[Pomp-commits] r1111 - in pkg/pomp: . R inst tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 27 03:58:17 CET 2015
Author: kingaa
Date: 2015-02-27 03:58:17 +0100 (Fri, 27 Feb 2015)
New Revision: 1111
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/mif.R
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/tests/bbs-trajmatch.Rout.save
pkg/pomp/tests/bbs.Rout.save
pkg/pomp/tests/blowflies.Rout.save
pkg/pomp/tests/dacca.Rout.save
pkg/pomp/tests/dimchecks.Rout.save
pkg/pomp/tests/fhn.Rout.save
pkg/pomp/tests/filtfail.Rout.save
pkg/pomp/tests/gillespie.Rout.save
pkg/pomp/tests/gompertz.Rout.save
pkg/pomp/tests/logistic.Rout.save
pkg/pomp/tests/ou2-abc.Rout.save
pkg/pomp/tests/ou2-bsmc.Rout.save
pkg/pomp/tests/ou2-bsmc2.Rout.save
pkg/pomp/tests/ou2-forecast.Rout.save
pkg/pomp/tests/ou2-kalman.Rout.save
pkg/pomp/tests/ou2-mif-fp.Rout.save
pkg/pomp/tests/ou2-mif.R
pkg/pomp/tests/ou2-mif.Rout.save
pkg/pomp/tests/ou2-mif2.R
pkg/pomp/tests/ou2-mif2.Rout.save
pkg/pomp/tests/ou2-nlf.Rout.save
pkg/pomp/tests/ou2-pmcmc.Rout.save
pkg/pomp/tests/ou2-probe.Rout.save
pkg/pomp/tests/ou2-procmeas.Rout.save
pkg/pomp/tests/ou2-simulate.Rout.save
pkg/pomp/tests/ou2-spect.Rout.save
pkg/pomp/tests/ou2-trajmatch.Rout.save
pkg/pomp/tests/partrans.Rout.save
pkg/pomp/tests/pfilter.Rout.save
pkg/pomp/tests/pomppomp.Rout.save
pkg/pomp/tests/prior.Rout.save
pkg/pomp/tests/ricker-bsmc.Rout.save
pkg/pomp/tests/ricker-probe.Rout.save
pkg/pomp/tests/ricker-spect.Rout.save
pkg/pomp/tests/ricker.Rout.save
pkg/pomp/tests/rw2.Rout.save
pkg/pomp/tests/sir.Rout.save
pkg/pomp/tests/skeleton.Rout.save
pkg/pomp/tests/steps.Rout.save
pkg/pomp/tests/synlik.Rout.save
pkg/pomp/tests/verhulst.Rout.save
Log:
- deprecate, but do not ignore, the 'pars' argument to 'mif'. It will be removed later.
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/DESCRIPTION 2015-02-27 02:58:17 UTC (rev 1111)
@@ -1,7 +1,7 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.62-1
+Version: 0.61-3
Date: 2015-02-26
Authors at R: c(person(given=c("Aaron","A."),family="King",
role=c("aut","cre"),email="kingaa at umich.edu"),
Modified: pkg/pomp/R/mif.R
===================================================================
--- pkg/pomp/R/mif.R 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/R/mif.R 2015-02-27 02:58:17 UTC (rev 1111)
@@ -114,27 +114,57 @@
if (is.null(start.names))
stop("mif error: ",sQuote("start")," must be a named vector",call.=FALSE)
- if (!is.null(pars)) {
- warning("mif warning: the ",sQuote("pars")," argument to ",sQuote("mif")," is unnecessary and deprecated and will be ignored.\n",
- "This behavior differs from that previous to ",sQuote("pomp")," version 0.62",call.=FALSE)
- }
-
rw.names <- names(rw.sd)
if (is.null(rw.names) || any(rw.sd<0))
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 <- rw.names[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)
- pars <- rw.names[!(rw.names%in%ivps)]
- if (!is.character(ivps) || !all(ivps%in%start.names))
- stop("mif error: ",sQuote("ivps")," must name model parameters",call.=FALSE)
-
-## rw.sd <- rw.sd[c(pars,ivps)]
-## rw.names <- names(rw.sd)
+ if (is.null(pars))
+ pars <- rw.names[!(rw.names%in%ivps)]
+ else
+ warning("mif warning: argument ",sQuote("pars")," is redundant and deprecated. It will be removed in a future release.",call.=FALSE)
+ if (
+ !is.character(pars) ||
+ !is.character(ivps) ||
+ !all(pars%in%start.names) ||
+ !all(ivps%in%start.names) ||
+ any(pars%in%ivps) ||
+ 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
+ )
+
+ 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
+ )
+ }
+ rw.sd <- rw.sd[c(pars,ivps)]
+ rw.names <- names(rw.sd)
+
ntimes <- length(time(object))
if (is.null(Np)) stop("mif error: ",sQuote("Np")," must be specified",call.=FALSE)
if (is.function(Np)) {
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/inst/NEWS 2015-02-27 02:58:17 UTC (rev 1111)
@@ -1,9 +1,9 @@
_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_2-_1:
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_1-_3:
- • ‘mif’'s ‘pars’ argument, which is redundant, is now ignored
- with a warning. In a future release, this argument will be
+ • ‘mif’'s ‘pars’ argument, which is redundant, is now
+ deprecated. In a future release, this argument will be
removed.
_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_1-_1:
