[Pomp-commits] r804 - pkg/pomp/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 9 23:58:24 CET 2013
Author: kingaa
Date: 2013-01-09 23:58:23 +0100 (Wed, 09 Jan 2013)
New Revision: 804
Modified:
pkg/pomp/tests/bbs-trajmatch.R
pkg/pomp/tests/bbs-trajmatch.Rout.save
pkg/pomp/tests/bbs.R
pkg/pomp/tests/bbs.Rout.save
pkg/pomp/tests/blowflies.R
pkg/pomp/tests/blowflies.Rout.save
pkg/pomp/tests/dacca.R
pkg/pomp/tests/dacca.Rout.save
pkg/pomp/tests/dimchecks.R
pkg/pomp/tests/dimchecks.Rout.save
pkg/pomp/tests/gillespie.R
pkg/pomp/tests/gillespie.Rout.save
pkg/pomp/tests/gompertz.R
pkg/pomp/tests/gompertz.Rout.save
pkg/pomp/tests/ou2-bsmc.R
pkg/pomp/tests/ou2-bsmc.Rout.save
pkg/pomp/tests/ou2-forecast.R
pkg/pomp/tests/ou2-forecast.Rout.save
pkg/pomp/tests/ou2-icfit.R
pkg/pomp/tests/ou2-icfit.Rout.save
pkg/pomp/tests/ou2-kalman.R
pkg/pomp/tests/ou2-kalman.Rout.save
pkg/pomp/tests/ou2-mif-fp.R
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-nlf.R
pkg/pomp/tests/ou2-nlf.Rout.save
pkg/pomp/tests/ou2-pmcmc.R
pkg/pomp/tests/ou2-pmcmc.Rout.save
pkg/pomp/tests/ou2-probe.R
pkg/pomp/tests/ou2-probe.Rout.save
pkg/pomp/tests/ou2-procmeas.R
pkg/pomp/tests/ou2-procmeas.Rout.save
pkg/pomp/tests/ou2-simulate.R
pkg/pomp/tests/ou2-simulate.Rout.save
pkg/pomp/tests/ou2-trajmatch.R
pkg/pomp/tests/ou2-trajmatch.Rout.save
pkg/pomp/tests/partrans.R
pkg/pomp/tests/partrans.Rout.save
pkg/pomp/tests/pfilter.R
pkg/pomp/tests/pfilter.Rout.save
pkg/pomp/tests/pomppomp.R
pkg/pomp/tests/pomppomp.Rout.save
pkg/pomp/tests/ricker-bsmc.R
pkg/pomp/tests/ricker-bsmc.Rout.save
pkg/pomp/tests/ricker-probe.R
pkg/pomp/tests/ricker-probe.Rout.save
pkg/pomp/tests/ricker-spect.R
pkg/pomp/tests/ricker-spect.Rout.save
pkg/pomp/tests/ricker.R
pkg/pomp/tests/ricker.Rout.save
pkg/pomp/tests/rw2.R
pkg/pomp/tests/rw2.Rout.save
pkg/pomp/tests/sir.R
pkg/pomp/tests/sir.Rout.save
pkg/pomp/tests/skeleton.R
pkg/pomp/tests/skeleton.Rout.save
pkg/pomp/tests/steps.R
pkg/pomp/tests/steps.Rout.save
pkg/pomp/tests/synlik.R
pkg/pomp/tests/synlik.Rout.save
pkg/pomp/tests/verhulst.R
pkg/pomp/tests/verhulst.Rout.save
Log:
- improved 'pompExample'
Modified: pkg/pomp/tests/bbs-trajmatch.R
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/bbs-trajmatch.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("bbs")
+pompExample(bbs)
guess <- c(
mu=0,gamma=1/3,beta=1,beta.sd=0,iota=0,
Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("bbs")
+> pompExample(bbs)
newly created pomp objects:
bbs
>
Modified: pkg/pomp/tests/bbs.R
===================================================================
--- pkg/pomp/tests/bbs.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/bbs.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("bbs")
+pompExample(bbs)
set.seed(48857734L)
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/bbs.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("bbs")
+> pompExample(bbs)
newly created pomp objects:
bbs
>
Modified: pkg/pomp/tests/blowflies.R
===================================================================
--- pkg/pomp/tests/blowflies.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/blowflies.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("blowflies")
+pompExample(blowflies)
init.state(blowflies1)
x1 <- simulate(blowflies1)
Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/blowflies.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("blowflies")
+> pompExample(blowflies)
newly created pomp objects:
blowflies1 blowflies2
>
Modified: pkg/pomp/tests/dacca.R
===================================================================
--- pkg/pomp/tests/dacca.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/dacca.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -2,7 +2,7 @@
set.seed(1420306530L)
-pompExample("dacca")
+pompExample(dacca)
x <- as.data.frame(dacca)
print(names(x))
Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/dacca.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -23,7 +23,7 @@
>
> set.seed(1420306530L)
>
-> pompExample("dacca")
+> pompExample(dacca)
newly created pomp objects:
dacca
>
Modified: pkg/pomp/tests/dimchecks.R
===================================================================
--- pkg/pomp/tests/dimchecks.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/dimchecks.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -2,7 +2,7 @@
set.seed(1420306530L)
-pompExample("ricker")
+pompExample(ricker)
po <- ricker
pars <- coef(po)
@@ -49,7 +49,7 @@
stopifnot(identical(g1,g3[,1:3,]))
stopifnot(identical(g1,g3[,4:6,]))
-pompExample("gompertz")
+pompExample(gompertz)
p <- parmat(coef(gompertz),5)
f1 <- partrans(gompertz,p,"inv")
f2 <- parmat(coef(gompertz,transform=TRUE),5)
Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/dimchecks.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -23,7 +23,7 @@
>
> set.seed(1420306530L)
>
-> pompExample("ricker")
+> pompExample(ricker)
newly created pomp objects:
ricker
> po <- ricker
@@ -153,7 +153,7 @@
> stopifnot(identical(g1,g3[,1:3,]))
> stopifnot(identical(g1,g3[,4:6,]))
>
-> pompExample("gompertz")
+> pompExample(gompertz)
newly created pomp objects:
gompertz
> p <- parmat(coef(gompertz),5)
Modified: pkg/pomp/tests/gillespie.R
===================================================================
--- pkg/pomp/tests/gillespie.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/gillespie.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -83,6 +83,6 @@
tail(as(gsir,"data.frame"))
-pompExample("gillespie.sir")
+pompExample(gillespie.sir)
tail(as.data.frame(simulate(gillespie.sir,times=time(gsir),t0=timezero(gsir),seed=1165270654L)))
Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/gillespie.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -118,7 +118,7 @@
104 0.1970810
105 0.1666667
>
-> pompExample("gillespie.sir")
+> pompExample(gillespie.sir)
newly created pomp objects:
gillespie.sir
>
Modified: pkg/pomp/tests/gompertz.R
===================================================================
--- pkg/pomp/tests/gompertz.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/gompertz.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,7 +1,7 @@
library(pomp)
options(digits=4)
-pompExample("gompertz")
+pompExample(gompertz)
po <- gompertz
coef(po)
Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/gompertz.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -22,7 +22,7 @@
Loading required package: deSolve
> options(digits=4)
>
-> pompExample("gompertz")
+> pompExample(gompertz)
newly created pomp objects:
gompertz
>
Modified: pkg/pomp/tests/ou2-bsmc.R
===================================================================
--- pkg/pomp/tests/ou2-bsmc.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-bsmc.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,7 +1,7 @@
library(pomp)
set.seed(398585L)
-pompExample("ou2")
+pompExample(ou2)
time(ou2) <- 1:10
Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -22,7 +22,7 @@
Loading required package: deSolve
>
> set.seed(398585L)
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/ou2-forecast.R
===================================================================
--- pkg/pomp/tests/ou2-forecast.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-forecast.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -2,7 +2,7 @@
set.seed(921625222L)
-pompExample("ou2")
+pompExample(ou2)
tm <- time(ou2)
y <- obs(ou2)
theta <- coef(ou2)
Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-forecast.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -23,7 +23,7 @@
>
> set.seed(921625222L)
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
> tm <- time(ou2)
Modified: pkg/pomp/tests/ou2-icfit.R
===================================================================
--- pkg/pomp/tests/ou2-icfit.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-icfit.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -2,7 +2,7 @@
set.seed(921625222L)
-pompExample("ou2")
+pompExample(ou2)
ics <- c("x1.0","x2.0") # names of the initial condition parameters
Modified: pkg/pomp/tests/ou2-icfit.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-icfit.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-icfit.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -23,7 +23,7 @@
>
> set.seed(921625222L)
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/ou2-kalman.R
===================================================================
--- pkg/pomp/tests/ou2-kalman.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-kalman.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -48,7 +48,7 @@
-kalman.filter(y,x0,a,b,sigma,tau)$loglik
}
-pompExample("ou2")
+pompExample(ou2)
# true coefficients
p.truth <- coef(ou2)
Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-kalman.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -69,7 +69,7 @@
+ -kalman.filter(y,x0,a,b,sigma,tau)$loglik
+ }
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/ou2-mif-fp.R
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-mif-fp.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ou2")
+pompExample(ou2)
set.seed(64857673L)
Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/ou2-mif.R
===================================================================
--- pkg/pomp/tests/ou2-mif.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-mif.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ou2")
+pompExample(ou2)
