[Pomp-commits] r365 - in pkg: data inst inst/doc src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Oct 5 22:39:25 CEST 2010
Author: kingaa
Date: 2010-10-05 22:39:24 +0200 (Tue, 05 Oct 2010)
New Revision: 365
Modified:
pkg/data/ou2.rda
pkg/inst/ChangeLog
pkg/inst/doc/advanced_topics_in_pomp.pdf
pkg/inst/doc/intro_to_pomp.pdf
pkg/inst/doc/ou2-first-mif.rda
pkg/inst/doc/ou2-trajmatch.rda
pkg/src/ou2.c
pkg/tests/gillespie.Rout.save
pkg/tests/logistic.Rout.save
pkg/tests/ou2-bsmc.Rout.save
pkg/tests/ou2-forecast.Rout.save
pkg/tests/ou2-kalman.Rout.save
pkg/tests/ou2-mif.Rout.save
pkg/tests/ou2-nlf.Rout.save
pkg/tests/ou2-pmcmc.Rout.save
pkg/tests/ou2-probe.Rout.save
pkg/tests/ou2-simulate.Rout.save
pkg/tests/ou2-trajmatch.Rout.save
pkg/tests/pfilter.Rout.save
pkg/tests/ricker-probe.Rout.save
pkg/tests/ricker.Rout.save
pkg/tests/rw2.Rout.save
pkg/tests/sir.Rout.save
pkg/tests/skeleton.Rout.save
Log:
- fix a bug in 'ou2'
Modified: pkg/data/ou2.rda
===================================================================
(Binary files differ)
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/inst/ChangeLog 2010-10-05 20:39:24 UTC (rev 365)
@@ -1,5 +1,7 @@
2010-10-05 kingaa
+ * [r364] R/aaa.R: - fiddle with the banner
+ * [r363] inst/ChangeLog:
* [r362] tests/ou2-pmcmc.Rout.save, tests/skeleton.R,
tests/skeleton.Rout.save: - add in results from ou2-pmcmc test
- add another set of tests in 'skeleton.R'
Modified: pkg/inst/doc/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/intro_to_pomp.pdf
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/ou2-first-mif.rda
===================================================================
(Binary files differ)
Modified: pkg/inst/doc/ou2-trajmatch.rda
===================================================================
(Binary files differ)
Modified: pkg/src/ou2.c
===================================================================
--- pkg/src/ou2.c 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/src/ou2.c 2010-10-05 20:39:24 UTC (rev 365)
@@ -35,23 +35,45 @@
// it is assumed that the times are consecutive (FIX THIS!)
void _ou2_adv (double *x, double *xstart, double *par, double *times, int *n, int *parindex)
{
- int nvar = n[0], npar = n[1], nrep = n[2], ntimes = n[3];
- double *xp, *pp;
+ int nvar = n[0], npar = n[1], nrep = n[2], ntimes = n[3], incr;
+ double tnow, tgoal, dt = 1.0;
+ double *xp0, *xp1, *pp;
int i, j, k;
+
+ incr = nrep*nvar;
+
GetRNGstate(); // initialize R's pseudorandom number generator
+
for (j = 0; j < nrep; j++) {
- xp = &x[nvar*j]; // get address of j-th state vector
- for (i = 0; i < nvar; i++) xp[i] = xstart[i+nvar*j]; // copy xstart into the first slice of x
- }
- for (k = 1; k < ntimes; k++) {
+
R_CheckUserInterrupt();
- for (j = 0; j < nrep; j++) {
- xp = &x[nvar*(j+nrep*k)];
- pp = &par[npar*j];
- for (i = 0; i < nvar; i++) xp[i] = x[i+nvar*(j+nrep*(k-1))];
- sim_ou2(xp,ALPHA1,ALPHA2,ALPHA3,ALPHA4,SIGMA1,SIGMA2,SIGMA3); // advance particle
+
+ xp0 = &xstart[nvar*j]; // pointer to j-th starting state
+ xp1 = &x[nvar*j]; // pointer to j-th state vector
+ pp = &par[npar*j]; // pointer to j-th parameter vector
+
+ for (i = 0; i < nvar; i++) xp1[i] = xp0[i]; // copy xstart into the first slice of x
+
+ tnow = times[0]; // initial time
+
+ for (k = 1; k < ntimes; k++) { // loop over times
+
+ xp0 = xp1;
+ xp1 += incr;
+
+ for (i = 0; i < nvar; i++) xp1[i] = xp0[i]; // copy state vector
+
+ tgoal = times[k];
+
+ while (tnow < tgoal) {
+ sim_ou2(xp1,ALPHA1,ALPHA2,ALPHA3,ALPHA4,SIGMA1,SIGMA2,SIGMA3); // advance state
+ tnow += dt; // advance time
+ }
+
}
+
}
+
PutRNGstate(); // finished with R's random number generator
}
Modified: pkg/tests/gillespie.Rout.save
===================================================================
--- pkg/tests/gillespie.Rout.save 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/tests/gillespie.Rout.save 2010-10-05 20:39:24 UTC (rev 365)
@@ -16,6 +16,16 @@
Type 'q()' to quit R.