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/inst/NEWS.Rd 2015-02-27 02:58:17 UTC (rev 1111)
@@ -1,8 +1,8 @@
\name{NEWS}
\title{News for package `pomp'}
-\section{Changes in \pkg{pomp} version 0.62-1}{
+\section{Changes in \pkg{pomp} version 0.61-3}{
\itemize{
- \item \code{mif}'s \code{pars} argument, which is redundant, is now ignored with a warning.
+ \item \code{mif}'s \code{pars} argument, which is redundant, is now deprecated.
In a future release, this argument will be removed.
}
}
Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -80,4 +80,4 @@
>
> proc.time()
user system elapsed
- 2.448 0.052 2.525
+ 2.480 0.052 2.555
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/bbs.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -73,4 +73,4 @@
>
> proc.time()
user system elapsed
- 6.916 0.056 7.013
+ 7.153 0.049 7.193
Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/blowflies.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -72,4 +72,4 @@
>
> proc.time()
user system elapsed
- 1.320 0.060 1.411
+ 1.304 0.044 1.380
Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/dacca.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -107,4 +107,4 @@
>
> proc.time()
user system elapsed
- 11.408 0.084 11.550
+ 10.852 0.064 10.968
Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/dimchecks.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -179,4 +179,4 @@
>
> proc.time()
user system elapsed
- 0.592 0.072 0.689
+ 0.560 0.092 0.677
Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/fhn.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -93,4 +93,4 @@
>
> proc.time()
user system elapsed
- 1.064 0.032 1.243
+ 1.084 0.064 1.285
Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/filtfail.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -116,4 +116,4 @@
>
> proc.time()
user system elapsed
- 0.624 0.048 0.693
+ 0.576 0.068 0.660
Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/gillespie.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -131,4 +131,4 @@
>
> proc.time()
user system elapsed
- 2.488 0.056 2.574
+ 2.564 0.048 2.635
Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/gompertz.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -133,4 +133,4 @@
>
> proc.time()
user system elapsed
- 1.616 0.052 1.820
+ 1.576 0.052 1.652
Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/logistic.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -124,4 +124,4 @@
>
> proc.time()
user system elapsed
- 0.944 0.072 1.143
+ 0.976 0.052 1.175
Modified: pkg/pomp/tests/ou2-abc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-abc.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-abc.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -139,4 +139,4 @@
>
> proc.time()
user system elapsed
- 11.092 0.068 11.369
+ 11.422 0.073 11.497
Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -59,7 +59,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 2.748923 secs
+Time difference of 2.789886 secs
>
> print(
+ cbind(
@@ -101,4 +101,4 @@
>
> proc.time()
user system elapsed
- 4.712 0.032 4.777
+ 4.688 0.064 4.785
Modified: pkg/pomp/tests/ou2-bsmc2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc2.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-bsmc2.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -56,7 +56,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 1.971769 secs
+Time difference of 2.022153 secs
>
> print(
+ cbind(
@@ -98,4 +98,4 @@
>
> proc.time()
user system elapsed
- 3.540 0.060 3.626
+ 3.588 0.084 3.697
Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-forecast.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -61,4 +61,4 @@
>
> proc.time()
user system elapsed
- 1.596 0.072 1.793
+ 1.420 0.036 1.559
Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-kalman.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -164,7 +164,7 @@
117 function evaluations used
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 3.520454 secs
+Time difference of 3.41739 secs
> tic <- Sys.time()
> print(loglik.mle <- -kalm.fit1$value,digits=4)
[1] -477.2
@@ -188,4 +188,4 @@
>
> proc.time()
user system elapsed
- 4.172 0.068 4.270
+ 3.933 0.035 3.954
Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -47,8 +47,7 @@
+ method="fp"
+ )
Warning message:
-mif warning: the 'pars' argument to 'mif' is unnecessary and deprecated and will be ignored.
