[Pomp-commits] r526 - in pkg: . src tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jul 24 02:11:14 CEST 2011
Author: kingaa
Date: 2011-07-24 02:11:13 +0200 (Sun, 24 Jul 2011)
New Revision: 526
Modified:
pkg/DESCRIPTION
pkg/src/SSA.f
pkg/tests/fhn.Rout.save
pkg/tests/filtfail.Rout.save
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-procmeas.Rout.save
pkg/tests/ou2-simulate.Rout.save
pkg/tests/ou2-trajmatch.Rout.save
pkg/tests/pfilter.Rout.save
pkg/tests/pomppomp.Rout.save
pkg/tests/ricker-probe.Rout.save
pkg/tests/ricker-spect.Rout.save
pkg/tests/ricker.Rout.save
pkg/tests/rw2.Rout.save
pkg/tests/sir-icfit.Rout.save
pkg/tests/sir.Rout.save
pkg/tests/skeleton.Rout.save
pkg/tests/synlik.Rout.save
Log:
- modify src/SSA.f to get rid of warning messages seen in gfortran-4.6
- update tests/*.Rout.save files
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/DESCRIPTION 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.38-6
-Date: 2011-07-12
+Version: 0.38-5
+Date: 2011-07-23
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
Maintainer: Aaron A. King <kingaa at umich.edu>
URL: http://pomp.r-forge.r-project.org
Modified: pkg/src/SSA.f
===================================================================
--- pkg/src/SSA.f 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/src/SSA.f 2011-07-24 00:11:13 UTC (rev 526)
@@ -3,6 +3,14 @@
& ncovar,icovar,lcov,mcov,tcov,cov)
implicit integer (i-n)
implicit double precision (a-h,o-z)
+ dimension xstart(nvar,nreps), times(ntimes)
+ dimension params(npar,nreps), par(npar)
+ dimension xout(nvar,nreps,ntimes)
+ dimension e(nvar),v(nvar,nevent),d(nvar,nevent)
+ dimension izero(nzero)
+ dimension istate(nvar), ipar(npar), icovar(ncovar)
+ dimension tcov(lcov), cov(lcov,mcov)
+ dimension covars(mcov)
external fprob
ntreeh=1+int(log(nevent*1.0)/log(2.0)+1)
do irep=1,nreps
@@ -91,7 +99,7 @@
dum=min(e(i)*y(i),dum)
if(dum.le.1.0)goto 50
enddo
- 50 kappa=max(dum,1.0)
+ 50 kappa=max(dum,1.0d0)
if(kappa.eq.1)then
call gillespie(fprob,t,f,y,v,d,par,n,m,ntreeh,npar,
& jevent,iflag,istate,ipar,ncovar,icovar,
@@ -276,7 +284,7 @@
enddo
500 return
end
-
+
subroutine tauleap(fprob,tau,t,f,y,v,d,par,n,m,ntreeh,npar,k,
& iflag,istate,ipar,ncovar,icovar,mcov,cov)
implicit integer (i-n)
Modified: pkg/tests/fhn.Rout.save
===================================================================
--- pkg/tests/fhn.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/fhn.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -127,9 +127,9 @@
, , 3
- [,1] [,2]
-V -1.471404 1.32437192
-R -0.586106 0.06164339
+ [,1] [,2]
+V -1.4714039 1.32437192
+R -0.5861061 0.06164339
> matplot(time(fhn),t(y["V",,]),type='l',lty=1)
> plot(y[1,,],y[2,,],type='n')
Modified: pkg/tests/filtfail.Rout.save
===================================================================
--- pkg/tests/filtfail.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/filtfail.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,6 +1,6 @@
-R version 2.12.1 (2010-12-16)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.13.1 (2011-07-08)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
Modified: pkg/tests/gillespie.Rout.save
===================================================================
--- pkg/tests/gillespie.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/gillespie.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,7 +1,8 @@
-R version 2.11.1 (2010-05-31)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.13.1 (2011-07-08)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -16,6 +17,9 @@
Type 'q()' to quit R.
> library(pomp)
+Loading required package: mvtnorm
+Loading required package: subplex
+Loading required package: deSolve
>
> params <- c(
+ nu=log(1/70),
Modified: pkg/tests/logistic.Rout.save
===================================================================
--- pkg/tests/logistic.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/logistic.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
Modified: pkg/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/tests/ou2-bsmc.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-bsmc.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,7 +1,8 @@
-R version 2.11.1 (2010-05-31)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.13.1 (2011-07-08)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -16,6 +17,9 @@
Type 'q()' to quit R.