> library(pomp)
+This is pomp version 0.34-1
+
+IMPORTANT NOTICE:
+The default behaviors of 'simulate' and 'trajectory' have changed as of release 0.34-1. You can ensure that your code will continue to function as you intend by specifying the values of the 'times' and 't0' arguments to these functions, thus removing dependence of your code on the defaults. In the meantime, using 'simulate' or 'trajectory' in such a way as to rely on the default will produce a warning. These warnings will be removed in a future release.
+
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+
+Subscribe to the pomp-announce list (go to pomp.r-forge.r-project.org) to receive email notification about new releases of pomp including descriptions of feature additions, changes, and fixes.
+
+
>
> params <- c(
+ nu=log(1/70),
Modified: pkg/tests/logistic.Rout.save
===================================================================
--- pkg/tests/logistic.Rout.save 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/tests/logistic.Rout.save 2010-10-05 20:39:24 UTC (rev 365)
@@ -16,6 +16,16 @@
Type 'q()' to quit R.
> library(pomp)
+This is pomp version 0.34-1
+
+IMPORTANT NOTICE:
+The default behaviors of 'simulate' and 'trajectory' have changed as of release 0.34-1. You can ensure that your code will continue to function as you intend by specifying the values of the 'times' and 't0' arguments to these functions, thus removing dependence of your code on the defaults. In the meantime, using 'simulate' or 'trajectory' in such a way as to rely on the default will produce a warning. These warnings will be removed in a future release.
+
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+
+Subscribe to the pomp-announce list (go to pomp.r-forge.r-project.org) to receive email notification about new releases of pomp including descriptions of feature additions, changes, and fixes.
+
+
>
> po <- pomp(
+ data=rbind(obs=rep(0,1000)),
Modified: pkg/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/tests/ou2-bsmc.Rout.save 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/tests/ou2-bsmc.Rout.save 2010-10-05 20:39:24 UTC (rev 365)
@@ -16,6 +16,16 @@
Type 'q()' to quit R.
> library(pomp)
+This is pomp version 0.34-1
+
+IMPORTANT NOTICE:
+The default behaviors of 'simulate' and 'trajectory' have changed as of release 0.34-1. You can ensure that your code will continue to function as you intend by specifying the values of the 'times' and 't0' arguments to these functions, thus removing dependence of your code on the defaults. In the meantime, using 'simulate' or 'trajectory' in such a way as to rely on the default will produce a warning. These warnings will be removed in a future release.
+
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+
+Subscribe to the pomp-announce list (go to pomp.r-forge.r-project.org) to receive email notification about new releases of pomp including descriptions of feature additions, changes, and fixes.
+
+
>
> set.seed(398585L)
> data(ou2)
@@ -58,7 +68,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 41.44052 secs
+Time difference of 41.84382 secs
>
> print(
+ cbind(
@@ -70,8 +80,8 @@
+ )
prior.mean posterior.mean truth 2.5% 50% 97.5%
alpha.1 0.8000000 0.8000000 0.8 0.8000000 0.8000000 0.8000000
-alpha.2 -0.4999287 -0.5254444 -0.5 -0.5480088 -0.5461081 -0.4576629
-alpha.3 0.2996065 0.2964690 0.3 0.2827214 0.3009050 0.3012988
+alpha.2 -0.4999287 -0.5043393 -0.5 -0.5112463 -0.5065709 -0.4767260
+alpha.3 0.2996065 0.3270662 0.3 0.3146781 0.3319924 0.3384011
alpha.4 0.9000000 0.9000000 0.9 0.9000000 0.9000000 0.9000000
sigma.1 3.0000000 3.0000000 3.0 3.0000000 3.0000000 3.0000000
sigma.2 -0.5000000 -0.5000000 -0.5 -0.5000000 -0.5000000 -0.5000000
@@ -81,5 +91,5 @@
x2.0 4.0000000 4.0000000 4.0 4.0000000 4.0000000 4.0000000
>
> print(min(smc$eff.sample.size))
-[1] 5.987632
+[1] 6.94596
>
Modified: pkg/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/tests/ou2-forecast.Rout.save 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/tests/ou2-forecast.Rout.save 2010-10-05 20:39:24 UTC (rev 365)
@@ -16,6 +16,16 @@
Type 'q()' to quit R.
