[Pomp-commits] r819 - in pkg/pomp: inst/examples tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 16 12:51:11 CET 2013
Author: kingaa
Date: 2013-01-16 12:51:10 +0100 (Wed, 16 Jan 2013)
New Revision: 819
Modified:
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.Rout.save
pkg/pomp/tests/gompertz.Rout.save
pkg/pomp/tests/ou2-mif.Rout.save
pkg/pomp/tests/skeleton.R
pkg/pomp/tests/skeleton.Rout.save
pkg/pomp/tests/verhulst.Rout.save
Log:
- the 'pompExample' examples no longer simulate data at run time
- update the tests
Modified: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R 2013-01-16 11:50:16 UTC (rev 818)
+++ pkg/pomp/inst/examples/euler.sir.R 2013-01-16 11:51:10 UTC (rev 819)
@@ -1,12 +1,229 @@
require(pomp)
+dat <- '"time";"reports"
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+'
+
+
po <- pomp(
- data=data.frame(
- time=seq(from=1/52,to=4,by=1/52),
- reports=NA
- ),
+ data=read.csv2(textConnection(dat)),
times="time",
t0=0,
+ params=c(
+ gamma=26,mu=0.02,iota=0.01,
+ beta1=400,beta2=480,beta3=320,
+ beta.sd=1e-3,
+ pop=2.1e6,
+ rho=0.6,
+ S.0=26/400,I.0=0.001,R.0=1-26/400
+ ),
rprocess=euler.sim(
step.fun="_sir_euler_simulator",
delta.t=1/52/20,
@@ -42,16 +259,8 @@
}
)
-coef(po) <- c(
- gamma=26,mu=0.02,iota=0.01,
- beta1=400,beta2=480,beta3=320,
- beta.sd=1e-3,
- pop=2.1e6,
- rho=0.6,
- S.0=26/400,I.0=0.001,R.0=1-26/400
- )
+## the following was originally used to generate the data
+## simulate(po,nsim=1,seed=329343545L) -> euler.sir
-simulate(po,nsim=1,seed=329343545L) -> euler.sir
-
-assign("euler.sir",euler.sir,envir=.GlobalEnv)
+assign("euler.sir",po,envir=.GlobalEnv)
c("euler.sir")
Modified: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R 2013-01-16 11:50:16 UTC (rev 818)
+++ pkg/pomp/inst/examples/gillespie.sir.R 2013-01-16 11:51:10 UTC (rev 819)
@@ -1,75 +1,592 @@
require(pomp)
-po <- pomp(
- data=data.frame(
- time=seq(from=0,to=10,by=1/52),
- reports=NA
- ),
- times="time",
- t0=0,
- rprocess=gillespie.sim(
- rate.fun="_sir_rates",
- PACKAGE="pomp",
- v=cbind(
- birth=c(1,0,0,1,0),
- sdeath=c(-1,0,0,-1,0),
- infection=c(-1,1,0,0,0),
- ideath=c(0,-1,0,-1,0),
- recovery=c(0,-1,1,0,1),
- rdeath=c(0,0,-1,-1,0)
- ),
- d=cbind(
- birth=c(0,0,0,1,0),
- sdeath=c(1,0,0,0,0),
- infection=c(1,1,0,1,0),
- ideath=c(0,1,0,0,0),
- recovery=c(0,1,0,0,0),
- rdeath=c(0,0,1,0,0)
- )
- ),
- skeleton.type="vectorfield",
- skeleton="_sir_ODE",
- measurement.model=reports~binom(size=cases,prob=rho),
- PACKAGE="pomp",
- obsnames = c("reports"),
- statenames=c("S","I","R","N","cases"),
- paramnames=c(
- "gamma","mu","iota",
- "beta1","beta.sd","pop","rho",
- "S.0","I.0","R.0"
- ),
- zeronames=c("cases"),
- comp.names=c("S","I","R"),
- ic.names=c("S.0","I.0","R.0"),
- parameter.transform="_sir_par_trans",
- parameter.inv.transform="_sir_par_untrans",
- nbasis=3L,
- degree=3L,
- period=1.0,
- initializer=function(params, t0, comp.names, ic.names, ...) {