> library(pomp)
+Loading required package: mvtnorm
+Loading required package: subplex
+Loading required package: deSolve
>
> set.seed(398585L)
> data(ou2)
@@ -58,7 +62,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 39.33551 secs
+Time difference of 38.74774 secs
>
> print(
+ cbind(
Modified: pkg/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/tests/ou2-forecast.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-forecast.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
Modified: pkg/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/tests/ou2-kalman.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-kalman.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,7 +1,8 @@
-R version 2.11.1 (2010-05-31)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.13.1 (2011-07-08)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -16,6 +17,9 @@
Type 'q()' to quit R.
> library(pomp)
+Loading required package: mvtnorm
+Loading required package: subplex
+Loading required package: deSolve
>
> set.seed(577639485L)
>
@@ -160,7 +164,7 @@
117 function evaluations used
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 11.83455 secs
+Time difference of 11.55296 secs
> tic <- Sys.time()
> print(loglik.mle <- -kalm.fit1$value,digits=4)
[1] -477.2
Modified: pkg/tests/ou2-mif.Rout.save
===================================================================
--- pkg/tests/ou2-mif.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-mif.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
Modified: pkg/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/tests/ou2-nlf.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-nlf.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,6 +1,6 @@
-R version 2.12.1 (2010-12-16)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.13.1 (2011-07-08)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
Modified: pkg/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/tests/ou2-pmcmc.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-pmcmc.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,7 +1,8 @@
-R version 2.11.1 (2010-05-31)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.13.1 (2011-07-08)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -16,6 +17,9 @@
Type 'q()' to quit R.
> library(pomp)
+Loading required package: mvtnorm
+Loading required package: subplex
+Loading required package: deSolve
>
> data(ou2)
>
Modified: pkg/tests/ou2-probe.Rout.save
===================================================================
--- pkg/tests/ou2-probe.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-probe.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -88,7 +88,7 @@
0.155688623 0.678642715 0.003992016 0.003992016
$synth.loglik
-[1] -108.7680
+[1] -108.768
>
> plot(pm.ou2)
Modified: pkg/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/tests/ou2-procmeas.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-procmeas.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
Modified: pkg/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/tests/ou2-simulate.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-simulate.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -35,7 +35,7 @@
> ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.009652853 secs
+Time difference of 0.007447004 secs
>
> coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
>
Modified: pkg/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/tests/ou2-trajmatch.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ou2-trajmatch.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -199,11 +199,11 @@
current params: 0.6368124 0.8539377 1.667453 -2.988615 4.334961
iter 55 val= 1295.452 , accept= TRUE
current params: 0.618709 0.8524734 1.694322 -2.997447 4.325407
-iter 56 val= 1270.420 , accept= TRUE
+iter 56 val= 1270.42 , accept= TRUE
