 'nlf'

Modified: pkg/pomp/NAMESPACE
===================================================================
--- pkg/pomp/NAMESPACE	2015-07-02 18:02:49 UTC (rev 1247)
+++ pkg/pomp/NAMESPACE	2015-07-02 18:02:54 UTC (rev 1248)
@@ -38,10 +38,9 @@
            points,polygon,lines,plot.default,legend,hist,rect,text)		
 importFrom(grDevices,rgb,dev.interactive)
 importFrom(stats,simulate,time,coef,logLik,window,
-           lm,residuals,fitted,sd,
-           dnorm,cov,runif,median,density,
-           spec.pgram,rnorm,weighted.mean,optim,.lm.fit,
-           setNames,cor,kernel,quantile)
+           dnorm,runif,sd,cov,cor,median,density,
+           spec.pgram,rnorm,weighted.mean,optim,
+           .lm.fit,setNames,kernel,quantile)
 importFrom(mvtnorm,dmvnorm,rmvnorm)
 importFrom(subplex,subplex)
 importFrom(deSolve,ode)

Modified: pkg/pomp/R/nlf-guts.R
===================================================================
--- pkg/pomp/R/nlf-guts.R	2015-07-02 18:02:49 UTC (rev 1247)
+++ pkg/pomp/R/nlf-guts.R	2015-07-02 18:02:54 UTC (rev 1248)
@@ -160,9 +160,9 @@
   model.residuals <- matrix(0,dim(model.pred)[1],nvar)
 
   for (jvar in seq_len(nvar)) {
-    model.lm <- lm(model.pred[,jvar]~rbfbasis.model-1)
-    model.residuals[,jvar] <- residuals(model.lm)
-    ck <- coef(model.lm)
+    model.lm <- .lm.fit(rbfbasis.model,model.pred[,jvar])
+    model.residuals[,jvar] <- model.lm$residuals
+    ck <- model.lm$coefficients
     if (verbose) {
       print(ck)
       print(summary(model.lm))


From noreply at r-forge.r-project.org  Mon Jul  6 12:49:42 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  6 Jul 2015 12:49:42 +0200 (CEST)
Subject: [Pomp-commits] r1249 - pkg/pomp pkg/pomp/inst www/vignettes
Message-ID: <20150706104942.9B8321878B4@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-06 12:49:42 +0200 (Mon, 06 Jul 2015)
New Revision: 1249

Added:
   pkg/pomp/inst/TODO.md
Removed:
   pkg/pomp/inst/TODO
Modified:
   pkg/pomp/DESCRIPTION
   www/vignettes/pompjss.Rnw
Log:
- change TODO to markdown format
- put VignetteEngine line in pompjss.Rnw

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-07-02 18:02:54 UTC (rev 1248)
+++ pkg/pomp/DESCRIPTION	2015-07-06 10:49:42 UTC (rev 1249)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.69-4
-Date: 2015-07-02
+Version: 0.69-5
+Date: 2015-07-06
 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")),

Deleted: pkg/pomp/inst/TODO
===================================================================
--- pkg/pomp/inst/TODO	2015-07-02 18:02:54 UTC (rev 1248)
+++ pkg/pomp/inst/TODO	2015-07-06 10:49:42 UTC (rev 1249)
@@ -1,31 +0,0 @@
-TO-DO LIST
-
-* write pompCBuilder support for 'onestep.dens' and 'gillespie.sim' plugins.
-
-* effects of replacing 'sample.int' with systematic resampling inside 'bsmc'
-
-* parameter transformations: put 'transform' option into each estimation routine
-  (spect.match)
-
-* unit tests for 'sannbox'
-
-* Improve 'pmcmc' to take advantage of all particles.
-
-* Partial rejection control for 'pfilter'?
-
-* Adaptive particle numbers in pfilter.
-
-* Write 'plot' and 'print' methods for 'pfilterd.pomp' objects.  
-  Would this display effective sample size, conditional log likelihood, filter means, prediction variances, prediction means?
-
-* Add plugin for adaptive tau leaping algorithm.
-
-* Parallel 'pfilter' algorithm.
-
-* Add LPA model examples.
-
-* SDE examples.
-
-* Extended Kalman filter.
-
-* Plugin for compartmental models.

Added: pkg/pomp/inst/TODO.md
===================================================================
--- pkg/pomp/inst/TODO.md	                        (rev 0)
+++ pkg/pomp/inst/TODO.md	2015-07-06 10:49:42 UTC (rev 1249)
@@ -0,0 +1,24 @@
+### pomp to-do list
+
+- improve 'pmcmc' to take advantage of all particles
+- documentation on 'mifList', 'pmcmcList', etc.
+- 'transform' argument for pmcmc?
+- 'initializer' -> 'rinit' and perhaps 'dinit'
+- documentation: "regular parameters" instead of "non-IVP"
+- add 'coef' method for 'mifList' objects
+- objective function for spectrum matching
+- one-point SCQL function for possible use in fitting initial conditions
+- save particle filtering variance?  Prediction means are optional.  Only interesting for end-user if one wants to look at residuals.
+- write pompCBuilder support for 'onestep.dens' and 'gillespie.sim' plugins.
+- parameter transformations: put 'transform' option into each estimation routine (spect.match)
+- unit tests for 'sannbox'
+- partial rejection control for 'pfilter'?
+- adaptive particle numbers in pfilter.
+- improve 'plot' and 'print' methods for 'pfilterd.pomp' objects.  
+    - Would this display effective sample size, conditional log likelihood, filter means, prediction variances, prediction means?
+- Add plugin for adaptive tau leaping algorithm.
+- Parallel 'pfilter' algorithm.
+- Add LPA model examples.
+- SDE examples.
+- Extended Kalman filter.
+- Plugin for compartmental models.

Modified: www/vignettes/pompjss.Rnw
===================================================================
--- www/vignettes/pompjss.Rnw	2015-07-02 18:02:54 UTC (rev 1248)
+++ www/vignettes/pompjss.Rnw	2015-07-06 10:49:42 UTC (rev 1249)
@@ -1,5 +1,5 @@
 \documentclass[article,pdftex,shortnames,nojss]{jss}
-
+%\VignetteEngine{knitr::knitr}
 \usepackage[ruled,noline,linesnumbered]{algorithm2e}
 \SetKwFor{For}{for}{do}{end}
 \SetKwFor{While}{while}{do}{end}


From noreply at r-forge.r-project.org  Mon Jul  6 18:49:14 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  6 Jul 2015 18:49:14 +0200 (CEST)
Subject: [Pomp-commits] r1250 - www
Message-ID: <20150706164914.5D3EC187A1A@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-06 18:49:14 +0200 (Mon, 06 Jul 2015)
New Revision: 1250

Added:
   www/index.html
Removed:
   www/index.php
Log:
- redirect to kingaa.github.io/pomp

Added: www/index.html
===================================================================
--- www/index.html	                        (rev 0)
+++ www/index.html	2015-07-06 16:49:14 UTC (rev 1250)
@@ -0,0 +1,18 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html>
+<head>
+  <title>pomp</title>
+  <meta http-equiv="refresh" content="0;url=http://kingaa.github.io/pomp/">
+<body>
+  <center>
+    <h2>pomp</h2>
+
+    <p><a href="http://kingaa.github.io/pomp">The <b>pomp</b> website has moved to<br>
+    http://kingaa.github.io/pomp/.</a></p>
+
+    <p><a href="http://kingaa.github.io/pomp">Please click on this
+    link to go there if you are not immediately redirected.</a></p>
+  </center>
+</body>
+</html>

