rmeasure, dmeasure, and skeleton are now specified by a function (or native routine) that does the computation for ONE state vector and ONE parameter vector.
This is analogous to the way that init.state has operated from the beginning.
It greatly simplifies model specification from the user's point of view without changing the low-level methods interfaces (pomp methods rmeasure, dmeasure, skeleton, init.states).
-However, this change is not backward-compatible: users will need to rewrite code for the rmeasure, dmeasure, and skeleton slots.
+However, this change is not backward-compatible: users will need to rewrite code for the rmeasure, dmeasure, and skeleton slots.
In practice, this should not be difficult.
It involves removing loops over times and columns of params and (if covariates are used in the measurement model or deterministic skeleton) making use of the covars argument passed to the user function.
Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf 2015-04-16 15:55:06 UTC (rev 1152)
+++ www/vignettes/pomp.pdf 2015-05-21 13:40:13 UTC (rev 1153)
@@ -10,8 +10,7 @@
?? ?@
-? ?????
!?W?O ?p???? ,??????????1???7G?6 SsU??Q|???9X?? _v|?|??= a|Mc|??l?? 6???Pt?(??m???e?\??? k!y?? ?^??E?????c????Fj?>??\??g?9?zH|??Zs?Z3??pM?????& ????G?]?\_??M?6????5X-c????>9V?7?x?1?y?"k?}?????????5Y?a?lU?????-?????????????c?#?c?&? ?s,?U? ?s,??<6??X?cy???%???????[g
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@@ -41,12 +40,12 @@
-
-2015-03-24T15:20:55-04:00
-2015-03-24T15:20:55-04:00
+
+2015-05-21T09:36:37-04:00
+2015-05-21T09:36:37-04:00
Raph Levien
-
-Inconsolata
+
+Inconsolata
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g?ssn??3?l????????V ?{?
Author: kingaa
Date: 2015-05-21 23:51:35 +0200 (Thu, 21 May 2015)
New Revision: 1154
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/inst/include/pomp.h
pkg/pomp/src/pomp.h
pkg/pomp/tests/synlik.Rout.save
Log:
- use 'const' where appropriate in pomp's C API
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-05-21 13:40:13 UTC (rev 1153)
+++ pkg/pomp/DESCRIPTION 2015-05-21 21:51:35 UTC (rev 1154)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.63-6
-Date: 2015-04-16
+Version: 0.63-7
+Date: 2015-05-21
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")),
Modified: pkg/pomp/inst/include/pomp.h
===================================================================
--- pkg/pomp/inst/include/pomp.h 2015-05-21 13:40:13 UTC (rev 1153)
+++ pkg/pomp/inst/include/pomp.h 2015-05-21 21:51:35 UTC (rev 1154)
@@ -65,7 +65,7 @@
// But note that when reulermultinom is called inside a pomp 'rprocess',
// there is no need to call {Get,Put}RNGState() as this is handled by pomp
-static R_INLINE void reulermultinom (int m, double size, double *rate,
+static R_INLINE void reulermultinom (int m, double size, const double *rate,
double dt, double *trans) {
double p = 0.0;
int j, k;
@@ -114,7 +114,7 @@
// See '?deulermultinom' and vignettes for more on the Euler-multinomial
// distributions.
-static R_INLINE double deulermultinom (int m, double size, double *rate,
+static R_INLINE double deulermultinom (int m, double size, const double *rate,
double dt, double *trans, int give_log) {
double p = 0.0;
double n = 0.0;
@@ -234,8 +234,8 @@
// prototype for stochastic simulation algorithm reaction-rate function, as used by "gillespie.sim":
typedef double pomp_ssa_rate_fn(int j, double t, const double *x, const double *p,
- int *stateindex, int *parindex, int *covindex,
- int ncovar, double *covars);
+ const int *stateindex, const int *parindex, const int *covindex,
+ int ncovar, const double *covars);
// Description:
// on input:
// j = integer specifying the number of the reaction whose rate is desired
@@ -283,7 +283,7 @@
// PROTOTYPE FOR ONE-STEP LOG PROBABILITY DENSITY FUNCTION, AS USED BY "ONESTEP.DENS":
typedef void pomp_onestep_pdf(double *f,
- double *x1, double *x2, double t1, double t2, const double *p,
+ const double *x1, const double *x2, double t1, double t2, const double *p,
const int *stateindex, const int *parindex, const int *covindex,
int ncovars, const double *covars);
// Description:
@@ -306,9 +306,9 @@
// f = pointer to the probability density (a single scalar)
// prototype for deterministic skeleton evaluation
-typedef void pomp_skeleton (double *f, double *x, double *p,
- int *stateindex, int *parindex, int *covindex,
- int ncovars, double *covars, double t);
+typedef void pomp_skeleton (double *f, const double *x, const double *p,
+ const int *stateindex, const int *parindex, const int *covindex,
+ int ncovars, const double *covars, double t);
// Description:
// on input:
@@ -328,9 +328,9 @@
// f = pointer to value of the map or vectorfield (a vector of the same length as 'x')
// prototype for measurement model simulation
-typedef void pomp_measure_model_simulator (double *y, double *x, double *p,
- int *obsindex, int *stateindex, int *parindex, int *covindex,
- int ncovars, double *covars, double t);
+typedef void pomp_measure_model_simulator (double *y, const double *x, const double *p,
+ const int *obsindex, const int *stateindex, const int *parindex, const int *covindex,
+ int ncovars, const double *covars, double t);
// Description:
// on input:
// x = pointer to state vector at time t
@@ -356,9 +356,9 @@
// prototype for measurement model density evaluator
-typedef void pomp_measure_model_density (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);
+typedef void pomp_measure_model_density (double *lik, const double *y, const double *x, const double *p, int give_log,
+ const int *obsindex, const int *stateindex, const int *parindex, const int *covindex,
+ int ncovars, const double *covars, double t);
// Description:
// on input:
// y = pointer to vector of observables at time t
@@ -381,7 +381,7 @@
// lik = pointer to scalar containing (log) likelihood
// prototype for prior simulation
-typedef void pomp_rprior (double *p, int *parindex);
+typedef void pomp_rprior (double *p, const int *parindex);
// Description:
// on input:
// p = pointer to parameter vector
@@ -395,7 +395,7 @@
// Inclusion of these calls in the user-defined function may result in significant slowdown.
// prototype for prior density evaluation
-typedef void pomp_dprior (double *lik, double *p, int give_log, int *parindex);
+typedef void pomp_dprior (double *lik, const double *p, int give_log, const int *parindex);
// Description:
// on input:
// p = pointer to parameter vector
@@ -406,6 +406,6 @@
// lik = pointer to vector containing likelihoods
// prototype for parameter transformation function.
-typedef void pomp_transform_fn (double *pt, double *p, int *parindex);
+typedef void pomp_transform_fn (double *pt, const double *p, const int *parindex);
#endif
Modified: pkg/pomp/src/pomp.h
===================================================================
--- pkg/pomp/src/pomp.h 2015-05-21 13:40:13 UTC (rev 1153)
+++ pkg/pomp/src/pomp.h 2015-05-21 21:51:35 UTC (rev 1154)
@@ -65,7 +65,7 @@
// But note that when reulermultinom is called inside a pomp 'rprocess',
// there is no need to call {Get,Put}RNGState() as this is handled by pomp
-static R_INLINE void reulermultinom (int m, double size, double *rate,
+static R_INLINE void reulermultinom (int m, double size, const double *rate,
double dt, double *trans) {
double p = 0.0;
int j, k;
@@ -114,7 +114,7 @@
// See '?deulermultinom' and vignettes for more on the Euler-multinomial
// distributions.