- x0 <- numeric(5)
- names(x0) <- c("S","I","R","N","cases")
- fracs <- params[ic.names]
- x0["N"] <- params["pop"]
- x0[comp.names] <- round(params["pop"]*fracs/sum(fracs))
- x0
- }
- )
+dat <- '"time";"reports"
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+9,92307692307692;3
+9,94230769230769;2
+9,96153846153846;3
+9,98076923076923;2
+10;6
+'
-coef(po) <- c(
- gamma=24,mu=1/70,iota=0.1,
- beta1=330,beta2=410,beta3=490,
- rho=0.1,
- S.0=0.05,I.0=1e-4,R.0=0.95,
- pop=1000000,
- beta.sd=0
- )
+pomp(
+ data=read.csv2(textConnection(dat)),
+ times="time",
+ t0=0,
+ params=c(
+ gamma=24,mu=1/70,iota=0.1,
+ beta1=330,beta2=410,beta3=490,
+ rho=0.1,
+ S.0=0.05,I.0=1e-4,R.0=0.95,
+ pop=1000000,
+ beta.sd=0
+ ),
+ rprocess=gillespie.sim(
+ rate.fun="_sir_rates",
+ PACKAGE="pomp",
+ v=cbind(
+ birth=c(1,0,0,1,0),
+ sdeath=c(-1,0,0,-1,0),
+ infection=c(-1,1,0,0,0),
+ ideath=c(0,-1,0,-1,0),
+ recovery=c(0,-1,1,0,1),
+ rdeath=c(0,0,-1,-1,0)
+ ),
+ d=cbind(
+ birth=c(0,0,0,1,0),
+ sdeath=c(1,0,0,0,0),
+ infection=c(1,1,0,1,0),
+ ideath=c(0,1,0,0,0),
+ recovery=c(0,1,0,0,0),
+ rdeath=c(0,0,1,0,0)
+ )
+ ),
+ skeleton.type="vectorfield",
+ skeleton="_sir_ODE",
+ measurement.model=reports~binom(size=cases,prob=rho),
+ PACKAGE="pomp",
+ obsnames = c("reports"),
+ statenames=c("S","I","R","N","cases"),
+ paramnames=c(
+ "gamma","mu","iota",
+ "beta1","beta.sd","pop","rho",
+ "S.0","I.0","R.0"
+ ),
+ zeronames=c("cases"),
+ comp.names=c("S","I","R"),
+ ic.names=c("S.0","I.0","R.0"),
+ parameter.transform="_sir_par_trans",
+ parameter.inv.transform="_sir_par_untrans",
+ nbasis=3L,
+ degree=3L,
+ period=1.0,
+ initializer=function(params, t0, comp.names, ic.names, ...) {
+ x0 <- numeric(5)
+ names(x0) <- c("S","I","R","N","cases")
+ fracs <- params[ic.names]
+ x0["N"] <- params["pop"]
+ x0[comp.names] <- round(params["pop"]*fracs/sum(fracs))
+ x0
+ }
+ ) -> po
-simulate(
- po,
- nsim=1,
- seed=1165270654L
- ) -> gillespie.sir
+## originally, the data were created via:
+## simulate(po,nsim=1,seed=1165270654L) -> gillespie.sir
-assign("gillespie.sir",gillespie.sir,envir=.GlobalEnv)
+assign("gillespie.sir",po,envir=.GlobalEnv)
c("gillespie.sir")
Modified: pkg/pomp/inst/examples/gompertz.R
===================================================================
--- pkg/pomp/inst/examples/gompertz.R 2013-01-16 11:50:16 UTC (rev 818)
+++ pkg/pomp/inst/examples/gompertz.R 2013-01-16 11:51:10 UTC (rev 819)
@@ -1,9 +1,114 @@
require(pomp)
+dat <- '"time";"X";"Y"
+0;1;1,07952841598157
+1;0,950636618475229;1,11861594539405
+2;0,83244916029991;0,828286900987495
+3;0,93103099656842;1,13600466557311
+4;0,911439385512777;0,806676551188204
+5;0,837105441016674;0,873084434929483
+6;1,00268501398128;1,04124835021771
+7;1,06579807727341;1,05979968381669
+8;1,04671681272393;1,14368595456944
+9;1,01143788899437;1,17581280964431
+10;1,12153364435953;1,16125775736251