current params: 0.5901194 0.8160746 1.711434 -3.027965 4.312765
-iter 57 val= 1270.420 , accept= FALSE
+iter 57 val= 1270.42 , accept= FALSE
current params: 0.5901194 0.8160746 1.711434 -3.027965 4.312765
-iter 58 val= 1270.420 , accept= FALSE
+iter 58 val= 1270.42 , accept= FALSE
current params: 0.5901194 0.8160746 1.711434 -3.027965 4.312765
iter 59 val= 1241.955 , accept= TRUE
current params: 0.581974 0.8179566 1.739656 -2.996623 4.348772
@@ -220,7 +220,7 @@
iter 65 val= 1205.706 , accept= FALSE
current params: 0.5690983 0.764269 1.774335 -2.973598 4.302674
iter 66 val= 1182.611 , accept= TRUE
-current params: 0.5710116 0.785939 1.801455 -2.993636 4.291691
+current params: 0.5710116 0.7859391 1.801455 -2.993636 4.291691
iter 67 val= 1167.827 , accept= TRUE
current params: 0.5732821 0.8225732 1.821809 -2.981542 4.293427
iter 68 val= 1167.827 , accept= FALSE
@@ -229,9 +229,9 @@
current params: 0.5732821 0.8225732 1.821809 -2.981542 4.293427
iter 70 val= 1159.736 , accept= TRUE
current params: 0.5633811 0.8360814 1.832664 -2.985213 4.272785
-iter 71 val= 1157.020 , accept= TRUE
+iter 71 val= 1157.02 , accept= TRUE
current params: 0.5707494 0.8370168 1.836375 -2.970371 4.271366
-iter 72 val= 1157.020 , accept= FALSE
+iter 72 val= 1157.02 , accept= FALSE
current params: 0.5707494 0.8370168 1.836375 -2.970371 4.271366
iter 73 val= 1146.235 , accept= TRUE
current params: 0.579767 0.8393374 1.850459 -2.980518 4.300226
@@ -239,7 +239,7 @@
current params: 0.5435931 0.8260895 1.906304 -2.961221 4.277552
iter 75 val= 1101.545 , accept= FALSE
current params: 0.5435931 0.8260895 1.906304 -2.961221 4.277552
-iter 76 val= 1086.000 , accept= TRUE
+iter 76 val= 1086 , accept= TRUE
current params: 0.5554613 0.8251125 1.928449 -2.969901 4.309415
iter 77 val= 1082.253 , accept= TRUE
current params: 0.5186073 0.7973389 1.931111 -2.964102 4.292897
@@ -250,23 +250,23 @@
iter 80 val= 1082.253 , accept= FALSE
current params: 0.5186073 0.7973389 1.931111 -2.964102 4.292897
iter 81 val= 1067.654 , accept= TRUE
-current params: 0.4905712 0.806781 1.953060 -2.915265 4.291014
+current params: 0.4905712 0.806781 1.95306 -2.915265 4.291014
iter 82 val= 1067.654 , accept= FALSE
-current params: 0.4905712 0.806781 1.953060 -2.915265 4.291014
-iter 83 val= 1066.480 , accept= TRUE
+current params: 0.4905712 0.806781 1.95306 -2.915265 4.291014
+iter 83 val= 1066.48 , accept= TRUE
current params: 0.5218239 0.7643546 1.953087 -2.897599 4.262599
iter 84 val= 1057.698 , accept= TRUE
-current params: 0.5419846 0.8110294 1.968900 -2.880169 4.286582
+current params: 0.5419846 0.8110294 1.9689 -2.880169 4.286582
iter 85 val= 1057.698 , accept= FALSE
-current params: 0.5419846 0.8110294 1.968900 -2.880169 4.286582
+current params: 0.5419846 0.8110294 1.9689 -2.880169 4.286582
iter 86 val= 1057.698 , accept= FALSE
-current params: 0.5419846 0.8110294 1.968900 -2.880169 4.286582
+current params: 0.5419846 0.8110294 1.9689 -2.880169 4.286582
iter 87 val= 1057.698 , accept= FALSE
-current params: 0.5419846 0.8110294 1.968900 -2.880169 4.286582
+current params: 0.5419846 0.8110294 1.9689 -2.880169 4.286582
iter 88 val= 1057.698 , accept= FALSE
-current params: 0.5419846 0.8110294 1.968900 -2.880169 4.286582
+current params: 0.5419846 0.8110294 1.9689 -2.880169 4.286582
iter 89 val= 1057.698 , accept= FALSE
-current params: 0.5419846 0.8110294 1.968900 -2.880169 4.286582
+current params: 0.5419846 0.8110294 1.9689 -2.880169 4.286582
iter 90 val= 1049.122 , accept= TRUE
current params: 0.5096302 0.8250705 1.982865 -2.874752 4.303329
iter 91 val= 1047.578 , accept= TRUE
@@ -284,12 +284,12 @@
iter 97 val= 1013.848 , accept= TRUE
current params: 0.5461696 0.8376482 2.043564 -2.947939 4.253507
iter 98 val= 1001.952 , accept= TRUE
-current params: 0.552347 0.840818 2.065274 -2.951199 4.265389
-iter 99 val= 999.435 , accept= TRUE