> library(pomp)
+This is pomp version 0.34-1
+
+IMPORTANT NOTICE:
+The default behaviors of 'simulate' and 'trajectory' have changed as of release 0.34-1. You can ensure that your code will continue to function as you intend by specifying the values of the 'times' and 't0' arguments to these functions, thus removing dependence of your code on the defaults. In the meantime, using 'simulate' or 'trajectory' in such a way as to rely on the default will produce a warning. These warnings will be removed in a future release.
+
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+
+Subscribe to the pomp-announce list (go to pomp.r-forge.r-project.org) to receive email notification about new releases of pomp including descriptions of feature additions, changes, and fixes.
+
+
>
> set.seed(921625222L)
>
Modified: pkg/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/tests/ou2-kalman.Rout.save 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/tests/ou2-kalman.Rout.save 2010-10-05 20:39:24 UTC (rev 365)
@@ -1,6 +1,6 @@
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,9 +16,16 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: deSolve
-Loading required package: subplex
-Loading required package: mvtnorm
+This is pomp version 0.34-1
+
+IMPORTANT NOTICE:
+The default behaviors of 'simulate' and 'trajectory' have changed as of release 0.34-1. You can ensure that your code will continue to function as you intend by specifying the values of the 'times' and 't0' arguments to these functions, thus removing dependence of your code on the defaults. In the meantime, using 'simulate' or 'trajectory' in such a way as to rely on the default will produce a warning. These warnings will be removed in a future release.
+
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+
+Subscribe to the pomp-announce list (go to pomp.r-forge.r-project.org) to receive email notification about new releases of pomp including descriptions of feature additions, changes, and fixes.
+
+
>
> set.seed(577639485L)
>
@@ -80,7 +87,7 @@
> cat("Kalman filter log likelihood at truth\n")
Kalman filter log likelihood at truth
> print(loglik.truth <- -kalman(p.truth,ou2,p.truth),digits=4)
-[1] -479.4
+[1] -479
>
> # make a wild guess
> p.guess <- p.truth[c('alpha.1','alpha.4','x1.0','x2.0')]*exp(rnorm(n=4,mean=0,sd=0.5))
@@ -92,7 +99,7 @@
> cat("Kalman filter log likelihood at guess\n")
Kalman filter log likelihood at guess
> print(loglik.guess <- -kalman(p.guess,ou2,p.truth),digits=4)
-[1] -511.4
+[1] -511.8
>
> # find MLE using Kalman filter starting at the guess
> cat("running Kalman filter estimation\n")
@@ -100,149 +107,70 @@
> tic <- Sys.time()
> kalm.fit1 <- optim(p.guess,kalman,object=ou2,params=p.truth,hessian=T,control=list(trace=2))
Nelder-Mead direct search function minimizer
-function value for initial parameters = 511.408754
- Scaled convergence tolerance is 7.62058e-06
+function value for initial parameters = 511.775815
+ Scaled convergence tolerance is 7.62605e-06
Stepsize computed as 0.493088
-BUILD 5 511.479973 505.078590
-REFLECTION 7 511.408754 477.669704
-LO-REDUCTION 9 511.265919 477.669704
-HI-REDUCTION 11 508.118826 477.669704
-HI-REDUCTION 13 505.078590 477.669704
-HI-REDUCTION 15 486.185588 477.669704
-LO-REDUCTION 17 482.985184 477.669704
-HI-REDUCTION 19 482.451265 477.669704
-HI-REDUCTION 21 479.401805 477.669704
-LO-REDUCTION 23 478.854608 477.669704
-HI-REDUCTION 25 478.170111 477.669704
-HI-REDUCTION 27 477.854748 477.669704
-HI-REDUCTION 29 477.842132 477.649565
-HI-REDUCTION 31 477.816787 477.636023
-HI-REDUCTION 33 477.712383 477.636023
-HI-REDUCTION 35 477.669704 477.631174
-REFLECTION 37 477.649565 477.604428
-HI-REDUCTION 39 477.642236 477.604428
-REFLECTION 41 477.636023 477.598062
-HI-REDUCTION 43 477.631174 477.598062
-LO-REDUCTION 45 477.606198 477.596516
-HI-REDUCTION 47 477.604428 477.589627
-HI-REDUCTION 49 477.600403 477.589627
-EXTENSION 51 477.598062 477.560652
-HI-REDUCTION 53 477.596516 477.560652
-LO-REDUCTION 55 477.591225 477.560652