-This behavior differs from that previous to 'pomp' version 0.62
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
>
> mif2 <- mif(ou2,Nmif=100,start=guess2,
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
@@ -65,8 +64,7 @@
+ method="fp"
+ )
Warning message:
-mif warning: the 'pars' argument to 'mif' is unnecessary and deprecated and will be ignored.
-This behavior differs from that previous to 'pomp' version 0.62
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
>
> plot(c(mif1,mif2))
>
@@ -76,4 +74,4 @@
>
> proc.time()
user system elapsed
- 20.933 0.064 21.259
+ 25.136 0.029 25.180
Modified: pkg/pomp/tests/ou2-mif.R
===================================================================
--- pkg/pomp/tests/ou2-mif.R 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-mif.R 2015-02-27 02:58:17 UTC (rev 1111)
@@ -19,7 +19,7 @@
guess2[c('x1.0','x2.0','alpha.2','alpha.3')] <- 1.5*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
mif1 <- mif(ou2,Nmif=30,start=guess1,
- ivps=c('x1.0','x2.0'),
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
rw.sd=c(
x1.0=5,x2.0=5,
alpha.2=0.1,alpha.3=0.1
@@ -33,7 +33,7 @@
)
mif2 <- mif(ou2,Nmif=30,start=guess2,
- ivps=c('x1.0','x2.0'),
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
transform=TRUE,
rw.sd=c(
x1.0=5,x2.0=5,
@@ -60,8 +60,9 @@
mif(
ou2,
Nmif=1,
+ pars=c("alpha.1","alpha.4","x1.0"),
ivps=c("x1.0","x2.0"),
- rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=-1),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
ic.lag=10,var.factor=1
)
@@ -70,6 +71,62 @@
try(
mif(
ou2,
+ Nmif=1,
+ pars=c("alpha.1","alpha.4"),
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
+ Np=100,
+ cooling.type="geometric",cooling.fraction=0.95^50,
+ ic.lag=10,var.factor=1
+ )
+ )
+
+try(
+ mif(
+ ou2,
+ Nmif=1,
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(alpha.1=0.1,alpha.4=0.2,alpha.3=0),
+ Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
+ cooling.factor=0.95,ic.lag=10,var.factor=1
+ )
+ )
+
+try(
+ mif(
+ ou2,
+ Nmif=1,
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
+ Np=100,ic.lag=10,var.factor=1
+ )
+ )
+
+try(
+ mif(
+ ou2,
+ Nmif=1,
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
+ Np=-10,cooling.type="geometric",cooling.fraction=0.95^50,
+ ic.lag=10,var.factor=1
+ )
+ )
+
+try(
+ mif(
+ ou2,
+ Nmif=-3,
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
+ Np=11.6,cooling.type="geometric",cooling.fraction=0.95^50,
+ ic.lag=10,var.factor=1
+ )
+ )
+
+try(
+ mif(
+ ou2,
Nmif=2,
start=c(alpha.1=0.9,alpha.2=0,alpha.3=0,alpha.4=-Inf,sigma.1=1,sigma.2=0,sigma.3=2,tau=1,x1.0=50,x2.0=-50),
ivps=c("x1.0","x2.0"),
@@ -94,6 +151,7 @@
fit <- mif(
ou2,
Nmif=0,
+ pars=c("alpha.2","alpha.3"),
ivps=c("x1.0","x2.0"),
