[Pomp-commits] r832 - in pkg/pomp: inst/examples tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 10 21:58:03 CET 2013
Author: kingaa
Date: 2013-03-10 21:58:03 +0100 (Sun, 10 Mar 2013)
New Revision: 832
Modified:
pkg/pomp/inst/examples/bbs.R
pkg/pomp/inst/examples/blowflies.R
pkg/pomp/inst/examples/euler.sir.R
pkg/pomp/inst/examples/gillespie.sir.R
pkg/pomp/inst/examples/gompertz.R
pkg/pomp/inst/examples/ou2.R
pkg/pomp/inst/examples/ricker.R
pkg/pomp/inst/examples/rw2.R
pkg/pomp/inst/examples/verhulst.R
pkg/pomp/tests/filtfail.R
pkg/pomp/tests/filtfail.Rout.save
Log:
- largely cosmetic streamlining
Modified: pkg/pomp/inst/examples/bbs.R
===================================================================
--- pkg/pomp/inst/examples/bbs.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/inst/examples/bbs.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -1,6 +1,6 @@
require(pomp)
-tc <- textConnection("
+flu <- read.csv2(text="
day;reports
1;3
2;8
@@ -18,9 +18,6 @@
14;5
")
-flu <- read.csv2(file=tc)
-close(tc)
-
po <- pomp(
data=flu,
times="day",
Modified: pkg/pomp/inst/examples/blowflies.R
===================================================================
--- pkg/pomp/inst/examples/blowflies.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/inst/examples/blowflies.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -868,14 +868,13 @@
718;8103;4
720;6803;4
'
-
raw.data <- subset(
- read.csv2(textConnection(blowfly.data),comment.char="#"),
- set==4
+ read.csv2(text=blowfly.data,comment.char="#"),
+ set==4,
+ select=-set
)
-
pomp(
- data=subset(raw.data[c("day","y")],day>14&day<400),
+ data=subset(raw.data,day>14&day<400),
times="day",
t0=14,
rprocess=discrete.time.sim(
Modified: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/inst/examples/euler.sir.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -213,7 +213,7 @@
po <- pomp(
- data=read.csv2(textConnection(dat)),
+ data=read.csv2(text=dat),
times="time",
t0=0,
params=c(
Modified: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/inst/examples/gillespie.sir.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -525,7 +525,7 @@
'
pomp(
- data=read.csv2(textConnection(dat)),
+ data=read.csv2(text=dat),
times="time",
t0=0,
params=c(
Modified: pkg/pomp/inst/examples/gompertz.R
===================================================================
--- pkg/pomp/inst/examples/gompertz.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/inst/examples/gompertz.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -105,7 +105,7 @@
'
po <- pomp(
- data=read.csv2(textConnection(dat)),
+ data=read.csv2(text=dat),
times="time",
t0=0,
params=c(K=1,r=0.1,sigma=0.1,tau=0.1,X.0=1),
Modified: pkg/pomp/inst/examples/ou2.R
===================================================================
--- pkg/pomp/inst/examples/ou2.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/inst/examples/ou2.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -104,7 +104,7 @@
'
pomp(
- data=read.csv2(textConnection(dat)),
+ data=read.csv2(text=dat),
times="time",
t0=0,
rprocess=discrete.time.sim("ou2_step",PACKAGE="pomp"),
Modified: pkg/pomp/inst/examples/ricker.R
===================================================================
--- pkg/pomp/inst/examples/ricker.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/inst/examples/ricker.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -55,7 +55,7 @@
'
pomp(
- data=read.csv2(textConnection(dat)),
+ data=read.csv2(text=dat),
times="time",
t0=0,
params=c(r=exp(3.8),sigma=0.3,phi=10,N.0=7,e.0=0), # originally used to generate the data
Modified: pkg/pomp/inst/examples/rw2.R
===================================================================
--- pkg/pomp/inst/examples/rw2.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/inst/examples/rw2.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -104,7 +104,7 @@
'
pomp(
- data=read.csv2(textConnection(dat)),
+ data=read.csv2(text=dat),
times="time",
t0=0,
params=c(x1.0=0,x2.0=0,s1=1,s2=3,tau=1), # parameters at which data were generated
Modified: pkg/pomp/inst/examples/verhulst.R
===================================================================
--- pkg/pomp/inst/examples/verhulst.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/inst/examples/verhulst.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -1004,7 +1004,7 @@
'
pomp(
- data=read.csv2(textConnection(dat)),
+ data=read.csv2(text=dat),
times="time",
t0=0,
params=c(n.0=10000,K=10000,r=0.9,sigma=0.4,tau=0.1),
Modified: pkg/pomp/tests/filtfail.R
===================================================================
--- pkg/pomp/tests/filtfail.R 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/tests/filtfail.R 2013-03-10 20:58:03 UTC (rev 832)
@@ -5,7 +5,8 @@
### the following example tests to make sure that states are updated properly
### upon filtering failures
-"time,admissions,discharges,patients,cases
+records <- read.csv(text="
+time,admissions,discharges,patients,cases
0,4,2,8,
1,0,1,10,2
2,2,0,9,1
@@ -27,12 +28,8 @@
18,4,0,7,1
19,0,0,11,0
20,1,4,11,
-" -> csvtext
+")
-tc <- textConnection(csvtext)
-records <- read.csv(tc)
-close(tc)
-
po <- pomp(
data=subset(records[c("time","cases")],!is.na(cases)),
times="time",
Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save 2013-03-10 20:49:19 UTC (rev 831)
+++ pkg/pomp/tests/filtfail.Rout.save 2013-03-10 20:58:03 UTC (rev 832)
@@ -1,6 +1,6 @@
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
+R version 2.15.3 (2013-03-01) -- "Security Blanket"
+Copyright (C) 2013 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -26,7 +26,8 @@
> ### the following example tests to make sure that states are updated properly
> ### upon filtering failures
>
-> "time,admissions,discharges,patients,cases
+> records <- read.csv(text="
++ time,admissions,discharges,patients,cases
+ 0,4,2,8,
+ 1,0,1,10,2
+ 2,2,0,9,1
@@ -48,12 +49,8 @@
+ 18,4,0,7,1
+ 19,0,0,11,0
+ 20,1,4,11,
-+ " -> csvtext
++ ")
>
-> tc <- textConnection(csvtext)
-> records <- read.csv(tc)
-> close(tc)
->
> po <- pomp(
+ data=subset(records[c("time","cases")],!is.na(cases)),
+ times="time",
@@ -121,4 +118,4 @@
>
> proc.time()
user system elapsed
- 0.456 0.052 0.526
+ 0.464 0.044 0.524
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