-LO-REDUCTION 57 477.589627 477.560652
-LO-REDUCTION 59 477.581884 477.560652
-LO-REDUCTION 61 477.576730 477.560652
-EXTENSION 63 477.576718 477.547516
-EXTENSION 65 477.565957 477.525920
-LO-REDUCTION 67 477.560890 477.525920
-EXTENSION 69 477.560652 477.509557
-LO-REDUCTION 71 477.547516 477.509557
-EXTENSION 73 477.530502 477.486327
-LO-REDUCTION 75 477.525920 477.486327
-LO-REDUCTION 77 477.513811 477.486327
-LO-REDUCTION 79 477.509557 477.486327
-LO-REDUCTION 81 477.503553 477.486327
-REFLECTION 83 477.493747 477.484757
-LO-REDUCTION 85 477.493230 477.484757
-LO-REDUCTION 87 477.492532 477.484757
-REFLECTION 89 477.487381 477.483024
-EXTENSION 91 477.486327 477.479960
-LO-REDUCTION 93 477.485973 477.479960
-LO-REDUCTION 95 477.484757 477.479960
-REFLECTION 97 477.483024 477.479805
-REFLECTION 99 477.482467 477.478335
-REFLECTION 101 477.479987 477.477966
-LO-REDUCTION 103 477.479960 477.477966
-LO-REDUCTION 105 477.479805 477.477966
-REFLECTION 107 477.478636 477.477531
-EXTENSION 109 477.478562 477.476522
-EXTENSION 111 477.478335 477.475747
-LO-REDUCTION 113 477.477966 477.475747
-EXTENSION 115 477.477531 477.474150
-EXTENSION 117 477.476522 477.469293
-LO-REDUCTION 119 477.475945 477.469293
-LO-REDUCTION 121 477.475747 477.469293
-EXTENSION 123 477.474150 477.465181
-EXTENSION 125 477.472564 477.461183
-EXTENSION 127 477.471851 477.456311
-LO-REDUCTION 129 477.469293 477.456311
-EXTENSION 131 477.465181 477.442594
-LO-REDUCTION 133 477.461183 477.442594
-LO-REDUCTION 135 477.457167 477.442594
-EXTENSION 137 477.456311 477.429887
-LO-REDUCTION 139 477.448140 477.429887
-LO-REDUCTION 141 477.445600 477.429887
-EXTENSION 143 477.442594 477.410597
-LO-REDUCTION 145 477.432656 477.410597
-LO-REDUCTION 147 477.432527 477.410597
-EXTENSION 149 477.429887 477.392977
-LO-REDUCTION 151 477.419644 477.392977
-EXTENSION 153 477.411056 477.370851
-LO-REDUCTION 155 477.410597 477.370851
-EXTENSION 157 477.393125 477.356665
-LO-REDUCTION 159 477.392977 477.356665
-EXTENSION 161 477.384415 477.340478
-EXTENSION 163 477.370851 477.328610
-LO-REDUCTION 165 477.367006 477.328610
-LO-REDUCTION 167 477.356665 477.328610
-LO-REDUCTION 169 477.343394 477.328610
-REFLECTION 171 477.340478 477.327623
-LO-REDUCTION 173 477.338392 477.327623
-EXTENSION 175 477.335102 477.316244
-LO-REDUCTION 177 477.333110 477.316244
-EXTENSION 179 477.328610 477.315156
-EXTENSION 181 477.327623 477.297605
-LO-REDUCTION 183 477.320547 477.297605
-LO-REDUCTION 185 477.316244 477.297605
-LO-REDUCTION 187 477.315156 477.297605
-EXTENSION 189 477.303700 477.269874
-LO-REDUCTION 191 477.301646 477.269874
-LO-REDUCTION 193 477.299419 477.269874
-EXTENSION 195 477.297605 477.255876
-EXTENSION 197 477.282615 477.230019
-LO-REDUCTION 199 477.274271 477.230019
-EXTENSION 201 477.269874 477.199711
-LO-REDUCTION 203 477.255876 477.199711
-LO-REDUCTION 205 477.233619 477.199711
-REFLECTION 207 477.230019 477.197257
-LO-REDUCTION 209 477.208884 477.195267
-LO-REDUCTION 211 477.202120 477.193313
-REFLECTION 213 477.199711 477.189386
-HI-REDUCTION 215 477.197257 477.189386
-LO-REDUCTION 217 477.195267 477.189386
-LO-REDUCTION 219 477.193313 477.189375
-HI-REDUCTION 221 477.192488 477.189375
-EXTENSION 223 477.190662 477.186951
-LO-REDUCTION 225 477.190145 477.186951
-LO-REDUCTION 227 477.189386 477.186951
-REFLECTION 229 477.189375 477.186325
-LO-REDUCTION 231 477.187184 477.186325
-LO-REDUCTION 233 477.187006 477.186251
-HI-REDUCTION 235 477.186951 477.186251
-REFLECTION 237 477.186602 477.185756
-LO-REDUCTION 239 477.186325 477.185756
-HI-REDUCTION 241 477.186313 477.185756
-LO-REDUCTION 243 477.186251 477.185756
-HI-REDUCTION 245 477.185922 477.185756
-EXTENSION 247 477.185856 477.185563
-LO-REDUCTION 249 477.185838 477.185563
-LO-REDUCTION 251 477.185776 477.185563
-LO-REDUCTION 253 477.185756 477.185563
-LO-REDUCTION 255 477.185655 477.185559
-REFLECTION 257 477.185630 477.185552
-LO-REDUCTION 259 477.185609 477.185552
-REFLECTION 261 477.185572 477.185522
