From noreply at r-forge.r-project.org  Tue Nov  5 15:05:35 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  5 Nov 2013 15:05:35 +0100 (CET)
Subject: [Pomp-commits] r864 - in branches/mif2: . R inst inst/include man
	src tests
Message-ID: <20131105140535.1EBAB185AC9@r-forge.r-project.org>

Author: kingaa
Date: 2013-11-05 15:05:32 +0100 (Tue, 05 Nov 2013)
New Revision: 864

Added:
   branches/mif2/src/SSA.f90
Removed:
   branches/mif2/inst/LICENSE
   branches/mif2/src/SSA.f
Modified:
   branches/mif2/.Rbuildignore
   branches/mif2/DESCRIPTION
   branches/mif2/NAMESPACE
   branches/mif2/R/builder.R
   branches/mif2/R/mif.R
   branches/mif2/R/pfilter-methods.R
   branches/mif2/R/pfilter.R
   branches/mif2/R/profile-design.R
   branches/mif2/inst/NEWS
   branches/mif2/inst/include/pomp.h
   branches/mif2/man/pfilter-methods.Rd
   branches/mif2/man/profile-design.Rd
   branches/mif2/src/SSA_wrapper.c
   branches/mif2/src/eulermultinom.c
   branches/mif2/src/lookup_table.c
   branches/mif2/src/pomp.h
   branches/mif2/tests/ou2-mif.Rout.save
   branches/mif2/tests/pfilter.R
   branches/mif2/tests/pfilter.Rout.save
Log:
- bring mif2 branch up to date with changes to trunk


Modified: branches/mif2/.Rbuildignore
===================================================================
--- branches/mif2/.Rbuildignore	2013-06-11 16:28:47 UTC (rev 863)
+++ branches/mif2/.Rbuildignore	2013-11-05 14:05:32 UTC (rev 864)
@@ -2,5 +2,3 @@
 inst/doc/(.+?)\.bst$
 inst/doc/(.+?)\.R$
 inst/doc/(.+?)\.png$
-^.*\.Rproj$
-^\.Rproj\.user$

Modified: branches/mif2/DESCRIPTION
===================================================================
--- branches/mif2/DESCRIPTION	2013-06-11 16:28:47 UTC (rev 863)
+++ branches/mif2/DESCRIPTION	2013-11-05 14:05:32 UTC (rev 864)
@@ -1,27 +1,28 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.44-1
-Date: 2013-03-26
-Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Dao Nguyen, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
-Maintainer: Aaron A. King <kingaa at umich.edu>
-Author at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
+Version: 0.46-1
+Date: 2013-10-30
+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")),
 	  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("Bruce","E."),family="Kendall",role=c("ctb")),
 	  person(given=c("Michael"),family="Lavine",role=c("ctb")),
-	  person(given=c("Dao"),family="Nguyen",role=c("ctb")),
 	  person(given=c("Daniel","C."),family="Reuman",role=c("ctb")),
 	  person(given=c("Helen"),family="Wearing",role=c("ctb")),
-	  person(given=c("Simon","N."),family="Wood",role=c("ctb")))
+	  person(given=c("Simon","N."),family="Wood",role=c("ctb")),
+	  person(given="Dao",family="Nguyen",role=c("ctb"))	)
+Maintainer: Aaron A. King <kingaa at umich.edu>
+Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman, Simon N. Wood, Dao Nguyen
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially-observed Markov processes
-Depends: R(>= 2.14.1), stats, methods, graphics, mvtnorm, subplex, deSolve
+Depends: R(>= 2.14.1), stats, graphics, mvtnorm, subplex, deSolve
+Imports: methods
 License: GPL(>= 2)
-LazyLoad: true
-LazyData: false
+LazyLoad: yes
+LazyData: no
 BuildVignettes: no
 Collate: aaa.R authors.R version.R eulermultinom.R plugins.R 
 	 parmat.R slice-design.R profile-design.R sobol.R bsplines.R sannbox.R

Modified: branches/mif2/NAMESPACE
===================================================================
--- branches/mif2/NAMESPACE	2013-06-11 16:28:47 UTC (rev 863)
+++ branches/mif2/NAMESPACE	2013-11-05 14:05:32 UTC (rev 864)
@@ -62,6 +62,7 @@
 
 export(
        as.data.frame.pomp,
+       as.data.frame.pfilterd.pomp,
        reulermultinom,
        deulermultinom,
        rgammawn,

Modified: branches/mif2/R/builder.R
===================================================================
--- branches/mif2/R/builder.R	2013-06-11 16:28:47 UTC (rev 863)
+++ branches/mif2/R/builder.R	2013-11-05 14:05:32 UTC (rev 864)
@@ -107,7 +107,6 @@
 
 decl <- list(
              periodic_bspline_basis_eval="\tvoid (*periodic_bspline_basis_eval)(double,double,int,int,double*);\nperiodic_bspline_basis_eval = (void (*)(double,double,int,int,double*)) R_GetCCallable(\"pomp\",\"periodic_bspline_basis_eval\");\n",
-             reulermultinom="\tvoid (*reulermultinom)(int,double,double*,double,double*);\nreulermultinom = (void (*)(int,double,double*,double,double*)) R_GetCCallable(\"pomp\",\"reulermultinom\");\n",
              get_pomp_userdata="\tconst SEXP (*get_pomp_userdata)(const char *);\npomp_get_userdata = (const SEXP (*)(const char*)) R_GetCCallable(\"pomp\",\"get_pomp_userdata\");\n",
              get_pomp_userdata_int="\tconst int * (*get_pomp_userdata_int)(const char *);\npomp_get_userdata_int = (const int *(*)(const char*)) R_GetCCallable(\"pomp\",\"get_pomp_userdata_int\");\n",
              get_pomp_userdata_double="\tconst double * (*get_pomp_userdata_double)(const char *);\npomp_get_userdata_double = (const double *(*)(const char*)) R_GetCCallable(\"pomp\",\"get_pomp_userdata_double\");\n"

Modified: branches/mif2/R/mif.R
===================================================================
--- branches/mif2/R/mif.R	2013-06-11 16:28:47 UTC (rev 863)
+++ branches/mif2/R/mif.R	2013-11-05 14:05:32 UTC (rev 864)
@@ -2,55 +2,55 @@
 
 default.pomp.particles.fun <- function (Np, center, sd, ...) {
   matrix(
-    data=rnorm(
-      n=Np*length(center),
-      mean=center,
-      sd=sd
-    ),
-    nrow=length(center),
-    ncol=Np,
-    dimnames=list(
-      names(center),
-      NULL
-    )
-  )
+         data=rnorm(
+           n=Np*length(center),
+           mean=center,
+           sd=sd
+           ),
+         nrow=length(center),
+         ncol=Np,
+         dimnames=list(
+           names(center),
+           NULL
+           )
+         )
 }
 
