[Pomp-commits] r1142 - pkg/pomp pkg/pomp/R pkg/pomp/inst pkg/pomp/tests www/content www/vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Mar 15 17:09:02 CET 2015 

Author: kingaa
Date: 2015-03-15 17:09:02 +0100 (Sun, 15 Mar 2015)
New Revision: 1142

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/minim.R
   pkg/pomp/R/nlf.R
   pkg/pomp/R/spect-match.R
   pkg/pomp/inst/NEWS
   pkg/pomp/inst/NEWS.Rd
   pkg/pomp/tests/bbs-trajmatch.R
   pkg/pomp/tests/bbs-trajmatch.Rout.save
   pkg/pomp/tests/ou2-probe.R
   pkg/pomp/tests/ou2-probe.Rout.save
   www/content/NEWS.html
   www/vignettes/pomp.pdf
Log:
- nloptr and subplex are no longer Dependencies but are Imported instead

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/DESCRIPTION	2015-03-15 16:09:02 UTC (rev 1142)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.62-9
-Date: 2015-03-14
+Version: 0.63-1
+Date: 2015-03-15
 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")),
@@ -18,8 +18,8 @@
 	  )
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially observed Markov processes (AKA stochastic dynamical systems, state-space models).
-Depends: R(>= 3.0.0), methods, subplex, nloptr
-Imports: stats, graphics, mvtnorm, deSolve, coda
+Depends: R(>= 3.0.0), methods
+Imports: stats, graphics, mvtnorm, deSolve, coda, subplex, nloptr
 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/R/minim.R
===================================================================
--- pkg/pomp/R/minim.R	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/R/minim.R	2015-03-15 16:09:02 UTC (rev 1142)
@@ -34,11 +34,11 @@
     opts <- list(...)
 
     if (method == 'subplex') {
-      opt <- subplex(par=guess,fn=objfun,control=opts)
+      opt <- subplex::subplex(par=guess,fn=objfun,control=opts)
     } else if (method=="sannbox") {
       opt <- sannbox(par=guess,fn=objfun,control=opts)
     } else if (method=="nloptr") {
-      opt <- nloptr(x0=guess,eval_f=objfun,opts=opts)
+      opt <- nloptr::nloptr(x0=guess,eval_f=objfun,opts=opts)
     } else {
       opt <- optim(par=guess,fn=objfun,method=method,control=opts)
     }

Modified: pkg/pomp/R/nlf.R
===================================================================
--- pkg/pomp/R/nlf.R	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/R/nlf.R	2015-03-15 16:09:02 UTC (rev 1142)
@@ -115,26 +115,26 @@
     opt <- list(params=params,value=val)
   } else {
     if (method == 'subplex') {
-      opt <- subplex(
-                     par=guess,
-                     fn=nlf.objfun,
-                     object=object,
-                     params=params,
-                     par.index=par.index, 
-                     transform=transform,
-                     times=times,
-                     t0=t0,
-                     lags=lags,
-                     period=period,
-                     tensor=tensor,
-                     seed=seed,
-                     transform.data=transform.data,
-                     nrbf=nrbf, 
-                     verbose=verbose,
-                     bootstrap=bootstrap,
-                     bootsamp=bootsamp,
-                     control=list(...)
-                     )
+      opt <- subplex::subplex(
+                              par=guess,
+                              fn=nlf.objfun,
+                              object=object,
+                              params=params,
+                              par.index=par.index, 
+                              transform=transform,
+                              times=times,
+                              t0=t0,
+                              lags=lags,
+                              period=period,
+                              tensor=tensor,
+                              seed=seed,
+                              transform.data=transform.data,
+                              nrbf=nrbf, 
+                              verbose=verbose,
+                              bootstrap=bootstrap,
+                              bootsamp=bootsamp,
+                              control=list(...)
+                              )
     } else {
       opt <- optim(
                    par=guess,

Modified: pkg/pomp/R/spect-match.R
===================================================================
--- pkg/pomp/R/spect-match.R	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/R/spect-match.R	2015-03-15 16:09:02 UTC (rev 1142)
@@ -174,23 +174,23 @@
     msg <- "no optimization performed"
   } else {
     if (method == 'subplex') {
-      opt <- subplex(
-                     par=guess,
-                     fn=obj.fn,
-                     est=par.index,
-                     object=object,
-                     params=params,
-                     vars=vars,
-                     ker=ker,
-                     nsim=nsim,
-                     seed=seed,
-                     transform=transform,
-                     detrend=detrend,
-                     weights=weights,
-                     data.spec=ds,
-                     fail.value=fail.value,
-                     control=list(...)
-                     )
+      opt <- subplex::subplex(
+                              par=guess,
+                              fn=obj.fn,
+                              est=par.index,
+                              object=object,
+                              params=params,
+                              vars=vars,
+                              ker=ker,
+                              nsim=nsim,
+                              seed=seed,
+                              transform=transform,
+                              detrend=detrend,
+                              weights=weights,
+                              data.spec=ds,
+                              fail.value=fail.value,
+                              control=list(...)
+                              )
     } else {
       opt <- optim(
                    par=guess,