-LO-REDUCTION 263 477.185563 477.185522
-REFLECTION 265 477.185559 477.185505
-LO-REDUCTION 267 477.185552 477.185505
-LO-REDUCTION 269 477.185523 477.185502
-LO-REDUCTION 271 477.185522 477.185501
-LO-REDUCTION 273 477.185512 477.185501
+BUILD 5 511.844749 505.360856
+REFLECTION 7 511.780782 477.413329
+LO-REDUCTION 9 511.775815 477.413329
+LO-REDUCTION 11 507.796383 477.413329
+HI-REDUCTION 13 505.360856 477.413329
+HI-REDUCTION 15 485.552686 477.413329
+LO-REDUCTION 17 484.509022 477.413329
+HI-REDUCTION 19 480.951298 477.413329
+HI-REDUCTION 21 478.596539 477.413329
+HI-REDUCTION 23 478.560567 477.413329
+HI-REDUCTION 25 478.123899 477.413329
+HI-REDUCTION 27 477.679801 477.413329
+HI-REDUCTION 29 477.675116 477.413329
+HI-REDUCTION 31 477.607881 477.413329
+HI-REDUCTION 33 477.554058 477.413329
+HI-REDUCTION 35 477.474282 477.413329
+REFLECTION 37 477.457729 477.391603
+LO-REDUCTION 39 477.443980 477.391603
+HI-REDUCTION 41 477.442964 477.391603
+REFLECTION 43 477.413329 477.363559
+HI-REDUCTION 45 477.401362 477.363559
+EXTENSION 47 477.400089 477.311957
+LO-REDUCTION 49 477.391603 477.311957
+LO-REDUCTION 51 477.380266 477.311957
+REFLECTION 53 477.363559 477.308763
+EXTENSION 55 477.343298 477.276752
+LO-REDUCTION 57 477.337915 477.276752
+REFLECTION 59 477.311957 477.264470
+REFLECTION 61 477.308763 477.256650
+LO-REDUCTION 63 477.289753 477.256650
+LO-REDUCTION 65 477.276752 477.256650
+EXTENSION 67 477.269605 477.244453
+REFLECTION 69 477.264470 477.243984
+LO-REDUCTION 71 477.260609 477.243984
+HI-REDUCTION 73 477.256650 477.243984
+REFLECTION 75 477.248262 477.243357
+LO-REDUCTION 77 477.245648 477.243282
+REFLECTION 79 477.244453 477.241804
+LO-REDUCTION 81 477.243984 477.241440
+HI-REDUCTION 83 477.243357 477.241378
+HI-REDUCTION 85 477.243282 477.241378
+LO-REDUCTION 87 477.241804 477.241378
+REFLECTION 89 477.241742 477.241190
+HI-REDUCTION 91 477.241702 477.241186
+HI-REDUCTION 93 477.241440 477.241186
+LO-REDUCTION 95 477.241378 477.241114
+HI-REDUCTION 97 477.241209 477.241114
+HI-REDUCTION 99 477.241190 477.241073
+LO-REDUCTION 101 477.241186 477.241059
+HI-REDUCTION 103 477.241123 477.241059
+HI-REDUCTION 105 477.241114 477.241057
+HI-REDUCTION 107 477.241073 477.241051
+HI-REDUCTION 109 477.241063 477.241047
+HI-REDUCTION 111 477.241059 477.241045
+HI-REDUCTION 113 477.241057 477.241042
+HI-REDUCTION 115 477.241051 477.241042
Exiting from Nelder Mead minimizer
- 275 function evaluations used
+ 117 function evaluations used
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 21.88590 secs
+Time difference of 11.85411 secs
> tic <- Sys.time()
> print(loglik.mle <- -kalm.fit1$value,digits=4)
[1] -477.2
@@ -258,9 +186,9 @@
+ digits=3
+ )
truth MLE SE
-alpha.1 0.8 0.685 0.0672
-alpha.4 0.9 0.875 0.0359
-x1.0 -3.0 -1.978 3.9679
-x2.0 4.0 6.431 2.6395
-loglik -479.4 -477.185 NA
+alpha.1 0.8 0.685 0.0676
+alpha.4 0.9 0.879 0.0358
+x1.0 -3.0 -3.996 3.9811
+x2.0 4.0 2.952 2.6278
+loglik -479.0 -477.241 NA
>
Modified: pkg/tests/ou2-mif.Rout.save
===================================================================
--- pkg/tests/ou2-mif.Rout.save 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/tests/ou2-mif.Rout.save 2010-10-05 20:39:24 UTC (rev 365)
@@ -1,6 +1,6 @@
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.11.1 (2010-05-31)
+Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,9 +16,16 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: deSolve
-Loading required package: subplex
-Loading required package: mvtnorm
+This is pomp version 0.34-1
+
+IMPORTANT NOTICE:
+The default behaviors of 'simulate' and 'trajectory' have changed as of release 0.34-1. You can ensure that your code will continue to function as you intend by specifying the values of the 'times' and 't0' arguments to these functions, thus removing dependence of your code on the defaults. In the meantime, using 'simulate' or 'trajectory' in such a way as to rely on the default will produce a warning. These warnings will be removed in a future release.
