Sorry for the late reply, maybe its is still of some help. See comments
below.
Sotiris Adamakis wrote:
Appologies for cross-posting
Dear R users,
I am using R2WinBUGS to call WinBUGS from R. After loading data, model, and
initial values I call this command
res <- bugs(data = dfile, inits = list(ifile), parameters.to.save = c("beta"),
model.file = mfile, working.directory = tdir, n.thin = nthin, n.chains = 1, n.iter =
niterations*nthin, n.burnin = 0, DIC = F, debug = T, save.history=F)
which opens WinBUGS and executes the following log file:
display(log)
check(C:/Documents and Settings/sbadamakis/Desktop/model_4/model_4.txt)
model is syntactically correct
data(C:/Documents and Settings/sbadamakis/Desktop/model_4/output1/data.txt)
data loaded
compile(1)
model compiled
inits(1,C:/Documents and Settings/sbadamakis/Desktop/model_4/output1/inits1.txt)
model is initialized
gen.inits()
command #Bugs:gen.inits cannot be executed (is greyed out)
thin.updater(1)
update(0)
set(beta)
update(20)
coda(*,C:/Documents and Settings/sbadamakis/Desktop/model_4/output1/coda)
stats(*)
Node statistics
node mean sd MC error 2.5% median 97.5% start sample
beta[1] 1.588 0.009812 0.003936 1.579 1.584 1.607 1 20
beta[2] -0.04272 0.00263 0.001137 -0.04592 -0.0433 -0.03688 1 20
beta[3] -0.07878 8.531E-4 2.829E-4 -0.07962 -0.07833 -0.07699 1 20
beta[4] -0.3035 0.01016 0.004509 -0.3194 -0.3028 -0.2841 1 20
beta[5] 1.241 0.00854 0.002739 1.228 1.242 1.258 1 20
beta[6] -4.155 0.01242 0.005405 -4.174 -4.152 -4.132 1 20
beta[7] 0.08322 0.001485 6.379E-4 0.08201 0.0824 0.08608 1 20
beta[8] -3.001 0.009335 0.003318 -3.013 -3.004 -2.981 1 20
beta[9] 0.07953 7.547E-4 3.198E-4 0.07777 0.07932 0.08035 1 20
save(C:/Documents and Settings/sbadamakis/Desktop/model_4/output1/log.odc)
save(C:/Documents and Settings/sbadamakis/Desktop/model_4/output1/log.txt)
So far so good. After the end of the last line of the log file, WinBUGS should close and
the bugs function in R should return the Markov chain values of the "beta"
parameters. The problem is that it doesn't and WinBUGS stays infinitely open. This is a
big problem as I have written a code in R and I want to call the bugs function several
times. Do you know if there's an option in the bugs function in R to FORCE WinBUGS to
close?
You can close WinBUGS and everything should be fine - or just set debug
= FALSE rather than debug = TRUE in your bugs() call.
Furthermore, some other times (the same code!!!) produces the following TRAP
message
undefined real result
GraphStack.Node.Value [00000C9AH]
.i INTEGER 6
.j INTEGER 2
.k INTEGER 1
.node GraphStack.Node [0138C5D0H]
.op INTEGER 6
.p GraphNodes.Node [01544D30H]
.top INTEGER 0
.work ARRAY 10 OF REAL
[0] REAL inf
[1] REAL inf
[2] REAL inf
[3] REAL 1.30212336033939
[4] REAL 4.534462964264759
[5] REAL 1.769649991139459E+167
[6] REAL 1.792592453177908E-307
[7] REAL 9.94060079432588E-321
[8] REAL 5.474495960374562E+67
[9] REAL 5.257527858867595E-308
MonitorsSamples.StdMonitor.Update [0000023DH]
.blocks POINTER NIL
.i INTEGER 1655837286
.index INTEGER 7
.monitor MonitorsSamples.StdMonitor [02155B50H]
.numBlocks INTEGER 0
.value REAL 1.0
SamplesMonitors.Monitor.Update [0000091BH]
.chain INTEGER 0
.i INTEGER 4480
.monitor SamplesMonitors.Monitor [01C0A4E0H]
.size INTEGER 6780
SamplesIndex.Monitor.Update [0000030CH]
.chain INTEGER 0
.cursor SamplesIndex.List [01AB2E30H]
.monitor SamplesIndex.Monitor [01C59510H]
.sampleMonitor SamplesMonitors.Monitor [01C0A4E0H]
UpdaterActions.UpdateMonitors [0000011CH]
.chain INTEGER 0
.monitor UpdaterActions.Monitor [01C59510H]
BugsCmds.Action.Step [00000BCAH]
.a BugsCmds.Action [011D40C0H]
.chain INTEGER 0
.i INTEGER 8
.j INTEGER 1000
.numChains INTEGER 1
BugsCmds.Action.Do [00000C58H]
.a BugsCmds.Action [011D40C0H]
.elapsedTime LONGINT 62EC21F162EB0384H
.profileList ARRAY 2024 OF CHAR "" ...