+current params: 0.552347 0.8408179 2.065274 -2.951199 4.265389
+iter 99 val= 999.4351 , accept= TRUE
current params: 0.569008 0.8631994 2.074306 -2.94497 4.265321
-iter 100 val= 999.435 , accept= FALSE
+iter 100 val= 999.4351 , accept= FALSE
current params: 0.569008 0.8631994 2.074306 -2.94497 4.265321
-best val= 999.435
+best val= 999.4351
$params
alpha.1 alpha.2 alpha.3 alpha.4 sigma.1 sigma.2 sigma.3
0.5690080 -0.5000000 0.3000000 0.8631994 3.0000000 -0.5000000 2.0000000
@@ -297,7 +297,7 @@
2.0743065 -2.9449702 4.2653209
$loglik
-[1] -999.435
+[1] -999.4351
$eval
[1] 101 NA
Modified: pkg/tests/pfilter.Rout.save
===================================================================
--- pkg/tests/pfilter.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/pfilter.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
Modified: pkg/tests/pomppomp.Rout.save
===================================================================
--- pkg/tests/pomppomp.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/pomppomp.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
Modified: pkg/tests/ricker-probe.Rout.save
===================================================================
--- pkg/tests/ricker-probe.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ricker-probe.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -240,7 +240,7 @@
0.34165834
$synth.loglik
-[1] -14.77430
+[1] -14.7743
$est
character(0)
@@ -312,7 +312,7 @@
+ )
+ )
user system elapsed
- 13.888 0.047 13.965
+ 13.267 0.002 13.271
> plot(pm)
>
> cbind(truth=coef(ricker),est=coef(pm),guess=coef(po))
@@ -371,7 +371,7 @@
+ )
+ )
user system elapsed
- 10.304 0.041 10.366
+ 10.041 0.021 10.064
> plot(pm)
> plot(as(pm,"pomp"),variables="y")
> plot(simulate(pm),variables="y")
Modified: pkg/tests/ricker-spect.Rout.save
===================================================================
--- pkg/tests/ricker-spect.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ricker-spect.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,7 +1,8 @@
-R version 2.11.1 (2010-05-31)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.13.1 (2011-07-08)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -16,6 +17,9 @@
Type 'q()' to quit R.
> library(pomp)
+Loading required package: mvtnorm
+Loading required package: subplex
+Loading required package: deSolve
>
> pdf(file="ricker-spect.pdf")
>
Modified: pkg/tests/ricker.Rout.save
===================================================================
--- pkg/tests/ricker.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/ricker.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -249,14 +249,14 @@
+ )
>
> print(res,digits=3)
- guess truth MLE PM
-log.r 3.00 3.80 3.79 3.74
-log.sigma 0.00 -1.20 -1.74 -1.12
-log.phi 3.00 2.30 2.32 2.41
-N.0 7.00 7.00 7.00 7.00
-e.0 0.00 0.00 0.00 0.00
-loglik -230.86 -139.55 -137.35 -143.33
-synth.loglik -12.28 17.47 16.47 20.34
+ guess truth MLE PM
+log.r 3.0 3.8 3.79 3.74
+log.sigma 0.0 -1.2 -1.74 -1.12
+log.phi 3.0 2.3 2.32 2.41
+N.0 7.0 7.0 7.00 7.00
+e.0 0.0 0.0 0.00 0.00
+loglik -230.9 -139.5 -137.35 -143.33
+synth.loglik -12.3 17.5 16.47 20.34
>
> plot(ricker)
> plot(simulate(guess))
Modified: pkg/tests/rw2.Rout.save
===================================================================
--- pkg/tests/rw2.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/rw2.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -253,7 +253,7 @@
}
y
}
-<environment: 0x1ba5950>
+<environment: 0x1acfdd0>
measurement model density, dmeasure =
function (y, x, t, params, log, covars, ...)
{
@@ -266,11 +266,11 @@
f
else exp(f)
}
-<environment: 0x1ba5950>
+<environment: 0x1acfdd0>
skeleton ( map ) =
function (x, t, params, covars, ...)
stop(sQuote("skeleton"), " not specified")
-<environment: 0x1c5dd08>
+<environment: 0x1b4b158>
initializer =
function (params, t0, ...)