+
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+
+Subscribe to the pomp-announce list (go to pomp.r-forge.r-project.org) to receive email notification about new releases of pomp including descriptions of feature additions, changes, and fixes.
+
+
>
> data(ou2)
>
@@ -33,7 +40,7 @@
> cat("particle filter log likelihood at truth\n")
particle filter log likelihood at truth
> print(fit1.pfilter$loglik,digits=4)
-[1] -479.9
+[1] -481.6
>
> p.truth <- coef(ou2)
> guess2 <- guess1 <- p.truth
Modified: pkg/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/tests/ou2-nlf.Rout.save 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/tests/ou2-nlf.Rout.save 2010-10-05 20:39:24 UTC (rev 365)
@@ -16,6 +16,16 @@
Type 'q()' to quit R.
> library(pomp)
+This is pomp version 0.34-1
+
+IMPORTANT NOTICE:
+The default behaviors of 'simulate' and 'trajectory' have changed as of release 0.34-1. You can ensure that your code will continue to function as you intend by specifying the values of the 'times' and 't0' arguments to these functions, thus removing dependence of your code on the defaults. In the meantime, using 'simulate' or 'trajectory' in such a way as to rely on the default will produce a warning. These warnings will be removed in a future release.
+
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+
+Subscribe to the pomp-announce list (go to pomp.r-forge.r-project.org) to receive email notification about new releases of pomp including descriptions of feature additions, changes, and fixes.
+
+
>
> set.seed(594861940L)
>
@@ -36,7 +46,7 @@
+ lql.frac = 0.025
+ )
> print(m1)
-[1] -555.448
+[1] -555.547
>
> m2 <- nlf(
+ object=ou2,
@@ -53,66 +63,76 @@
+ lql.frac = 0.025
+ )
Nelder-Mead direct search function minimizer
-function value for initial parameters = 555.447984
- Scaled convergence tolerance is 8.27682e-06
+function value for initial parameters = 555.547033
+ Scaled convergence tolerance is 8.2783e-06
Stepsize computed as 0.100000
-BUILD 4 559.766061 555.447984
-HI-REDUCTION 6 557.051562 555.447984
-HI-REDUCTION 8 556.036042 555.166021
-LO-REDUCTION 10 555.512890 555.166021
-REFLECTION 12 555.447984 555.147214
-HI-REDUCTION 14 555.192349 555.110296
-HI-REDUCTION 16 555.166021 555.067342
-HI-REDUCTION 18 555.147214 555.061950
-HI-REDUCTION 20 555.110296 555.057410
-HI-REDUCTION 22 555.067342 555.049678
-HI-REDUCTION 24 555.061950 555.047266
-HI-REDUCTION 26 555.057410 555.044069
-HI-REDUCTION 28 555.049678 555.044069
-HI-REDUCTION 30 555.047266 555.040984
-REFLECTION 32 555.044378 555.040622
-REFLECTION 34 555.044069 555.037871
-REFLECTION 36 555.040984 555.036847
-HI-REDUCTION 38 555.040622 555.036847
-HI-REDUCTION 40 555.037871 555.036847
-LO-REDUCTION 42 555.037321 555.036508
-EXTENSION 44 555.037037 555.034319
-HI-REDUCTION 46 555.036847 555.034319
-LO-REDUCTION 48 555.036508 555.034319
-LO-REDUCTION 50 555.035578 555.034319
-EXTENSION 52 555.034913 555.033759
-LO-REDUCTION 54 555.034753 555.033759
-LO-REDUCTION 56 555.034319 555.033759
-HI-REDUCTION 58 555.034253 555.033759
-EXTENSION 60 555.034001 555.033182
-LO-REDUCTION 62 555.033917 555.033182
-EXTENSION 64 555.033759 555.032580
-EXTENSION 66 555.033343 555.032098
-EXTENSION 68 555.033182 555.031949
-REFLECTION 70 555.032580 555.031649
-HI-REDUCTION 72 555.032098 555.031649
-LO-REDUCTION 74 555.031949 555.031649
-LO-REDUCTION 76 555.031943 555.031649
-HI-REDUCTION 78 555.031739 555.031649