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/inst/NEWS	2015-03-15 16:09:02 UTC (rev 1142)
@@ -1,5 +1,11 @@
 _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_3-_1:
+
+        • The optimization packages ‘nloptr’ and ‘subplex’ are no
+          longer dependencies of ‘pomp’ that will be loaded at the time
+          ‘pomp’ is.  Instead, they are imported as needed.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_2-_2:
 
         • Bug fix in ‘partrans’ when transformations are implemented

Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/inst/NEWS.Rd	2015-03-15 16:09:02 UTC (rev 1142)
@@ -1,5 +1,11 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.63-1}{
+  \itemize{
+    \item The optimization packages \pkg{nloptr} and \pkg{subplex} are no longer dependencies of \pkg{pomp} that will be loaded at the time \pkg{pomp} is.
+    Instead, they are imported as needed.
+  }
+}
 \section{Changes in \pkg{pomp} version 0.62-2}{
   \itemize{
     \item Bug fix in \code{partrans} when transformations are implemented using \code{Csnippet}s.

Modified: pkg/pomp/tests/bbs-trajmatch.R
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.R	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/tests/bbs-trajmatch.R	2015-03-15 16:09:02 UTC (rev 1142)
@@ -19,6 +19,7 @@
 
 tmf <- traj.match.objfun(bbs,params=guess,est=est,transform=TRUE,hmax=0.001)
 
+require(subplex)
 fit <- subplex(fn=tmf,par=log(guess[est]),control=list(reltol=1e-7))
 tm2 <- bbs
 coef(tm2) <- guess

Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-03-15 16:09:02 UTC (rev 1142)
@@ -1,6 +1,6 @@
 
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
+Copyright (C) 2015 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,8 +16,6 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
 > 
 > pompExample(bbs)
 newly created object(s):
@@ -54,6 +52,8 @@
 > 
 > tmf <- traj.match.objfun(bbs,params=guess,est=est,transform=TRUE,hmax=0.001)
 > 
+> require(subplex)
+Loading required package: subplex
 > fit <- subplex(fn=tmf,par=log(guess[est]),control=list(reltol=1e-7))
 > tm2 <- bbs
 > coef(tm2) <- guess
@@ -80,4 +80,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.480   0.052   2.555 
+  2.709   0.041   2.740 

Modified: pkg/pomp/tests/ou2-probe.R
===================================================================
--- pkg/pomp/tests/ou2-probe.R	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/tests/ou2-probe.R	2015-03-15 16:09:02 UTC (rev 1142)
@@ -138,6 +138,8 @@
                            probes=good$probes,nsim=100,
                            seed=349956868L
                            )
+
+require(nloptr)
 fit1 <- nloptr(
                coef(good,c("alpha.1","alpha.2")),
                ofun,

Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save	2015-03-13 18:43:50 UTC (rev 1141)
+++ pkg/pomp/tests/ou2-probe.Rout.save	2015-03-15 16:09:02 UTC (rev 1142)
@@ -1,6 +1,6 @@
 
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
+Copyright (C) 2015 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,8 +16,6 @@
 Type 'q()' to quit R.
 
 > library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
 > set.seed(1066L)
 > 
 > pdf(file="ou2-probe.pdf")
@@ -312,6 +310,9 @@
 +                            probes=good$probes,nsim=100,
 +                            seed=349956868L
 +                            )
+> 
+> require(nloptr)
+Loading required package: nloptr
 > fit1 <- nloptr(
 +                coef(good,c("alpha.1","alpha.2")),
 +                ofun,
@@ -340,4 +341,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  7.892   0.092   8.187 
+  9.307   0.094   9.395 

Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html	2015-03-13 18:43:50 UTC (rev 1141)
+++ www/content/NEWS.html	2015-03-15 16:09:02 UTC (rev 1142)
@@ -8,6 +8,17 @@
 
 <h2>News for package ‘pomp’</h2>
 
+<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>
 
 

Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf	2015-03-13 18:43:50 UTC (rev 1141)
+++ www/vignettes/pomp.pdf	2015-03-15 16:09:02 UTC (rev 1142)
@@ -17,27 +17,38 @@
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