set.seed(64857673L)
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/ou2-nlf.R
===================================================================
--- pkg/pomp/tests/ou2-nlf.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-nlf.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -2,7 +2,7 @@
set.seed(594861940L)
-pompExample("ou2")
+pompExample(ou2)
estnames=c("alpha.2","alpha.3","tau")
theta.truth <- coef(ou2)
theta.guess <- theta.truth
Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-nlf.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -23,7 +23,7 @@
>
> set.seed(594861940L)
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
> estnames=c("alpha.2","alpha.3","tau")
Modified: pkg/pomp/tests/ou2-pmcmc.R
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-pmcmc.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ou2")
+pompExample(ou2)
dprior.ou2 <- function (params, hyperparams, ..., log) {
f <- sum(dunif(params,min=hyperparams$min,max=hyperparams$max,log=TRUE))
Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/ou2-probe.R
===================================================================
--- pkg/pomp/tests/ou2-probe.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-probe.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,7 +1,7 @@
library(pomp)
set.seed(1066L)
-pompExample("ou2")
+pompExample(ou2)
pm.ou2 <- probe(
ou2,
Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-probe.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -22,7 +22,7 @@
Loading required package: deSolve
> set.seed(1066L)
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/ou2-procmeas.R
===================================================================
--- pkg/pomp/tests/ou2-procmeas.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-procmeas.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ou2")
+pompExample(ou2)
po <- window(ou2,end=10)
Modified: pkg/pomp/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-procmeas.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-procmeas.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/ou2-simulate.R
===================================================================
--- pkg/pomp/tests/ou2-simulate.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-simulate.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ou2")
+pompExample(ou2)
## fix some parameters
p <- c(
Modified: pkg/pomp/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-simulate.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-simulate.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/ou2-trajmatch.R
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-trajmatch.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -2,7 +2,7 @@
set.seed(93885485L)
-pompExample("ou2")
+pompExample(ou2)
true.p <- coef(ou2)
simdata <- simulate(ou2,nsim=5,params=true.p,seed=394885)
guess.p <- true.p
@@ -48,7 +48,7 @@
print(fit)
stopifnot(fit$convergence==0)
-pompExample("ou2")
+pompExample(ou2)
p <- coef(ou2)
ou2 at params <- numeric(0)
res <- traj.match(
Modified: pkg/pomp/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ou2-trajmatch.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -23,7 +23,7 @@
>
> set.seed(93885485L)
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
> true.p <- coef(ou2)
@@ -156,7 +156,7 @@
> stopifnot(fit$convergence==0)
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
> p <- coef(ou2)
Modified: pkg/pomp/tests/partrans.R
===================================================================
--- pkg/pomp/tests/partrans.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/partrans.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("gompertz")
+pompExample(gompertz)
pars <- coef(gompertz)
Modified: pkg/pomp/tests/partrans.Rout.save
===================================================================
--- pkg/pomp/tests/partrans.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/partrans.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("gompertz")
+> pompExample(gompertz)
newly created pomp objects:
gompertz
>
Modified: pkg/pomp/tests/pfilter.R
===================================================================
--- pkg/pomp/tests/pfilter.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/pfilter.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ou2")
+pompExample(ou2)
set.seed(9994847L)
@@ -15,7 +15,7 @@
ll.se <- sd(exp(pf.ll-mean(pf.ll)))/exp(ll.est-mean(pf.ll))/sqrt(length(pf))
print(round(c(loglik=ll.est,loglik.se=ll.se),digits=2))
-pompExample("euler.sir")
+pompExample(euler.sir)
pf <- pfilter(euler.sir,Np=100,seed=394343L)
print(coef(pf))
print(pf$loglik,digits=4)
Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/pfilter.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
@@ -44,7 +44,7 @@
loglik loglik.se
-479.61 0.46
>
-> pompExample("euler.sir")
+> pompExample(euler.sir)
newly created pomp objects:
euler.sir
> pf <- pfilter(euler.sir,Np=100,seed=394343L)
Modified: pkg/pomp/tests/pomppomp.R
===================================================================
--- pkg/pomp/tests/pomppomp.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/pomppomp.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ricker")
+pompExample(ricker)
y1 <- obs(simulate(ricker,seed=1066L))
r2 <- pomp(ricker,measurement.model=y~pois(lambda=N*phi))
coef(r2) <- coef(ricker)
Modified: pkg/pomp/tests/pomppomp.Rout.save
===================================================================
--- pkg/pomp/tests/pomppomp.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/pomppomp.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ricker")
+> pompExample(ricker)
newly created pomp objects:
ricker
> y1 <- obs(simulate(ricker,seed=1066L))
Modified: pkg/pomp/tests/ricker-bsmc.R
===================================================================
--- pkg/pomp/tests/ricker-bsmc.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ricker-bsmc.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ricker")
+pompExample(ricker)
pdf(file="ricker-bsmc.pdf")
Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ricker")
+> pompExample(ricker)
newly created pomp objects:
ricker
>
Modified: pkg/pomp/tests/ricker-probe.R
===================================================================
--- pkg/pomp/tests/ricker-probe.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ricker-probe.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ricker")
+pompExample(ricker)
pdf(file="ricker-probe.pdf")
Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ricker-probe.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ricker")
+> pompExample(ricker)
newly created pomp objects:
ricker
>
Modified: pkg/pomp/tests/ricker-spect.R
===================================================================
--- pkg/pomp/tests/ricker-spect.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ricker-spect.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -2,7 +2,7 @@
pdf(file="ricker-spect.pdf")
-pompExample("ricker")
+pompExample(ricker)
set.seed(6457673L)
Modified: pkg/pomp/tests/ricker-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-spect.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ricker-spect.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -23,7 +23,7 @@
>
> pdf(file="ricker-spect.pdf")
>
-> pompExample("ricker")
+> pompExample(ricker)
newly created pomp objects:
ricker
>
Modified: pkg/pomp/tests/ricker.R
===================================================================
--- pkg/pomp/tests/ricker.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ricker.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ricker")
+pompExample(ricker)
pdf(file="ricker.pdf")
Modified: pkg/pomp/tests/ricker.Rout.save
===================================================================
--- pkg/pomp/tests/ricker.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/ricker.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ricker")
+> pompExample(ricker)
newly created pomp objects:
ricker
>
Modified: pkg/pomp/tests/rw2.R
===================================================================
--- pkg/pomp/tests/rw2.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/rw2.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -168,7 +168,7 @@
stopifnot(max(abs(d1-d2),na.rm=T)<.Machine$double.eps*100)
stopifnot(max(abs(e1-e2),na.rm=T)<.Machine$double.eps*100)
-pompExample("rw2")
+pompExample(rw2)
a3 <- dmeasure(po,y=y[,1,1:4],x=x[,,1:4,drop=F],times=time(rw2)[1:4],p)
b3 <- dmeasure(po,y=y[,2,1:4],x=x[,,1:4,drop=F],times=time(rw2)[1:4],p)
Modified: pkg/pomp/tests/rw2.Rout.save
===================================================================
--- pkg/pomp/tests/rw2.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/rw2.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -375,7 +375,7 @@
> stopifnot(max(abs(d1-d2),na.rm=T)<.Machine$double.eps*100)
> stopifnot(max(abs(e1-e2),na.rm=T)<.Machine$double.eps*100)
>
-> pompExample("rw2")
+> pompExample(rw2)
newly created pomp objects:
rw2
>
Modified: pkg/pomp/tests/sir.R
===================================================================
--- pkg/pomp/tests/sir.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/sir.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -198,7 +198,7 @@
print(h1[c("S","I","R"),,],digits=4)
## now repeat using the compiled native codes built into the package
-pompExample("euler.sir")