-HI-REDUCTION 80 555.031714 555.031649
-LO-REDUCTION 82 555.031673 555.031643
-HI-REDUCTION 84 555.031661 555.031636
-HI-REDUCTION 86 555.031649 555.031636
+BUILD 4 559.966959 555.547033
+HI-REDUCTION 6 556.890993 555.547033
+HI-REDUCTION 8 556.217248 555.181704
+LO-REDUCTION 10 555.617125 555.174895
+REFLECTION 12 555.547033 555.100277
+HI-REDUCTION 14 555.181704 555.100277
+HI-REDUCTION 16 555.174895 555.060649
+HI-REDUCTION 18 555.158167 555.060649
+HI-REDUCTION 20 555.100277 555.060649
+HI-REDUCTION 22 555.073319 555.046470
+HI-REDUCTION 24 555.064516 555.046470
+HI-REDUCTION 26 555.060649 555.046470
+LO-REDUCTION 28 555.049690 555.044469
+REFLECTION 30 555.047655 555.041210
+HI-REDUCTION 32 555.046470 555.041210
+HI-REDUCTION 34 555.044469 555.040900
+HI-REDUCTION 36 555.041431 555.040037
+HI-REDUCTION 38 555.041210 555.039984
+HI-REDUCTION 40 555.040900 555.039847
+LO-REDUCTION 42 555.040037 555.039534
+HI-REDUCTION 44 555.039984 555.039516
+EXTENSION 46 555.039847 555.038378
+HI-REDUCTION 48 555.039534 555.038378
+LO-REDUCTION 50 555.039516 555.038378
+LO-REDUCTION 52 555.039124 555.038378
+REFLECTION 54 555.038819 555.038336
+EXTENSION 56 555.038601 555.037899
+LO-REDUCTION 58 555.038378 555.037899
+LO-REDUCTION 60 555.038336 555.037899
+REFLECTION 62 555.038103 555.037848
+EXTENSION 64 555.038074 555.037593
+EXTENSION 66 555.037899 555.037354
+EXTENSION 68 555.037848 555.037335
+EXTENSION 70 555.037593 555.036537
+LO-REDUCTION 72 555.037354 555.036537
+LO-REDUCTION 74 555.037335 555.036537
+EXTENSION 76 555.037012 555.036094
+LO-REDUCTION 78 555.036938 555.036094
+EXTENSION 80 555.036537 555.035295
+LO-REDUCTION 82 555.036148 555.035295
+LO-REDUCTION 84 555.036094 555.035295
+REFLECTION 86 555.035627 555.035238
+REFLECTION 88 555.035311 555.035071
+LO-REDUCTION 90 555.035295 555.035071
+HI-REDUCTION 92 555.035238 555.035071
+REFLECTION 94 555.035152 555.035045
+LO-REDUCTION 96 555.035150 555.035045
+REFLECTION 98 555.035071 555.035010
+LO-REDUCTION 100 555.035065 555.035010
+LO-REDUCTION 102 555.035045 555.035010
+LO-REDUCTION 104 555.035022 555.035009
+LO-REDUCTION 106 555.035017 555.035009
Exiting from Nelder Mead minimizer
- 88 function evaluations used
+ 108 function evaluations used
h in NLF = 0.1
-epsilon in NLF = 0.07723393 0.08606162 1.499432
-Fitted param 1 -5.935289 -5.935289 up in 'nlf'
-Fitted param 1 -5.924214 down in 'NLF'
-Fitted param 2 -5.92809 -5.92809 up in 'nlf'
-Fitted param 2 -5.941322 down in 'NLF'
-Fitted param 3 -5.953709 -5.953709 up in 'nlf'
-Fitted param 3 -5.905519 down in 'NLF'
+epsilon in NLF = 0.07620834 0.0830427 1.496106
+Fitted param 1 -5.935533 -5.935533 up in 'nlf'
+Fitted param 1 -5.923885 down in 'NLF'
+Fitted param 2 -5.923836 -5.923836 up in 'nlf'
+Fitted param 2 -5.941826 down in 'NLF'
+Fitted param 3 -5.952844 -5.952844 up in 'nlf'
+Fitted param 3 -5.905505 down in 'NLF'
>
> se <- m2$se
> print(cbind(truth=p.truth[names(se)],fit=m2$params[names(se)],se=se),digits=3)
truth fit se
-alpha.2 -0.5 -0.467 0.0454
-alpha.3 0.3 0.299 0.0541
-tau 1.0 0.930 0.5491
+alpha.2 -0.5 -0.465 0.0433
+alpha.3 0.3 0.292 0.0508
+tau 1.0 0.917 0.5458
>
Modified: pkg/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/tests/ou2-pmcmc.Rout.save 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/tests/ou2-pmcmc.Rout.save 2010-10-05 20:39:24 UTC (rev 365)
@@ -16,6 +16,16 @@
Type 'q()' to quit R.