-static R_INLINE double deulermultinom (int m, double size, double *rate,
+static R_INLINE double deulermultinom (int m, double size, const double *rate,
double dt, double *trans, int give_log) {
double p = 0.0;
double n = 0.0;
@@ -234,8 +234,8 @@
// prototype for stochastic simulation algorithm reaction-rate function, as used by "gillespie.sim":
typedef double pomp_ssa_rate_fn(int j, double t, const double *x, const double *p,
- int *stateindex, int *parindex, int *covindex,
- int ncovar, double *covars);
+ const int *stateindex, const int *parindex, const int *covindex,
+ int ncovar, const double *covars);
// Description:
// on input:
// j = integer specifying the number of the reaction whose rate is desired
@@ -283,7 +283,7 @@
// PROTOTYPE FOR ONE-STEP LOG PROBABILITY DENSITY FUNCTION, AS USED BY "ONESTEP.DENS":
typedef void pomp_onestep_pdf(double *f,
- double *x1, double *x2, double t1, double t2, const double *p,
+ const double *x1, const double *x2, double t1, double t2, const double *p,
const int *stateindex, const int *parindex, const int *covindex,
int ncovars, const double *covars);
// Description:
@@ -306,9 +306,9 @@
// f = pointer to the probability density (a single scalar)
// prototype for deterministic skeleton evaluation
-typedef void pomp_skeleton (double *f, double *x, double *p,
- int *stateindex, int *parindex, int *covindex,
- int ncovars, double *covars, double t);
+typedef void pomp_skeleton (double *f, const double *x, const double *p,
+ const int *stateindex, const int *parindex, const int *covindex,
+ int ncovars, const double *covars, double t);
// Description:
// on input:
@@ -328,9 +328,9 @@
// f = pointer to value of the map or vectorfield (a vector of the same length as 'x')
// prototype for measurement model simulation
-typedef void pomp_measure_model_simulator (double *y, double *x, double *p,
- int *obsindex, int *stateindex, int *parindex, int *covindex,
- int ncovars, double *covars, double t);
+typedef void pomp_measure_model_simulator (double *y, const double *x, const double *p,
+ const int *obsindex, const int *stateindex, const int *parindex, const int *covindex,
+ int ncovars, const double *covars, double t);
// Description:
// on input:
// x = pointer to state vector at time t
@@ -356,9 +356,9 @@
// prototype for measurement model density evaluator
-typedef void pomp_measure_model_density (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);
+typedef void pomp_measure_model_density (double *lik, const double *y, const double *x, const double *p, int give_log,
+ const int *obsindex, const int *stateindex, const int *parindex, const int *covindex,
+ int ncovars, const double *covars, double t);
// Description:
// on input:
// y = pointer to vector of observables at time t
@@ -381,7 +381,7 @@
// lik = pointer to scalar containing (log) likelihood
// prototype for prior simulation
-typedef void pomp_rprior (double *p, int *parindex);
+typedef void pomp_rprior (double *p, const int *parindex);
// Description:
// on input:
// p = pointer to parameter vector
@@ -395,7 +395,7 @@
// Inclusion of these calls in the user-defined function may result in significant slowdown.
// prototype for prior density evaluation
-typedef void pomp_dprior (double *lik, double *p, int give_log, int *parindex);
+typedef void pomp_dprior (double *lik, const double *p, int give_log, const int *parindex);
// Description:
// on input:
// p = pointer to parameter vector
@@ -406,6 +406,6 @@
// lik = pointer to vector containing likelihoods
// prototype for parameter transformation function.
-typedef void pomp_transform_fn (double *pt, double *p, int *parindex);
+typedef void pomp_transform_fn (double *pt, const double *p, const int *parindex);
#endif
Modified: pkg/pomp/tests/synlik.Rout.save
===================================================================
--- pkg/pomp/tests/synlik.Rout.save 2015-05-21 13:40:13 UTC (rev 1153)
+++ pkg/pomp/tests/synlik.Rout.save 2015-05-21 21:51:35 UTC (rev 1154)
@@ -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 3.2.0 (2015-04-16) -- "Full of Ingredients"
+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(ou2)
newly created object(s):
@@ -87,14 +85,14 @@
Kruskal-Wallis rank sum test
data: list(loglik.probe, loglik.pfilter)
-Kruskal-Wallis chi-squared = 10.5617, df = 1, p-value = 0.001155
+Kruskal-Wallis chi-squared = 10.562, df = 1, p-value = 0.001155
> wilcox.test(loglik.probe,loglik.pfilter)
Wilcoxon rank sum test with continuity correction
data: loglik.probe and loglik.pfilter
-W = 139841, p-value = 0.001155
+W = 139840, p-value = 0.001155
alternative hypothesis: true location shift is not equal to 0
> ks.test(loglik.pfilter,loglik.probe)
@@ -116,4 +114,4 @@
>
> proc.time()
user system elapsed
- 7.286 0.042 7.322
+ 5.628 0.060 5.764
From noreply at r-forge.r-project.org Fri May 22 12:52:15 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 22 May 2015 12:52:15 +0200 (CEST)
Subject: [Pomp-commits] r1155 - pkg/pomp/R
Message-ID: <20150522105216.09D51186A83@r-forge.r-project.org>
Author: kingaa
Date: 2015-05-22 12:52:15 +0200 (Fri, 22 May 2015)
New Revision: 1155
Modified:
pkg/pomp/R/builder.R
Log:
- use 'const' where appropriate in pomp's C API
Modified: pkg/pomp/R/builder.R
===================================================================
--- pkg/pomp/R/builder.R 2015-05-21 21:51:35 UTC (rev 1154)
+++ pkg/pomp/R/builder.R 2015-05-22 10:52:15 UTC (rev 1155)
@@ -312,14 +312,14 @@
header <- list(
file="/* pomp model file: {%name%} */\n\n#include <{%pompheader%}>\n#include \n\n",
registration="\nvoid R_init_{%name%} (DllInfo *info)\n{\n",
- rmeasure="\nvoid __pomp_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 __pomp_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",
+ rmeasure="\nvoid __pomp_rmeasure (double *__y, const double *__x, const double *__p, const int *__obsindex, const int *__stateindex, const int *__parindex, const int *__covindex, int __ncovars, const double *__covars, double t)\n{\n",
+ dmeasure= "\nvoid __pomp_dmeasure (double *__lik, const double *__y, const double *__x, const double *__p, int give_log, const int *__obsindex, const int *__stateindex, const int *__parindex, const int *__covindex, int __ncovars, const double *__covars, double t)\n{\n",
step.fn="\nvoid __pomp_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",
- skeleton="\nvoid __pomp_skelfn (double *__f, double *__x, double *__p, int *__stateindex, int *__parindex, int *__covindex, int __ncovars, double *__covars, double t)\n{\n",
- parameter.transform="\nvoid __pomp_par_trans (double *__pt, double *__p, int *__parindex)\n{\n",
- parameter.inv.transform="\nvoid __pomp_par_untrans (double *__pt, double *__p, int *__parindex)\n{\n",
- rprior="\nvoid __pomp_rprior (double *__p, int *__parindex)\n{\n",
- dprior="\nvoid __pomp_dprior (double *__lik, double *__p, int give_log, int *__parindex)\n{\n"
+ skeleton="\nvoid __pomp_skelfn (double *__f, const double *__x, const double *__p, const int *__stateindex, const int *__parindex, const int *__covindex, int __ncovars, const double *__covars, double t)\n{\n",
+ parameter.transform="\nvoid __pomp_par_trans (double *__pt, const double *__p, const int *__parindex)\n{\n",
+ parameter.inv.transform="\nvoid __pomp_par_untrans (double *__pt, const double *__p, const int *__parindex)\n{\n",
+ rprior="\nvoid __pomp_rprior (double *__p, const int *__parindex)\n{\n",
+ dprior="\nvoid __pomp_dprior (double *__lik, const double *__p, int give_log, const int *__parindex)\n{\n"
)
fnames <- list(
From noreply at r-forge.r-project.org Fri May 22 18:38:43 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 22 May 2015 18:38:43 +0200 (CEST)
Subject: [Pomp-commits] r1156 - pkg/pompExamples
Message-ID: <20150522163843.EE563187A72@r-forge.r-project.org>
Author: kingaa
Date: 2015-05-22 18:38:43 +0200 (Fri, 22 May 2015)
New Revision: 1156
Modified:
pkg/pompExamples/DESCRIPTION
