[Pomp-commits] r454 - in pkg: . data inst inst/data-R src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 4 23:31:46 CEST 2011
Author: kingaa
Date: 2011-05-04 23:31:45 +0200 (Wed, 04 May 2011)
New Revision: 454
Modified:
pkg/DESCRIPTION
pkg/data/dacca.rda
pkg/data/euler.sir.rda
pkg/data/gillespie.sir.rda
pkg/data/gompertz.rda
pkg/data/ou2.rda
pkg/data/ricker.rda
pkg/data/rw2.rda
pkg/data/verhulst.rda
pkg/inst/ChangeLog
pkg/inst/NEWS
pkg/inst/data-R/dacca.R
pkg/inst/data-R/euler.sir.R
pkg/inst/data-R/gillespie.sir.R
pkg/inst/data-R/gompertz.R
pkg/inst/data-R/ou2.R
pkg/inst/data-R/ricker.R
pkg/inst/data-R/rw2.R
pkg/inst/data-R/verhulst.R
pkg/src/blowfly.c
pkg/src/probe_acf.c
Log:
- fix bug in error message in 'probe_acf.c'
- update data()-loadable examples
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/DESCRIPTION 2011-05-04 21:31:45 UTC (rev 454)
@@ -1,7 +1,7 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.36-6
+Version: 0.36-7
Date: 2011-05-04
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing,
Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
@@ -16,7 +16,7 @@
slice-design.R profile-design.R sobol.R bsplines.R sannbox.R
pomp-fun.R pomp.R pomp-methods.R rmeasure-pomp.R rprocess-pomp.R init-state-pomp.R
dmeasure-pomp.R dprocess-pomp.R skeleton-pomp.R simulate-pomp.R trajectory-pomp.R plot-pomp.R
- pfilter.R traj-match.R bsmc.R
+ pfilter.R pfilter-methods.R traj-match.R bsmc.R
mif-class.R particles-mif.R mif.R mif-methods.R compare-mif.R
pmcmc.R pmcmc-methods.R compare-pmcmc.R
nlf-funcs.R nlf-guts.R nlf-objfun.R nlf.R
Modified: pkg/data/dacca.rda
===================================================================
(Binary files differ)
Modified: pkg/data/euler.sir.rda
===================================================================
(Binary files differ)
Modified: pkg/data/gillespie.sir.rda
===================================================================
(Binary files differ)
Modified: pkg/data/gompertz.rda
===================================================================
(Binary files differ)
Modified: pkg/data/ou2.rda
===================================================================
(Binary files differ)
Modified: pkg/data/ricker.rda
===================================================================
(Binary files differ)
Modified: pkg/data/rw2.rda
===================================================================
(Binary files differ)
Modified: pkg/data/verhulst.rda
===================================================================
(Binary files differ)
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/ChangeLog 2011-05-04 21:31:45 UTC (rev 454)
@@ -1,5 +1,20 @@
2011-05-03 kingaa
+ * [r453] inst/doc/intro_to_pomp.pdf:
+ * [r452] inst/doc/intro_to_pomp.Rnw, inst/doc/intro_to_pomp.pdf: -
+ minor improvement to 'compare.mif' figure
+ * [r451] tests/filtfail.R, tests/filtfail.Rout.save,
+ tests/sir-icfit.R, tests/sir-icfit.Rout.save: - two new tests:
+ 'sir-icfit' and 'filtfail'
+ * [r450] DESCRIPTION, R/pfilter.R, inst/ChangeLog,
+ inst/doc/advanced_topics_in_pomp.pdf, inst/doc/intro_to_pomp.Rnw,
+ inst/doc/intro_to_pomp.pdf, src/pfilter.c, src/resample.c,
+ tests/ou2-probe.Rout.save, tests/ricker-probe.Rout.save,
+ tests/ricker.Rout.save: - move resampling and random-walking
+ inside 'pfilter.internal' into C (pfilter.c)
+ - move resampling codes from 'resample.c' to 'pfilter.c'
+ - update test .save files
+ - minor corrections in 'intro_to_pomp' vignette
* [r449] R/bsplines.R, man/bsplines.Rd: - add 'names' argument
2011-04-27 kingaa
Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/NEWS 2011-05-04 21:31:45 UTC (rev 454)
@@ -1,3 +1,15 @@
+NEW IN VERSION 0.36-7:
+
+ o 'trajectory' now gives a more informative error when no skeleton is present
+
+ o 'pred.mean', 'pred.var', and 'filter.mean' methods are now defined for 'pfilterd.pomp' objects (and not just 'mif' objects)
+
+ o A new 'data()'-loadable example is included: do '?blowflies' to read about it.
+
+NEW IN VERSION 0.36-6:
+
+ o The B-spline basis construction functions 'bspline.basis' and 'periodic.bspline.basis' now take a 'names' argument that allows one to give names to the basis functions.
+
NEW IN VERSION 0.36-5:
o The "intro_to_pomp" vignette has been updated. The first part of the vignette centers on a new, more transparent first example.