Deleted: www/index.php
===================================================================
--- www/index.php	2015-07-06 10:49:42 UTC (rev 1249)
+++ www/index.php	2015-07-06 16:49:14 UTC (rev 1250)
@@ -1,105 +0,0 @@
-<?php
-$domain=ereg_replace('[^\.]*\.(.*)$','\1',$_SERVER['HTTP_HOST']);
-$group_name=ereg_replace('([^\.]*)\..*$','\1',$_SERVER['HTTP_HOST']);
-$themeroot='http://r-forge.r-project.org/themes/rforge/';
-$rforgepkgs = "http://r-forge.r-project.org/R/?group_id=214";
-$tracker = "http://r-forge.r-project.org/tracker/?group_id=214";
-$scm = "http://r-forge.r-project.org/scm/viewvc.php/?root=pomp";
-$cranpage = "http://cran.at.r-project.org/web/packages/pomp/";
-$crancontents = file_get_contents($cranpage);
-preg_match("/<tr>\\n*<td>Version:<\/td>\\n*<td>(.+?)<\/td>/",$crancontents,$matches);
-$cranversion = $matches[1];
-$rforgepage = file_get_contents($rforgepkgs);
-preg_match_all("/Rev\.: <b>(.+?)<\/b>/",$rforgepage,&$matches);
-$svnrevision = $matches[1][0];
-echo '<?xml version="1.0" encoding="UTF-8"?>';
-?>
-<!DOCTYPE html
-	PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-	"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en   ">
-
-  <head>
-  	<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-	<meta name="keywords" content="stochastic dynamics, inference, hidden Markov model, state space model" />
-	<title><?php echo $group_name; ?></title>
-	<link href="./whitestyle.css" rel="stylesheet" type="text/css">
-  </head>
-
-<body>
-<! --- R-Forge Logo --- >
-
-<table border="0" width="80%" cellspacing="0" cellpadding="0">
-<tr>
-<td>
-<a href="http://R-Forge.R-Project.org"><img src="<?php echo $themeroot; ?>/imagesrf/logo.png" border="0" alt="R-Forge Logo" /> </a> 
-</td> 
-</tr>
-</table>
-
-<table width="80%" align="left" border="0" cellspacing="0" cellpadding="0">
-<tr>
-<td>
-<table border="0" cellspacing="0" cellpadding="0">
-<tr>
-<td align="right" width="60%">
-<h2><span class="emph">pomp</span>:<br> 
-statistical inference for<br>
-<span class="emph">p</span>artially-<span class="emph">o</span>bserved&nbsp;<span class="emph">M</span>arkov&nbsp;<span class="emph">p</span>rocesses</h2>
-</td>
-<td align="left" width="40%">
-<ul>
-<li><a href="./index.php?nav=about">About <i>pomp</i></a></li>
-<li><a href="<?php echo $rforgepkgs;?>">Development Version (Rev. <?php print $svnrevision; ?>)</a></li>
-<li><a href="<?php echo $cranpage;?>">Release Version (<?php print $cranversion; ?>) on CRAN</a></li>
-<li><a target="_blank" href="./vignettes/pomp.pdf"><i>pomp</i> manual (PDF)</a></li>
-<li><a href="http://lists.r-forge.r-project.org/pipermail/pomp-announce/"><i>pomp-announce</i> mailing list archives</a></li>
-<li><a href="./index.php?nav=news">Package NEWS</a></li>
-<li><a href="./index.php?nav=vignettes">Tutorial vignettes</a></li>
-<li><a href="<?php echo $tracker;?>">Bug reports, feature &amp; support requests</a></li>
-<li><a href="<?php echo $scm;?>">Source code repository</a></li>
-<li><a href="./index.php?nav=bib">References to the literature</a></li>
-<li><a href="./index.php?nav=authors">Authors' homepages</a></li>
-</ul>
-</td>
-</tr>
-</table>
-</td>
-</tr>
-<tr>
-<td>
-<table border="0" cellspacing="0" cellpadding="0">
-<tr>
-<td>
-<?php
-$nav = $_REQUEST["nav"];
-switch ($nav) {
-    case "vignettes":
-        $dfile = "content/vignettes.htm";
-        break;
-    case "news":
-        $dfile = "content/NEWS.html";
-        break;
-    case "bib":
-        $dfile = "content/refs.htm";
-        break;
-    case "soft":
-        $dfile = "content/links.htm";
-        break;
-    case "authors":
-        $dfile = "content/authors.htm";
-        break;
-    default:
-        $dfile = "content/about.htm";
-        break;
-}
-include($dfile);
-?>
-</td>
-</tr>
-</table>
-</td>
-</tr>
-</table>
-</body>
-</html>


From noreply at r-forge.r-project.org  Tue Jul  7 15:16:47 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  7 Jul 2015 15:16:47 +0200 (CEST)
Subject: [Pomp-commits] r1251 - pkg/pompExamples pkg/pompExamples/R
	pkg/pompExamples/inst pkg/pompExamples/inst/examples
	pkg/pompExamples/man pkg/pompExamples/src
	pkg/pompExamples/tests www/vignettes
Message-ID: <20150707131647.EEA57183C4E@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-07 15:16:46 +0200 (Tue, 07 Jul 2015)
New Revision: 1251

Removed:
   pkg/pompExamples/.Rbuildignore
   pkg/pompExamples/.Rinstignore
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/NAMESPACE
   pkg/pompExamples/R/aaa.R
   pkg/pompExamples/R/pertussis.R
   pkg/pompExamples/inst/GPL
   pkg/pompExamples/inst/NEWS
   pkg/pompExamples/inst/NEWS.Rd
   pkg/pompExamples/inst/examples/bbp.R
   pkg/pompExamples/inst/examples/bsflu.R
   pkg/pompExamples/inst/examples/bsflu3.R
   pkg/pompExamples/inst/examples/budmoth.R
   pkg/pompExamples/inst/examples/ebola.R
   pkg/pompExamples/inst/examples/parus.R
   pkg/pompExamples/man/budmoth.Rd
   pkg/pompExamples/man/parus.Rd
   pkg/pompExamples/man/pertussis.Rd
   pkg/pompExamples/src/bbp.c
   pkg/pompExamples/src/budmoth.c
   pkg/pompExamples/src/cholmodel.c
   pkg/pompExamples/src/parus.c
   pkg/pompExamples/src/pertussis.c
   pkg/pompExamples/tests/bbp.R
   pkg/pompExamples/tests/bbp.Rout.save
   pkg/pompExamples/tests/budmoth.R
   pkg/pompExamples/tests/budmoth.Rout.save
   pkg/pompExamples/tests/ebola.R
   pkg/pompExamples/tests/ebola.Rout.save
   pkg/pompExamples/tests/parus.R
   pkg/pompExamples/tests/parus.Rout.save
   pkg/pompExamples/tests/pertussis.R
   pkg/pompExamples/tests/pertussis.Rout.save
   www/vignettes/Makefile
   www/vignettes/abc.rda
   www/vignettes/advanced_topics_in_pomp.R
   www/vignettes/advanced_topics_in_pomp.Rnw
   www/vignettes/advanced_topics_in_pomp.pdf
   www/vignettes/algorithm2e.sty
   www/vignettes/bbp.Rmd
   www/vignettes/bbp.html
   www/vignettes/bsflu-mf1.rds
   www/vignettes/bsflu-mf3.rds
   www/vignettes/bsflu-tm1.rds
   www/vignettes/bsflu-tm3.rds
   www/vignettes/bsflu.Rmd
   www/vignettes/bsflu.html
   www/vignettes/cleveref.sty
   www/vignettes/ecology.csl
   www/vignettes/fullnat.bst
   www/vignettes/getting_started.R
   www/vignettes/getting_started.Rmd
   www/vignettes/getting_started.html
   www/vignettes/gompertz-mif.rda
   www/vignettes/intro_to_pomp.R
   www/vignettes/intro_to_pomp.Rnw
   www/vignettes/intro_to_pomp.pdf
   www/vignettes/jss.bst
   www/vignettes/jss.cls
   www/vignettes/mif2.R
   www/vignettes/mif2.Rmd
   www/vignettes/mif2.html
   www/vignettes/nlf-mif-compare.rda
   www/vignettes/parus-mf.rds
   www/vignettes/parus-tm1.rds
   www/vignettes/parus.Rmd
   www/vignettes/parus.html
   www/vignettes/pmcmc.rda
   www/vignettes/pomp.bib
   www/vignettes/pomp.pdf
   www/vignettes/pompjss.R
   www/vignettes/pompjss.Rnw
   www/vignettes/pompjss.bib
   www/vignettes/pompjss.pdf
   www/vignettes/ricker-comparison.rda
   www/vignettes/ricker-mif.rda
   www/vignettes/ricker-probe-match.rda
   www/vignettes/timing.rda
Log:
- remove pompExamples and vignettes

Deleted: pkg/pompExamples/.Rbuildignore
===================================================================
--- pkg/pompExamples/.Rbuildignore	2015-07-06 16:49:14 UTC (rev 1250)
+++ pkg/pompExamples/.Rbuildignore	2015-07-07 13:16:46 UTC (rev 1251)
@@ -1,3 +0,0 @@
-vignettes/Makefile
-inst/data-R/Makefile
-vignettes/(.+?)\.pbs$

Deleted: pkg/pompExamples/.Rinstignore
===================================================================
--- pkg/pompExamples/.Rinstignore	2015-07-06 16:49:14 UTC (rev 1250)
+++ pkg/pompExamples/.Rinstignore	2015-07-07 13:16:46 UTC (rev 1251)
@@ -1,5 +0,0 @@
-inst/doc/Makefile
-inst/data-R/Makefile
-inst/doc/(.+?)\.bst$
-inst/doc/(.+?)\.rda$
-inst/doc/(.+?)\.pbs$

Deleted: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2015-07-06 16:49:14 UTC (rev 1250)
+++ pkg/pompExamples/DESCRIPTION	2015-07-07 13:16:46 UTC (rev 1251)
@@ -1,24 +0,0 @@
-Package: pompExamples
-Type: Package
-Title: Additional POMP Examples
-Version: 0.28-2
-Date: 2015-06-25
-Maintainer: Aaron A. King <kingaa at umich.edu>
-Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
-	   email="kingaa at umich.edu"),
-	  person(given=c("Carles"),family="Breto",role=c("aut")),
-	  person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),
-	  person(given=c("Matthew","J."),family="Ferrari",role=c("ctb")),
-	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
-	  person(given=c("Bruce","E."),family="Kendall",role=c("ctb")),
-	  person(given=c("Michael"),family="Lavine",role=c("ctb")),
-	  person(given=c("Daniel","C."),family="Reuman",role=c("ctb")),
-	  person(given=c("Helen"),family="Wearing",role=c("ctb")))
-URL: http://pomp.r-forge.r-project.org
-Description: Provides more 'pomp' examples.
-Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.65-1)
-Suggests: plyr, reshape2
-LinkingTo: pomp
-License: GPL (>= 2)
-LazyData: false
-Collate: aaa.R pertussis.R