+11;1,23274218227861;1,22891596556583
+12;1,32655395564463;1,38234823254117
+13;1,35069512981151;1,13856582462482
+14;1,13875163542966;1,10278598215362
+15;1,26066897039704;1,29730413792106
+16;1,24543791707035;1,33112792763266
+17;1,23134905281316;1,20013316479374
+18;1,15533668996193;1,1748481850297
+19;1,19423810951996;1,37677723538777
+20;1,20635310746995;1,30467220974374
+21;1,04307227953634;0,933048055379677
+22;1,04107912990884;1,08563062740614
+23;1,00318246871677;1,02180297594675
+24;0,970849938478495;1,25099936514459
+25;0,79243164319502;0,79761814762639
+26;0,771762127953167;0,68253288426557
+27;0,760988977405389;0,785573183621746
+28;0,836517935205031;0,880032437134315
+29;0,7939171601806;0,817662333089958
+30;0,723293224297652;0,682204778379272
+31;0,775999242794153;0,609158268599648
+32;0,801813842772822;0,953075868457542
+33;0,76994574267228;0,64000611215012
+34;0,746021978630474;0,824778708853423
+35;0,81336335287903;0,75477831785326
+36;0,923882876057083;1,05020086682025
+37;1,02216853265321;1,07915643829565
+38;0,953397077328701;0,910377207219948
+39;1,01222135734455;1,07196221241156
+40;0,978288274555936;0,927402543398725
+41;1,07783628249536;1,13562270683309
+42;1,18185012207163;1,15138433126514
+43;0,952520534180798;0,979766621130238
+44;0,84439364958955;0,932583376950161
+45;0,85025855989352;0,874190322172554
+46;0,868591242831582;0,917317195376153
+47;0,96734181848679;0,810217908784557
+48;0,90424208054782;0,91751282983596
+49;0,77998160754507;0,777229472252738
+50;0,807245881695201;0,984536558782125
+51;0,796994124555762;0,829289645018853
+52;0,811536735801658;0,738549113698673
+53;0,817376297833073;0,751664773418347
+54;0,911274275731693;0,901320737117393
+55;1,09671858179842;1,02114400728858
+56;1,17782304259497;1,15480952716325
+57;1,48974254173377;1,52171146422867
+58;1,59363218853134;1,60303998339523
+59;1,33894250041079;1,3673888909755
+60;1,24282152770653;1,07557075960246
+61;1,21473587944885;1,26679772028961
+62;1,31898738946143;1,22392737161959
+63;1,45195233453426;1,40639369164472
+64;1,58364437767931;1,61885414154031
+65;1,60727226980948;1,70623639556045
+66;1,55648312498095;1,87962959035064
+67;1,66568956879442;1,73633383185204
+68;1,71151559987914;1,59157235244771
+69;1,53634236355877;1,58129601393277
+70;1,62285253887348;1,66169160756609
+71;1,27898023105463;1,35952077984963
+72;1,1818761514106;1,22549784715231
+73;1,09002630947639;1,2025122303878
+74;1,2232879353834;1,25096891846816
+75;1,43006968443063;1,41018069268411
+76;1,41189860111872;1,43675715990225
+77;1,55201995283258;1,44229999201853
+78;1,45818570565819;1,38883706742128
+79;1,22002519977696;1,25058856058262
+80;1,23865238275549;1,23288019435894
+81;1,48621496132753;1,58848483557968
+82;1,36483886467245;1,23628960315986
+83;1,51299070383272;1,60393599831722
+84;1,25759262244331;1,1541357227336
+85;1,19746015105645;1,35609775043505
+86;1,05742547057021;0,855756862528805