Log:
- bump
Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION 2015-05-22 10:52:15 UTC (rev 1155)
+++ pkg/pompExamples/DESCRIPTION 2015-05-22 16:38:43 UTC (rev 1156)
@@ -1,8 +1,8 @@
Package: pompExamples
Type: Package
Title: Additional pomp examples
-Version: 0.27-1
-Date: 2015-03-02
+Version: 0.27-2
+Date: 2015-05-22
Maintainer: Aaron A. King
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 Fri May 22 19:40:17 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 22 May 2015 19:40:17 +0200 (CEST)
Subject: [Pomp-commits] r1157 - pkg/pomp pkg/pomp/R pkg/pomp/inst
pkg/pomp/man pkg/pomp/tests www/content www/vignettes
Message-ID: <20150522174017.3A66218743E@r-forge.r-project.org>
Author: kingaa
Date: 2015-05-22 19:40:16 +0200 (Fri, 22 May 2015)
New Revision: 1157
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/mif.R
pkg/pomp/inst/CITATION
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/man/mif.Rd
pkg/pomp/tests/ou2-mif.Rout.save
www/content/NEWS.html
www/vignettes/pomp.pdf
Log:
- replace 'cooling.factor' with 'cooling.factor.50' in 'mif'
- update NEWS file
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/DESCRIPTION 2015-05-22 17:40:16 UTC (rev 1157)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.63-7
-Date: 2015-05-21
+Version: 0.64-1
+Date: 2015-05-22
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")),
Modified: pkg/pomp/R/mif.R
===================================================================
--- pkg/pomp/R/mif.R 2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/R/mif.R 2015-05-22 17:40:16 UTC (rev 1157)
@@ -13,7 +13,7 @@
var.factor='numeric',
ic.lag='integer',
cooling.type='character',
- cooling.fraction='numeric',
+ cooling.fraction.50='numeric',
method='character',
random.walk.sd = 'numeric',
conv.rec = 'matrix'
@@ -57,7 +57,7 @@
hyperbolic={
if (fraction>=1)
stop(
- "mif error: ",sQuote("cooling.fraction"),
+ "mif error: ",sQuote("cooling.fraction.50"),
" must be < 1 when cooling.type = ",
sQuote("hyperbolic"),
call.=FALSE
@@ -86,7 +86,7 @@
particles,
rw.sd,
Np, var.factor, ic.lag,
- cooling.type, cooling.fraction,
+ cooling.type, cooling.fraction.50,
method,
tol, max.fail,
verbose, transform, .ndone = 0L,
@@ -206,16 +206,16 @@
)
}
- if (missing(cooling.fraction))
- stop("mif error: ",sQuote("cooling.fraction")," must be specified",call.=FALSE)
- cooling.fraction <- as.numeric(cooling.fraction)
- if ((length(cooling.fraction)!=1)||(cooling.fraction<0)||(cooling.fraction>1))
- stop("mif error: ",sQuote("cooling.fraction")," must be a number between 0 and 1",call.=FALSE)
+ if (missing(cooling.fraction.50))
+ stop("mif error: ",sQuote("cooling.fraction.50")," must be specified",call.=FALSE)
+ cooling.fraction.50 <- as.numeric(cooling.fraction.50)
+ if ((length(cooling.fraction.50)!=1)||(cooling.fraction.50<0)||(cooling.fraction.50>1))
+ stop("mif error: ",sQuote("cooling.fraction.50")," must be a number between 0 and 1",call.=FALSE)
cooling <- cooling.function(
type=cooling.type,
perobs=(method=="mif2"),
- fraction=cooling.fraction,
+ fraction=cooling.fraction.50,
ntimes=ntimes
)
@@ -370,7 +370,7 @@
conv.rec=conv.rec,
method=method,
cooling.type=cooling.type,
- cooling.fraction=cooling.fraction,
+ cooling.fraction.50=cooling.fraction.50,
paramMatrix=if (method=="mif2") paramMatrix else array(data=numeric(0),dim=c(0,0))
)
}
@@ -384,7 +384,7 @@
particles, rw.sd,
Np, ic.lag, var.factor = 1,
cooling.type = c("geometric","hyperbolic"),
- cooling.fraction,
+ cooling.fraction.50,
method = c("mif","unweighted","fp","mif2"),
tol = 1e-17, max.fail = Inf,
verbose = getOption("verbose"),
@@ -434,7 +434,7 @@
rw.sd=rw.sd,
Np=Np,
cooling.type=cooling.type,
- cooling.fraction=cooling.fraction,
+ cooling.fraction.50=cooling.fraction.50,
var.factor=var.factor,
ic.lag=ic.lag,
method=method,
@@ -476,7 +476,7 @@
ivps,
particles, rw.sd,
Np, ic.lag, var.factor,
- cooling.type, cooling.fraction,
+ cooling.type, cooling.fraction.50,
method,
tol,
transform,
@@ -490,7 +490,7 @@
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(cooling.fraction.50)) cooling.fraction.50 <- object at cooling.fraction.50
if (missing(method)) method <- object at method
if (missing(transform)) transform <- object at transform
@@ -506,7 +506,7 @@
rw.sd=rw.sd,
Np=Np,
cooling.type=cooling.type,
- cooling.fraction=cooling.fraction,
+ cooling.fraction.50=cooling.fraction.50,
var.factor=var.factor,
ic.lag=ic.lag,
method=method,
Modified: pkg/pomp/inst/CITATION
===================================================================
--- pkg/pomp/inst/CITATION 2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/inst/CITATION 2015-05-22 17:40:16 UTC (rev 1157)
@@ -27,7 +27,7 @@
)
citEntry(
- header="The correct citation of the package itself is:",
+ header="Additionally, please cite the package itself:",
entry="Manual",
title="{pomp}: {S}tatistical Inference for Partially Observed {M}arkov Processes",
author=personList(
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/inst/NEWS 2015-05-22 17:40:16 UTC (rev 1157)
@@ -1,5 +1,21 @@
_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_4-_1:
+
+ ??? The ???mif??? option ???cooling.fraction??? has been replaced by the
+ more descriptive ???cooling.fraction.50???. Recall that this
+ parameter specifies the fraction of random-walk remaining
+ after 50 ???mif??? iterations.
+
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_3-_6:
+
+ ??? Fixed bug arising when using ???pomp??? with ???Csnippets??? under
+ windows. Thanks to Hamish McCallum for reporting it.
+
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_3-_3:
+
+ ??? Improvements to documentation.
+
_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
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/inst/NEWS.Rd 2015-05-22 17:40:16 UTC (rev 1157)
@@ -1,5 +1,22 @@
\name{NEWS}
\title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.64-1}{
+ \itemize{
+ \item The \code{mif} option \code{cooling.fraction} has been replaced by the more descriptive \code{cooling.fraction.50}.
+ Recall that this parameter specifies the fraction of random-walk remaining after 50 \code{mif} iterations.
+ }
+}
+\section{Changes in \pkg{pomp} version 0.63-6}{
+ \itemize{
+ \item Fixed bug arising when using \code{pomp} with \code{Csnippets} under windows.
+ Thanks to Hamish McCallum for reporting it.
+ }
+}
+\section{Changes in \pkg{pomp} version 0.63-3}{
+ \itemize{
+ \item Improvements to documentation.
+ }
+}
\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.
Modified: pkg/pomp/man/mif.Rd
===================================================================
--- pkg/pomp/man/mif.Rd 2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/man/mif.Rd 2015-05-22 17:40:16 UTC (rev 1157)
@@ -38,14 +38,14 @@
\usage{
\S4method{mif}{pomp}(object, Nmif = 1, start, ivps = character(0),
particles, rw.sd, Np, ic.lag, var.factor = 1,
- cooling.type, cooling.fraction,
+ cooling.type, cooling.fraction.50,
method = c("mif","unweighted","fp","mif2"),
tol = 1e-17, max.fail = Inf,
verbose = getOption("verbose"), transform = FALSE, \dots)
\S4method{mif}{pfilterd.pomp}(object, Nmif = 1, Np, tol, \dots)
\S4method{mif}{mif}(object, Nmif, start, ivps,
particles, rw.sd, Np, ic.lag, var.factor,
- cooling.type, cooling.fraction,
+ cooling.type, cooling.fraction.50,
method, tol, transform, \dots)
\S4method{continue}{mif}(object, Nmif = 1, \dots)
\S4method{logLik}{mif}(object, \dots)
@@ -107,14 +107,14 @@
the scaling coefficient relating the width of the starting particle distribution to \code{rw.sd}.
In particular, the width of the distribution of particles at the start of the first \code{mif} iteration will be \code{random.walk.sd*var.factor}.
}
- \item{cooling.type, cooling.fraction}{
+ \item{cooling.type, cooling.fraction.50}{
specifications for the cooling schedule, i.e., the manner in which the intensity of the parameter perturbations is reduced with successive filtering iterations.