{
Modified: pkg/tests/sir-icfit.Rout.save
===================================================================
--- pkg/tests/sir-icfit.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/sir-icfit.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -39,12 +39,12 @@
>
> summary(pm.true <- probe(po,probes=plist,nsim=100,seed=1066L))
$coef
- gamma mu iota nbasis degree period
- 3.25809654 -3.91202301 -4.60517019 3.00000000 3.00000000 1.00000000
- beta1 beta2 beta3 beta.sd pop rho
- 7.09007684 7.49554194 6.39692966 -6.90775528 14.55744790 -0.51082562
- S.0 I.0 R.0
--3.83198030 -6.90775528 -0.02292750
+ gamma mu iota nbasis degree period beta1
+ 3.2580965 -3.9120230 -4.6051702 3.0000000 3.0000000 1.0000000 7.0900768
+ beta2 beta3 beta.sd pop rho S.0 I.0
+ 7.4955419 6.3969297 -6.9077553 14.5574479 -0.5108256 -3.8319803 -6.9077553
+ R.0
+-0.0229275
$nsim
[1] 100
@@ -67,12 +67,12 @@
>
> summary(pm.guess <- probe(po,params=guess,probes=plist,nsim=100,seed=1066L))
$coef
- gamma mu iota nbasis degree period
- 3.25809654 -3.91202301 -4.60517019 3.00000000 3.00000000 1.00000000
- beta1 beta2 beta3 beta.sd pop rho
- 7.09007684 7.49554194 6.39692966 -6.90775528 14.55744790 -0.51082562
- S.0 I.0 R.0
--3.63198030 -7.10775528 -0.02292750
+ gamma mu iota nbasis degree period beta1
+ 3.2580965 -3.9120230 -4.6051702 3.0000000 3.0000000 1.0000000 7.0900768
+ beta2 beta3 beta.sd pop rho S.0 I.0
+ 7.4955419 6.3969297 -6.9077553 14.5574479 -0.5108256 -3.6319803 -7.1077553
+ R.0
+-0.0229275
$nsim
[1] 100
@@ -214,12 +214,12 @@
>
> summary(tm.true <- traj.match(po,eval.only=TRUE))
$params
- gamma mu iota nbasis degree period
- 3.25809654 -3.91202301 -4.60517019 3.00000000 3.00000000 1.00000000
- beta1 beta2 beta3 beta.sd pop rho
- 7.09007684 7.49554194 6.39692966 -6.90775528 14.55744790 -0.51082562
- S.0 I.0 R.0
--3.83198030 -6.90775528 -0.02292750
+ gamma mu iota nbasis degree period beta1
+ 3.2580965 -3.9120230 -4.6051702 3.0000000 3.0000000 1.0000000 7.0900768
+ beta2 beta3 beta.sd pop rho S.0 I.0
+ 7.4955419 6.3969297 -6.9077553 14.5574479 -0.5108256 -3.8319803 -6.9077553
+ R.0
+-0.0229275
$loglik
[1] -49.09745
@@ -236,12 +236,12 @@
>
> summary(tm.guess <- traj.match(po,start=guess,eval.only=TRUE))
$params
- gamma mu iota nbasis degree period
- 3.25809654 -3.91202301 -4.60517019 3.00000000 3.00000000 1.00000000
- beta1 beta2 beta3 beta.sd pop rho
- 7.09007684 7.49554194 6.39692966 -6.90775528 14.55744790 -0.51082562
- S.0 I.0 R.0
--3.63198030 -7.10775528 -0.02292750
+ gamma mu iota nbasis degree period beta1
+ 3.2580965 -3.9120230 -4.6051702 3.0000000 3.0000000 1.0000000 7.0900768
+ beta2 beta3 beta.sd pop rho S.0 I.0
+ 7.4955419 6.3969297 -6.9077553 14.5574479 -0.5108256 -3.6319803 -7.1077553
+ R.0
+-0.0229275
$loglik
[1] -1768.807
@@ -294,7 +294,7 @@
iter 26 val= 1548.83 , accept= FALSE
iter 27 val= 1389.144 , accept= TRUE
iter 28 val= 1389.144 , accept= FALSE
-iter 29 val= 1375.290 , accept= TRUE
+iter 29 val= 1375.29 , accept= TRUE
iter 30 val= 976.1314 , accept= TRUE
iter 31 val= 976.1314 , accept= FALSE
iter 32 val= 976.1314 , accept= FALSE
Modified: pkg/tests/sir.Rout.save
===================================================================
--- pkg/tests/sir.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/sir.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -394,7 +394,7 @@
zeronames = zeronames, tcovar = tcovar, covar = covar,
args = pairlist(...))
}
-<environment: 0x192ae10>
+<environment: 0x2d238f0>
process model density, dprocess =
function (x, times, params, ..., statenames = character(0), paramnames = character(0),
covarnames = character(0), tcovar, covar, log = FALSE)
@@ -404,7 +404,7 @@
covarnames = covarnames, tcovar = tcovar, covar = covar,
log = log, args = pairlist(...))