> library(pomp)
+This is pomp version 0.34-1
+
+IMPORTANT NOTICE:
+The default behaviors of 'simulate' and 'trajectory' have changed as of release 0.34-1. You can ensure that your code will continue to function as you intend by specifying the values of the 'times' and 't0' arguments to these functions, thus removing dependence of your code on the defaults. In the meantime, using 'simulate' or 'trajectory' in such a way as to rely on the default will produce a warning. These warnings will be removed in a future release.
+
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+
+Subscribe to the pomp-announce list (go to pomp.r-forge.r-project.org) to receive email notification about new releases of pomp including descriptions of feature additions, changes, and fixes.
+
+
>
> data(ou2)
>
Modified: pkg/tests/ou2-probe.Rout.save
===================================================================
--- pkg/tests/ou2-probe.Rout.save 2010-10-05 18:12:11 UTC (rev 364)
+++ pkg/tests/ou2-probe.Rout.save 2010-10-05 20:39:24 UTC (rev 365)
@@ -16,6 +16,16 @@
Type 'q()' to quit R.
> library(pomp)
+This is pomp version 0.34-1
+
+IMPORTANT NOTICE:
+The default behaviors of 'simulate' and 'trajectory' have changed as of release 0.34-1. You can ensure that your code will continue to function as you intend by specifying the values of the 'times' and 't0' arguments to these functions, thus removing dependence of your code on the defaults. In the meantime, using 'simulate' or 'trajectory' in such a way as to rely on the default will produce a warning. These warnings will be removed in a future release.
+
+See the documentation ("pomp?simulate", "pomp?trajectory") for a description of the new default behaviors.
+
+Subscribe to the pomp-announce list (go to pomp.r-forge.r-project.org) to receive email notification about new releases of pomp including descriptions of feature additions, changes, and fixes.
+
+
> set.seed(1066L)
>
> data(ou2)
@@ -57,11 +67,11 @@
$quantiles
y1.mean y2.mean y1.sd y2.sd
- 0.104 0.526 0.026 0.048
+ 0.122 0.542 0.020 0.050
$pvals
y1.mean y2.mean y1.sd y2.sd
-0.21157685 0.95009980 0.05588822 0.09980040
+0.24750499 0.91816367 0.04391218 0.10379242
> summary(pm.po)
$coef
@@ -73,11 +83,11 @@
$quantiles
y1.mean y2.mean y1.sd y2.sd
- 0.052 0.642 1.000 1.000
+ 0.074 0.650 1.000 1.000
$pvals
y1.mean y2.mean y1.sd y2.sd
-0.107784431 0.718562874 0.003992016 0.003992016
+0.151696607 0.702594810 0.003992016 0.003992016
>
> plot(pm.ou2)
@@ -103,15 +113,15 @@
$quantiles
y1acf.acf.1.y1 y1acf.acf.2.y1 y2acf.acf.0.y2 y2acf.acf.1.y2 y2acf.acf.2.y2
- 0.104 0.054 0.048 0.050 0.050
+ 0.084 0.036 0.050 0.044 0.044
y12ccf.ccf.3 y12ccf.ccf.8
- 0.058 0.366
+ 0.048 0.326
$pvals
y1acf.acf.1.y1 y1acf.acf.2.y1 y2acf.acf.0.y2 y2acf.acf.1.y2 y2acf.acf.2.y2
- 0.2115768 0.1117764 0.0998004 0.1037924 0.1037924
+ 0.17165669 0.07584830 0.10379242 0.09181637 0.09181637
y12ccf.ccf.3 y12ccf.ccf.8
- 0.1197605 0.7345309
+ 0.09980040 0.65469062
>
> pb <- probe(
@@ -133,19 +143,19 @@
$quantiles
y1.10% y1.20% y1.30% y1.40% y1.50% y1.60% y1.70% y1.80%
- 0.780 0.805 0.750 0.600 0.365 0.145 0.025 0.020
+ 0.755 0.760 0.800 0.620 0.355 0.125 0.025 0.010
y1.90% acf.0.y1 acf.1.y1 acf.2.y1 acf.3.y1 acf.4.y1 acf.0.y2 acf.1.y2
- 0.005 0.025 0.040 0.025 0.120 0.790 0.060 0.065
+ 0.005 0.020 0.035 0.025 0.100 0.835 0.060 0.070
acf.2.y2 acf.3.y2 acf.4.y2 pd
- 0.075 0.110 0.435 0.075
+ 0.070 0.090 0.430 0.060
$pvals
y1.10% y1.20% y1.30% y1.40% y1.50% y1.60% y1.70%
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 365
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