\code{cooling.type} specifies the nature of the cooling schedule.
- When \code{cooling.type="geometric"}, on the n-th \code{mif} iteration, the relative perturbation intensity is \code{cooling.fraction^(n/50)}.
+ When \code{cooling.type="geometric"}, on the n-th \code{mif} iteration, the relative perturbation intensity is \code{cooling.fraction.50^(n/50)}.
- When \code{cooling.type="hyperbolic"}, on the n-th \code{mif} iteration, the relative perturbation intensity is \code{(s+1)/(s+n)}, where \code{(s+1)/(s+50)=cooling.fraction}.
- \code{cooling.fraction} is the relative magnitude of the parameter perturbations after 50 \code{mif} iterations.
+ When \code{cooling.type="hyperbolic"}, on the n-th \code{mif} iteration, the relative perturbation intensity is \code{(s+1)/(s+n)}, where \code{(s+1)/(s+50)=cooling.fraction.50}.
+ \code{cooling.fraction.50} is the relative magnitude of the parameter perturbations after 50 \code{mif} iterations.
}
\item{method}{
\code{method} sets the update rule used in the algorithm.
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2015-05-22 16:38:43 UTC (rev 1156)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2015-05-22 17:40:16 UTC (rev 1157)
@@ -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 3.2.0 (2015-04-16) -- "Full of Ingredients"
+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(ou2)
newly created object(s):
@@ -137,7 +135,7 @@
+ Np=100,ic.lag=10,var.factor=1
+ )
+ )
-Error : mif error: 'cooling.fraction' must be specified
+Error : mif error: 'cooling.fraction.50' must be specified
>
> try(
+ mif(
@@ -279,4 +277,4 @@
>
> proc.time()
user system elapsed
- 15.232 0.060 15.274
+ 11.468 0.028 11.712
Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html 2015-05-22 16:38:43 UTC (rev 1156)
+++ www/content/NEWS.html 2015-05-22 17:40:16 UTC (rev 1157)
@@ -7,6 +7,38 @@
News for package ‘pomp’
+Changes in pomp version 0.64-1
+
+
+
+
+
+
+Changes in pomp version 0.63-6
+
+
+
+
+
+
+Changes in pomp version 0.63-3
+
+
+
+
+
+
Changes in pomp version 0.63-1
Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf 2015-05-22 16:38:43 UTC (rev 1156)
+++ www/vignettes/pomp.pdf 2015-05-22 17:40:16 UTC (rev 1157)
@@ -1,305 +1,340 @@
%PDF-1.5
%????
1 0 obj
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+???
Author: kingaa
Date: 2015-05-24 19:24:31 +0200 (Sun, 24 May 2015)
New Revision: 1158
Modified:
pkg/pompExamples/DESCRIPTION
pkg/pompExamples/inst/examples/ebola.R
Log:
- add R-Forge to 'Additional_repositories' field.
- fix const declarations in Ebola example that give warnings
Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION 2015-05-22 17:40:16 UTC (rev 1157)
+++ pkg/pompExamples/DESCRIPTION 2015-05-24 17:24:31 UTC (rev 1158)
@@ -2,7 +2,7 @@
Type: Package
Title: Additional pomp examples
Version: 0.27-2
-Date: 2015-05-22
+Date: 2015-05-24
Maintainer: Aaron A. King
Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),
email="kingaa at umich.edu"),
@@ -19,6 +19,7 @@
Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.58-6)
Suggests: plyr, reshape2, ggplot2, knitr, markdown
LinkingTo: pomp
+Additional_repositories: http://r-forge.r-rproject.org
License: GPL (>= 2)
LazyData: false
BuildVignettes: true
Modified: pkg/pompExamples/inst/examples/ebola.R
===================================================================
--- pkg/pompExamples/inst/examples/ebola.R 2015-05-22 17:40:16 UTC (rev 1157)
+++ pkg/pompExamples/inst/examples/ebola.R 2015-05-24 17:24:31 UTC (rev 1158)
@@ -55,7 +55,7 @@
paruntrans <- Csnippet('
- double *IC = &S_0;
+ const double *IC = &S_0;
double *TIC = &TS_0;
TN = log(N);
TR0 = log(R0);
@@ -68,7 +68,7 @@
')
partrans <- Csnippet('
- double *IC = &S_0;
+ const double *IC = &S_0;
double *TIC = &TS_0;
TN = exp(N);
TR0 = exp(R0);
@@ -146,7 +146,7 @@
skel <- Csnippet('
double lambda, beta;
- double *E = &E1;
+ const double *E = &E1;
double *DE = &DE1;
beta = R0 * gamma; // Transmission rate
lambda = beta * I / N; // Force of infection
From noreply at r-forge.r-project.org Thu May 28 16:55:45 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 28 May 2015 16:55:45 +0200 (CEST)
Subject: [Pomp-commits] r1159 - pkg/pomp pkg/pomp/R pkg/pomp/inst
pkg/pomp/inst/examples pkg/pomp/man pkg/pomp/src
pkg/pomp/tests www/content www/vignettes
Message-ID: <20150528145545.3693A18625C@r-forge.r-project.org>
Author: kingaa
Date: 2015-05-28 16:55:44 +0200 (Thu, 28 May 2015)
New Revision: 1159
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/builder.R
pkg/pomp/R/pomp-class.R
pkg/pomp/R/pomp-methods.R
pkg/pomp/R/pomp.R
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/inst/examples/bbs.R
pkg/pomp/inst/examples/blowflies.R
pkg/pomp/inst/examples/dacca.R
pkg/pomp/inst/examples/euler.sir.R
pkg/pomp/inst/examples/gillespie.sir.R
pkg/pomp/inst/examples/gompertz.R
pkg/pomp/inst/examples/ricker.R
pkg/pomp/man/builder.Rd
pkg/pomp/man/pomp-methods.Rd
pkg/pomp/man/pomp.Rd
pkg/pomp/src/partrans.c
pkg/pomp/tests/getting_started.R
pkg/pomp/tests/getting_started.Rout.save
pkg/pomp/tests/partrans.R
pkg/pomp/tests/partrans.Rout.save
pkg/pomp/tests/rw2.Rout.save
pkg/pomp/tests/sir.Rout.save
www/content/NEWS.html
www/vignettes/getting_started.R
www/vignettes/getting_started.Rmd
www/vignettes/pomp.pdf
www/vignettes/pompjss.R
www/vignettes/pompjss.Rnw
www/vignettes/pompjss.pdf
Log:
- the unfortunately named 'pomp' arguments 'parameter.inv.transform' and 'parameter.transform' have been deprecated in favor of the more mnemonic 'toEstimationScale' and 'fromEstimationScale'
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/DESCRIPTION 2015-05-28 14:55:44 UTC (rev 1159)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.64-1
-Date: 2015-05-22
+Version: 0.65-1
+Date: 2015-05-28
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")),
Modified: pkg/pomp/R/builder.R
===================================================================
--- pkg/pomp/R/builder.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/R/builder.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -1,7 +1,7 @@
pompCBuilder <- function (name = NULL, dir = NULL,
statenames, paramnames, covarnames, obsnames,
rmeasure, dmeasure, step.fn, skeleton,
- parameter.transform, parameter.inv.transform,
+ fromEstimationScale, toEstimationScale,
rprior, dprior, globals,