+87;1,22304508672589;1,38718382523001
+88;1,25379301734834;1,24797305664899
+89;1,13949050640685;1,35307215916429
+90;0,817425730431819;0,970652163066452
+91;0,802233823759296;0,847914335870894
+92;0,857912063302802;0,897827069767532
+93;1,05787680391846;1,16338321886402
+94;1,05448994160666;1,04849780806396
+95;1,11773425002073;1,02168552045925
+96;1,03321705886828;1,23012631227719
+97;0,985172093658399;1,06931864474828
+98;0,942026595214108;1,14999282942163
+99;1,16257505590149;0,972309774206453
+100;1,28071364632546;1,23495259845453
+'
+
po <- pomp(
- data=data.frame(time=seq(0,100,by=1),Y=NA),
+ data=read.csv2(textConnection(dat)),
times="time",
t0=0,
+ params=c(K=1,r=0.1,sigma=0.1,tau=0.1,X.0=1),
rprocess=discrete.time.sim(
step.fun="_gompertz_simulator"
),
@@ -22,9 +127,8 @@
}
)
-coef(po) <- c(K=1,r=0.1,sigma=0.1,tau=0.1,X.0=1)
+## the following was used to create the data included
+## simulate(po,nsim=1,seed=299438676L) -> gompertz
-simulate(po,nsim=1,seed=299438676L) -> gompertz
-
-assign("gompertz",gompertz,envir=.GlobalEnv)
+assign("gompertz",po,envir=.GlobalEnv)
c("gompertz")
Modified: pkg/pomp/inst/examples/ou2.R
===================================================================
--- pkg/pomp/inst/examples/ou2.R 2013-01-16 11:50:16 UTC (rev 818)
+++ pkg/pomp/inst/examples/ou2.R 2013-01-16 11:51:10 UTC (rev 819)
@@ -1,40 +1,133 @@
require(pomp)
-simulate(
- pomp(
- times=seq(1,101),
- data=rbind(
- y1=rep(0,101),
- y2=rep(0,101)
- ),
- t0=1,
- rprocess=discrete.time.sim("ou2_step",PACKAGE="pomp"),
- dprocess=onestep.dens("ou2_pdf",PACKAGE="pomp"),
- dmeasure = "ou2_dmeasure",
- rmeasure = "ou2_rmeasure",
- skeleton.type="map",
- skeleton = "ou2_skel",
- PACKAGE="pomp",
- paramnames = c(
- "alpha.1","alpha.2","alpha.3","alpha.4",
- "sigma.1","sigma.2","sigma.3",
- "tau"
- ),
- statenames = c("x1","x2"),
- obsnames = c("y1","y2")
- ),
- params=c(
- alpha.1=0.8, alpha.2=-0.5, alpha.3=0.3, alpha.4=0.9,
- sigma.1=3, sigma.2=-0.5, sigma.3=2,
- tau=1,
- x1.0=-3, x2.0=4
- ),
- nsim=1,
- seed=377456545L
- ) -> ou2
+dat <- '"time";"y1";"y2"
+1;-1,70081613181228;4,24746468495763
+2;0,242170113354698;7,03941580692464
+3;3,76758938785925;2,97520908716299
+4;5,68588808149477;-1,47040054732921
+5;3,77452601600709;-4,43380857201258
+6;-3,08021312625511;-3,91887931755601
+7;-2,62344860290795;-1,03202457662666
+8;-2,86592128836057;4,35432873921529
+9;-0,57760946681527;3,39758289565346
+10;2,74097620676726;4,91071465265353
+11;-0,95441253676346;10,1937011763325
+12;-0,991464112428821;6,61823476151473
+13;3,84297778313153;7,16145392465002
+14;11,0789623105051;4,16444989466932
+15;8,59819025333584;-4,90334695500249
+16;2,19964347503517;-10,2511439107283
+17;-1,13492397511025;-10,3624312929729
+18;-2,56413579798821;-8,16885880550387
+19;-4,91536849799727;-7,2203116145846
+20;-4,33899642531645;-2,31022153289937
+21;-1,35937286561288;2,99698279033669