rw.sd=c(x1.0=5,x2.0=5,alpha.2=0.1,alpha.3=0.2,alpha.3=0),
Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
@@ -113,7 +171,7 @@
ff <- pfilter(fit,pred.mean=T,filter.mean=T,pred.var=T,max.fail=100,verbose=T)
ff <- pfilter(ff)
fit <- mif(fit,rw.sd=c(x1.0=5,x2.0=5,alpha.2=0.1,alpha.3=0.1))
-fit <- continue(fit,Nmif=2,ivps=c("x1.0"),rw.sd=c(x1.0=5,alpha.2=0.1))
+fit <- continue(fit,Nmif=2,ivps=c("x1.0"),pars=c("alpha.2"))
s <- coef(fit)
s[2] <- 0.01
fit <- mif(fit,Nmif=3,start=s)
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -52,7 +52,7 @@
> guess2[c('x1.0','x2.0','alpha.2','alpha.3')] <- 1.5*guess1[c('x1.0','x2.0','alpha.2','alpha.3')]
>
> mif1 <- mif(ou2,Nmif=30,start=guess1,
-+ ivps=c('x1.0','x2.0'),
++ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ rw.sd=c(
+ x1.0=5,x2.0=5,
+ alpha.2=0.1,alpha.3=0.1
@@ -64,12 +64,13 @@
+ cooling.factor=0.95,
+ max.fail=100
+ )
-Warning message:
-'cooling.factor' is deprecated.
+Warning messages:
+1: mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
+2: 'cooling.factor' is deprecated.
See '?mif' for instructions on specifying the cooling schedule.
>
> mif2 <- mif(ou2,Nmif=30,start=guess2,
-+ ivps=c('x1.0','x2.0'),
++ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ transform=TRUE,
+ rw.sd=c(
+ x1.0=5,x2.0=5,
@@ -82,6 +83,8 @@
+ cooling.fraction=0.95^50,
+ max.fail=100
+ )
+Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
>
> pdf(file="ou2-mif.pdf")
> plot(mif1)
@@ -100,17 +103,84 @@
+ mif(
+ ou2,
+ Nmif=1,
++ pars=c("alpha.1","alpha.4","x1.0"),
+ ivps=c("x1.0","x2.0"),
-+ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=-1),
++ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
+ Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
+ ic.lag=10,var.factor=1
+ )
+ )
-Error : mif error: 'rw.sd' must be a named non-negative numerical vector
+Error : mif error: 'pars' and 'ivps' must be mutually disjoint subsets of 'names(start)' and must have a positive random-walk SDs specified in 'rw.sd'
+In addition: Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
>
> try(
+ mif(
+ ou2,
++ Nmif=1,
++ pars=c("alpha.1","alpha.4"),
++ ivps=c("x1.0","x2.0"),
++ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
++ Np=100,
++ cooling.type="geometric",cooling.fraction=0.95^50,
++ ic.lag=10,var.factor=1
++ )
++ )
+Error : mif error: 'pars' and 'ivps' must be mutually disjoint subsets of 'names(start)' and must have a positive random-walk SDs specified in 'rw.sd'
+In addition: Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
+>
+> try(
++ mif(
++ ou2,
++ Nmif=1,
++ ivps=c("x1.0","x2.0"),
++ rw.sd=c(alpha.1=0.1,alpha.4=0.2,alpha.3=0),
++ Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
++ cooling.factor=0.95,ic.lag=10,var.factor=1
++ )
++ )