Deleted: pkg/pompExamples/NAMESPACE
===================================================================
--- pkg/pompExamples/NAMESPACE	2015-07-06 16:49:14 UTC (rev 1250)
+++ pkg/pompExamples/NAMESPACE	2015-07-07 13:16:46 UTC (rev 1251)
@@ -1,3 +0,0 @@
-useDynLib(pompExamples)
-import(pomp)
-export(pertussis.sim)

Deleted: pkg/pompExamples/R/aaa.R
===================================================================
--- pkg/pompExamples/R/aaa.R	2015-07-06 16:49:14 UTC (rev 1250)
+++ pkg/pompExamples/R/aaa.R	2015-07-07 13:16:46 UTC (rev 1251)
@@ -1,12 +0,0 @@
-.onAttach <- function (...) {
-  exampleDir <- getOption("pomp.examples")
-  newDir <- system.file("examples",package="pompExamples")
-  options(pomp.examples=c(exampleDir,newDir,recursive=TRUE))
-}
-
-.onDetach <- function (...) {
-  exampleDir <- getOption("pomp.examples")
-  newDir <- system.file("examples",package="pompExamples")
-  exampleDir <- exampleDir[exampleDir!=newDir]
-  options(pomp.examples=exampleDir)
-}

Deleted: pkg/pompExamples/R/pertussis.R
===================================================================
--- pkg/pompExamples/R/pertussis.R	2015-07-06 16:49:14 UTC (rev 1250)
+++ pkg/pompExamples/R/pertussis.R	2015-07-07 13:16:46 UTC (rev 1251)
@@ -1,133 +0,0 @@
-## This file constructs a pomp object for one of several continuous time Markov chain models
-## for pertussis containing simulated data.
-## Simulations from the process model are approximated using an Euler approximation.
-
-pertussis.sim <- function (which) {
-  if (missing(which)) {
-    datasets <- c(
-                  "SEIR.small","SEIR.big",
-                  "SEIRS.small","SEIRS.big",
-                  "SEIRR.small","SEIRR.big",
-                  "full.small","full.big"
-                  )
-
-    cat("available datasets:",sQuote(datasets),"\n")
-    invisible(datasets)
-  } else {
-    which <- as.character(substitute(which))
-    suppressMessages(
-                     simulate(
-                              pomp(
-                                   data=data.frame(time=seq(from=0,to=20,by=1/52),reports=NA),
-                                   times="time",
-                                   t0=-1/52,
-                                   params=switch(
-                                     which,
-                                     SEIR.small=c(
-                                       birthrate=0.02, deathrate=0.02, mean.beta=450, ampl.beta=0.15,
-                                       imports=10, sigma=46, gamma=26, alpha=0, alpha.ratio=1,
-                                       report.prob=0.3, boost.prob=0, polar.prob=0, foi.mod=0,
-                                       popsize=5e+5, noise.sigma=0, tau=0.01,
-                                       S.0=0.0574148031949802, E.0=0.0004081763321755, I.0=0.00067028956509212,
-                                       R1.0=0.941506730907752, R2.0=0),
-                                     SEIR.big=c(
-                                       birthrate=0.02, deathrate=0.02, mean.beta=450, ampl.beta=0.15,
-                                       imports=10, sigma=46, gamma=26, alpha=0, alpha.ratio=1,
-                                       report.prob=0.3, boost.prob=0, polar.prob=0, foi.mod=0,
-                                       popsize=5e+6, noise.sigma=0, tau=0.01,
-                                       S.0=0.0515635231482973, E.0=0.000437143470487014, I.0=0.000734641109212043,
-                                       R1.0=0.947264692272004, R2.0=0),
-                                     SEIRS.small=c(
-                                       birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
-                                       imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
-                                       report.prob=0.1, boost.prob=0, polar.prob=0, foi.mod=0,
-                                       popsize=5e+5, noise.sigma=0, tau=0.01,
-                                       S.0=0.157360395940609, E.0=0.000837874318852172, I.0=0.00124181372794081,
-                                       R1.0=0.45913512973054, R2.0=0.381424786282058),
-                                     SEIRS.big=c(
-                                       birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
-                                       imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
-                                       report.prob=0.1, boost.prob=0, polar.prob=0, foi.mod=0,
-                                       popsize=5e+6, noise.sigma=0, tau=0.01,
-                                       S.0=0.157398354546347, E.0=0.00132093662562661, I.0=0.0022558671035406,
-                                       R1.0=0.457185201591761, R2.0=0.381839640132725),
-                                     SEIRR.small=c(
-                                       birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
-                                       imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
-                                       report.prob=0.11, boost.prob=0.75, polar.prob=0, foi.mod=0.5,
-                                       popsize=5e+5, noise.sigma=0, tau=0.01,
-                                       S.0=0.128943112158304, E.0=0.00068688724266688, I.0=0.00114414648269803,
-                                       R1.0=0.638074319602244, R2.0=0.231151534514087),
-                                     SEIRR.big=c(
-                                       birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
-                                       imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
-                                       report.prob=0.11, boost.prob=0.75, polar.prob=0, foi.mod=0.5,
-                                       popsize=5e+6, noise.sigma=0, tau=0.01,
-                                       S.0=0.127128689912424, E.0=0.00126497004491763, I.0=0.00216092385991776,
-                                       R1.0=0.639879739889535, R2.0=0.229565676293206),
-                                     full.small=c(
-                                       birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
-                                       imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
-                                       report.prob=0.1, boost.prob=0.75, polar.prob=0.1, foi.mod=0.5,
-                                       popsize=5e+5, noise.sigma=0.01, tau=0.01,
-                                       S.0=0.132553922599906, E.0=0.0010539075727066, I.0=0.00166100642162314,
-                                       R1.0=0.641737544956371, R2.0=0.222993618449393),
-                                     full.big=c(
-                                       birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
-                                       imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
-                                       report.prob=0.1, boost.prob=0.75, polar.prob=0.1, foi.mod=0.5,
-                                       popsize=5e+6, noise.sigma=0.01, tau=0.01,
-                                       S.0=0.130980596244438, E.0=0.00115096693013597, I.0=0.0018994251960431,
-                                       R1.0=0.643957103848235, R2.0=0.222011907781148),
-                                     stop("unrecognized dataset ",sQuote(which),call.=FALSE)
-                                     ),
-                                   rprocess = euler.sim(
-                                     step.fun="pertussis_sveirr_EM",
-                                     delta.t=1/52/7,          # Euler stepsize
-                                     PACKAGE="pompExamples"
-                                     ),
-                                   skeleton.type="vectorfield",
-                                   skeleton="pertussis_sveirr_skel",
-                                   PACKAGE="pompExamples",
-                                   paramnames=c(
-                                     "birthrate","deathrate","mean.beta","ampl.beta",
-                                     "imports","sigma","gamma","alpha","alpha.ratio",
-                                     "report.prob","boost.prob","polar.prob",
-                                     "foi.mod","noise.sigma","popsize","tau",
-                                     "S.0","E.0","I.0","R1.0","R2.0"
-                                     ),
-                                   statenames=c("S","E","I","R1","R2","cases","W","err","simpop"),
-                                   zeronames=c("cases","err"),
-                                   ivps=c("S.0","E.0","I.0","R1.0","R2.0"),
-                                   comp.names=c("S","E","I","R1","R2"),
-                                   rmeasure = "negbin_rmeasure",
-                                   dmeasure = "negbin_dmeasure",
-                                   toEstimationScale="pertussis_par_untrans",
-                                   fromEstimationScale="pertussis_par_trans",
-                                   varnames=c("S","E","I","R1","R2","cases","W","err","simpop"),
-                                   initializer = function (params, t0, varnames, comp.names, ivps, ...) {
-                                     states <- numeric(length(varnames))
-                                     names(states) <- varnames
-                                     ## translate fractions into initial conditions
-                                     frac <- params[ivps]
-                                     states[comp.names] <- round(params['popsize']*frac/sum(frac))
-                                     states["simpop"] <- params["popsize"]
-                                     states
-                                   }
-                                   ),
-                              seed=switch(
-                                which,
-                                SEIR.small=1831650124L,
-                                SEIR.big=908022490L,
-                                SEIRS.small=1111340406L,
-                                SEIRS.big=1751228386L,
-                                SEIRR.small=350421545L,
-                                SEIRR.big=748454784L,
-                                full.small=581894515L,
-                                full.big=301057392L,
-                                stop("unrecognized dataset ",sQuote(which),call.=FALSE)
-                                )
-                              )
-                     )
-  }
-}

Deleted: pkg/pompExamples/inst/GPL
===================================================================
--- pkg/pompExamples/inst/GPL	2015-07-06 16:49:14 UTC (rev 1250)
+++ pkg/pompExamples/inst/GPL	2015-07-07 13:16:46 UTC (rev 1251)
@@ -1,118 +0,0 @@
- GNU GENERAL PUBLIC LICENSE Version 2, June 1991
-
-Copyright (C) 1989, 1991 Free Software Foundation, Inc. 675 Mass Ave, Cambridge, MA 02139, USA 
-Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
-
-Preamble
-
-The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too.
-
-When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.
-
-To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it.
-
-For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.
-
-We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software.
-
-Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations.
-
-Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all.
-
-The precise terms and conditions for copying, distribution and modification follow.
-
-GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
-
-0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you".
-
-Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does.
-
-1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program.
-
-You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.
-
-2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions:
-
-a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change.
-
-b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License.
-
-c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.)
-
-These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it.
-
-Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program.
-
-In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License.
-
-3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following:
-
-a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,
-
-b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,
-
-c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.)
-
-The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable.
-
-If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code.
-
-4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance.
-
-5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it.
-
-6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License.
-
-7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program.
-
-If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances.
-
-It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice.
-
-This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.
-
-8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License.
-
-9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.
-
-Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.
-
-10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally.
-
-NO WARRANTY
-
-11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
-12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
-
-END OF TERMS AND CONDITIONS
-
-How to Apply These Terms to Your New Programs
-
-If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
-
-To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found.
-
-<one line to give the program's name and a brief idea of what it does.> Copyright (C) 19yy <name of author>
-
-This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-
-Also add information on how to contact you by electronic and paper mail.
-
-If the program is interactive, make it output a short notice like this when it starts in an interactive mode:
-
-Gnomovision version 69, Copyright (C) 19yy name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program.
-
-You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names:
-
-Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker.
-
-<signature of Ty Coon>, 1 April 1989 Ty Coon, President of Vice
-
-This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License.