+22;-4,0242840268505;3,69116465405162
+23;2,9387644957218;6,15414586126603
+24;4,31828658150857;5,69290844809883
+25;3,53319543208941;3,46054629112961
+26;6,44281783433088;-4,79748856413256
+27;0,718035321052913;-7,62976005316743
+28;1,28027528075623;-6,25270934959545
+29;3,70910008919496;-9,94125507650066
+30;1,48104366840107;-10,2850854614516
+31;-0,209117126395869;-8,80046618352614
+32;-5,81639714549404;-13,2283385097361
+33;-10,0225182259708;-6,4113389217938
+34;-6,89506104214256;-0,998400718547352
+35;-6,08611873904796;1,29299352993825
+36;-7,74305796307499;5,90263448168222
+37;0,0287081408447805;5,88274335246936
+38;9,62512958922631;2,54860024892302
+39;4,61772012246597;-4,51699357410536
+40;-1,40028864684968;-3,66192759013006
+41;-6,10811040670547;-4,38003912739696
+42;-0,658058036920092;-1,7236046423518
+43;-3,49326574531689;-4,14959269754278
+44;2,54826871576915;-1,40873093710545
+45;-0,640114486048052;0,896862978414845
+46;-1,67566665036179;0,379384529694427
+47;0,488141779118929;2,07741847310818
+48;0,975197260459797;2,83822178936221
+49;-1,0207098675894;0,112186038274661
+50;0,0342598900248652;3,50605179482128
+51;-2,39842556182189;2,92854885312383
+52;5,19015239107048;-0,0089221935515531
+53;4,14310779510487;0,268899079252409
+54;2,63260618646816;1,60371893328454
+55;-1,55607266713321;-0,764379706108408
+56;-0,545766983243217;-0,837246196106889
+57;1,34912551213756;-4,15285169037281
+58;0,970330264719094;0,379978231358855
+59;-5,04652345030695;-0,444477177942712
+60;-3,97209430320528;1,10490455647656
+61;-3,20325965055922;5,69632695844117
+62;1,03436272221434;7,86129746544832
+63;0,667898750837872;10,4068175981576
+64;3,50430639591665;9,2816749036714
+65;0,925079731276049;5,05429708955105
+66;1,46558192088153;0,403851869094214
+67;2,69317536547979;-4,51756265008713
+68;-2,41608073604264;-8,3370959564069
+69;-4,53015031919341;-3,20513929382432
+70;-11,0133845324347;-1,33315487824171
+71;-10,7508370993112;5,17621264446314
+72;-10,5218612264298;8,61966772995883
+73;-8,57143649619155;11,4982952428018
+74;-3,99562214384817;12,5937325399812
+75;-2,71455145450133;15,5796601067951
+76;0,512617531996642;16,8599826830534
+77;8,77766626349685;11,8289064956647
+78;9,92868196527894;5,40891154021026
+79;4,66011726941136;1,15575075091348
+80;2,67821752937628;-0,585565498904033
+81;1,15068730079675;-5,26069159041533
+82;-2,203829735812;-7,73574749590483
+83;-1,36113119160702;-6,51696428184672
+84;-4,49088592785424;-6,88875950760792
+85;-6,95435086585582;-5,73210381080353
+86;-7,54286719246903;-2,04743677554387
+87;-7,25975156626116;-1,10509448997233
+88;-5,31555444374504;2,94363686064014
+89;1,9728018375925;4,08030586218171
+90;2,87436582964618;1,2087743319357
+91;2,96600944673318;1,85680168956727
+92;4,63179378892858;3,07085679112279
+93;5,62360583343836;-2,89483235988436
+94;1,87661311794902;-3,00789937429844
+95;-0,0144619140532691;-2,67204400181558
+96;1,94214418106964;-6,14711561527305