+Error : mif error: 'pars' and 'ivps' must be mutually disjoint subsets of 'names(start)' and must have a positive random-walk SDs specified in 'rw.sd'
+>
+> try(
++ mif(
++ ou2,
++ Nmif=1,
++ ivps=c("x1.0","x2.0"),
++ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0.1,alpha.4=0.2,alpha.3=0),
++ Np=100,ic.lag=10,var.factor=1
++ )
++ )
+Error : mif error: 'cooling.fraction' must be specified
+>
+> try(
++ mif(
++ ou2,
++ Nmif=1,
++ ivps=c("x1.0","x2.0"),
++ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
++ Np=-10,cooling.type="geometric",cooling.fraction=0.95^50,
++ ic.lag=10,var.factor=1
++ )
++ )
+Error in mif.internal(object = object, Nmif = Nmif, start = start, ivps = ivps, :
+ number of particles, 'Np', must always be positive
+>
+> try(
++ mif(
++ ou2,
++ Nmif=-3,
++ ivps=c("x1.0","x2.0"),
++ rw.sd=c(x1.0=5,x2.0=5,alpha.1=0,alpha.4=0.2,alpha.3=0),
++ Np=11.6,cooling.type="geometric",cooling.fraction=0.95^50,
++ ic.lag=10,var.factor=1
++ )
++ )
+Error : mif error: 'Nmif' must be a positive integer
+>
+> try(
++ mif(
++ ou2,
+ Nmif=2,
+ start=c(alpha.1=0.9,alpha.2=0,alpha.3=0,alpha.4=-Inf,sigma.1=1,sigma.2=0,sigma.3=2,tau=1,x1.0=50,x2.0=-50),
+ ivps=c("x1.0","x2.0"),
@@ -139,11 +209,14 @@
> fit <- mif(
+ ou2,
+ Nmif=0,
++ pars=c("alpha.2","alpha.3"),
+ ivps=c("x1.0","x2.0"),
+ rw.sd=c(x1.0=5,x2.0=5,alpha.2=0.1,alpha.3=0.2,alpha.3=0),
+ Np=100,cooling.type="geometric",cooling.fraction=0.95^50,
+ ic.lag=10,var.factor=1
+ )
+Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
> fit <- mif(
+ fit,
+ Nmif=2,
@@ -178,7 +251,10 @@
pfilter timestep 100 of 100 finished
> ff <- pfilter(ff)
> fit <- mif(fit,rw.sd=c(x1.0=5,x2.0=5,alpha.2=0.1,alpha.3=0.1))
-> fit <- continue(fit,Nmif=2,ivps=c("x1.0"),rw.sd=c(x1.0=5,alpha.2=0.1))
+> fit <- continue(fit,Nmif=2,ivps=c("x1.0"),pars=c("alpha.2"))
+Warning messages:
+1: mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
+2: mif warning: the variables 'alpha.3', 'x2.0' have positive random-walk SDs specified, but are included in neither 'pars' nor 'ivps'. These random walk SDs will be ignored.
> s <- coef(fit)
> s[2] <- 0.01
> fit <- mif(fit,Nmif=3,start=s)
@@ -217,4 +293,4 @@
>
> proc.time()
user system elapsed
- 12.032 0.080 12.261
+ 15.048 0.037 15.088
Modified: pkg/pomp/tests/ou2-mif2.R
===================================================================
--- pkg/pomp/tests/ou2-mif2.R 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-mif2.R 2015-02-27 02:58:17 UTC (rev 1111)
@@ -11,7 +11,7 @@
set.seed(64857673L)
mif1a <- mif(ou2,Nmif=100,start=guess1,
- ivps=c('x1.0','x2.0'),
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
rw.sd=c(
x1.0=.5,x2.0=.5,
alpha.2=0.1,alpha.3=0.1),
@@ -26,7 +26,7 @@
)
mif2a <- mif(ou2,Nmif=100,start=guess1,