 cooling.function <- function (type, perobs, fraction, ntimes) {
   switch(
-    type,
-    geometric={
-      factor <- fraction^(1/50)
-      if (perobs) {
-        function (nt, m) {
-          alpha <- factor^(nt/ntimes+m-1)
-          list(alpha=alpha,gamma=alpha^2)
-        }
-      } else {
-        function (nt, m) {
-          alpha <- factor^(m-1)
-          list(alpha=alpha,gamma=alpha^2)
-        }
-      }
-    },
-    hyperbolic={
-      if (perobs) {
-        scal <- (50*ntimes*fraction-1)/(1-fraction)
-        function (nt, m) {
-          alpha <- (1+scal)/(scal+nt+ntimes*(m-1))
-          list(alpha=alpha,gamma=alpha^2)
-        }
-      } else {
-        scal <- (50*fraction-1)/(1-fraction)
-        function (nt, m) {
-          alpha <- (1+scal)/(scal+m-1)
-          list(alpha=alpha,gamma=alpha^2)
-        }
-        
-      }
-    },
-    stop("unrecognized cooling schedule type ",sQuote(type))
-  )
+         type,
+         geometric={
+           factor <- fraction^(1/50)
+           if (perobs) {
+             function (nt, m) {
+               alpha <- factor^(nt/ntimes+m-1)
+               list(alpha=alpha,gamma=alpha^2)
+             }
+           } else {
+             function (nt, m) {
+               alpha <- factor^(m-1)
+               list(alpha=alpha,gamma=alpha^2)
+             }
+           }
+         },
+         hyperbolic={
+           if (perobs) {
+             scal <- (50*ntimes*fraction-1)/(1-fraction)
+             function (nt, m) {
+               alpha <- (1+scal)/(scal+nt+ntimes*(m-1))
+               list(alpha=alpha,gamma=alpha^2)
+             }
+           } else {
+             scal <- (50*fraction-1)/(1-fraction)
+             function (nt, m) {
+               alpha <- (1+scal)/(scal+m-1)
+               list(alpha=alpha,gamma=alpha^2)
+             }
+             
+           }
+         },
+         stop("unrecognized cooling schedule type ",sQuote(type))
+         )
 }
 
 mif.cooling <- function (factor, n) {   # default geometric cooling schedule
@@ -95,10 +95,10 @@
   
   if (length(start)==0)
     stop(
-      "mif error: ",sQuote("start")," must be specified if ",
-      sQuote("coef(object)")," is NULL",
-      call.=FALSE
-    )
+         "mif error: ",sQuote("start")," must be specified if ",
+         sQuote("coef(object)")," is NULL",
+         call.=FALSE
+         )
   
   if (transform)
     start <- partrans(object,start,dir="inverse")
@@ -112,7 +112,7 @@
     stop("mif error: ",sQuote("rw.sd")," must be a named non-negative numerical vector",call.=FALSE)
   if (!all(rw.names%in%start.names))
     stop("mif error: all the names of ",sQuote("rw.sd")," must be names of ",sQuote("start"),call.=FALSE)
-  #rw.names <- names(rw.sd[rw.sd>0])
+                                        #rw.names <- names(rw.sd[rw.sd>0])
   if (length(rw.names) == 0)
     stop("mif error: ",sQuote("rw.sd")," must have one positive entry for each parameter to be estimated",call.=FALSE)
   
@@ -120,7 +120,7 @@
   if (missing(ivps)) stop("mif error: ",sQuote("ivps")," must be specified",call.=FALSE)
   
   if (
-    !is.character(pars) ||
+      !is.character(pars) ||
       !is.character(ivps) ||
       !all(pars%in%start.names) ||
       !all(ivps%in%start.names) ||
@@ -128,32 +128,32 @@
       any(ivps%in%pars) ||
       !all(pars%in%rw.names) ||
       !all(ivps%in%rw.names)
-  )
+      )
     stop(
-      "mif error: ",
-      sQuote("pars")," and ",sQuote("ivps"),
-      " must be mutually disjoint subsets of ",
-      sQuote("names(start)"),
-      " and must have a positive random-walk SDs specified in ",
-      sQuote("rw.sd"),
-      call.=FALSE
-    )
+         "mif error: ",
+         sQuote("pars")," and ",sQuote("ivps"),
+         " must be mutually disjoint subsets of ",
+         sQuote("names(start)"),
+         " and must have a positive random-walk SDs specified in ",
+         sQuote("rw.sd"),
+         call.=FALSE
+         )
   
   if (!all(rw.names%in%c(pars,ivps))) {
     extra.rws <- rw.names[!(rw.names%in%c(pars,ivps))]
     warning(
-      ngettext(length(extra.rws),"mif warning: the variable ",
-               "mif warning: the variables "),
-      paste(sQuote(extra.rws),collapse=", "),
-      ngettext(length(extra.rws)," has positive random-walk SD specified, but is included in neither ",
-               " have positive random-walk SDs specified, but are included in neither "),
-      sQuote("pars")," nor ",sQuote("ivps"),
-      ngettext(length(extra.rws),". This random walk SD will be ignored.",
-               ". These random walk SDs will be ignored."),
-      call.=FALSE
-    )
+            ngettext(length(extra.rws),"mif warning: the variable ",
+                     "mif warning: the variables "),
+            paste(sQuote(extra.rws),collapse=", "),
+            ngettext(length(extra.rws)," has positive random-walk SD specified, but is included in neither ",
+                     " have positive random-walk SDs specified, but are included in neither "),
+            sQuote("pars")," nor ",sQuote("ivps"),
+            ngettext(length(extra.rws),". This random walk SD will be ignored.",
+                     ". These random walk SDs will be ignored."),
+            call.=FALSE
+            )
   }
-  #rw.sd <- rw.sd[c(pars,ivps)]
+                                        #rw.sd <- rw.sd[c(pars,ivps)]
   rw.names <- colnames(rw.sd)
   rwsdMat <-rw.sd
   if (missing(particles))
@@ -163,9 +163,9 @@
   if (missing(Np)) stop("mif error: ",sQuote("Np")," must be specified",call.=FALSE)
   if (is.function(Np)) {
     Np <- try(
-      vapply(seq.int(from=0,to=ntimes,by=1),Np,numeric(1)),
-      silent=FALSE
-    )
+              vapply(seq.int(from=0,to=ntimes,by=1),Np,numeric(1)),
+              silent=FALSE
+              )
     if (inherits(Np,"try-error"))
       stop("if ",sQuote("Np")," is a function, it must return a single positive integer")
   }
@@ -185,20 +185,20 @@
     stop("mif error: ",sQuote("ic.lag")," must be a positive integer",call.=FALSE)
   if (ic.lag>ntimes) {
     warning(
-      "mif warning: ",sQuote("ic.lag")," = ",ic.lag," > ",ntimes,
-      " = length(time(",sQuote("object"),"))",
-      " is nonsensical.  Setting ",sQuote("ic.lag")," = ",ntimes,".",
-      call.=FALSE
-    )
+            "mif warning: ",sQuote("ic.lag")," = ",ic.lag," > ",ntimes,
+            " = length(time(",sQuote("object"),"))",
+            " is nonsensical.  Setting ",sQuote("ic.lag")," = ",ntimes,".",
+            call.=FALSE
+            )
     ic.lag <- length(time(object))
   }
   if ((length(pars)==0)&&(ic.lag<length(time(object)))) {
     warning(
-      "mif warning: only IVPs are to be estimated, yet ",sQuote("ic.lag")," = ",ic.lag,
-      " < ",ntimes," = length(time(",sQuote("object"),")),",
-      " so unnecessary work is to be done.",
-      call.=FALSE
-    )
+            "mif warning: only IVPs are to be estimated, yet ",sQuote("ic.lag")," = ",ic.lag,
+            " < ",ntimes," = length(time(",sQuote("object"),")),",
+            " so unnecessary work is to be done.",
+            call.=FALSE
+            )
   }
   