Deleted: pkg/pompExamples/inst/NEWS
===================================================================
--- pkg/pompExamples/inst/NEWS	2015-07-06 16:49:14 UTC (rev 1250)
+++ pkg/pompExamples/inst/NEWS	2015-07-07 13:16:46 UTC (rev 1251)
@@ -1,34 +0,0 @@
-_N_e_w_s _f_o_r _P_a_c_k_a_g_e '_p_o_m_p_E_x_a_m_p_l_e_s'
-
-_C_h_a_n_g_e_s _i_n '_p_o_m_p_E_x_a_m_p_l_e_s' _v_e_r_s_i_o_n _0._2_7-_1:
-
-        ? _Parus major_ example (?pompExample(parus)?) reworked
-          slightly.
-
-_C_h_a_n_g_e_s _i_n '_p_o_m_p_E_x_a_m_p_l_e_s' _v_e_r_s_i_o_n _0._2_4-_1:
-
-        ? Examples included in the package can now be accessed using
-          ?pomp?'s ?pompExample? function.
-
-        ? New _Parus major_ example.
-
-_C_h_a_n_g_e_s _i_n '_p_o_m_p_E_x_a_m_p_l_e_s' _v_e_r_s_i_o_n _0._2_3-_2:
-
-        ? Update for use with ?pomp? version 0.50.
-
-_C_h_a_n_g_e_s _i_n '_p_o_m_p_E_x_a_m_p_l_e_s' _v_e_r_s_i_o_n _0._2_2-_1:
-
-        ? The pomp objects are no longer accessed using ?data?.
-          Instead, ?pertussis.sim? and ?budmoth.sim? are functions that
-          return the pomp objects.
-
-_C_h_a_n_g_e_s _i_n '_p_o_m_p_E_x_a_m_p_l_e_s' _v_e_r_s_i_o_n _0._2_1-_1:
-
-        ? Changed ?t0? for the budmoth model from 0 to -1.  The data
-          are different as well.
-
-_C_h_a_n_g_e_s _i_n '_p_o_m_p_E_x_a_m_p_l_e_s' _v_e_r_s_i_o_n _0._2_0-_1:
-
-        ? Ported these examples from ?pomp.devel?.  The data are not
-          identical to those in ?pomp.devel?, however.
-

Deleted: pkg/pompExamples/inst/NEWS.Rd
===================================================================
--- pkg/pompExamples/inst/NEWS.Rd	2015-07-06 16:49:14 UTC (rev 1250)
+++ pkg/pompExamples/inst/NEWS.Rd	2015-07-07 13:16:46 UTC (rev 1251)
@@ -1,36 +0,0 @@
-\name{NEWS}
-\title{News for Package 'pompExamples'}
-\section{Changes in \pkg{pompExamples} version 0.27-1}{
-  \itemize{
-    \item \emph{Parus major} example (\code{pompExample(parus)}) reworked slightly.
-  }
-}
-\section{Changes in \pkg{pompExamples} version 0.24-1}{
-  \itemize{
-    \item Examples included in the package can now be accessed using \pkg{pomp}'s \code{pompExample} function.
-    \item New \emph{Parus major} example.
-  }
-}
-\section{Changes in \pkg{pompExamples} version 0.23-2}{
-  \itemize{
-    \item Update for use with \pkg{pomp} version 0.50.
-  }
-}
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1251

From noreply at r-forge.r-project.org  Tue Jul  7 15:20:45 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  7 Jul 2015 15:20:45 +0200 (CEST)
Subject: [Pomp-commits] r1252 - / www www/content www/graphics
Message-ID: <20150707132046.063CB18784F@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-07 15:20:45 +0200 (Tue, 07 Jul 2015)
New Revision: 1252

Removed:
   TODO.md
   www/content/Makefile
   www/content/NEWS.html
   www/content/about.htm
   www/content/authors.htm
   www/content/ecology.bst
   www/content/refs.htm
   www/content/refs.tex
   www/content/vignettes.htm
   www/graphics/NSF_logo.jpg
   www/graphics/abstract.gif
   www/graphics/cc-by-nc.png
   www/graphics/cc0.png
   www/graphics/pomp_schematic1.png
   www/graphics/pomp_schematic2.png
   www/whitestyle.css
Log:
- remove unneeded web content

Deleted: TODO.md
===================================================================
--- TODO.md	2015-07-07 13:16:46 UTC (rev 1251)
+++ TODO.md	2015-07-07 13:20:45 UTC (rev 1252)
@@ -1,10 +0,0 @@
-### pomp to-do list
-
-- documentation on 'mifList', 'pmcmcList', etc.
-- 'transform' argument for pmcmc?
-- 'initializer' -> 'rinit' and perhaps 'dinit'
-- documentation: "regular parameters" instead of "non-IVP"
-- add 'coef' method for 'mifList' objects
-- objective function for spectrum matching
-- one-point SCQL function for possible use in fitting initial conditions
-- save particle filtering variance?  Prediction means are optional.  Only interesting for end-user if one wants to look at residuals.

Deleted: www/content/Makefile
===================================================================
--- www/content/Makefile	2015-07-07 13:16:46 UTC (rev 1251)
+++ www/content/Makefile	2015-07-07 13:20:45 UTC (rev 1252)
@@ -1,137 +0,0 @@
-INSTALLDIR = $(HOME)
-
-LATEX = latex
-PDFLATEX = pdflatex
-BIBTEX = bibtex
-MAKEIDX = makeindex
-DVIPS = dvips -t letter -Ppdf
-RM = rm -f
-CP = cp
-TAR = tar
-TARFLAGS = zcvf
-PSTOPDF = ps2pdf
-EPSTOPDF = epstopdf
-
-CC = gcc
-CXX = g++
-CFLAGS = -O2 -I. -Wall -static
-LDLIBS = -L. -L/usr/X11/lib 
-FC = g77
-FFLAGS = -O2 -fno-underscoring
-AR = ar
-ARFLAGS = rs
-INSTALL = install
-
-AWK = gawk
-L2H = latex2html
-L2HFLAGS = -scalable_fonts -style "whitestyle.css" -short_extn -local_icons -noinfo -split 0 -no_navigation -nosubdir -noaddress -nofootnode
-TIDY = tidy
-F2D = fig2dev
-GZIP = gzip
-ZIP = zip
-
-PSFIX = /usr/local/bin/psfix
-
-GRAPH = graph
-GRAPHFLAGS = -Tfig -K2 --max-line 256 --title-font-name "times-bolditalic" -F"times-bold" -W0.005 -B
-
-TABLES = 
-
-FIGS = 
-
-EPSFIGS = $(addsuffix .eps, $(FIGS))
-
-PDFFIGS = $(addsuffix .pdf, $(FIGS))
-
-%.ps: %.dvi
-	$(DVIPS) $* -o $*.ps
-
-%.dvi: %.tex
-	$(LATEX) $*
-	-$(BIBTEX) $*
-	$(LATEX) $*
-	$(LATEX) $*
-
-%.pdf: %.tex
-	$(PDFLATEX) $*
-	-$(BIBTEX) $*
-	$(PDFLATEX) $*
-	$(PDFLATEX) $*
-
-%.pdf: %.ps
-	$(PSTOPDF) $*.ps $*.pdf
-
-%.idx: %.tex
-	-$(LATEX) $*
-
-%.ind: %.idx
-	$(MAKEIDX) $*
-
-%.pdf: %.eps
-	$(EPSTOPDF) $*.eps --outfile=$*.pdf
-
-%.pdf: %.fig
-	$(F2D) -Lpdf $*.fig $@
-
-%.eps: %.fig
-	$(F2D) -Leps $*.fig $@
-
-%.gif: %.fig
-	$(F2D) -Lgif -t"#ffffff" $*.fig $@
-
-%.png: %.fig
-	$(F2D) -Lpng $*.fig $@
-
-%.pdf: %.fig
-	$(F2D) -Lpdf $*.fig $@
-
-%.pcx: %.fig
-	$(F2D) -Lpcx $*.fig $@
-
-%.htm: %.tex %.pdf
-	$(L2H) $(L2HFLAGS) $*
-	$(AWK) '{gsub("H2", "H3"); print;}' $*.htm > $*_1.htm
-	$(AWK) '{gsub("<BR><HR>", ""); print;}' $*_1.htm > $*_2.htm
-	-$(TIDY) -i -w --show-body-only yes $*_2.htm > $*.htm
-	$(RM) $*_1.htm $*_2.htm
-
-%.ps: %.nb.ps
-	$(PSFIX) $*.nb.ps > $@
-
-%.gz: %
-	$(GZIP) < $* > $*.gz
-
-%.tgz: %
-	$(TAR) $(TARFLAGS) $*.tgz $*
-
-%: %.c
-	$(CC) $(CFLAGS) $*.c $(LDLIBS) -o $*
-
-%: %.cc
-	$(CXX) $(CFLAGS) $*.cc $(LDLIBS) -o $*
-
-%: %.f
-	$(FC) $(FFLAGS) $*.f $(LDLIBS) -o $*
-
-(%.o): %.c
-	$(CC) -c $(CFLAGS) $*.c -o $*.o
-	$(AR) $(ARFLAGS) $@ $*.o
-	$(RM) $*.o 
-
-(%.o): %.cc
-	$(CXX) -c $(CFLAGS) $*.cc -o $*.o
-	$(AR) $(ARFLAGS) $@ $*.o
-	$(RM) $*.o 
-
-(%.o): %.f
-	$(FC) -c $(FFLAGS) $*.f -o $*.o
-	$(AR) $(ARFLAGS) $@ $*.o
-	$(RM) $*.o
-
-$(LIB):	$(LIB)($(addsuffix .o, $(basename $(SRC))))
-
-clean:
-	$(RM) *.log *.blg *.ilg *.aux *.lof *.lot *.toc *.idx *.ttt *.fff *.out internals.pl labels.pl
-
-fresh: clean
-	$(RM) *.bbl *.ind *.dvi *.ps