verbose = getOption("verbose",FALSE))
{
@@ -65,19 +65,19 @@
registry <- c("load_stack_incr","load_stack_decr")
## parameter transformation function
- if (!missing(parameter.transform)) {
+ if (!missing(fromEstimationScale)) {
registry <- c(registry,"par_trans")
- cat(file=out,render(header$parameter.transform,name=name))
- cat(file=out,callable.decl(parameter.transform))
- cat(file=out,parameter.transform,footer$parameter.transform)
+ cat(file=out,render(header$fromEstimationScale,name=name))
+ cat(file=out,callable.decl(fromEstimationScale))
+ cat(file=out,fromEstimationScale,footer$fromEstimationScale)
}
## inverse parameter transformation function
- if (!missing(parameter.inv.transform)) {
+ if (!missing(toEstimationScale)) {
registry <- c(registry,"par_untrans")
- cat(file=out,render(header$parameter.inv.transform,name=name))
- cat(file=out,callable.decl(parameter.inv.transform))
- cat(file=out,parameter.inv.transform,footer$parameter.inv.transform)
+ cat(file=out,render(header$toEstimationScale,name=name))
+ cat(file=out,callable.decl(toEstimationScale))
+ cat(file=out,toEstimationScale,footer$toEstimationScale)
}
## rmeasure function
@@ -224,7 +224,7 @@
rmeasure, dmeasure, step.fn, step.fn.delta.t,
skeleton, skeleton.type = c("map","vectorfield"),
skelmap.delta.t = 1,
- parameter.transform, parameter.inv.transform,
+ fromEstimationScale, toEstimationScale,
rprior, dprior,
globals, ..., save = FALSE) {
@@ -245,8 +245,8 @@
if (missing(statenames)) stop(sQuote("statenames")," must be supplied");
if (missing(paramnames)) stop(sQuote("paramnames")," must be supplied");
- mpt <- missing(parameter.transform)
- mpit <- missing(parameter.inv.transform)
+ mpt <- missing(fromEstimationScale)
+ mpit <- missing(toEstimationScale)
if (xor(mpt,mpit))
stop("if you supply one transformation function, you must supply its inverse")
@@ -260,8 +260,8 @@
dmeasure=dmeasure,
step.fn=step.fn,
skeleton=skeleton,
- parameter.transform=parameter.transform,
- parameter.inv.transform=parameter.inv.transform,
+ fromEstimationScale=fromEstimationScale,
+ toEstimationScale=toEstimationScale,
rprior=rprior,
dprior=dprior,
globals=globals,
@@ -284,8 +284,8 @@
skeleton=render(fnames$skeleton,name=name),
skeleton.type=skeleton.type,
skelmap.delta.t=skelmap.delta.t,
- parameter.transform=render(fnames$parameter.transform,name=name),
- parameter.inv.transform=render(fnames$parameter.inv.transform,name=name),
+ fromEstimationScale=render(fnames$fromEstimationScale,name=name),
+ toEstimationScale=render(fnames$toEstimationScale,name=name),
rprior=render(fnames$rprior,name=name),
dprior=render(fnames$dprior,name=name),
PACKAGE=name,
@@ -316,8 +316,8 @@
dmeasure= "\nvoid __pomp_dmeasure (double *__lik, const double *__y, const double *__x, const double *__p, int give_log, const int *__obsindex, const int *__stateindex, const int *__parindex, const int *__covindex, int __ncovars, const double *__covars, double t)\n{\n",
step.fn="\nvoid __pomp_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",
skeleton="\nvoid __pomp_skelfn (double *__f, const double *__x, const double *__p, const int *__stateindex, const int *__parindex, const int *__covindex, int __ncovars, const double *__covars, double t)\n{\n",
- parameter.transform="\nvoid __pomp_par_trans (double *__pt, const double *__p, const int *__parindex)\n{\n",
- parameter.inv.transform="\nvoid __pomp_par_untrans (double *__pt, const double *__p, const int *__parindex)\n{\n",
+ fromEstimationScale="\nvoid __pomp_par_trans (double *__pt, const double *__p, const int *__parindex)\n{\n",
+ toEstimationScale="\nvoid __pomp_par_untrans (double *__pt, const double *__p, const int *__parindex)\n{\n",
rprior="\nvoid __pomp_rprior (double *__p, const int *__parindex)\n{\n",
dprior="\nvoid __pomp_dprior (double *__lik, const double *__p, int give_log, const int *__parindex)\n{\n"
)
@@ -327,8 +327,8 @@
dmeasure= "__pomp_dmeasure",
step.fn="__pomp_stepfn",
skeleton="__pomp_skelfn",
- parameter.transform="__pomp_par_trans",
- parameter.inv.transform="__pomp_par_untrans",
+ fromEstimationScale="__pomp_par_trans",
+ toEstimationScale="__pomp_par_untrans",
rprior="__pomp_rprior",
dprior="__pomp_dprior"
)
@@ -347,8 +347,8 @@
dmeasure="\n}\n\n",
step.fn="\n}\n\n",
skeleton="\n}\n\n",
- parameter.transform="\n}\n\n",
- parameter.inv.transform="\n}\n\n",
+ fromEstimationScale="\n}\n\n",
+ toEstimationScale="\n}\n\n",
rprior="\n}\n\n",
dprior="\n}\n\n",
globals="\n",
Modified: pkg/pomp/R/pomp-class.R
===================================================================
--- pkg/pomp/R/pomp-class.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/R/pomp-class.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -32,8 +32,8 @@
tcovar = 'numeric',
zeronames = 'character',
has.trans = 'logical',
- par.trans = 'pomp.fun',
- par.untrans = 'pomp.fun',
+ from.trans = 'pomp.fun',
+ to.trans = 'pomp.fun',
solibfile = 'list',
userdata = 'list'
),
@@ -57,8 +57,8 @@
tcovar=numeric(0),
zeronames=character(0),
has.trans=FALSE,
- par.trans=pomp.fun(),
- par.untrans=pomp.fun(),
+ from.trans=pomp.fun(),
+ to.trans=pomp.fun(),
solibfile=list(),
userdata=list()
),
Modified: pkg/pomp/R/pomp-methods.R
===================================================================
--- pkg/pomp/R/pomp-methods.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/R/pomp-methods.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -25,18 +25,20 @@
as.data.frame.pomp <- function (x, row.names, optional, ...) as(x,"data.frame")
## parameter transformations
-partrans.internal <- function (object, params, dir = c("forward","inverse"),
+partrans.internal <- function (object, params,
+ dir = c("fromEstimationScale","toEstimationScale",
+ "forward","inverse"),
.getnativesymbolinfo = TRUE, ...) {
if (!object at has.trans) return(params)
pompLoad(object)
- dir <- switch(match.arg(dir),forward=1L,inverse=-1L)
+ dir <- switch(match.arg(dir),fromEstimationScale=1L,toEstimationScale=-1L,forward=1L,inverse=-1L)
rv <- .Call(do_partrans,object,params,dir,.getnativesymbolinfo)
pompUnload(object)
rv
}
setMethod("partrans","pomp",
- function (object, params, dir = c("forward","inverse"), ...)
+ function (object, params, dir = c("fromEstimationScale","toEstimationScale", "forward","inverse"),...)
partrans.internal(object=object,params=params,dir=dir,...)