}
-<environment: 0x2012898>
+<environment: 0x222b818>
measurement model simulator, rmeasure =
function (x, t, params, covars, ...)
{
@@ -471,7 +471,7 @@
> x <- simulate(po,params=log(params),nsim=3)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 2.064163 secs
+Time difference of 2.030447 secs
>
> pdf(file='sir.pdf')
>
@@ -488,7 +488,7 @@
> X3 <- trajectory(po,params=log(params),times=t3,hmax=1/52)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 2.758715 secs
+Time difference of 2.690172 secs
> plot(t3,X3['I',1,],type='l')
>
> f1 <- dprocess(
@@ -529,10 +529,10 @@
+ params=as.matrix(log(params))
+ )
> print(h1[c("S","I","R"),,],digits=4)
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
-S 39607.5 39770.1 39222.4 39000 38470.0 37635 36130 34844 33808 30538
-I 243.0 246.8 415.5 519 722.8 1047 1628 2172 2649 4006
-R -39852.3 -40019.5 -39639.0 -39520 -39191.5 -38682 -37758 -37016 -36456 -34544
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
+S 39608 39770.1 39222.4 39000 38470.0 37635 36130 34844 33808 30538
+I 243 246.8 415.5 519 722.8 1047 1628 2172 2649 4006
+R -39852 -40019.5 -39639.0 -39520 -39191.5 -38682 -37758 -37016 -36456 -34544
[,11] [,12] [,13] [,14] [,15] [,16]
S 27082 20266 13528 2809 -8808 -26739.3
I 5473 8300 11076 15339 19697 25951.9
@@ -548,7 +548,7 @@
> x <- simulate(po,nsim=100)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 1.99654 secs
+Time difference of 1.987663 secs
> plot(x[[1]],variables=c("S","I","R","cases","W"))
>
> t3 <- seq(0,20,by=1/52)
@@ -556,7 +556,7 @@
> X4 <- trajectory(po,times=t3,hmax=1/52)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.1497879 secs
+Time difference of 0.1495709 secs
> plot(t3,X4['I',1,],type='l')
>
> g2 <- dmeasure(
@@ -582,10 +582,10 @@
+ params=as.matrix(c(log(params),nbasis=3,degree=3,period=1))
+ )
> print(h2[c("S","I","R"),,],digits=4)
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
-S 39607.5 39770.1 39222.4 39000 38470.0 37635 36130 34844 33808 30538
-I 243.0 246.8 415.5 519 722.8 1047 1628 2172 2649 4006
-R -39852.3 -40019.5 -39639.0 -39520 -39191.5 -38682 -37758 -37016 -36456 -34544
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
+S 39608 39770.1 39222.4 39000 38470.0 37635 36130 34844 33808 30538
+I 243 246.8 415.5 519 722.8 1047 1628 2172 2649 4006
+R -39852 -40019.5 -39639.0 -39520 -39191.5 -38682 -37758 -37016 -36456 -34544
[,11] [,12] [,13] [,14] [,15] [,16]
S 27082 20266 13528 2809 -8808 -26739.3
I 5473 8300 11076 15339 19697 25951.9
Modified: pkg/tests/skeleton.Rout.save
===================================================================
--- pkg/tests/skeleton.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/skeleton.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -109,9 +109,9 @@
, , 3
- [,1]
-N 0.0001788570
-e 0.0000000000
+ [,1]
+N 0.000178857
+e 0.000000000
, , 4
@@ -211,9 +211,9 @@
, , 20
- [,1]
-N 0.0001788570
-e 0.0000000000
+ [,1]
+N 0.000178857
+e 0.000000000
, , 21
@@ -313,9 +313,9 @@
, , 37
- [,1]
-N 0.0001788570
-e 0.0000000000
+ [,1]
+N 0.000178857
+e 0.000000000
, , 38
Modified: pkg/tests/synlik.Rout.save
===================================================================
--- pkg/tests/synlik.Rout.save 2011-07-11 11:35:37 UTC (rev 525)
+++ pkg/tests/synlik.Rout.save 2011-07-24 00:11:13 UTC (rev 526)
@@ -1,5 +1,5 @@
-R version 2.12.2 (2011-02-25)
+R version 2.13.1 (2011-07-08)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
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