Deleted: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html	2015-07-07 13:16:46 UTC (rev 1251)
+++ www/content/NEWS.html	2015-07-07 13:20:45 UTC (rev 1252)
@@ -1,1622 +0,0 @@
-<!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 style="text-align: right;">R Documentation</td></tr></table>
-
-<h2>News for package &lsquo;pomp&rsquo;</h2>
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.69-2</h3>
-
-
-<ul>
-<li><p> Measles data from England and Wales, kindly provided by Ben Bolker, are now included as <code>ewmeas</code> and <code>ewcitmeas</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.68-2</h3>
-
-
-<ul>
-<li><p> When using <code>Csnippet</code>s, by default, the C codes and shared-object files are stored in the R session's temporary directory.
-One can override this behavior by setting the global <code>pomp.cache</code> option.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.67-1</h3>
-
-
-<ul>
-<li><p> A 'pomp' object's initializer can now be specified as a Csnippet.
-</p>
-</li>
-<li><p> The default initializer is now considerably faster.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.66-4</h3>
-
-
-<ul>
-<li><p> A full-featured version of IF2, an improved iterated filtering algorithm, is now available as <code>mif2</code>.
-This allows a more general structure for the random perturbations applied to parameters and is generally more efficient and stable than IF1.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.65-2</h3>
-
-
-<ul>
-<li><p> In the <code>pomp</code> constructor, unrecognized arguments are stored internally for use with user-supplied model functions.
-As of this version, an informative message is generated when this happens.
-Previously, this silent behavior was a source of confusion for some users.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.65-1</h3>
-
-
-<ul>
-<li><p> The unfortunately named <code>pomp</code> arguments <code>parameter.transform</code> and <code>parameter.inv.transform</code> have been deprecated in favor of the more mnemonic <code>toEstimationScale</code> and <code>fromEstimationScale</code>.
-Using the old arguments will result in the same behavior as previously, but a warning will be generated.
-</p>
-</li></ul>
-
-
-
-<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>
-
-
-<ul>
-<li><p> The optimization packages <span class="pkg">nloptr</span> and <span class="pkg">subplex</span> are no longer dependencies of <span class="pkg">pomp</span> that will be loaded at the time <span class="pkg">pomp</span> is.
-Instead, they are imported as needed.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.62-2</h3>
-
-
-<ul>
-<li><p> Bug fix in <code>partrans</code> when transformations are implemented using <code>Csnippet</code>s.
-</p>
-</li>
-<li><p> Remove the <code>verhulst</code> example.
-</p>
-</li></ul>
-
-
-
-<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.
-</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>
-
-
-<ul>
-<li> <p><code>mif</code>'s <code>pars</code> argument, which is redundant, is now deprecated.
-In a future release, this argument will be removed.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.61-1</h3>
-
-
-<ul>
-<li><p> When using <code>Csnippet</code>s or <code>pompBuilder</code>, it is no longer necessary to manually load and unload the dynamically loadable library.
-This is now handled automatically.
-Accordingly, the <code>link</code> argument of <code>pompBuilder</code> has been removed.
-The <code>pompLoad</code> and <code>pompUnload</code> functions introduced in 0.58-1 remain available, though they should rarely be needed.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.60-1</h3>
-
-
-<ul>
-<li> <p><code>pmcmc</code> and <code>abc</code> can now use arbitrary symmetric proposal distributions via the <code>proposal</code> argument.
-For the moment, these are constrained to be symmetric.
-Two new functions, <code>mvn.diag.rw</code> and <code>mvn.rw</code> generate suitable proposal functions.
-The first generates a multivariate normal random-walk proposal with diagonal variance-covariance matrix; this duplicates the old behavior of both <code>abc</code> and <code>pmcmc</code>.
-The second, <code>mvn.rw</code>, corresponds to a multivariate normal random-walk proposal with arbitrary variance-covariance matrix.
-</p>
-</li>
-<li><p> In <code>pmcmc</code> and <code>abc</code>, the arguments <code>pars</code> and <code>rw.sd</code> are now unneeded and have been deprecated.
-Use of <code>rw.sd</code> will generate a warning and result in behavior equivalent to choosing <code>proposal=mvn.diag.rw(rw.sd)</code>.
-Use of <code>pars</code> will be ignored, with a warning.
-</p>
-</li>
-<li><p> In <code>nlf</code>, the <code>transform.params</code> argument is now deprecated;
-use instead the <code>transform</code> argument, as in the other inference methods.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.59-1</h3>
-
-
-<ul>
-<li><p> A bug in <code>spect.match</code> has been fixed.
-Thanks to Karsten Hempel for finding it and contributing the fix.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.58-1</h3>
-
-
-<ul>
-<li><p> Compiler messages are now suppressed by default when <code>Csnippet</code>s are used in construction of a <code>pomp</code> object.
-These can be enabled by setting <code>options(verbose=TRUE)</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.58-1</h3>
-
-
-<ul>
-<li><p> A <code>pomp</code> object created with <code>Csnippet</code>s or <code>pompBuilder</code> will now remember its associated shared-object file, which can be unloaded and reloaded using the new <code>pompUnload</code> and <code>pompLoad</code> methods.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.57-1</h3>
-
-
-<ul>
-<li> <p><code>simulate</code> has a new argument, <code>include.data</code>, that when used in conjuncion with <code>as.data.frame=TRUE</code> will include the actual data in the resulting data frame along with the simulations.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.56-1</h3>
-
-
-<ul>
-<li><p> Revamped the <code>pompExample</code> function.
-A search path for example directories is now stored in global option &quot;pomp.examples&quot;.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.55-1</h3>
-
-
-<ul>
-<li><p> New <code>values</code> method extracts simulated probe values on <code>probed.pomp</code> object.
-</p>
-</li>
-<li><p> Better documentation in the &lsquo;<span class="file">pomp.h</span>&rsquo; header file.
-</p>
-</li>
-<li><p> Vignettes now feature <code>bsmc2</code> instead of <code>bsmc</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.54-1</h3>
-
-
-<ul>
-<li><p> A modified version of the Liu and West (2001) algorithm is included as <code>bsmc2</code>.
-</p>
-</li>
-<li><p> By default, when <code>B</code> is of class <code>bsmcd.pomp</code>, <code>plot(B)</code> ignores fixed parameters.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.53-6</h3>
-
-
-<ul>
-<li><p> A bug having to do with paths to the temporary C files, encountered when using <code>Csnippet</code>s under windows, has been fixed.
-</p>
-</li>
-<li><p> Package demos are now checked by <code>R CMD check</code> on all platforms.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.53-1</h3>
-
-
-<ul>
-<li> <p><code>nlf</code> now returns an S4 object of class <code>nlfd.pomp</code> with a <code>logLik</code> method for extracting the log quasi likelihood and a <code>$</code> method for extracting arbitrary components.
-</p>
-</li>
-<li><p> The <code>transform</code> argument (for providing a function to transform the data) has been removed in favor of <code>transform.data</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.52-1</h3>
-
-
-<ul>
-<li><p> The new <code>mifList</code> class facilitates approaches based on multiple <code>mif</code> runs.
-The <code>c</code> method constructs <code>mifList</code>s from <code>mif</code>s.
-The <code>plot</code> method produces diagnostic plots.
-</p>
-</li>
-<li> <p><code>compare.mif</code> is now deprecated in favor of <code>plot</code> applied to a <code>mif</code> or <code>mifList</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.51-3</h3>
-
-
-<ul>
-<li> <p><code>transform</code> argument for <code>pmcmc</code> and <code>abc</code> has been removed.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.51-2</h3>
-
-
-<ul>
-<li><p> More informative error messages are generated when a needed variable cannot be found.
-</p>
-</li>
-<li><p> Features that facilitate multiple ABC chains have been added.
-There is a <code>c</code> method to combine <code>abc</code> objects into an <code>abcList</code> object and to combine <code>abcList</code> objects.
-Running <code>conv.rec</code> on an <code>abc</code> or <code>abcList</code> object produces <span class="pkg">coda</span> <code>mcmc</code> and <code>mcmc.list</code> objects, respectively.
-Diagnostic plots are produced by running <code>plot</code> on such objects.
-</p>
-</li>
-<li><p> Basic structure of <code>pmcmcList</code> and <code>abcList</code> objects is changed: these objects now inherit directly from <code>list</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.51-1</h3>
-
-
-<ul>
-<li><p> Package <span class="pkg">coda</span> is now a dependency of <span class="pkg">pomp</span>.
-This package provides various generic MCMC diagnostics.
-</p>
-</li>
-<li><p> Features that facilitate multiple PMCMC chains have been added.
-There is a <code>c</code> method to combine <code>pmcmc</code> objects into a <code>pmcmcList</code> object and to combine <code>pmcmcList</code> objects.
-Running <code>conv.rec</code> on a <code>pmcmc</code> or <code>pmcmcList</code> object now produces <span class="pkg">coda</span> <code>mcmc</code> and <code>mcmc.list</code> objects, respectively.
-Diagnostic plots are produced by running <code>plot</code> on such objects.
-</p>
-</li>
-<li><p> The <code>compare.pmcmc</code> and <code>compare.abc</code> methods have been removed as obsolete.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.50-9</h3>
-
-
-<ul>
-<li><p> Fix bug in <code>compare.pmcmc</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.50-8</h3>
-
-
-<ul>
-<li><p> Introduced new <code>compare.pmcmc</code> and <code>compare.abc</code> functions, comparable to <code>compare.mif</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.50-6</h3>
-
-
-<ul>
-<li><p> The package manual and tutorials are no longer included with the package source.
-Instead, links are provided to the <span class="pkg">pomp</span> website.
-</p>
-</li>
-<li><p> The package help pages have been revisited for accuracy and completeness.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.50-1</h3>
-
-
-<ul>
-<li> <p><code>pomp</code> can now take snippets of C code directly as definitions of the various basic functions.
-This is accomplished through the use of a new <code>Csnippet</code> function.
-See the &lsquo;sir&rsquo; demo for a demonstration.
-</p>
-</li>
-<li><p> It is now possible to specify global variables and typedefs using the <code>globals</code> argument to <code>pompBuilder</code> and <code>pomp</code>.
-See the &lsquo;sir&rsquo; demo for a demonstration.
-Thanks to Carl Pearson for the suggestion.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.49-1</h3>
-
-
-<ul>
-<li><p> A new method, <code>probe.match.objfun</code>, constructs objective functions suitable for use in optimizers.
-</p>
-</li>
-<li> <p><code>pomp</code> now depends on <code>nloptr</code>, which provides a suite of optimization algorithms.
-This package can now be used in various methods for optimization of an objective function.
-</p>
-</li>
-<li><p> New inline C functions <code>to_log_barycentric</code> and <code>from_log_barycentric</code> are provided in &lsquo;<span class="file">pomp.h</span>&rsquo; to facilitate log-barycentric transformations.
-These have proven very useful in dealing with parameters constrained to sum to one (e.g., initial conditions of compartmental models).
-</p>
-</li>
-<li><p> Bug fix in <code>periodic.bspline.basis</code>.
-</p>
-</li>
-<li><p> Package vignettes are no longer available via <code>vignette()</code> but can be reached from the help index.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.48-3</h3>
-
-
-<ul>
-<li><p> Correct a bug in <code>abc</code> to do with parameter transformation.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.48-1</h3>
-
-
-<ul>
-<li><p> Create new <code>dprior</code> and <code>rprior</code> slots for <code>pomp</code> objects.
-These will be used by the Bayesian methods (currently <code>abc</code>, <code>bsmc</code>, and <code>pmcmc</code>).
-The <code>hyperparams</code> argument to these methods has been removed;
-hyperparameters are now treated just as any others.
-</p>
-</li>
-<li> <p><code>bsmc</code> can now be called so that the particles are drawn from the prior distribution (as set by the <code>rprior</code> slot).
-</p>
-</li>
-<li><p> Some of the longer tests will only be run if an environment variable is set.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.47-4</h3>
-
-
-<ul>
-<li><p> Revisit <code>dacca</code> bug.  Set negative compartments to zero along with compartments immediately downstream.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.47-3</h3>
-
-
-<ul>
-<li><p> Fix bug that arises only very occasionally in the <code>dacca</code> cholera example.
-</p>
-</li>
-<li><p> Modify <code>dacca</code> model so that rare positivity violations are punished in a different way.