   ## the following deals with the deprecated option 'cooling.factor'
@@ -225,11 +225,11 @@
     stop("mif error: ",sQuote("cooling.fraction")," must be a number between 0 and 1",call.=FALSE)
   
   cooling <- cooling.function(
-    type=cooling.type,
-    perobs=(method=="mif2"),
-    fraction=cooling.fraction,
-    ntimes=ntimes
-  )
+                              type=cooling.type,
+                              perobs=(method=="mif2"),
+                              fraction=cooling.fraction,
+                              ntimes=ntimes
+                              )
   
   if ((method=="mif2")&&(Np[1L]!=Np[ntimes+1]))
     stop("the first and last values of ",sQuote("Np")," must agree when method = ",sQuote("mif2"))
@@ -245,26 +245,26 @@
   
   
   conv.rec <- matrix(
-    data=NA,
-    nrow=Nmif+1,
-    ncol=length(theta)+2,
-    dimnames=list(
-      seq(.ndone,.ndone+Nmif),
-      c('loglik','nfail',names(theta))
-    )
-  )
+                     data=NA,
+                     nrow=Nmif+1,
+                     ncol=length(theta)+2,
+                     dimnames=list(
+                       seq(.ndone,.ndone+Nmif),
+                       c('loglik','nfail',names(theta))
+                       )
+                     )
   conv.rec[1L,] <- c(NA,NA,theta)
   
   if (!all(is.finite(theta[c(pars,ivps)]))) {
     stop(
-      sQuote("mif")," cannot estimate non-finite parameters.\n",
-      "The following ",if (transform) "transformed ", "parameters are non-finite: ",
-      paste(
-        sQuote(c(pars,ivps)[!is.finite(theta[c(pars,ivps)])]),
-        collapse=","
-      ),
-      call.=FALSE
-    )
+         sQuote("mif")," cannot estimate non-finite parameters.\n",
+         "The following ",if (transform) "transformed ", "parameters are non-finite: ",
+         paste(
+               sQuote(c(pars,ivps)[!is.finite(theta[c(pars,ivps)])]),
+               collapse=","
+               ),
+         call.=FALSE
+         )
   }
   
   obj <- as(object,"pomp")
@@ -286,14 +286,14 @@
     
     ## initialize the parameter portions of the particles
     P <- try(
-      particles(
-        tmp.mif,
-        Np=Np[1L],
-        center=theta,
-        sd=sigma.n*var.factor
-      ),
-      silent = FALSE
-    )
+             particles(
+                       tmp.mif,
+                       Np=Np[1L],
+                       center=theta,
+                       sd=sigma.n*var.factor
+                       ),
+             silent = FALSE
+             )
     if (inherits(P,"try-error")) 
       stop("mif error: error in ",sQuote("particles"),call.=FALSE)
     
@@ -303,27 +303,27 @@
     }
     colnames(rwsdMat) <- names(start)
     pfp <- try(
-      pfilter.internal(
-        object=obj,
-        params=P, 
-        Np=Np,
-        tol=tol,
-        max.fail=max.fail,
-        pred.mean=(n==Nmif),
-        pred.var=((method=="mif")||(n==Nmif)),
-        filter.mean=TRUE,
-        cooling=cooling,
-        cooling.m=.ndone+n,
-        .mif2=(method=="mif2"),
-        .rw.sd=rwsdMat*cool.sched$alpha,
-        .transform=transform,
-        save.states=FALSE, 
-        save.params=FALSE,
-        verbose=verbose,
-        .getnativesymbolinfo=gnsi
-      ),
-      silent=FALSE
-    )
+               pfilter.internal(
+                                object=obj,
+                                params=P, 
+                                Np=Np,
+                                tol=tol,
+                                max.fail=max.fail,
+                                pred.mean=(n==Nmif),
+                                pred.var=((method=="mif")||(n==Nmif)),
+                                filter.mean=TRUE,
+                                cooling=cooling,
+                                cooling.m=.ndone+n,
+                                .mif2=(method=="mif2"),
+                                .rw.sd=rwsdMat*cool.sched$alpha,
+                                .transform=transform,
+                                save.states=FALSE, 
+                                save.params=FALSE,
+                                verbose=verbose,
+                                .getnativesymbolinfo=gnsi
+                                ),
+               silent=FALSE
+               )
     if (inherits(pfp,"try-error")) 
       stop("mif error: error in ",sQuote("pfilter"),call.=FALSE)
     
@@ -331,26 +331,26 @@
     
     ## update parameters
     switch(
-      method,
-      mif={              # original Ionides et al. (2006) average
-        theta <- .Call(mif_update,pfp,theta,cool.sched$gamma,var.factor,rwsdMat[1,],pars)
-        theta[ivps] <- pfp at filter.mean[ivps,ic.lag]
-      },
-      unweighted={                 # unweighted average
-        theta[pars] <- rowMeans(pfp at filter.mean[pars,,drop=FALSE])
-        theta[ivps] <- pfp at filter.mean[ivps,ic.lag]
-      },
-      fp={                         # fixed-point iteration
-        theta[pars] <- pfp at filter.mean[pars,ntimes,drop=FALSE]
-        theta[ivps] <- pfp at filter.mean[ivps,ic.lag]
-      },
-      mif2={                     # "efficient" iterated filtering
-        paramMatrix <- pfp at paramMatrix
-        theta[pars] <- rowMeans(paramMatrix[pars,,drop=FALSE])
-        theta[ivps] <- pfp at filter.mean[ivps,ntimes]
-      },
-      stop("unrecognized method ",sQuote(method))
-    )
+           method,
+           mif={              # original Ionides et al. (2006) average
+             theta <- .Call(mif_update,pfp,theta,cool.sched$gamma,var.factor,rwsdMat[1,],pars)
+             theta[ivps] <- pfp at filter.mean[ivps,ic.lag]
+           },
+           unweighted={                 # unweighted average
+             theta[pars] <- rowMeans(pfp at filter.mean[pars,,drop=FALSE])
+             theta[ivps] <- pfp at filter.mean[ivps,ic.lag]
+           },
+           fp={                         # fixed-point iteration
+             theta[pars] <- pfp at filter.mean[pars,ntimes,drop=FALSE]
+             theta[ivps] <- pfp at filter.mean[ivps,ic.lag]
+           },
+           mif2={                     # "efficient" iterated filtering
+             paramMatrix <- pfp at paramMatrix
+             theta[pars] <- rowMeans(paramMatrix[pars,,drop=FALSE])
+             theta[ivps] <- pfp at filter.mean[ivps,ntimes]
+           },
+           stop("unrecognized method ",sQuote(method))
+           )
     
     conv.rec[n+1,-c(1,2)] <- theta
     conv.rec[n,c(1,2)] <- c(pfp at loglik,pfp at nfail)
@@ -363,266 +363,266 @@
   if (transform) theta <- partrans(pfp,theta,dir="forward")
   
   new(
-    "mif",
-    pfp,
-    transform=transform,
-    params=theta,
-    ivps=ivps,
-    pars=pars,
-    Nmif=Nmif,
-    particles=particles,
-    var.factor=var.factor,
-    ic.lag=ic.lag,
-    random.walk.sd=rwsdMat,
-    tol=tol,
-    conv.rec=conv.rec,
-    method=method,
-    cooling.type=cooling.type,
-    cooling.fraction=cooling.fraction,
-    paramMatrix=if (method=="mif2") paramMatrix else array(data=numeric(0),dim=c(0,0))
-  )
+      "mif",
+      pfp,
+      transform=transform,
+      params=theta,
+      ivps=ivps,
+      pars=pars,
+      Nmif=Nmif,
+      particles=particles,
+      var.factor=var.factor,
+      ic.lag=ic.lag,
+      random.walk.sd=rwsdMat,
+      tol=tol,
+      conv.rec=conv.rec,
+      method=method,
+      cooling.type=cooling.type,
+      cooling.fraction=cooling.fraction,
+      paramMatrix=if (method=="mif2") paramMatrix else array(data=numeric(0),dim=c(0,0))
+      )
 }
 