Modified: pkg/inst/data-R/dacca.R
===================================================================
--- pkg/inst/data-R/dacca.R 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/data-R/dacca.R 2011-05-04 21:31:45 UTC (rev 454)
@@ -192,3 +192,4 @@
}
coef(dacca$po) <- dacca$transform(mle,dir="forward")
+save(dacca,file="dacca.rda")
Modified: pkg/inst/data-R/euler.sir.R
===================================================================
--- pkg/inst/data-R/euler.sir.R 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/data-R/euler.sir.R 2011-05-04 21:31:45 UTC (rev 454)
@@ -52,3 +52,5 @@
nsim=1,
seed=329348545L
) -> euler.sir
+
+save(euler.sir,file="euler.sir.rda")
Modified: pkg/inst/data-R/gillespie.sir.R
===================================================================
--- pkg/inst/data-R/gillespie.sir.R 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/data-R/gillespie.sir.R 2011-05-04 21:31:45 UTC (rev 454)
@@ -73,3 +73,4 @@
seed=1165270654L
) -> gillespie.sir
+save(gillespie.sir,file="gillespie.sir.rda")
Modified: pkg/inst/data-R/gompertz.R
===================================================================
--- pkg/inst/data-R/gompertz.R 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/data-R/gompertz.R 2011-05-04 21:31:45 UTC (rev 454)
@@ -25,3 +25,5 @@
nsim=1,
seed=299438676L
) -> gompertz
+
+save(gompertz,file="gompertz.rda")
Modified: pkg/inst/data-R/ou2.R
===================================================================
--- pkg/inst/data-R/ou2.R 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/data-R/ou2.R 2011-05-04 21:31:45 UTC (rev 454)
@@ -87,3 +87,5 @@
ou2 <- window(ou2,end=100)
timezero(ou2) <- 0
+
+save(ou2,file="ou2.rda")
Modified: pkg/inst/data-R/ricker.R
===================================================================
--- pkg/inst/data-R/ricker.R 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/data-R/ricker.R 2011-05-04 21:31:45 UTC (rev 454)
@@ -25,3 +25,5 @@
nsim=1,
seed=73691676L
) -> ricker
+
+save(ricker,file="ricker.rda")
Modified: pkg/inst/data-R/rw2.R
===================================================================
--- pkg/inst/data-R/rw2.R 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/data-R/rw2.R 2011-05-04 21:31:45 UTC (rev 454)
@@ -38,3 +38,5 @@
nsim=1,
seed=738377475L
) -> rw2
+
+save(rw2,file="rw2.rda")
Modified: pkg/inst/data-R/verhulst.R
===================================================================
--- pkg/inst/data-R/verhulst.R 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/inst/data-R/verhulst.R 2011-05-04 21:31:45 UTC (rev 454)
@@ -50,3 +50,5 @@
nsim=1,
seed=73658676L
) -> verhulst
+
+save(verhulst,file="verhulst.rda")
Modified: pkg/src/blowfly.c
===================================================================
--- pkg/src/blowfly.c 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/src/blowfly.c 2011-05-04 21:31:45 UTC (rev 454)
@@ -25,12 +25,13 @@
{
double var_p = exp(2*LOG_SIGMAP)/dt;
double var_d = exp(2*LOG_SIGMAD)/dt;
+ double nzero = exp(LOG_NZERO);
double e = (var_p > 0.0) ? rgamma(1.0/var_p,var_p) : 1.0;
double eps = (var_d > 0.0) ? rgamma(1.0/var_d,var_d) : 1.0;
double P = exp(LOG_P);
int tau = (int) TAU;
int k;
- R = rpois(P*N[tau]*exp(-N[tau]/exp(LOG_NZERO))*dt*e);
+ R = rpois(P*N[tau]*exp(-N[tau]/nzero)*dt*e);
S = rbinom(N[0],exp(-exp(LOG_DELTA)*dt*eps));
E = e;
EPS = eps;
Modified: pkg/src/probe_acf.c
===================================================================
--- pkg/src/probe_acf.c 2011-05-03 16:11:22 UTC (rev 453)
+++ pkg/src/probe_acf.c 2011-05-04 21:31:45 UTC (rev 454)
@@ -20,7 +20,7 @@
ct++;
}
}
- if (ct < 1) error("series %ld has no data",j);
+ if (ct < 1) error("series %ld has no data",j+1);
xx /= ct; // mean of x[j,]
for (k = 0, p0 = p; k < n; p0 += nvars, k++)
if (R_FINITE(*p0)) *p0 -= xx;
@@ -54,7 +54,7 @@
ct++;
}
}
- if (ct < 1) error("series 'x' has no data");
+ if (ct < 1) error("series 1 has no data");
xx /= ct; // mean of x[j]
for (k = 0, p = x; k < n; k++, p++)
if (R_FINITE(*p)) *p -= xx;
@@ -66,7 +66,7 @@
ct++;
}
}
- if (ct < 1) error("series 'y' has no data");
+ if (ct < 1) error("series 2 has no data");
xx /= ct; // mean of y[j]
for (k = 0, p = y; k < n; k++, p++)
if (R_FINITE(*p)) *p -= xx;
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