-This modifies the formal model slightly.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.47-2</h3>
-
-
-<ul>
-<li><p> By default, <code>pompBuilder</code> now creates all files in the temporary directory.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.47-1</h3>
-
-
-<ul>
-<li> <p><code>abc</code> implements Approximate Bayesian Computation for pomp models.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.46-1</h3>
-
-
-<ul>
-<li> <p><code>pompExample</code> now has an optional argument, <code>envir</code>, determining which environment the <code>pomp</code> object will be loaded into.
-</p>
-</li>
-<li> <p><code>logmeanexp</code> now has an optional argument, <code>se</code>, allowing for computation of an approximate standard error.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-8</h3>
-
-
-<ul>
-<li><p> bug fix in <code>gompertz</code> example.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-7</h3>
-
-
-<ul>
-<li><p> bug fix in <code>pmcmc</code>: Metropolis-Hastings ratio was incorrect except for flat priors!
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-6</h3>
-
-
-<ul>
-<li><p> a fix so that <code>pompBuilder</code> will find &lsquo;<span class="file">pomp.h</span>&rsquo; header file on Windows machines.  Thanks to Dave Hayman for finding the problem.
-</p>
-</li>
-<li><p> new <code>logmeanexp</code> function.
-</p>
-</li>
-<li><p> some reorganization of the source package structure.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-4</h3>
-
-
-<ul>
-<li><p> changes in the way <code>reulermultinom</code>, <code>deulermultinom</code>, <code>dot_product</code> are exported to other packages.  Rather than just being exported as linkables, these are now also defined as static inline functions in the &lsquo;<span class="file">pomp.h</span>&rsquo; header.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-3</h3>
-
-
-<ul>
-<li><p> Fix bug with <code>continue</code> and method <code>"mif2"</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-2</h3>
-
-
-<ul>
-<li><p> new method to coerce <code>pfilterd.pomp</code> objects to data-frames.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-1</h3>
-
-
-<ul>
-<li> <p><code>profileDesign</code> can now handle variables of mixed type.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.44-1</h3>
-
-
-<ul>
-<li><p> New <code>"mif2"</code> option for <code>mif</code>.
-</p>
-</li>
-<li><p> The default behavior for <code>mif</code> and <code>pfilter</code> with respect to filtering failures has been changed.
-Before, the default behavior has been to stop with an error on the first filtering failure (<code>max.fail=0</code>).
-Now, the default is <code>max.fail=Inf</code>, i.e., an error is never triggered.
-</p>
-</li>
-<li><p> The implementation of MIF cooling schedules has been changed to make it more general.
-The cooling schedule is now specified by a <code>type</code> and a <code>fraction</code>.
-Currently, supported <code>cooling.type</code>s include <code>geometric</code> (the old behavior) and <code>hyperbolic</code>, i.e., a <i>1/(1+n)</i> schedule.
-The <code>cooling.fraction</code> argument specifies the cooling at 50 iterations.
-That is, if <code>s</code> is the intensity of the random-walk perturbation to parameters at the first iteration (<code>rw.sd</code>), then the intensity at iteration 50 is <code>s*cooling.fraction</code>.
-</p>
-</li>
-<li><p> Remove all <code>data()</code>-loadable <code>pomp</code> objects.
-To load the prebuilt example <code>pomp</code> objects from previous versions, use the new <code>pompExample</code> function.
-E.g., instead of <code>data(euler.sir)</code>, do <code>pompExample("euler.sir")</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.43-4</h3>
-
-
-<ul>
-<li><p> Clean up tests.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.43-3</h3>
-
-
-<ul>
-<li><p> Fix bug in <code>pompBuilder</code> on mac.
-</p>
-</li>
-<li><p> Fix bug in <code>dmeasure</code> when <code>log=TRUE</code>.  Bug located by R. Reiner.
-</p>
-</li>
-<li><p> Add <code>eff.sample.size</code> and <code>cond.logLik</code> methods for <code>pfilterd.pomp</code> objects.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.43-1</h3>
-
-
-<ul>
-<li><p> Modify <code>traj.match.objfun</code> to allow arbitrary parameters to be passed to the ODE integrator.
-</p>
-</li>
-<li><p> Add <code>params</code> argument to <code>pomp</code> so that parameters can be specified at the time the <code>pomp</code> object is created.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.42-6</h3>
-
-
-<ul>
-<li><p> Improve error checking in <code>pomp</code>.
-</p>
-</li>
-<li><p> Add support for covariates to <code>pompBuilder</code>.
-</p>
-</li>
-<li><p> Add native parameter transformation routines to the demos.
-</p>
-</li>
-<li><p> Change the warning behavior in <code>lookup_table</code> so that warnings are not generated unless true extrapolation is performed (i.e., eliminate the warnings at the boundary).
-</p>
-</li>
-<li><p> Some small modifications to the &lsquo;<span class="file">pomp.h</span>&rsquo; header file.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.42-4</h3>
-
-
-<ul>
-<li><p> When <code>trajectory</code> calls <code>ode</code>, there is a need to preserve information across calls to the vectorfield-evaluating function.
-The code has been modified to do this in a cleaner way.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.42-2</h3>
-
-
-<ul>
-<li><p> Several minor bugs have been fixed.
-See the ChangeLog for details.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.42-1</h3>
-
-
-<ul>
-<li><p> An EXPERIMENTAL facility for constructing <code>pomp</code> objects out of native C routines is now included (pompBuilder).
-This facility is being actively developed and future changes may not be backward compatible.
-</p>
-</li>
-<li><p> A new facility allowing access to the <code>userdata</code> slot of a <code>pomp</code> object from compiled <code>rprocess</code>, <code>rmeasure</code>, <code>dprocess</code>, <code>dmeasure</code>, <code>skeleton</code>, and <code>partrans</code> codes is now available.
-Calls to the new C routines <code>get_pomp_userdata</code>, <code>get_pomp_userdata_int</code>, and <code>get_pomp_userdata_double</code> allow retrieval of these elements.
-</p>
-</li>
-<li><p> Some of the <code>data()</code>-loadable examples have been reworked to make use of the above facility.
-The parameterization of these examples has changed.
-These changes are not backward compatible: codes that depend on the <code>data()</code>-loadable examples may be broken.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-8</h3>
-
-
-<ul>
-<li><p> A demonstration of <code>pompBuilder</code> has been put into the &ldquo;advanced topics&rdquo; vignette.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-7</h3>
-
-
-<ul>
-<li><p> A bug in the <code>blowflies</code> example has been fixed.
-Thanks to Greg Minshall for discovering it.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-6</h3>
-
-
-<ul>
-<li><p> The <code>gompertz</code> example parameter transformations have been changed.
-No longer are the names of the parameter vector changed in the transformation.
-This change is not backward-compatible, but only codes using this example are affected.
-</p>
-</li>
-<li><p> The <code>euler.sir</code> and <code>gillespie.sir</code> examples have been changed.
-The transmission rate <i>&beta;(t)</i> is now the arithmetic sum of the seasonality basis functions.
-Before, it was the geometric sum.
-<i>R_0</i> is now given by the arithmetic average of the <i>&beta;</i> parameters divided by <i>&gamma;+&mu;</i>.
-This change is not backward-compatible, but only codes using these examples are affected.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-5</h3>
-
-
-<ul>
-<li><p> An experimental facility for constructing <code>pomp</code> objects with native C routines is now included.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-4</h3>
-
-
-<ul>
-<li><p> The <code>blowflies</code>, <code>euler.sir</code>, <code>gillespie.sir</code>, <code>bbs</code>, and <code>ricker</code> <code>data()</code>-loadable examples have been changed to make the parameterization simpler and more natural.
-This change is not backward-compatible, but only codes using this example are affected.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-3</h3>
-
-
-<ul>
-<li><p> In <code>trajectory</code>, all vectorfield and map evaluation is now done in C for speed.
-For continuous-time dynamical systems, this gives an approximately 4-fold speedup.
-</p>
-</li>
-<li><p> Demos have been created to show some examples.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-2</h3>
-
-
-<ul>
-<li><p> A segfault bug in <code>bbs</code> example has been fixed.
-</p>
-</li>
-<li><p> The posterior medians (not means) are now stored in the <code>params</code> slot of the <code>bsmcd.pomp</code> object.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-1</h3>
-
-
-<ul>
-<li><p> New arguments in <code>mif</code>, <code>nlf</code>, <code>bsmc</code>, <code>pmcmc</code>, <code>probe-match</code>, and <code>traj-match</code> allow the estimation to be done on a transformed parameter space.
-When <code>transform=TRUE</code> in these commands (<code>transform.params=TRUE</code> for <code>nlf</code>), estimation is performed on the transformed parameter space.
-This is described and demonstrated in the &ldquo;intro_to_pomp&rdquo; vignette.
-</p>
-</li>
-<li><p> The <code>data()</code>-loadable examples have been re-implemented to make use of the above-mentioned facility.
-Note that this new functionality makes it unnecessary to un-transform model parameters within the user-specified <code>rprocess</code>, <code>dprocess</code>, <code>rmeasure</code>, <code>dmeasure</code>, <code>skeleton</code>, and <code>initializer</code> codes.
-This change is not backward-compatible, but only codes using these <code>data()</code>-loadable example are affected.
-</p>
-</li>
-<li><p> The Bayesian sequential Monte Carlo command <code>bsmc</code> now returns not a list but an object of class <code>bsmcd.pomp</code>.
-An experimental <code>plot</code> method for objects of this class now exists.
-Also, the parameter posterior means are now stored in the <code>params</code> slot of the <code>bsmcd.pomp</code> object:
-access them with the <code>coef</code> command as usual.
-</p>
-</li>
-<li><p> A new example, using data from an influenza outbreak in a British boarding school and an SIR model, has been included.
-Do <code>data(bbs)</code> to load it.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-9</h3>
-
-
-<ul>
-<li><p> Setting the new argument <code>as.data.frame</code> to <code>TRUE</code> in <code>simulate</code> and <code>trajectory</code> causes the results to be returned as a data-frame.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-8</h3>
-
-
-<ul>
-<li><p> A new method <code>partrans</code> allows transformation of vectors or matrices of parameters.
-The parameter transformations have been pushed into C for speed.
-It is possible to specify native parameter transformation routines in addition to C functions, but this last facility has not yet been extensively tested.
-A new slot <code>has.trans</code> has been introduced into the <code>pomp</code> class, and the types of slots <code>par.trans</code> and <code>par.untrans</code> have changed.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-7</h3>
-
-
-<ul>
-<li> <p><code>parmat</code> now gracefully handles the case when <code>params</code> is already a matrix.
-</p>
-</li>
-<li><p> Error in the documentation of <code>pfilter</code> repaired.
-Thanks to Alex Smith for pointing this out.
-</p>
-</li>
-<li><p> Improvements in the documentation of the Nicholson blowflies data <code>data(blowflies)</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-6</h3>
-
-
-<ul>
-<li><p> When a <code>pomp</code> object is updated using <code>pomp</code>, the <code>params</code> slot will now be copied over (appropriately transformed).
-Before, it was simply dropped.
-</p>
-</li>
-<li><p> The <code>gillespie.sir</code> example has been changed to make the reporting rate equal to <code>rho</code>.
-Before, it was fixed at 10%.
-</p>
-</li>
-<li><p> A new error-trap has been put into <code>probe</code> and <code>probe.match</code> for the case <code>nsim &lt; nprobes</code>.
-Thanks to Dani Jonas for finding this error.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-5</h3>
-
-
-<ul>
-<li><p> More informative error messages when dimension of state space or data space disagree internally.
-</p>
-</li>
-<li><p> The <code>weighted</code> argument to <code>mif</code> and <code>continue</code> is now deprecated in favor of a new argument <code>method</code>.
-The old <code>weighted=TRUE</code> corresponds to <code>method="mif"</code> while the old <code>weighted=FALSE</code> corresponds to <code>method="unweighted"</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-4</h3>
-
-
-<ul>
-<li><p> New functions <code>traj.match.objfun</code> and <code>probe.match.objfun</code> have been added.
-These functions construct functions of one argument suitable for use as objective functions in <code>optim</code>-like optimizers (iincluding <code>subplex</code> and <code>sannbox</code>).
-Minimizing these functions solves the trajectory-matching problem and probe-matching problem, respectively.
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1252