.res INTEGER 1635734111
.s ARRAY 120 OF CHAR 3X ...
Services.Exec [00000136H]
.a Services.Action [011D40C0H]
.t POINTER [62EB0384H]
Services.IterateOverActions [000002F4H]
.p Services.Action [011D40C0H]
.t POINTER NIL
.time LONGINT 300843187
Services.StdHook.Step [0000034DH]
.h Services.StdHook [0101E380H]
HostWindows.Idle [00004A86H]
.focus BOOLEAN FALSE
.tick Controllers.TickMsg Fields
.w HostWindows.Window NIL
HostMenus.TimerTick [00003422H]
.lParam INTEGER 0
.ops Controllers.PollOpsMsg Fields
.wParam INTEGER 1
.wnd INTEGER 1770006
Kernel.Try [00003A61H]
.a INTEGER 1770006
.b INTEGER 1
.c INTEGER 0
.h PROCEDURE HostMenus.TimerTick
HostMenus.ApplWinHandler [00003841H]
.Proc PROCEDURE NIL
.hit BOOLEAN FALSE
.lParam INTEGER 0
.message INTEGER 275
.res INTEGER 4243644
.s ARRAY 256 OF SHORTCHAR "¯B", 1X ...
.w INTEGER 2147348480
.wParam INTEGER 1
.wnd INTEGER 1770006
<system> (pc=7E418733H, fp=0022FB84H)
<system> (pc=7E418815H, fp=0022FBECH)
<system> (pc=7E4189CCH, fp=0022FC4CH)
<system> (pc=7E4196C6H, fp=0022FC5CH)
HostMenus.Loop [00003BDEH]
.done BOOLEAN FALSE
.f SET {0..5}
.n INTEGER 0
.res INTEGER 0
.w HostWindows.Window NIL
Kernel.Start [00002B8CH]
.code PROCEDURE HostMenus.Loop
Is there anyone who can explain what does this mean and how to understand trap
messages? For me, it seems that the problem lies here:
.work ARRAY 10 OF REAL
[0] REAL inf
[1] REAL inf
[2] REAL inf
[3] REAL 1.30212336033939
[4] REAL 4.534462964264759
[5] REAL 1.769649991139459E+167
[6] REAL 1.792592453177908E-307
[7] REAL 9.94060079432588E-321
[8] REAL 5.474495960374562E+67
[9] REAL 5.257527858867595E-308
where it says that it produces some inf parameter values. I do not understand
why this happens as the program was working fine for 5*10^5 iterations. I tried
to change the Seed values but there was no use.
This is a BUGS rather than an R question, hence please ask on their
mailing list.
Anyway, without having your model file etc, I can guess that you have
some division by almost zero from sampling from some distribution that
may return some extremely small values close to zero.
Uwe Ligges
A bit of background:
1) I am running multilevel models for small area estimation and the above
problems seem to appear only with the spatial random effects model. The
spatial+non-spatial random effects model seems to behave properly without any
problems.
2) As mentioned above the program was working fine for more than 500000
iterations. This means that I got no trap messages and I called the bugs
function for more than 10 times without any problems.
It's so frustrating...
Kind regards,
Sotiris
Dr. Sotiris Adamakis
Senior Statistician - Ipsos MORI
T +44 20 7347 3828
s<mailto:ssotiris.adama...@ipsos.com>otiris.adamakis<mailto:ssotiris.adama...@ipsos.com>@ipsos.com<mailto:ssotiris.adama...@ipsos.com>
www.ipsos-mori.com<http://www.ipsos-mori.com/>
79-81 Borough Road, London, SE1 1FY
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