 setGeneric('mif',function(object,...)standardGeneric("mif"))
 
 setMethod(
-  "mif",
-  signature=signature(object="pomp"),
-  function (object, Nmif = 1,
-            start,
-            pars, ivps = character(0),
-            particles, rw.sd,
-            Np, ic.lag, var.factor,
-            cooling.type = c("geometric","hyperbolic"),
-            cooling.fraction, cooling.factor,
-            method = c("mif","unweighted","fp","mif2"),
-            tol = 1e-17, max.fail = Inf,
-            verbose = getOption("verbose"),
-            transform = FALSE,
-            ...) {
-    
-    transform <- as.logical(transform)
-    method <- match.arg(method)
-    
-    
-    ntimes <- length(time(object))
-    if (missing(start)) start <- coef(object)
-    if (missing(rw.sd))
-      stop("mif error: ",sQuote("rw.sd")," must be specified",call.=FALSE)
-    if (missing(pars)) {
-      stop("mif error: ",sQuote("par")," must be specified",call.=FALSE)
-    }
-    rw.names <- c(pars,ivps)
-    dtheta <- length(start)
-    rwsdMat <- matrix(rep(0, dtheta*(ntimes+1)), ncol=dtheta, nrow = (ntimes+1))
-    colnames(rwsdMat) <- names(start)
-    
-    if (is.matrix(rw.sd)) rwsdMat<-rw.sd
-    else if (is.list(rw.sd))
-    {
-      for (i in 1:length(rw.names))
-      { if (rw.names[i] %in% ivps)
-      { 
-        if (length((rw.sd[[rw.names[i]]])==1))
-        {
-          rwsdMat[1,rw.names[i]] <- rw.sd[[rw.names[i]]][1]
-        }
-        else
-        {
-          stop(sQuote("rw.sd")," must have length 1 or length ",ntimes+1)
-          
-        }
-      }
-        else if (rw.names[i] %in% pars)
-        { 
-          if (length(rw.sd[[rw.names[i]]])==1)
-          {
-            rwsdMat[,rw.names[i]] <- rep(rw.sd[[rw.names[i]]],(ntimes+1))
-          }
-          else if (length(rw.sd[[rw.names[i]]])==(ntimes+1))
-          { 
-            rwsdMat[,rw.names[i]] <- rw.sd[[rw.names[i]]]  
-          }
-          else
-          {
-            stop(sQuote("rw.sd")," must have length 1 or length ",ntimes+1)
+          "mif",
+          signature=signature(object="pomp"),
+          function (object, Nmif = 1,
+                    start,
+                    pars, ivps = character(0),
+                    particles, rw.sd,
+                    Np, ic.lag, var.factor,
+                    cooling.type = c("geometric","hyperbolic"),
+                    cooling.fraction, cooling.factor,
+                    method = c("mif","unweighted","fp","mif2"),
+                    tol = 1e-17, max.fail = Inf,
+                    verbose = getOption("verbose"),
+                    transform = FALSE,
+                    ...) {
             
+            transform <- as.logical(transform)
+            method <- match.arg(method)
+            
+            
+            ntimes <- length(time(object))
+            if (missing(start)) start <- coef(object)
+            if (missing(rw.sd))
+              stop("mif error: ",sQuote("rw.sd")," must be specified",call.=FALSE)
+            if (missing(pars)) {
+              stop("mif error: ",sQuote("par")," must be specified",call.=FALSE)
+            }
+            rw.names <- c(pars,ivps)
+            dtheta <- length(start)
+            rwsdMat <- matrix(rep(0, dtheta*(ntimes+1)), ncol=dtheta, nrow = (ntimes+1))
+            colnames(rwsdMat) <- names(start)
+            
+            if (is.matrix(rw.sd)) rwsdMat<-rw.sd
+            else if (is.list(rw.sd))
+              {
+                for (i in 1:length(rw.names))
+                  { if (rw.names[i] %in% ivps)
+                      { 
+                        if (length((rw.sd[[rw.names[i]]])==1))
+                          {
+                            rwsdMat[1,rw.names[i]] <- rw.sd[[rw.names[i]]][1]
+                          }
+                        else
+                          {
+                            stop(sQuote("rw.sd")," must have length 1 or length ",ntimes+1)
+                            
+                          }
+                      }
+                  else if (rw.names[i] %in% pars)
+                    { 
+                      if (length(rw.sd[[rw.names[i]]])==1)
+                        {
+                          rwsdMat[,rw.names[i]] <- rep(rw.sd[[rw.names[i]]],(ntimes+1))
+                        }
+                      else if (length(rw.sd[[rw.names[i]]])==(ntimes+1))
+                        { 
+                          rwsdMat[,rw.names[i]] <- rw.sd[[rw.names[i]]]  
+                        }
+                      else
+                        {
+                          stop(sQuote("rw.sd")," must have length 1 or length ",ntimes+1)
+                          
+                        }
+                    }
+                    
+                  }
+                
+              }
+            else if (is.vector(rw.sd))
+              {
+                if (missing(pars)) {
+                  rw.names <- names(rw.sd)[rw.sd>0]
+                  pars <- rw.names[!(rw.names%in%ivps)]
+                }
+                for (i in 1:length(rw.names))
+                  { if (rw.names[i] %in% ivps)
+                      { 
+                        rwsdMat[1,rw.names[i]] <- rw.sd[rw.names[i]]
+                        
+                      }
+                  else if (rw.names[i] %in% pars)
+                    { 
+                      rwsdMat[,rw.names[i]] <- rep(rw.sd[rw.names[i]],(ntimes+1))
+                    }
+                    
+                  }
+                
+                
+                
+              }
+            
+            
+            
+            if (missing(Np))
+              stop("mif error: ",sQuote("Np")," must be specified",call.=FALSE)
+            if (missing(ic.lag) && length(ivps)>0)
+              stop("mif error: ",sQuote("ic.lag")," must be specified if ",sQuote("ivps")," are",call.=FALSE)
+            if (missing(var.factor))
+              stop("mif error: ",sQuote("var.factor")," must be specified",call.=FALSE)
+            
+            cooling.type <- match.arg(cooling.type)
+            
+            if (missing(particles)) { # use default: normal distribution
+              particles <- default.pomp.particles.fun
+            } else {
+              particles <- match.fun(particles)
+              if (!all(c('Np','center','sd','...')%in%names(formals(particles))))
+                stop(
+                     "mif error: ",
+                     sQuote("particles"),
+                     " must be a function of prototype ",
+                     sQuote("particles(Np,center,sd,...)"),
+                     call.=FALSE
+                     )
+            }
+            
+            mif.internal(
+                         object=object,
+                         Nmif=Nmif,
+                         start=start,
+                         pars=pars,
+                         ivps=ivps,
+                         particles=particles,
+                         rw.sd=rwsdMat,
+                         Np=Np,
+                         cooling.type=cooling.type,
+                         cooling.factor=cooling.factor,
+                         cooling.fraction=cooling.fraction,
+                         var.factor=var.factor,
+                         ic.lag=ic.lag,
+                         method=method,
+                         tol=tol,
+                         max.fail=max.fail,
+                         verbose=verbose,
+                         transform=transform
+                         )
+            
           }
-        }
-        
-      }
-      
-    }
-    else if (is.vector(rw.sd))
-    {
-      if (missing(pars)) {
-        rw.names <- names(rw.sd)[rw.sd>0]
-        pars <- rw.names[!(rw.names%in%ivps)]
-      }
-      for (i in 1:length(rw.names))
-      { if (rw.names[i] %in% ivps)
-      { 
-        rwsdMat[1,rw.names[i]] <- rw.sd[rw.names[i]]
-        
-      }
-        else if (rw.names[i] %in% pars)
-        { 
-          rwsdMat[,rw.names[i]] <- rep(rw.sd[rw.names[i]],(ntimes+1))
-        }
-        
-      }
-      
-      
-      
-    }
-    
-    
-    
-    if (missing(Np))
-      stop("mif error: ",sQuote("Np")," must be specified",call.=FALSE)
-    if (missing(ic.lag) && length(ivps)>0)
-      stop("mif error: ",sQuote("ic.lag")," must be specified if ",sQuote("ivps")," are",call.=FALSE)
-    if (missing(var.factor))
-      stop("mif error: ",sQuote("var.factor")," must be specified",call.=FALSE)
-    
-    cooling.type <- match.arg(cooling.type)
-    
-    if (missing(particles)) { # use default: normal distribution
-      particles <- default.pomp.particles.fun
-    } else {
-      particles <- match.fun(particles)
-      if (!all(c('Np','center','sd','...')%in%names(formals(particles))))
-        stop(
-          "mif error: ",
-          sQuote("particles"),
-          " must be a function of prototype ",
-          sQuote("particles(Np,center,sd,...)"),
-          call.=FALSE
-        )
-    }
-    
-    mif.internal(
-      object=object,
-      Nmif=Nmif,
-      start=start,
-      pars=pars,
-      ivps=ivps,
-      particles=particles,
-      rw.sd=rwsdMat,
-      Np=Np,
-      cooling.type=cooling.type,
-      cooling.factor=cooling.factor,
-      cooling.fraction=cooling.fraction,
-      var.factor=var.factor,
-      ic.lag=ic.lag,
-      method=method,
-      tol=tol,
-      max.fail=max.fail,
-      verbose=verbose,
-      transform=transform
-    )
-    
-  }
-)
+          )
 