From noreply at r-forge.r-project.org  Tue Jul  7 15:20:48 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  7 Jul 2015 15:20:48 +0200 (CEST)
Subject: [Pomp-commits] r1253 - /
Message-ID: <20150707132048.1EC1F18784F@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-07 15:20:47 +0200 (Tue, 07 Jul 2015)
New Revision: 1253

Modified:
   README.md
Log:
- update README

Modified: README.md
===================================================================
--- README.md	2015-07-07 13:20:45 UTC (rev 1252)
+++ README.md	2015-07-07 13:20:47 UTC (rev 1253)
@@ -1,6 +1,3 @@
 **pomp**, an *R* package for statistical inference using partially observed Markov processes
 
-- the `pkg` directory contains the source code for several `R` packages  
-- the `www` directory contains the `pomp` website
-
-The package's official website is [pomp.r-forge.r-project.org](http://pomp.r-forge.r-project.org).
+Development has moved to [github](http://kingaa.github.io/pomp).


From noreply at r-forge.r-project.org  Tue Jul  7 15:20:49 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  7 Jul 2015 15:20:49 +0200 (CEST)
Subject: [Pomp-commits] r1254 - /
Message-ID: <20150707132049.C44BC18784F@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-07 15:20:49 +0200 (Tue, 07 Jul 2015)
New Revision: 1254

Added:
   README
Removed:
   README.md
Log:
- use plain text for README

Added: README
===================================================================
--- README	                        (rev 0)
+++ README	2015-07-07 13:20:49 UTC (rev 1254)
@@ -0,0 +1,4 @@
+pomp, an R package for statistical inference using partially observed Markov processes
+
+Development has moved to github: http://kingaa.github.io/pomp.
+

Deleted: README.md
===================================================================
--- README.md	2015-07-07 13:20:47 UTC (rev 1253)
+++ README.md	2015-07-07 13:20:49 UTC (rev 1254)
@@ -1,3 +0,0 @@
-**pomp**, an *R* package for statistical inference using partially observed Markov processes
-
-Development has moved to [github](http://kingaa.github.io/pomp).