)
@@ -168,7 +170,7 @@
function (object, pars, transform = FALSE, ...) {
if (length(object at params)>0) {
if (transform)
- params <- partrans(object,params=object at params,dir="inverse")
+ params <- partrans(object,params=object at params,dir="toEstimationScale")
else
params <- object at params
if (missing(pars))
@@ -198,7 +200,7 @@
if (missing(pars)) { ## replace the whole params slot with 'value'
if (length(value)>0) {
if (transform)
- value <- partrans(object,params=value,dir="forward")
+ value <- partrans(object,params=value,dir="fromEstimationScale")
pars <- names(value)
if (is.null(pars)) {
if (transform)
@@ -220,7 +222,7 @@
names(val) <- pars
val[] <- value
if (transform)
- value <- partrans(object,params=val,dir="forward")
+ value <- partrans(object,params=val,dir="fromEstimationScale")
object at params <- value
} else { ## pre-existing params slot
params <- coef(object,transform=transform)
@@ -240,7 +242,7 @@
}
params[pars] <- val
if (transform)
- params <- partrans(object,params=params,dir="forward")
+ params <- partrans(object,params=params,dir="fromEstimationScale")
object at params <- params
}
}
@@ -296,10 +298,10 @@
}
cat("initializer = \n")
show(object at initializer)
- cat("parameter transform function = \n")
- show(object at par.trans)
- cat("parameter inverse transform function = \n")
- show(object at par.untrans)
+ cat("parameter transformation (to estimation scale) = \n")
+ show(object at to.trans)
+ cat("parameter transformation (from estimation scale) = \n")
+ show(object at from.trans)
if (length(coef(object))>0) {
cat("parameter(s):\n")
print(coef(object))
Modified: pkg/pomp/R/pomp.R
===================================================================
--- pkg/pomp/R/pomp.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/R/pomp.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -8,7 +8,8 @@
params, covar, tcovar,
obsnames, statenames, paramnames, covarnames,
zeronames, PACKAGE,
- parameter.transform, parameter.inv.transform,
+ fromEstimationScale, toEstimationScale,
+ parameter.transform = NULL, parameter.inv.transform = NULL,
globals, userdata, ...,
.solibfile, .filename, .filedir,
verbose = getOption("verbose",FALSE)) {
@@ -39,9 +40,39 @@
if (missing(dmeasure)) dmeasure <- NULL
if (missing(rprior)) rprior <- NULL
if (missing(dprior)) dprior <- NULL
- if (missing(parameter.transform)) parameter.transform <- NULL
- if (missing(parameter.inv.transform)) parameter.inv.transform <- NULL
+ if (missing(fromEstimationScale)) fromEstimationScale <- NULL
+ if (missing(toEstimationScale)) toEstimationScale <- NULL
+ ## deal with deprecated arguments
+ if (!is.null(parameter.transform)) {
+ warning("the ",sQuote("parameter.transform")," argument of ",
+ sQuote("pomp")," is deprecated, ",
+ "and will be removed in a future release.\n",
+ "Use ",sQuote("fromEstimationScale")," instead.",call.=FALSE)
+ if (!is.null(fromEstimationScale) && !is(fromEstimationScale,"pomp.fun")) {
+ warning("both ",sQuote("fromEstimationScale")," and ",
+ sQuote("parameter.transform")," have been specified in a call to ",
+ sQuote("pomp"),".\n",
+ "The latter will be ignored.",call.=FALSE)
+ } else {
+ fromEstimationScale <- parameter.transform
+ }
+ }
+ if (!is.null(parameter.inv.transform)) {
+ warning("the ",sQuote("parameter.inv.transform")," argument of ",
+ sQuote("pomp")," is deprecated, ",
+ "and will be removed in a future release.\n",
+ "Use ",sQuote("toEstimationScale")," instead.",call.=FALSE)
+ if (!is.null(toEstimationScale) && !is(toEstimationScale,"pomp.fun")) {
+ warning("both ",sQuote("toEstimationScale")," and ",
+ sQuote("parameter.inv.transform")," have been specified in a call to ",
+ sQuote("pomp"),".\n",
+ "The latter will be ignored.",call.=FALSE)
+ } else {
+ toEstimationScale <- parameter.inv.transform
+ }
+ }
+
## defaults for names of states, parameters, and accumulator variables
if (missing(statenames)) statenames <- character(0)
if (missing(paramnames)) paramnames <- character(0)
@@ -60,7 +91,7 @@
storage.mode(data) <- 'double'
if (missing(obsnames) || length(obsnames)==0) obsnames <- rownames(data)
obsnames <- as.character(obsnames)
-
+
## check times
if (!is.numeric(times) || !all(diff(times)>0))
stop("pomp error: ",sQuote("times")," must be an increasing numeric vector")
@@ -132,10 +163,10 @@
snips <- c(snips,rprior=rprior at text)
if (is(dprior,"Csnippet"))
snips <- c(snips,dprior=dprior at text)
- if (is(parameter.transform,"Csnippet"))
- snips <- c(snips,parameter.transform=parameter.transform at text)
- if (is(parameter.inv.transform,"Csnippet"))
- snips <- c(snips,parameter.inv.transform=parameter.inv.transform at text)
+ if (is(fromEstimationScale,"Csnippet"))
+ snips <- c(snips,fromEstimationScale=fromEstimationScale at text)
+ if (is(toEstimationScale,"Csnippet"))
+ snips <- c(snips,toEstimationScale=toEstimationScale at text)
if (length(snips)>0) {
libname <- try(
do.call(
@@ -288,44 +319,44 @@
}
## handle parameter transformations
- mpt <- is.null(parameter.transform)
- mpit <- is.null(parameter.inv.transform)
+ mpt <- is.null(fromEstimationScale)
+ mpit <- is.null(toEstimationScale)
if (xor(mpt,mpit)) {
- stop("if one of ",sQuote("parameter.transform"),", ",
- sQuote("parameter.inv.transform"),
+ stop("if one of ",sQuote("fromEstimationScale"),", ",
+ sQuote("toEstimationScale"),
" is supplied, then so must the other")
}
has.trans <- !mpt
if (has.trans) {
- par.trans <- pomp.fun(
- f=parameter.transform,
- PACKAGE=PACKAGE,
- proto=quote(par.trans(params,...)),
- slotname="parameter.transform",
- libname=libname,
- statenames=statenames,
- paramnames=paramnames,
- obsnames=obsnames,
- covarnames=covarnames
- )
- par.untrans <- pomp.fun(
- f=parameter.inv.transform,
- PACKAGE=PACKAGE,
- proto=quote(par.untrans(params,...)),
- slotname="parameter.inv.transform",
- libname=libname,
- statenames=statenames,
- paramnames=paramnames,
- obsnames=obsnames,
- covarnames=covarnames
- )
+ from.trans <- pomp.fun(
+ f=fromEstimationScale,
+ PACKAGE=PACKAGE,
+ proto=quote(from.trans(params,...)),
+ slotname="fromEstimationScale",
+ libname=libname,
+ statenames=statenames,
+ paramnames=paramnames,
+ obsnames=obsnames,
+ covarnames=covarnames
+ )
+ to.trans <- pomp.fun(
+ f=toEstimationScale,
+ PACKAGE=PACKAGE,
+ proto=quote(to.trans(params,...)),
+ slotname="toEstimationScale",
+ libname=libname,
+ statenames=statenames,
+ paramnames=paramnames,
+ obsnames=obsnames,
+ covarnames=covarnames
+ )
} else {
- par.trans <- pomp.fun()
- par.untrans <- pomp.fun()
+ from.trans <- pomp.fun()
+ to.trans <- pomp.fun()
}
if (has.trans &&
- par.trans at mode==pompfunmode$undef &&
- par.untrans at mode==pompfunmode$undef
+ from.trans at mode==pompfunmode$undef &&
+ to.trans at mode==pompfunmode$undef
) has.trans <- FALSE
if (nrow(covar)>0) {
@@ -381,8 +412,8 @@
tcovar = tcovar,
zeronames = zeronames,
has.trans = has.trans,
- par.trans = par.trans,
- par.untrans = par.untrans,
+ from.trans = from.trans,
+ to.trans = to.trans,
solibfile = .solibfile,
userdata = userdata
)
@@ -477,7 +508,7 @@
initializer, rprior, dprior,
params, covar, tcovar,
obsnames, statenames, paramnames, covarnames, zeronames,
- PACKAGE, parameter.transform, parameter.inv.transform,
+ PACKAGE, fromEstimationScale, toEstimationScale,
globals) {
data <- t(sapply(data,as.numeric))
@@ -519,8 +550,8 @@
covarnames=covarnames,
zeronames=zeronames,
PACKAGE=PACKAGE,
- parameter.transform=parameter.transform,
- parameter.inv.transform=parameter.inv.transform,
+ fromEstimationScale=fromEstimationScale,
+ toEstimationScale=toEstimationScale,
globals=globals,
...
)
@@ -536,7 +567,7 @@
skelmap.delta.t = 1,
initializer, rprior, dprior, params, covar, tcovar,
obsnames, statenames, paramnames, covarnames, zeronames,
- PACKAGE, parameter.transform, parameter.inv.transform,
+ PACKAGE, fromEstimationScale, toEstimationScale,
globals) {
pomp.constructor(
@@ -563,8 +594,8 @@
covarnames=covarnames,
zeronames=zeronames,
PACKAGE=PACKAGE,
- parameter.transform=parameter.transform,
- parameter.inv.transform=parameter.inv.transform,
+ fromEstimationScale=fromEstimationScale,
+ toEstimationScale=toEstimationScale,
globals=globals,
...
)
@@ -581,7 +612,7 @@
skelmap.delta.t = 1,
initializer, rprior, dprior, params, covar, tcovar,
obsnames, statenames, paramnames, covarnames, zeronames,
- PACKAGE, parameter.transform, parameter.inv.transform,
+ PACKAGE, fromEstimationScale, toEstimationScale,
globals) {
pomp.constructor(
@@ -608,8 +639,8 @@
covarnames=covarnames,
zeronames=zeronames,
PACKAGE=PACKAGE,
- parameter.transform=parameter.transform,
- parameter.inv.transform=parameter.inv.transform,
+ fromEstimationScale=fromEstimationScale,
+ toEstimationScale=toEstimationScale,
globals=globals,
...