 
 setMethod(
-  "mif",
-  signature=signature(object="pfilterd.pomp"),
-  function (object, Nmif = 1, Np, tol,
-            ...) {
-    
-    if (missing(Np)) Np <- object at Np
-    if (missing(tol)) tol <- object at tol
-    
-    mif(
-      object=as(object,"pomp"),
-      Nmif=Nmif,
-      Np=Np,
-      tol=tol,
-      ...
-    )
-  }
-)
+          "mif",
+          signature=signature(object="pfilterd.pomp"),
+          function (object, Nmif = 1, Np, tol,
+                    ...) {
+            
+            if (missing(Np)) Np <- object at Np
+            if (missing(tol)) tol <- object at tol
+            
+            mif(
+                object=as(object,"pomp"),
+                Nmif=Nmif,
+                Np=Np,
+                tol=tol,
+                ...
+                )
+          }
+          )
 
 setMethod(
-  "mif",
-  signature=signature(object="mif"),
-  function (object, Nmif,
-            start,
-            pars, ivps,
-            particles, rw.sd,
-            Np, ic.lag, var.factor,
-            cooling.type, cooling.fraction,
-            method,
-            tol,
-            transform,
-            ...) {
-    
-    if (missing(Nmif)) Nmif <- object at Nmif
-    if (missing(start)) start <- coef(object)
-    if (missing(pars)) pars <- object at pars
-    if (missing(ivps)) ivps <- object at ivps
-    if (missing(particles)) particles <- object at particles
-    if (missing(rw.sd)) rw.sd <- object at random.walk.sd
-    if (missing(ic.lag)) ic.lag <- object at ic.lag
-    if (missing(var.factor)) var.factor <- object at var.factor
-    if (missing(cooling.type)) cooling.type <- object at cooling.type
-    if (missing(cooling.fraction)) cooling.fraction <- object at cooling.fraction
-    if (missing(method)) method <- object at method
-    if (missing(transform)) transform <- object at transform
-    transform <- as.logical(transform)
-    
-    if (missing(Np)) Np <- object at Np
-    if (missing(tol)) tol <- object at tol
-    
-    mif(
-      object=as(object,"pomp"),
-      Nmif=Nmif,
-      start=start,
-      pars=pars,
-      ivps=ivps,
-      particles=particles,
-      rw.sd=rw.sd,
-      Np=Np,
-      cooling.type=cooling.type,
-      cooling.fraction=cooling.fraction,
-      var.factor=var.factor,
-      ic.lag=ic.lag,
-      method=method,
-      tol=tol,
-      transform=transform,
-      ...
-    )
-  }
-)
+          "mif",
+          signature=signature(object="mif"),
+          function (object, Nmif,
+                    start,
+                    pars, ivps,
+                    particles, rw.sd,
+                    Np, ic.lag, var.factor,
+                    cooling.type, cooling.fraction,
+                    method,
+                    tol,
+                    transform,
+                    ...) {
+            
+            if (missing(Nmif)) Nmif <- object at Nmif
+            if (missing(start)) start <- coef(object)
+            if (missing(pars)) pars <- object at pars
+            if (missing(ivps)) ivps <- object at ivps
+            if (missing(particles)) particles <- object at particles
+            if (missing(rw.sd)) rw.sd <- object at random.walk.sd
+            if (missing(ic.lag)) ic.lag <- object at ic.lag
+            if (missing(var.factor)) var.factor <- object at var.factor
+            if (missing(cooling.type)) cooling.type <- object at cooling.type
+            if (missing(cooling.fraction)) cooling.fraction <- object at cooling.fraction
+            if (missing(method)) method <- object at method
+            if (missing(transform)) transform <- object at transform
+            transform <- as.logical(transform)
+            
+            if (missing(Np)) Np <- object at Np
+            if (missing(tol)) tol <- object at tol
+            
+            mif(
+                object=as(object,"pomp"),
+                Nmif=Nmif,
+                start=start,
+                pars=pars,
+                ivps=ivps,
+                particles=particles,
+                rw.sd=rw.sd,
+                Np=Np,
+                cooling.type=cooling.type,
+                cooling.fraction=cooling.fraction,
+                var.factor=var.factor,
+                ic.lag=ic.lag,
+                method=method,
+                tol=tol,
+                transform=transform,
+                ...
+                )
+          }
+          )
 
 setMethod(
-  'continue',
-  signature=signature(object='mif'),
-  function (object, Nmif = 1,
-            ...) {
-    
-    ndone <- object at Nmif
-    
-    obj <- mif(
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 864

From noreply at r-forge.r-project.org  Tue Nov  5 18:22:33 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  5 Nov 2013 18:22:33 +0100 (CET)
Subject: [Pomp-commits] r865 - in pkg/pompExamples: . inst vignettes
Message-ID: <20131105172233.6B619184724@r-forge.r-project.org>

Author: kingaa
Date: 2013-11-05 18:22:33 +0100 (Tue, 05 Nov 2013)
New Revision: 865