From noreply at r-forge.r-project.org  Tue Jul  7 15:21:39 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  7 Jul 2015 15:21:39 +0200 (CEST)
Subject: [Pomp-commits] r1255 - pkg
Message-ID: <20150707132139.A4FE118784F@r-forge.r-project.org>

Author: kingaa
Date: 2015-07-07 15:21:39 +0200 (Tue, 07 Jul 2015)
New Revision: 1255

Removed:
   pkg/Makefile
   pkg/Rprofile
Log:
- remove unneeded files

Deleted: pkg/Makefile
===================================================================
--- pkg/Makefile	2015-07-07 13:20:49 UTC (rev 1254)
+++ pkg/Makefile	2015-07-07 13:21:39 UTC (rev 1255)
@@ -1,181 +0,0 @@
-REPOS=/var/www/html/R/
-SRCREPOS=src/contrib
-WINREPOS=bin/windows/contrib/3.2
-DOCREPOS=doc/packages
-ARCHIVE=./dists
-INSTALL_DIR=./library
-
-REXE = R --vanilla
-RCMD = $(REXE) CMD
-RCMD_ALT = R --no-save --no-restore CMD
-RSCRIPT = Rscript --vanilla
-
-PDFLATEX = pdflatex
-BIBTEX = bibtex
-MAKEIDX = makeindex
-
-RM = rm -f
-CP = cp
-TOUCH = touch
-INSTALL = install
-
-default:
-
-.PHONY:
-
-pomp.dist: pomp/inst/include/pomp.h
-
-pomp/inst/include/pomp.h: pomp/src/pomp.h
-	$(CP) $^ $@
-
-pomp.vignettes: export POMP_BUILD_VIGNETTES=yes
-%.dist %.manual %.vignettes: export R_QPDF=qpdf
-%.dist %.manual %.vignettes: export R_GSCMD=gs
-%.dist %.manual %.vignettes: export GS_QUALITY=ebook
-%.dist %.manual %.vignettes: export R_HOME=$(shell $(REXE) RHOME)
-%.check %.xcheck: export POMP_FULL_TESTS=yes
-%.crancheck: export R_PROFILE_USER=./Rprofile
-%.crancheck: export R_PROFILE_USER=$(CURDIR)/Rprofile
-%.vignettes %.data: export R_LIBS=$(CURDIR)/library
-%.xcheck: export R_LIBS=$(CURDIR)/check
-%.bin %.check %.qcheck %.qqcheck %.xcheck %.crancheck %.upload %.publish %.clean %.install %.win: PKG = $*_$(shell perl -ne 'print $$1 if /Version:\s+(\d+\.\d+-\d+)/;' $*/DESCRIPTION)
-
-pomp.vignettes: pomp.install pomp.manual
-	(cd ../www/vignettes; make)
-	cp pomp.pdf ../www/vignettes
-	$(RCMD) Rdconv -t html pomp/inst/NEWS.Rd -o ../www/content/NEWS.html
-
-pompExamples.vignettes: pompExamples.install
-	(cd pompExamples/vignettes; make)
-
-%.data: %.install
-	cd $*/inst/data-R; make
-
-%.win: %.dist
-	ncftpput -v win-builder.r-project.org R-release $(PKG).tar.gz
-	$(TOUCH) $@
-
-%.upload: %.dist
-	ncftpput -v cran.r-project.org incoming $(PKG).tar.gz
-	$(TOUCH) $@
-
-%.crandist: %.cransrc
-	$(RCMD) build --resave-data --compact-vignettes --md5 cran/$*
-	$(TOUCH) $@
-
-%.crancheck: %.crandist
-	$(RCMD_ALT) check --as-cran --library=check $(PKG).tar.gz
-	$(TOUCH) $@
-
-%.cransrc:
-	mkdir -p cran check
-	$(RM) -r cran/$*
-	git archive --format=tar HEAD $* | (cd cran; tar -xf -)
-	$(RM) -r cran/$*/tests 
-	$(TOUCH) $@
-
-%.xcheck: %.check
-	mkdir -p check
-	$(REXE) -d "valgrind --tool=memcheck --track-origins=yes --leak-check=full" < $*.Rcheck/$*-Ex.R
-	$(TOUCH) $@
-
-%.check: %.dist
-	mkdir -p check
-	$(RCMD) check --library=check $(PKG).tar.gz
-	$(TOUCH) $@
-
-%.qcheck: %.dist
-	mkdir -p check
-	$(RCMD) check --library=check --no-vignettes --no-tests $(PKG).tar.gz
-	$(TOUCH) $@
-
-%.qqcheck: %.dist
-	mkdir -p check
-	$(RCMD) check --library=check --no-codoc --no-examples --no-vignettes --no-manual --no-tests $(PKG).tar.gz
-	$(TOUCH) $@
-
-%.manual:
-	$(RM) $*.pdf
-	$(RCMD) Rd2pdf --no-preview --pdf $*
-	$(RSCRIPT) -e "tools::compactPDF(\"$*.pdf\")";
-	$(TOUCH) $@
-
-%.included_manual: %.manual
-	$(CP) $*.pdf $*/inst/doc/manual.pdf
-	$(TOUCH) $@
-
-%.dist:
-	-$(RCMD) Rdconv -t txt $*/inst/NEWS.Rd -o $*/inst/NEWS
-	$(RCMD) build --force --no-manual --resave-data --compact-vignettes=both $*
-	$(TOUCH) $@
-
-%.bin: %.dist
-	$(RCMD) build --force --binary $(PKG).tar.gz
-	$(TOUCH) $@
-
-%.clean: clean
-	$(RM) $*.dist $*.check $*.qcheck $*.qqcheck $*.xcheck $*.crancheck $*.manual $*.cransrc
-	$(RM) -r $*.Rcheck check/$* cran/$*
-	$(RM) $*/src/*.o $*/src/*.so $*/src/symbols.rds $*/vignettes/Rplots.*
-	$(RM) $(PKG).tar.gz $(PKG).zip $*.pdf
-
-%.distclean: %.clean
-	$(RM) $*.win $*.upload $*.bin $*.changelog $*.crandist $*.included_manual
-
-%.install: %.dist
-	mkdir -p $(INSTALL_DIR)
-	$(RCMD) INSTALL --library=$(INSTALL_DIR) $(PKG).tar.gz
-	$(TOUCH) $@
-
-%.remove:
-	-$(RCMD) REMOVE --library=$(INSTALL_DIR) $*
-	$(RM) $*.install
-
-%.publish: %.dist %.manual
-	mkdir -m0755 -p $(REPOS)/$(WINREPOS)
-	mkdir -m0755 -p $(REPOS)/$(SRCREPOS)
-	mkdir -m0755 -p $(REPOS)/$(DOCREPOS)
-	(cd $(REPOS)/$(WINREPOS); $(RM) $*_*.zip)
-	(cd $(REPOS)/$(SRCREPOS); $(RM) $*_*.tar.gz)
-	(cd $(REPOS)/$(DOCREPOS); $(RM) $*.pdf)
-	-$(INSTALL) -m0644 $(PKG).zip $(REPOS)/$(WINREPOS)
-	-$(INSTALL) -m0644 $(PKG).tar.gz $(REPOS)/$(SRCREPOS)
-	-$(INSTALL) -m0644 $*.pdf $(REPOS)/$(DOCREPOS)
-	$(RSCRIPT) -e 'Sys.umask("0022"); tools::write_PACKAGES(dir="$(REPOS)/$(WINREPOS)",type="win.binary")'
-	$(RSCRIPT) -e 'Sys.umask("0022"); tools::write_PACKAGES(dir="$(REPOS)/$(SRCREPOS)",type="source")'
-	mkdir -p $(ARCHIVE)
-	-$(INSTALL) -m0644 $(PKG).zip $(ARCHIVE)
-	-$(INSTALL) -m0644 $(PKG).tar.gz $(ARCHIVE)
-	-$(INSTALL) -m0644 $*.pdf $(ARCHIVE)
-	$(RSCRIPT) -e 'Sys.umask("0022"); tools::write_PACKAGES(dir="dists",type="source")'
-
-%.tex: %.Rnw
-	$(RSCRIPT) -e "library(knitr); knit(\"$*.Rnw\")"
-
-%.R: %.Rnw
-	$(RSCRIPT) -e "library(knitr); purl(\"$*.Rnw\")"
-
-%.pdf: %.tex
-	$(PDFLATEX) $*
-	-$(BIBTEX) $*
-	$(PDFLATEX) $*
-	$(PDFLATEX) $*
-
-%.bbl: %.tex
-	-$(PDFLATEX) $*
-	$(BIBTEX) $*
-
-%.idx: %.tex
-	-$(PDFLATEX) $*
-
-%.ind: %.idx
-	$(MAKEIDX) $*
-
-clean:
-	$(RM) *.o *.so *.tex *.log *.aux *.out *.nav *.snm *.toc *.bak
-	$(RM) Rplots.ps Rplots.pdf
-
-fresh: clean
-	$(RM) -r library check cran
-
-.SECONDARY:

Deleted: pkg/Rprofile
===================================================================
--- pkg/Rprofile	2015-07-07 13:20:49 UTC (rev 1254)
+++ pkg/Rprofile	2015-07-07 13:21:39 UTC (rev 1255)
@@ -1 +0,0 @@
-options(repos = c(CRAN="http://cran.r-project.org"))