)
@@ -624,7 +655,7 @@
skeleton, skeleton.type, skelmap.delta.t,
initializer, rprior, dprior, params, covar, tcovar,
obsnames, statenames, paramnames, covarnames, zeronames,
- PACKAGE, parameter.transform, parameter.inv.transform,
+ PACKAGE, fromEstimationScale, toEstimationScale,
globals) {
if (missing(times)) times <- data at times
@@ -660,23 +691,23 @@
if (missing(skeleton.type)) skeleton.type <- data at skeleton.type
if (missing(skeleton)) skeleton <- data at skeleton
if (missing(skelmap.delta.t)) skelmap.delta.t <- data at skelmap.delta.t
- if (missing(parameter.transform)) {
- if (missing(parameter.inv.transform)) {
- par.trans <- data at par.trans
- par.untrans <- data at par.untrans
+ if (missing(fromEstimationScale)) {
+ if (missing(toEstimationScale)) {
+ from.trans <- data at from.trans
+ to.trans <- data at to.trans
} else {
- stop("pomp error: if ",sQuote("parameter.inv.transform"),
+ stop("pomp error: if ",sQuote("toEstimationScale"),
" is supplied, then " ,
- sQuote("parameter.transform")," must also be supplied")
+ sQuote("fromEstimationScale")," must also be supplied")
}
} else {
- if (missing(parameter.inv.transform)) {
- stop("pomp error: if ",sQuote("parameter.transform"),
+ if (missing(toEstimationScale)) {
+ stop("pomp error: if ",sQuote("fromEstimationScale"),
" is supplied, then " ,
- sQuote("parameter.inv.transform")," must also be supplied")
+ sQuote("toEstimationScale")," must also be supplied")
} else {
- par.trans <- parameter.transform
- par.untrans <- parameter.inv.transform
+ from.trans <- fromEstimationScale
+ to.trans <- toEstimationScale
}
}
@@ -708,8 +739,8 @@
covarnames=covarnames,
zeronames=zeronames,
PACKAGE=PACKAGE,
- parameter.transform=par.trans,
- parameter.inv.transform=par.untrans,
+ fromEstimationScale=from.trans,
+ toEstimationScale=to.trans,
params=params,
globals=globals,
.solibfile=data at solibfile,
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/NEWS 2015-05-28 14:55:44 UTC (rev 1159)
@@ -1,5 +1,14 @@
_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_5-_1:
+
+ ? The unfortunately named ?pomp? arguments
+ ?parameter.transform? and ?parameter.inv.transform? have been
+ deprecated in favor of the more mnemonic ?toEstimationScale?
+ and ?fromEstimationScale?. Using the old arguments will
+ result in the same behavior as previously, but a warning will
+ be generated.
+
_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_4-_1:
? The ?mif? option ?cooling.fraction? has been replaced by the
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/NEWS.Rd 2015-05-28 14:55:44 UTC (rev 1159)
@@ -1,5 +1,11 @@
\name{NEWS}
\title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.65-1}{
+ \itemize{
+ \item The unfortunately named \code{pomp} arguments \code{parameter.transform} and \code{parameter.inv.transform} have been deprecated in favor of the more mnemonic \code{toEstimationScale} and \code{fromEstimationScale}.
+ Using the old arguments will result in the same behavior as previously, but a warning will be generated.
+ }
+}
\section{Changes in \pkg{pomp} version 0.64-1}{
\itemize{
\item The \code{mif} option \code{cooling.fraction} has been replaced by the more descriptive \code{cooling.fraction.50}.
Modified: pkg/pomp/inst/examples/bbs.R
===================================================================
--- pkg/pomp/inst/examples/bbs.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/bbs.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -57,12 +57,12 @@
"S.0","I.0","R.0"
),
logitvar="rho",
- parameter.inv.transform=function (params, logvar, logitvar, ...) {
+ toEstimationScale=function (params, logvar, logitvar, ...) {
params[logvar] <- log(params[logvar])
params[logitvar] <- qlogis(params[logitvar])
params
},
- parameter.transform=function (params, logvar, logitvar, ...) {
+ fromEstimationScale=function (params, logvar, logitvar, ...) {
params[logvar] <- exp(params[logvar])
params[logitvar] <- plogis(params[logitvar])
params
Modified: pkg/pomp/inst/examples/blowflies.R
===================================================================
--- pkg/pomp/inst/examples/blowflies.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/blowflies.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -892,10 +892,10 @@
approx(x=day,y=y,xout=seq(from=0,to=14,by=1),rule=2)$y
),
# y.init=c(948, 948, 942, 930, 911, 885, 858, 833.7, 801, 748.3, 676, 589.8, 504, 434.9, 397),
- parameter.inv.transform=function(params,...) {
+ toEstimationScale=function(params,...) {
log(params)
},
- parameter.transform=function(params,...) {
+ fromEstimationScale=function(params,...) {
exp(params)
},
initializer=function (params, t0, y.init, ...) {
Modified: pkg/pomp/inst/examples/dacca.R
===================================================================
--- pkg/pomp/inst/examples/dacca.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/dacca.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -128,8 +128,8 @@
all.state.names=c("S","I","Rs",paste("R",1:nrstage,sep=''),"M","W","count"),
comp.names=c("S","I","Rs",paste("R",1:nrstage,sep='')),
comp.ic.names=c("S.0","I.0","Rs.0",paste("R",1:nrstage,".0",sep='')),
- parameter.transform="_cholmodel_trans",
- parameter.inv.transform="_cholmodel_untrans",
+ fromEstimationScale="_cholmodel_trans",
+ toEstimationScale="_cholmodel_untrans",
initializer = function (params, t0, covars, nrstage, comp.ic.names, comp.names, all.state.names, ...) {
states <- numeric(length(all.state.names))
names(states) <- all.state.names
Modified: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/euler.sir.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -243,8 +243,8 @@
zeronames=c("cases"),
comp.names=c("S","I","R"),
ic.names=c("S.0","I.0","R.0"),
- parameter.transform="_sir_par_trans",
- parameter.inv.transform="_sir_par_untrans",
+ fromEstimationScale="_sir_par_trans",
+ toEstimationScale="_sir_par_untrans",
nbasis=3L,
degree=3L,
period=1.0,
Modified: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/gillespie.sir.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -570,8 +570,8 @@
zeronames=c("cases"),
comp.names=c("S","I","R"),
ic.names=c("S.0","I.0","R.0"),
- parameter.transform="_sir_par_trans",
- parameter.inv.transform="_sir_par_untrans",
+ fromEstimationScale="_sir_par_trans",
+ toEstimationScale="_sir_par_untrans",
nbasis=3L,
degree=3L,
period=1.0,
Modified: pkg/pomp/inst/examples/gompertz.R
===================================================================
--- pkg/pomp/inst/examples/gompertz.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/gompertz.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -119,10 +119,10 @@
paramnames=c("r","K","sigma","tau"),
statenames=c("X"),
obsnames=c("Y"),
- parameter.transform=function(params,...){
+ fromEstimationScale=function(params,...){
exp(params)
},
- parameter.inv.transform=function(params,...){
+ toEstimationScale=function(params,...){
log(params)
}
) -> gompertz
Modified: pkg/pomp/inst/examples/ricker.R
===================================================================
--- pkg/pomp/inst/examples/ricker.R 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/inst/examples/ricker.R 2015-05-28 14:55:44 UTC (rev 1159)
@@ -69,11 +69,11 @@
paramnames=c("r","sigma","phi"),
statenames=c("N","e"),
obsnames=c("y"),
- parameter.inv.transform=function(params,...) {
+ toEstimationScale=function(params,...) {
params[c("r","sigma","phi","N.0")] <- log(params[c("r","sigma","phi","N.0")])
params
},
- parameter.transform=function(params,...) {
+ fromEstimationScale=function(params,...) {
params[c("r","sigma","phi","N.0")] <- exp(params[c("r","sigma","phi","N.0")])
params
},
Modified: pkg/pomp/man/builder.Rd
===================================================================
--- pkg/pomp/man/builder.Rd 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/man/builder.Rd 2015-05-28 14:55:44 UTC (rev 1159)
@@ -12,7 +12,7 @@
rmeasure, dmeasure, step.fn, step.fn.delta.t,
skeleton, skeleton.type = c("map","vectorfield"),
skelmap.delta.t = 1,
- parameter.transform, parameter.inv.transform,
+ fromEstimationScale, toEstimationScale,
rprior, dprior, globals, \dots, save = FALSE)
}
\arguments{
@@ -44,10 +44,10 @@
As in \code{\link{pomp}}, \code{skeleton.type} indicates whether the skeleton is a map (discrete-time) or vectorfield (continuous-time).