Added:
   pkg/pompExamples/vignettes/
Removed:
   pkg/pompExamples/inst/LICENSE
   pkg/pompExamples/inst/doc/
Modified:
   pkg/pompExamples/.Rbuildignore
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/NAMESPACE
   pkg/pompExamples/vignettes/budmoth-model.Rnw
   pkg/pompExamples/vignettes/budmoth-model.pdf
   pkg/pompExamples/vignettes/pertussis-model.Rnw
   pkg/pompExamples/vignettes/pertussis-model.pdf
Log:
- changes to bring 'pompExamples' up to date with the package building and checking process
- vignettes are now rebuilt


Modified: pkg/pompExamples/.Rbuildignore
===================================================================
--- pkg/pompExamples/.Rbuildignore	2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/.Rbuildignore	2013-11-05 17:22:33 UTC (rev 865)
@@ -1,6 +1,3 @@
-inst/doc/Makefile
+vignettes/Makefile
 inst/data-R/Makefile
-inst/doc/(.+?)\.bst$
-inst/doc/(.+?)\.R$
-inst/doc/(.+?)\.png$
-inst/doc/(.+?)\.pbs$
+vignettes/(.+?)\.pbs$

Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/DESCRIPTION	2013-11-05 17:22:33 UTC (rev 865)
@@ -1,23 +1,24 @@
 Package: pompExamples
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.21-3
-Date: 2013-06-11
+Version: 0.21-4
+Date: 2013-11-05
 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("Edward","L."),family="Ionides",role=c("aut")),
 	  person(given=c("Carles"),family="Breto",role=c("aut")),
 	  person(given=c("Stephen","P."),family="Ellner",role=c("ctb")),
+	  person(given=c("Bruce","E."),family="Kendall",role=c("ctb")),
+	  person(given=c("Helen"),family="Wearing",role=c("ctb")),
 	  person(given=c("Matthew","J."),family="Ferrari",role=c("ctb")),
-	  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")))
+	  person(given=c("Daniel","C."),family="Reuman",role=c("ctb")))
+Maintainer: Aaron A. King <kingaa at umich.edu>
 URL: http://pomp.r-forge.r-project.org
 Description: More 'pomp' examples.
-Depends: R(>= 3.0.0), stats, methods, graphics, pomp(>= 0.45-4)
+Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.45-4)
+Suggests: Rmpi,mpifarm,plyr,reshape2,ggplot2,xtable
 License: GPL (>= 2)
-LazyLoad: true
 LazyData: false
-BuildVignettes: no
+BuildVignettes: true
 Collate: version.R budmoth.R pertussis.R

Modified: pkg/pompExamples/NAMESPACE
===================================================================
--- pkg/pompExamples/NAMESPACE	2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/NAMESPACE	2013-11-05 17:22:33 UTC (rev 865)
@@ -1,3 +1,3 @@
 useDynLib(pompExamples)
-importFrom(pomp)
+import(pomp)
 export(pertussis.sim,budmoth.sim)

Deleted: pkg/pompExamples/inst/LICENSE
===================================================================
--- pkg/pompExamples/inst/LICENSE	2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/inst/LICENSE	2013-11-05 17:22:33 UTC (rev 865)
@@ -1,16 +0,0 @@
-The POMP package: Inference for partially-observed Markov processes
-
-This package 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 package 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., 675 Mass Ave., Cambridge, MA 02139 USA.
-

Modified: pkg/pompExamples/vignettes/budmoth-model.Rnw
===================================================================
--- pkg/pompExamples/inst/doc/budmoth-model.Rnw	2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/vignettes/budmoth-model.Rnw	2013-11-05 17:22:33 UTC (rev 865)
@@ -24,7 +24,7 @@
 \newcommand\logit{{\mathrm{logit}}}
 \newcommand\expit{{\mathrm{expit}}}
 
-\SweaveOpts{echo=T,results=verbatim,print=F,eps=F,pdf=F,png=T,keep.source=T,split=T,prefix=T,prefix.string=budmoth-model,resolution=150}
+\SweaveOpts{echo=T,results=verbatim,print=F,eps=F,pdf=F,png=T,keep.source=T,split=F,prefix=T,prefix.string=budmoth-model,resolution=150}
 
 \title{Larch Budmoth State-Space Model}
 \author{AAK, ELI, SPE, KBN}
@@ -159,7 +159,7 @@
 <<data-plot,fig=T,height=6,width=8,pdf=T,png=F,echo=F>>=
 require(pompExamples)
 require(plyr)
-require(reshape)
+require(reshape2)
 require(ggplot2)
 data(budmoth.sim)
 x <- ldply(budmoth.sim,as.data.frame)
@@ -429,9 +429,11 @@
 <<slices-plot,fig=T,png=T,pdf=F,echo=F,height=7,width=7>>=
 require(ggplot2)
 require(plyr)
-require(reshape)
-x <- melt(slices,id.vars=c(".id","dataset","slice","loglik","nfail","etime"))
-x$.id <- NULL
+require(reshape2)
+slices$.id <- NULL
+slices$etime <- NULL
+slices$nfail <- NULL
+x <- melt(slices,id.vars=c("dataset","slice","loglik"))
 x$slice <- factor(x$slice,levels=levels(x$variable))
 x <- subset(x,slice==variable)
 x <- ddply(x,~dataset+slice,subset,loglik>max(loglik)-50)

Modified: pkg/pompExamples/vignettes/budmoth-model.pdf
===================================================================
(Binary files differ)

Modified: pkg/pompExamples/vignettes/pertussis-model.Rnw
===================================================================
--- pkg/pompExamples/inst/doc/pertussis-model.Rnw	2013-11-05 14:05:32 UTC (rev 864)
+++ pkg/pompExamples/vignettes/pertussis-model.Rnw	2013-11-05 17:22:33 UTC (rev 865)
@@ -370,7 +370,7 @@
 <<dataplots,fig=T,echo=F,png=T,pdf=F,height=8,width=6>>=
 require(ggplot2)
 require(plyr)
-require(reshape)
+require(reshape2)
 require(pompExamples)
 data(pertussis.sim)
 x <- ldply(pertussis.sim,as.data.frame)

Modified: pkg/pompExamples/vignettes/pertussis-model.pdf
===================================================================
(Binary files differ)


From noreply at r-forge.r-project.org  Tue Nov  5 18:47:53 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  5 Nov 2013 18:47:53 +0100 (CET)
Subject: [Pomp-commits] r866 - in pkg/pomp: . inst
Message-ID: <20131105174753.B7F3C184F3E@r-forge.r-project.org>

Author: kingaa
Date: 2013-11-05 18:47:53 +0100 (Tue, 05 Nov 2013)
New Revision: 866

Added:
   pkg/pomp/vignettes/
Removed:
   pkg/pomp/inst/LICENSE
   pkg/pomp/inst/doc/
Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/NAMESPACE
Log:
- keeping up with changes to the package build and check processes