+pompExample(euler.sir)
po <- euler.sir
set.seed(3049953)
@@ -252,7 +252,7 @@
## test of vectorfield integrator
-pompExample("euler.sir")
+pompExample(euler.sir)
po <- pomp(
window(euler.sir,end=2),
Modified: pkg/pomp/tests/sir.Rout.save
===================================================================
--- pkg/pomp/tests/sir.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/sir.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -525,7 +525,7 @@
R -31549.7 -30472.3 -30226.0 -29798.8 -29007.2 -28580 -27634 -26740
>
> ## now repeat using the compiled native codes built into the package
-> pompExample("euler.sir")
+> pompExample(euler.sir)
newly created pomp objects:
euler.sir
> po <- euler.sir
@@ -595,7 +595,7 @@
>
> ## test of vectorfield integrator
>
-> pompExample("euler.sir")
+> pompExample(euler.sir)
newly created pomp objects:
euler.sir
>
Modified: pkg/pomp/tests/skeleton.R
===================================================================
--- pkg/pomp/tests/skeleton.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/skeleton.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ricker")
+pompExample(ricker)
pdf(file="skeleton.pdf")
pdf.options(useDingbats=FALSE)
@@ -20,7 +20,7 @@
## non-autonomous case
-pompExample("euler.sir")
+pompExample(euler.sir)
x <- states(euler.sir)
p <- parmat(coef(euler.sir),nrep=3)
p["beta2",2:3] <- exp(c(3,5)) ## try different values of one of the seasonality parameters
Modified: pkg/pomp/tests/skeleton.Rout.save
===================================================================
--- pkg/pomp/tests/skeleton.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/skeleton.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ricker")
+> pompExample(ricker)
newly created pomp objects:
ricker
>
@@ -43,7 +43,7 @@
>
> ## non-autonomous case
>
-> pompExample("euler.sir")
+> pompExample(euler.sir)
newly created pomp objects:
euler.sir
> x <- states(euler.sir)
Modified: pkg/pomp/tests/steps.R
===================================================================
--- pkg/pomp/tests/steps.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/steps.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -2,14 +2,14 @@
set.seed(54588699L)
-pompExample("ricker")
+pompExample(ricker)
coef(ricker,"sigma") <- 0
tm <- sort(runif(n=20,max=3))
x <- trajectory(ricker,times=tm)["N",,]
y <- simulate(ricker,times=tm,states=TRUE)["N",,]
stopifnot(identical(x,y))
-pompExample("verhulst")
+pompExample(verhulst)
coef(verhulst,c("n.0","sigma")) <- c(15,0)
tm <- sort(runif(n=100,max=1))
x <- trajectory(verhulst,times=tm)["n",,]
Modified: pkg/pomp/tests/steps.Rout.save
===================================================================
--- pkg/pomp/tests/steps.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/steps.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -23,7 +23,7 @@
>
> set.seed(54588699L)
>
-> pompExample("ricker")
+> pompExample(ricker)
newly created pomp objects:
ricker
> coef(ricker,"sigma") <- 0
@@ -32,7 +32,7 @@
> y <- simulate(ricker,times=tm,states=TRUE)["N",,]
> stopifnot(identical(x,y))
>
-> pompExample("verhulst")
+> pompExample(verhulst)
newly created pomp objects:
verhulst
> coef(verhulst,c("n.0","sigma")) <- c(15,0)
Modified: pkg/pomp/tests/synlik.R
===================================================================
--- pkg/pomp/tests/synlik.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/synlik.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("ou2")
+pompExample(ou2)
set.seed(6457673L)
Modified: pkg/pomp/tests/synlik.Rout.save
===================================================================
--- pkg/pomp/tests/synlik.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/synlik.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("ou2")
+> pompExample(ou2)
newly created pomp objects:
ou2
>
Modified: pkg/pomp/tests/verhulst.R
===================================================================
--- pkg/pomp/tests/verhulst.R 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/verhulst.R 2013-01-09 22:58:23 UTC (rev 804)
@@ -1,6 +1,6 @@
library(pomp)
-pompExample("verhulst")
+pompExample(verhulst)
tail(as(verhulst,"data.frame"))
tail(as.data.frame(verhulst))
Modified: pkg/pomp/tests/verhulst.Rout.save
===================================================================
--- pkg/pomp/tests/verhulst.Rout.save 2013-01-09 22:56:49 UTC (rev 803)
+++ pkg/pomp/tests/verhulst.Rout.save 2013-01-09 22:58:23 UTC (rev 804)
@@ -21,7 +21,7 @@
Loading required package: subplex
Loading required package: deSolve
>
-> pompExample("verhulst")
+> pompExample(verhulst)
newly created pomp objects:
verhulst
>
More information about the pomp-commits
mailing list