- ivps=c('x1.0','x2.0'),
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
rw.sd=c(
x1.0=0.5,x2.0=.5,
alpha.2=0.1,alpha.3=0.1),
@@ -45,7 +45,7 @@
set.seed(64857673L)
mif1b <- mif(ou2,Nmif=50,start=guess1,
- ivps=c('x1.0','x2.0'),
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
rw.sd=c(
x1.0=.5,x2.0=.5,
alpha.2=0.1,alpha.3=0.1),
@@ -60,7 +60,7 @@
mif1b <- continue(mif1b,Nmif=50)
mif2b <- mif(ou2,Nmif=50,start=guess1,
- ivps=c('x1.0','x2.0'),
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
rw.sd=c(
x1.0=0.5,x2.0=.5,
alpha.2=0.1,alpha.3=0.1),
@@ -77,7 +77,7 @@
mif2b <- continue(mif2b,Nmif=50)
mif2c <- mif(ou2,Nmif=50,start=guess1,
- ivps=c('x1.0','x2.0'),
+ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
rw.sd=c(
x1.0=0.5,x2.0=.5,
alpha.2=0.1,alpha.3=0.1),
Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-mif2.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -32,7 +32,7 @@
>
> set.seed(64857673L)
> mif1a <- mif(ou2,Nmif=100,start=guess1,
-+ ivps=c('x1.0','x2.0'),
++ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ rw.sd=c(
+ x1.0=.5,x2.0=.5,
+ alpha.2=0.1,alpha.3=0.1),
@@ -45,9 +45,11 @@
+ method="mif2",
+ tol=1e-8
+ )
+Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
>
> mif2a <- mif(ou2,Nmif=100,start=guess1,
-+ ivps=c('x1.0','x2.0'),
++ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ rw.sd=c(
+ x1.0=0.5,x2.0=.5,
+ alpha.2=0.1,alpha.3=0.1),
@@ -61,12 +63,14 @@
+ method="mif",
+ tol=1e-8
+ )
+Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
>
> plot(c(mif1a,mif2a))
>
> set.seed(64857673L)
> mif1b <- mif(ou2,Nmif=50,start=guess1,
-+ ivps=c('x1.0','x2.0'),
++ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ rw.sd=c(
+ x1.0=.5,x2.0=.5,
+ alpha.2=0.1,alpha.3=0.1),
@@ -78,10 +82,12 @@
+ cooling.fraction=0.05,
+ method="mif2"
+ )
+Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
> mif1b <- continue(mif1b,Nmif=50)
>
> mif2b <- mif(ou2,Nmif=50,start=guess1,
-+ ivps=c('x1.0','x2.0'),
++ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ rw.sd=c(
+ x1.0=0.5,x2.0=.5,
+ alpha.2=0.1,alpha.3=0.1),
@@ -95,13 +101,14 @@
+ max.fail=100,
+ method="mif"
+ )
-Warning message:
-'cooling.factor' is deprecated.
+Warning messages:
+1: mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
+2: 'cooling.factor' is deprecated.
See '?mif' for instructions on specifying the cooling schedule.
> mif2b <- continue(mif2b,Nmif=50)
>
> mif2c <- mif(ou2,Nmif=50,start=guess1,
-+ ivps=c('x1.0','x2.0'),
++ pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
+ rw.sd=c(
+ x1.0=0.5,x2.0=.5,
+ alpha.2=0.1,alpha.3=0.1),
@@ -113,6 +120,8 @@
+ max.fail=100,
+ method="mif2"
+ )
+Warning message:
+mif warning: argument 'pars' is redundant and deprecated. It will be removed in a future release.