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2013-11-05 17:22:33 UTC (rev 865)
+++ pkg/pomp/DESCRIPTION	2013-11-05 17:47:53 UTC (rev 866)
@@ -1,9 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.45-4
-Date: 2013-06-06
-Maintainer: Aaron A. King <kingaa at umich.edu>
+Version: 0.45-5
+Date: 2013-11-05
 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")),
 	  person(given=c("Carles"),family="Breto",role=c("aut")),
@@ -15,13 +14,14 @@
 	  person(given=c("Helen"),family="Wearing",role=c("ctb")),
 	  person(given=c("Simon","N."),family="Wood",role=c("ctb")),
 	  person(given="Dao",family="Nguyen",role=c("ctb"))	)
+Maintainer: Aaron A. King <kingaa at umich.edu>
+Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman, Simon N. Wood, Dao Nguyen
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially-observed Markov processes
-Depends: R(>= 2.14.1), stats, methods, graphics, mvtnorm, subplex, deSolve
+Depends: R(>= 2.14.1), stats, graphics, methods, mvtnorm, subplex, deSolve
 License: GPL(>= 2)
-LazyLoad: true
-LazyData: false
-BuildVignettes: no
+LazyData: true
+BuildVignettes: true
 Collate: aaa.R authors.R version.R eulermultinom.R plugins.R 
 	 parmat.R slice-design.R profile-design.R sobol.R bsplines.R sannbox.R
 	 pomp-fun.R pomp-class.R pomp.R pomp-methods.R 

Modified: pkg/pomp/NAMESPACE
===================================================================
--- pkg/pomp/NAMESPACE	2013-11-05 17:22:33 UTC (rev 865)
+++ pkg/pomp/NAMESPACE	2013-11-05 17:47:53 UTC (rev 866)
@@ -29,6 +29,7 @@
           do_init_state
           )
 
+import(methods)
 importFrom(graphics,plot)		
 importFrom(stats,simulate,time,coef,logLik,window)
 importFrom(mvtnorm,dmvnorm,rmvnorm)

Deleted: pkg/pomp/inst/LICENSE
===================================================================
--- pkg/pomp/inst/LICENSE	2013-11-05 17:22:33 UTC (rev 865)
+++ pkg/pomp/inst/LICENSE	2013-11-05 17:47:53 UTC (rev 866)
@@ -1,16 +0,0 @@
-The POMP package: Inference for partially-observed Markov processes
-
-This package 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 package 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., 675 Mass Ave., Cambridge, MA 02139 USA.
-


From noreply at r-forge.r-project.org  Tue Nov  5 23:58:31 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  5 Nov 2013 23:58:31 +0100 (CET)
Subject: [Pomp-commits] r867 - www/vignettes
Message-ID: <20131105225831.87959184FD6@r-forge.r-project.org>

Author: kingaa
Date: 2013-11-05 23:58:31 +0100 (Tue, 05 Nov 2013)
New Revision: 867

Modified:
   www/vignettes/advanced_topics_in_pomp.pdf
   www/vignettes/intro_to_pomp.pdf
Log:
- update vignettes


Modified: www/vignettes/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)

Modified: www/vignettes/intro_to_pomp.pdf
===================================================================
(Binary files differ)


From noreply at r-forge.r-project.org  Mon Nov 11 02:28:49 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 11 Nov 2013 02:28:49 +0100 (CET)
Subject: [Pomp-commits] r868 - in pkg/pomp: . R inst man
Message-ID: <20131111012849.294E21853F5@r-forge.r-project.org>

Author: kingaa
Date: 2013-11-11 02:28:48 +0100 (Mon, 11 Nov 2013)
New Revision: 868

Added:
   pkg/pomp/R/logmeanexp.R
   pkg/pomp/man/logmeanexp.Rd
Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/NAMESPACE
   pkg/pomp/R/builder.R
   pkg/pomp/inst/NEWS
   pkg/pomp/man/builder.Rd
Log:
- add 'logmeanexp'
- fix 'pompBuilder' codes for windows


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2013-11-05 22:58:31 UTC (rev 867)
+++ pkg/pomp/DESCRIPTION	2013-11-11 01:28:48 UTC (rev 868)
@@ -1,21 +1,24 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.45-5
-Date: 2013-11-05
-Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
+Version: 0.45-6
+Date: 2013-11-10
+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")),
 	  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("Bruce","E."),family="Kendall",role=c("ctb")),
 	  person(given=c("Michael"),family="Lavine",role=c("ctb")),
+	  person(given="Dao",family="Nguyen",role=c("ctb")),
 	  person(given=c("Daniel","C."),family="Reuman",role=c("ctb")),
 	  person(given=c("Helen"),family="Wearing",role=c("ctb")),
-	  person(given=c("Simon","N."),family="Wood",role=c("ctb")),
-	  person(given="Dao",family="Nguyen",role=c("ctb"))	)
+	  person(given=c("Simon","N."),family="Wood",role=c("ctb"))
+	  )
 Maintainer: Aaron A. King <kingaa at umich.edu>
-Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman, Simon N. Wood, Dao Nguyen
+Author: Aaron A. King, Edward L. Ionides, Carles Breto, Stephen P. Ellner, Matthew J. Ferrari, Bruce E. Kendall, Michael Lavine, Dao Nguyen, Daniel C. Reuman, Helen Wearing, Simon N. Wood
 URL: http://pomp.r-forge.r-project.org
 Description: Inference methods for partially-observed Markov processes
 Depends: R(>= 2.14.1), stats, graphics, methods, mvtnorm, subplex, deSolve
@@ -23,7 +26,8 @@
 LazyData: true
 BuildVignettes: true
 Collate: aaa.R authors.R version.R eulermultinom.R plugins.R 
-	 parmat.R slice-design.R profile-design.R sobol.R bsplines.R sannbox.R
+	 parmat.R logmeanexp.R slice-design.R 
+	 profile-design.R sobol.R bsplines.R sannbox.R
 	 pomp-fun.R pomp-class.R pomp.R pomp-methods.R 
 	 rmeasure-pomp.R rprocess-pomp.R init-state-pomp.R dmeasure-pomp.R dprocess-pomp.R skeleton-pomp.R 
 	 simulate-pomp.R trajectory-pomp.R plot-pomp.R 

Modified: pkg/pomp/NAMESPACE
===================================================================
--- pkg/pomp/NAMESPACE	2013-11-05 22:58:31 UTC (rev 867)
+++ pkg/pomp/NAMESPACE	2013-11-11 01:28:48 UTC (rev 868)
@@ -81,6 +81,7 @@
        compare.mif,
        nlf,
        parmat,
+       logmeanexp,
        probe.mean,
        probe.median,
        probe.var,

Modified: pkg/pomp/R/builder.R
===================================================================
--- pkg/pomp/R/builder.R	2013-11-05 22:58:31 UTC (rev 867)
+++ pkg/pomp/R/builder.R	2013-11-11 01:28:48 UTC (rev 868)
@@ -96,7 +96,7 @@
                  )
 
 header <- list(
-               file="/* pomp model file: {%name%} */\n\n#include <pomp.h>\n#include <R_ext/Rdynload.h>\n\n",
+               file="/* pomp model file: {%name%} */\n\n#include <{%pompheader%}>\n#include <R_ext/Rdynload.h>\n\n",
                rmeasure="\nvoid {%name%}_rmeasure (double *__y, double *__x, double *__p, int *__obsindex, int *__stateindex, int *__parindex, int *__covindex, int __ncovars, double *__covars, double t)\n{\n",
                dmeasure= "\nvoid {%name%}_dmeasure (double *__lik, double *__y, double *__x, double *__p, int give_log, int *__obsindex, int *__stateindex, int *__parindex, int *__covindex, int __ncovars, double *__covars, double t)\n{\n",
                step.fn="\nvoid {%name%}_stepfn (double *__x, const double *__p, const int *__stateindex, const int *__parindex, const int *__covindex, int __covdim, const double *__covars, double t, double dt)\n{\n",
@@ -148,10 +148,15 @@
 
   modelfile <- paste0(name,".c")
   solib <- paste0(name,.Platform$dynlib.ext)
-
+  if (.Platform$OS.type=="unix") {
+    pompheader <- "pomp.h"
+  } else {
+    pompheader <- system.file("include/pomp.h",package="pomp")
+  }
+  
   out <- file(description=modelfile,open="w")
   