If the former, \code{skelmap.delta.t} is the time-step of the map.
}
- \item{parameter.transform, parameter.inv.transform}{
+ \item{fromEstimationScale, toEstimationScale}{
optional C codes that implement parameter transformations.
- \code{parameter.transform} maps parameters from the estimation scale to the natural scale;
- \code{parameter.inv.transformation} maps them from the natural scale to the estimation scale.
+ \code{toEstimationScale} maps parameters from the model scale to the estimation scale.
+ \code{fromEstimationScale} maps them from the estimation scale to the model scale;
}
\item{rprior, dprior}{
C codes implementing the prior distribution
Modified: pkg/pomp/man/pomp-methods.Rd
===================================================================
--- pkg/pomp/man/pomp-methods.Rd 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/man/pomp-methods.Rd 2015-05-28 14:55:44 UTC (rev 1159)
@@ -47,7 +47,8 @@
\S4method{coef}{pomp}(object, pars, transform = FALSE, \dots)
\S4method{coef}{pomp}(object, pars, transform = FALSE, \dots) <- value
\S4method{obs}{pomp}(object, vars, \dots)
-\S4method{partrans}{pomp}(object, params, dir = c("forward","inverse"), \dots)
+\S4method{partrans}{pomp}(object, params, dir = c("fromEstimationScale",
+ "toEstimationScale","forward","inverse"), \dots)
\S4method{plot}{pomp}(x, y, variables, panel = lines,
nc = NULL, yax.flip = FALSE,
mar = c(0, 5.1, 0, if (yax.flip) 5.1 else 2.1),
Modified: pkg/pomp/man/pomp.Rd
===================================================================
--- pkg/pomp/man/pomp.Rd 2015-05-24 17:24:31 UTC (rev 1158)
+++ pkg/pomp/man/pomp.Rd 2015-05-28 14:55:44 UTC (rev 1159)
@@ -24,24 +24,24 @@
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1159
From noreply at r-forge.r-project.org Thu May 28 17:54:55 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 28 May 2015 17:54:55 +0200 (CEST)
Subject: [Pomp-commits] r1160 - www/vignettes
Message-ID: <20150528155455.630A7186229@r-forge.r-project.org>
Author: kingaa
Date: 2015-05-28 17:54:54 +0200 (Thu, 28 May 2015)
New Revision: 1160
Modified:
www/vignettes/pomp.pdf
www/vignettes/pompjss.R
www/vignettes/pompjss.Rnw
www/vignettes/pompjss.pdf
Log:
- update pompjss vignette
Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf 2015-05-28 14:55:44 UTC (rev 1159)
+++ www/vignettes/pomp.pdf 2015-05-28 15:54:54 UTC (rev 1160)
@@ -10,7 +10,7 @@
?? ?@
-? ?????
!?W?O ?p???? ,??????????1???7G?6 SsU??Q|???9X?? _v|?|??= a|Mc|??l?? 6???Pt?(??m???e?\??? k!y?? ?^??E?????c????Fj???|???????e=$>M\?9e??b??&p?r?F[?J????Y??Y??U?j??????Yn?q? ???F?O???
????k"???!D??? ?1??jH?????(U?k??????3?,???F????4?????% m??????h? S?G??l:%?/?????v???Y?t~rz?t4?,????G? f?X??'?-6V~h???f,{!
4Qu?}?j?p?ov?m????a ???????
@@ -39,7 +39,7 @@
w?v??d?\D???S?.?m??zc??3Z}D?@?O`?s?Y85?^ ?d)?B?0?h?@???????q???????{?>?k?`Z?lw???RP> ??:.G?????o?:???S~b?_
>
@@ -48,12 +48,12 @@
-
-2015-05-28T10:51:52-04:00
-2015-05-28T10:51:52-04:00
+
+2015-05-28T11:42:30-04:00
+2015-05-28T11:42:30-04:00
Raph Levien
-
-Inconsolata
+
+Inconsolata
@@ -2633,7 +2633,7 @@
%??{?P???endstream
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+<< /Type /XRef /Length 441 /Filter /FlateDecode /DecodeParms << /Columns 5 /Predictor 12 >> /W [ 1 3 1 ] /Info 3 0 R /Root 2 0 R /Size 1092 /ID [<41a992de9a1335d5ff63527c20725e2b>] >>
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Modified: www/vignettes/pompjss.R
===================================================================
--- www/vignettes/pompjss.R 2015-05-28 14:55:44 UTC (rev 1159)
+++ www/vignettes/pompjss.R 2015-05-28 15:54:54 UTC (rev 1160)
@@ -11,7 +11,7 @@
require(reshape2)
require(xtable)
-stopifnot(packageVersion("pomp")>="0.63-4")
+stopifnot(packageVersion("pomp")>="0.65-1")
## ----set-opts,include=F,cache=F------------------------------------------
Modified: www/vignettes/pompjss.Rnw
===================================================================
--- www/vignettes/pompjss.Rnw 2015-05-28 14:55:44 UTC (rev 1159)
+++ www/vignettes/pompjss.Rnw 2015-05-28 15:54:54 UTC (rev 1160)
@@ -145,7 +145,7 @@
require(reshape2)
require(xtable)
-stopifnot(packageVersion("pomp")>="0.63-4")
+stopifnot(packageVersion("pomp")>="0.65-1")
<>=
options(
Modified: www/vignettes/pompjss.pdf
===================================================================
--- www/vignettes/pompjss.pdf 2015-05-28 14:55:44 UTC (rev 1159)
+++ www/vignettes/pompjss.pdf 2015-05-28 15:54:54 UTC (rev 1160)
@@ -14142,8 +14142,8 @@
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-/CreationDate (D:20150528082357-04'00')
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1160
From noreply at r-forge.r-project.org Sat May 30 12:54:23 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat, 30 May 2015 12:54:23 +0200 (CEST)
Subject: [Pomp-commits] r1161 - pkg/pomp www/vignettes
Message-ID: <20150530105423.5532B1868B2@r-forge.r-project.org>
Author: kingaa
Date: 2015-05-30 12:54:22 +0200 (Sat, 30 May 2015)
New Revision: 1161
Modified:
pkg/pomp/DESCRIPTION
www/vignettes/pomp.pdf
www/vignettes/pompjss.bib
Log:
- bump to trigger rebuild
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-05-28 15:54:54 UTC (rev 1160)
+++ pkg/pomp/DESCRIPTION 2015-05-30 10:54:22 UTC (rev 1161)
@@ -2,7 +2,7 @@
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
Version: 0.65-1
-Date: 2015-05-28
+Date: 2015-05-30
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")),
Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf 2015-05-28 15:54:54 UTC (rev 1160)
+++ www/vignettes/pomp.pdf 2015-05-30 10:54:22 UTC (rev 1161)
@@ -1,7 +1,7 @@
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%%EOF
Modified: www/vignettes/pompjss.bib
===================================================================
--- www/vignettes/pompjss.bib 2015-05-28 15:54:54 UTC (rev 1160)
+++ www/vignettes/pompjss.bib 2015-05-30 10:54:22 UTC (rev 1161)
@@ -593,7 +593,7 @@
@Manual{pomp,
Title = {\pkg{pomp}: {S}tatistical Inference for Partially Observed {M}arkov Processes},
Author = {Aaron A. King and Edward L. Ionides and Carles Martinez Bret\'o and Stephen P. Ellner and Matthew J. Ferrari and Bruce E. Kendall and Michael Lavine and Dao Nguyen and Daniel C. Reuman and Helen Wearing and Simon N. Wood},
- Note = {\proglang{R} package version 0.63-4},
+ Note = {\proglang{R} package version 0.65-1},
Year = {2015},
Url = {http://pomp.r-forge.r-project.org}