+97;1,98468512734267;-5,61898548532659
+98;-1,41012196458721;-11,086585198673
+99;-7,29715227580992;-4,07855448780968
+100;-4,81538906352058;-1,00365875150418
+'
-ou2 <- window(ou2,end=100)
-timezero(ou2) <- 0
+pomp(
+ data=read.csv2(textConnection(dat)),
+ times="time",
+ t0=0,
+ rprocess=discrete.time.sim("ou2_step",PACKAGE="pomp"),
+ dprocess=onestep.dens("ou2_pdf",PACKAGE="pomp"),
+ dmeasure = "ou2_dmeasure",
+ rmeasure = "ou2_rmeasure",
+ skeleton.type="map",
+ skeleton = "ou2_skel",
+ PACKAGE="pomp",
+ paramnames = c(
+ "alpha.1","alpha.2","alpha.3","alpha.4",
+ "sigma.1","sigma.2","sigma.3",
+ "tau"
+ ),
+ statenames = c("x1","x2"),
+ obsnames = c("y1","y2"),
+ params=c(
+ alpha.1=0.8, alpha.2=-0.5, alpha.3=0.3, alpha.4=0.9,
+ sigma.1=3, sigma.2=-0.5, sigma.3=2,
+ tau=1,
+ x1.0=-3, x2.0=4
+ )
+ ) -> po
-assign("ou2",ou2,envir=.GlobalEnv)
+assign("ou2",po,envir=.GlobalEnv)
c("ou2")
Modified: pkg/pomp/inst/examples/ricker.R
===================================================================
--- pkg/pomp/inst/examples/ricker.R 2013-01-16 11:50:16 UTC (rev 818)
+++ pkg/pomp/inst/examples/ricker.R 2013-01-16 11:51:10 UTC (rev 819)
@@ -1,40 +1,84 @@
require(pomp)
-simulate(
- pomp(
- data=data.frame(time=seq(0,50,by=1),y=NA),
- times="time",
- t0=0,
- rprocess=discrete.time.sim(
- step.fun="_ricker_simulator"
- ),
- rmeasure="_ricker_poisson_rmeasure",
- dmeasure="_ricker_poisson_dmeasure",
- skeleton.type="map",
- skeleton="_ricker_skeleton",
- paramnames=c("r","sigma","phi"),
- statenames=c("N","e"),
- obsnames=c("y"),
- parameter.inv.transform=function(params,...) {
- params[c("r","sigma","phi","N.0")] <- log(params[c("r","sigma","phi","N.0")])
- params
- },
- parameter.transform=function(params,...) {
- params[c("r","sigma","phi","N.0")] <- exp(params[c("r","sigma","phi","N.0")])
- params
- },
- PACKAGE="pomp"
- ),
- params=c(
- r=exp(3.8),
- sigma=0.3,
- phi=10,
- N.0=7,
- e.0=0
- ),
- nsim=1,
- seed=73691676L
- ) -> ricker
+dat <- '"time";"y"
+0;68
+1;2
+2;87
+3;0
+4;12
+5;174
+6;0
+7;0
+8;1
+9;57
+10;11
+11;178
+12;0
+13;1
+14;0
+15;34
+16;72
+17;3
+18;101
+19;0
+20;8
+21;156
+22;0
+23;0
+24;3
+25;93
+26;0
+27;17
+28;121
+29;0
+30;0
+31;19
+32;107
+33;0
+34;4
+35;127
+36;0
+37;1
+38;47
+39;8
+40;117
+41;0
+42;3
+43;82
+44;2
+45;39
+46;70
+47;11
+48;275
+49;0
+50;0
+'
-assign("ricker",ricker,envir=.GlobalEnv)
+pomp(
+ data=read.csv2(textConnection(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
+ rprocess=discrete.time.sim(
+ step.fun="_ricker_simulator"
+ ),
+ rmeasure="_ricker_poisson_rmeasure",
+ dmeasure="_ricker_poisson_dmeasure",
+ skeleton.type="map",
+ skeleton="_ricker_skeleton",
+ paramnames=c("r","sigma","phi"),
+ statenames=c("N","e"),
+ obsnames=c("y"),
+ parameter.inv.transform=function(params,...) {
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 819
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