-  cat(file=out,render(header$file,name=name))
+  cat(file=out,render(header$file,name=name,pompheader=pompheader))
 
   for (f in utility.fns) {
     cat(file=out,f)

Added: pkg/pomp/R/logmeanexp.R
===================================================================
--- pkg/pomp/R/logmeanexp.R	                        (rev 0)
+++ pkg/pomp/R/logmeanexp.R	2013-11-11 01:28:48 UTC (rev 868)
@@ -0,0 +1,4 @@
+logmeanexp <- function (x) {
+  mx <- max(x)
+  mx+log(mean(exp(x-mx)))
+}

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2013-11-05 22:58:31 UTC (rev 867)
+++ pkg/pomp/inst/NEWS	2013-11-11 01:28:48 UTC (rev 868)
@@ -1,4 +1,9 @@
 NEWS
+0.45-5
+     o	a fix so that 'pompBuilder' will find 'pomp.h' header file on Windows machines.  Thanks to Dave Hayman for finding the problem.
+
+     o	some reorganization of the source package structure.
+
 0.45-4
      o	changes in the way 'reulermultinom', 'deulermultinom', 'dot_product' are exported to other packages.  Rather than just being exported as linkables, these are now also defined as static inline functions in the 'pomp.h' header.
 

Modified: pkg/pomp/man/builder.Rd
===================================================================
--- pkg/pomp/man/builder.Rd	2013-11-05 22:58:31 UTC (rev 867)
+++ pkg/pomp/man/builder.Rd	2013-11-11 01:28:48 UTC (rev 868)
@@ -55,12 +55,20 @@
 }
 \value{
   The constructed \code{pomp} object.
-  A side-effect is the writing and compilation of a C code into a shared-object library.
+  A side-effect is the writing and compilation of a C code into a dynamics shared object.
   These files will reside in the current working directory (see \code{\link{getwd}}).
-  If \code{pompBuilder} has been called with \code{link=FALSE}, this shared-object library must be linked (see \code{\link{dyn.load}}) before the \code{pomp} object can be used.
+  If \code{pompBuilder} has been called with \code{link=FALSE}, this dynamic shared object must be linked (see \code{\link{dyn.load}}) before the \code{pomp} object can be used.
+
+  \strong{Parallel computing caution:}
+  note that, since a side-effect of running \code{pompBuilder} is the writing and compilation of a file, caution must be used when running parallel computations.
+  Simultaneous execution of \code{pompBuilder} on nodes sharing a common disk will cause all nodes to attempt to write the same file at the same time;
+  the results will be undefined.
+  If multiple nodes are to work on the same \code{pomp} object built by \code{pompBuilder}, first run \code{pompBuilder} once (perhaps with \code{link=FALSE}) to write the C file and compile it into a dynamic shared object file.
+  The \code{pomp} object returned by \code{pompBuilder} can then be shared with all worker nodes.
+  Note, however, that all worker nodes must dynamically load (using \code{\link{dyn.load}}) the dynamic shared object file before anything can be done with the \code{pomp} object.
 }
 \details{
-  \code{pompBuilder} assumes that files can be written to the current working directory and that shared-object libraries can be compiled and linked, i.e., that \code{R CMD SHLIB} will work.
+  \code{pompBuilder} assumes that files can be written to the current working directory and that dynamic shared objects can be compiled and linked, i.e., that \code{R CMD SHLIB} will work.
   This will not typically be the case in out-of-the-box Windows installations.
 }
 \seealso{

Added: pkg/pomp/man/logmeanexp.Rd
===================================================================
--- pkg/pomp/man/logmeanexp.Rd	                        (rev 0)
+++ pkg/pomp/man/logmeanexp.Rd	2013-11-11 01:28:48 UTC (rev 868)
@@ -0,0 +1,23 @@
+\name{logmeanexp}
+\alias{logmeanexp}
+\title{The log-mean-exp trick}
+\description{
+  \code{logmeanexp} computes the log-mean-exp of a set of numbers.
+}
+\usage{
+logmeanexp(x)
+}
+\arguments{
+  \item{x}{numeric}
+}
+\value{
+  \code{log(mean(exp(x)))} computed so as to avoid over- or underflow.
+}
+\author{Aaron A. King \email{kingaa at umich dot edu}}
+\examples{
+  ## generate a bifurcation diagram for the Ricker map
+  pompExample(ricker)
+  ll <- replicate(n=5,logLik(pfilter(ricker,Np=1000)))
+  ## an estimate of the log likelihood:
+  logmeanexp(ll)
+}


From noreply at r-forge.r-project.org  Mon Nov 11 02:43:33 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 11 Nov 2013 02:43:33 +0100 (CET)
Subject: [Pomp-commits] r869 - www/vignettes
Message-ID: <20131111014333.B36831853F5@r-forge.r-project.org>

Author: kingaa
Date: 2013-11-11 02:43:33 +0100 (Mon, 11 Nov 2013)
New Revision: 869

Modified:
   www/vignettes/advanced_topics_in_pomp.pdf
   www/vignettes/intro_to_pomp.pdf
   www/vignettes/pomp.bib
Log:
- update vignettes


Modified: www/vignettes/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)

Modified: www/vignettes/intro_to_pomp.pdf
===================================================================
(Binary files differ)

Modified: www/vignettes/pomp.bib
===================================================================
--- www/vignettes/pomp.bib	2013-11-11 01:28:48 UTC (rev 868)
+++ www/vignettes/pomp.bib	2013-11-11 01:43:33 UTC (rev 869)
@@ -478,8 +478,7 @@
   journal = {Proceedings of the National Academy of Sciences of the U.S.A.},
   year = {2006},
   volume = {103},
-  pages = {18860--18865 },
-  url = {http://dx.doi.org/10.1073/pnas.0608571103}
+  pages = {18860--18865 }
 }
 
 @ARTICLE{Smith1993,
@@ -527,8 +526,7 @@
 	future.},
   file = {Tidd1993.pdf:Tidd1993.pdf:PDF},
   owner = {kingaa},
-  timestamp = {2009.09.22},
-  url = {http://links.jstor.org/sici?sici=0962-8452%2819931222%29254%3A1341%3C257%3ATCFCIC%3E2.0.CO%3B2-G}
+  timestamp = {2009.09.22}
 }
 
 @ARTICLE{Wearing2009,


From noreply at r-forge.r-project.org  Mon Nov 11 16:30:44 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 11 Nov 2013 16:30:44 +0100 (CET)
Subject: [Pomp-commits] r870 - pkg/pompExamples
Message-ID: <20131111153044.26D4618622D@r-forge.r-project.org>

Author: kingaa
Date: 2013-11-11 16:30:43 +0100 (Mon, 11 Nov 2013)
New Revision: 870

Modified:
   pkg/pompExamples/DESCRIPTION
Log:
- bump for rebuild


Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2013-11-11 01:43:33 UTC (rev 869)
+++ pkg/pompExamples/DESCRIPTION	2013-11-11 15:30:43 UTC (rev 870)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.21-4
-Date: 2013-11-05
+Date: 2013-11-11
 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("Edward","L."),family="Ionides",role=c("aut")),