[Pomp-commits] r741 - in pkg/pomp: inst tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jun 29 23:25:50 CEST 2012
Author: kingaa
Date: 2012-06-29 23:25:50 +0200 (Fri, 29 Jun 2012)
New Revision: 741
Modified:
pkg/pomp/inst/ChangeLog
pkg/pomp/tests/sir.Rout.save
Log:
- update changelog and unit test
Modified: pkg/pomp/inst/ChangeLog
===================================================================
--- pkg/pomp/inst/ChangeLog 2012-06-29 21:12:06 UTC (rev 740)
+++ pkg/pomp/inst/ChangeLog 2012-06-29 21:25:50 UTC (rev 741)
@@ -1,3 +1,50 @@
+2012-06-29 kingaa
+
+ * [r740] DESCRIPTION, R/pomp.R, inst/NEWS, man/pomp.Rd,
+ tests/sir.R: - add 'params' argument to 'pomp' constructor
+ * [r739] R/traj-match.R, man/traj-match.Rd, tests/bbs-trajmatch.R,
+ tests/bbs-trajmatch.Rout.save: - extra arguments (...) to
+ 'traj.match.objfun' are now passed on to the ODE integrator in
+ case the skeleton is a vectorfield
+
+2012-06-18 kingaa
+
+ * [r732] inst/include/pomp.h: - update installed version of
+ 'pomp.h'
+ * [r731] DESCRIPTION, inst/NEWS, src/pomp.h: - update NEWS file
+ - minor changes to 'pomp.h'
+
+2012-06-12 kingaa
+
+ * [r729] inst/doc/pomp.bib: - update bibliography database
+
+2012-06-01 kingaa
+
+ * [r727] DESCRIPTION, demo/sir.R, inst/include/pomp.h,
+ src/lookup_table.c, src/pomp.h: - remove superfluous warnings
+ from 'lookup_table'
+ - fix 'sir' demo to work with covariate table
+ - add some inline functions to 'pomp.h'
+ * [r726] DESCRIPTION, R/builder.R, demo/gompertz.R, man/builder.Rd:
+ - fix incorrect error messages in 'pompBuilder'
+ - allow 'pompBuilder' to deal with covariates
+
+2012-05-29 kingaa
+
+ * [r725] DESCRIPTION, R/builder.R, R/pomp.R, demo/gompertz.R,
+ demo/sir.R, man/builder.Rd, man/pomp.Rd: - add support for
+ parameter transformations to 'pompBuilder'
+ - more error-trapping in 'pomp'
+ - update demos to use compiled parameter transformations
+ - fix minor omission in 'pomp' man page
+
+2012-05-14 kingaa
+
+ * [r722] DESCRIPTION: - update DESCRIPTION
+ * [r721] inst/ChangeLog, inst/NEWS,
+ inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.pdf:
+ - update changelog NEWS file and vignettes
+
2012-05-12 kingaa
* [r716] DESCRIPTION, R/dmeasure-pomp.R, R/dprocess-pomp.R,
Modified: pkg/pomp/tests/sir.Rout.save
===================================================================
--- pkg/pomp/tests/sir.Rout.save 2012-06-29 21:12:06 UTC (rev 740)
+++ pkg/pomp/tests/sir.Rout.save 2012-06-29 21:25:50 UTC (rev 741)
@@ -1,5 +1,5 @@
-R version 2.15.0 (2012-03-30)
+R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -39,6 +39,7 @@
> po <- pomp(
+ times=1/52*seq.int(length=4*52),
+ data=rbind(reports=numeric(52*4)),
++ params=params,
+ t0=0,
+ tcovar=tbasis,
+ covar=basis,
@@ -376,7 +377,11 @@
207 3.98076923 0 0.66343428 0.13948471 0.19708101
208 4.00000000 0 0.66666667 0.16666667 0.16666667
zero time, t0 = 0
-parameter(s) unspecified
+parameter(s):
+ gamma mu iota beta1 beta2 beta3 beta.sd pop
+2.60e+01 2.00e-02 1.00e-02 4.00e+02 4.80e+02 3.20e+02 1.00e-03 2.10e+06
+ rho S.0 I.0 R.0
+6.00e-01 6.50e-02 1.00e-03 9.35e-01
process model simulator, rprocess =
function (xstart, times, params, ..., statenames = character(0),
paramnames = character(0), covarnames = character(0), zeronames = character(0),
@@ -388,7 +393,7 @@
zeronames = zeronames, tcovar = tcovar, covar = covar,
args = pairlist(...))
}
-<environment: 0x2277ff8>
+<environment: 0x28d9c78>
process model density, dprocess =
function (x, times, params, ..., statenames = character(0), paramnames = character(0),
covarnames = character(0), tcovar, covar, log = FALSE)
@@ -398,7 +403,7 @@
covarnames = covarnames, tcovar = tcovar, covar = covar,
log = log, args = pairlist(...))
}
-<environment: 0x22dc348>
+<environment: 0x18821e0>
measurement model simulator, rmeasure =
function (x, t, params, covars, ...)
{
@@ -459,27 +464,27 @@
> set.seed(3049953)
> ## simulate from the model
> tic <- Sys.time()
-> x <- simulate(po,params=params,nsim=3)
+> x <- simulate(po,nsim=3)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 1.053949 secs
+Time difference of 1.041633 secs
>
> pdf(file='sir.pdf')
>
> plot(x[[1]],variables=c("S","I","R","cases","W"))
>
> t1 <- seq(0,4/52,by=1/52/25)
-> X1 <- simulate(po,params=params,nsim=10,states=TRUE,obs=TRUE,times=t1)
+> X1 <- simulate(po,nsim=10,states=TRUE,obs=TRUE,times=t1)
>
> t2 <- seq(0,2,by=1/52)
-> X2 <- simulate(po,params=params,nsim=1,states=TRUE,obs=TRUE,times=t2)
+> X2 <- simulate(po,nsim=1,states=TRUE,obs=TRUE,times=t2)
>
> t3 <- seq(0,20,by=1/52)
> tic <- Sys.time()
-> X3 <- trajectory(po,params=params,times=t3,hmax=1/52)
+> X3 <- trajectory(po,times=t3,hmax=1/52)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.6904695 secs
+Time difference of 0.6949608 secs
> plot(t3,X3['I',1,],type='l')
>
> f1 <- dprocess(
@@ -529,7 +534,7 @@
> x <- simulate(po,nsim=100)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 1.30669 secs
+Time difference of 1.300245 secs
> plot(x[[1]],variables=c("S","I","R","cases","W"))
>
> t3 <- seq(0,20,by=1/52)
@@ -537,7 +542,7 @@
> X4 <- trajectory(po,times=t3,hmax=1/52)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.008178949 secs
+Time difference of 0.008083344 secs
> plot(t3,X4['I',1,],type='l')
>
> g2 <- dmeasure(
@@ -650,4 +655,4 @@
>
> proc.time()
user system elapsed
- 3.896 0.036 4.149
+ 4.052 0.052 4.349
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