> mif2c <- continue(mif2c,Nmif=50)
>
> plot(c(mif1b,mif2b))
@@ -135,4 +144,4 @@
>
> proc.time()
user system elapsed
- 51.303 0.148 51.806
+ 66.333 0.037 66.430
Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-nlf.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -85,4 +85,4 @@
>
> proc.time()
user system elapsed
- 4.416 0.048 4.523
+ 4.380 0.092 6.425
Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -138,4 +138,4 @@
>
> proc.time()
user system elapsed
- 32.378 0.076 32.745
+ 28.662 0.057 28.743
Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-probe.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -340,4 +340,4 @@
>
> proc.time()
user system elapsed
- 7.692 0.072 7.942
+ 7.892 0.092 8.187
Modified: pkg/pomp/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-procmeas.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-procmeas.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -54,4 +54,4 @@
>
> proc.time()
user system elapsed
- 0.588 0.076 0.684
+ 0.408 0.048 0.479
Modified: pkg/pomp/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-simulate.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-simulate.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -35,7 +35,7 @@
> ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.004848957 secs
+Time difference of 0.006910086 secs
>
> coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
>
@@ -46,4 +46,4 @@
>
> proc.time()
user system elapsed
- 0.608 0.052 0.680
+ 0.508 0.040 0.572
Modified: pkg/pomp/tests/ou2-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-spect.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-spect.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -38,4 +38,4 @@
>
> proc.time()
user system elapsed
- 22.417 0.048 22.562
+ 21.537 0.040 21.670
Modified: pkg/pomp/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ou2-trajmatch.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -175,4 +175,4 @@
>
> proc.time()
user system elapsed
- 2.188 0.040 2.279
+ 1.712 0.060 1.801
Modified: pkg/pomp/tests/partrans.Rout.save
===================================================================
--- pkg/pomp/tests/partrans.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/partrans.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -52,4 +52,4 @@
>
> proc.time()
user system elapsed
- 0.600 0.052 0.668
+ 0.600 0.060 0.678
Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/pfilter.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -77,4 +77,4 @@
>
> proc.time()
user system elapsed
- 8.604 0.040 8.824
+ 8.448 0.080 8.699
Modified: pkg/pomp/tests/pomppomp.Rout.save
===================================================================
--- pkg/pomp/tests/pomppomp.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/pomppomp.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -55,4 +55,4 @@
>
> proc.time()
user system elapsed
- 0.556 0.088 0.667
+ 0.580 0.064 0.663
Modified: pkg/pomp/tests/prior.Rout.save
===================================================================
--- pkg/pomp/tests/prior.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/prior.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -73,4 +73,4 @@
>
> proc.time()
user system elapsed
- 0.796 0.040 0.857
+ 0.736 0.056 0.809
Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -54,4 +54,4 @@
>
> proc.time()
user system elapsed
- 2.608 0.076 2.850
+ 2.604 0.072 2.860
Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ricker-probe.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -297,4 +297,4 @@
>
> proc.time()
user system elapsed
- 12.064 0.080 12.363
+ 11.976 0.072 12.278
Modified: pkg/pomp/tests/ricker-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-spect.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ricker-spect.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -70,4 +70,4 @@
>
> proc.time()
user system elapsed
- 2.320 0.064 2.577
+ 2.284 0.084 3.241
Modified: pkg/pomp/tests/ricker.Rout.save
===================================================================
--- pkg/pomp/tests/ricker.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/ricker.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -83,4 +83,4 @@
>
> proc.time()
user system elapsed
- 0.708 0.056 0.884
+ 0.704 0.048 0.884
Modified: pkg/pomp/tests/rw2.Rout.save
===================================================================
--- pkg/pomp/tests/rw2.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/rw2.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -164,7 +164,7 @@
}
y
}
-<environment: 0x2b3ac50>
+<environment: 0x2300468>
measurement model density, dmeasure =
function (y, x, t, params, log, covars, ...)
{
@@ -177,7 +177,7 @@
f
else exp(f)
}
-<environment: 0x2b3ac50>
+<environment: 0x2300468>
prior simulator, rprior =
function not specified
prior density, dprior =
@@ -342,4 +342,4 @@
>
> proc.time()
user system elapsed
- 0.996 0.040 1.062
+ 0.870 0.033 0.889
Modified: pkg/pomp/tests/sir.Rout.save
===================================================================
--- pkg/pomp/tests/sir.Rout.save 2015-02-27 02:58:10 UTC (rev 1110)
+++ pkg/pomp/tests/sir.Rout.save 2015-02-27 02:58:17 UTC (rev 1111)
@@ -192,7 +192,7 @@
method = 0L, zeronames = zeronames, tcovar = tcovar,
covar = covar, args = pairlist(...), gnsi = .getnativesymbolinfo)
}
-<environment: 0x297a5b0>
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1111
More information about the pomp-commits
mailing list