• using R Under development (unstable) (2012-05-24 r59432)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘glmmBUGS/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘glmmBUGS’ version ‘2.0’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
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• checking whether package ‘glmmBUGS’ can be installed ... [10s/11s] OK
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• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
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• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking for unstated dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
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• checking Rd files ... NOTE
  prepare_Rd: CondSimuPosterior.Rd:51-52: Dropping empty section \examples
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  prepare_Rd: muscleResult.Rd:15-17: Dropping empty section \source
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  prepare_Rd: winBugsRaggedArray.Rd:39: Dropping empty section \note
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• checking examples ... ERROR
  Running examples in ‘glmmBUGS-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: glmmBUGS
  > ### Title: A function to run Generalised Linear Mixed Models in Bugs
  > ### Aliases: glmmBUGS
  >
  > ### ** Examples
  >
  > library(nlme)
  > data(Muscle)
  >
  >
  > muscleRagged = glmmBUGS(conc ~ length, data=Muscle, effects="Strip", family="gaussian")
  iteration 1
  iteration 2
  > startingValues = muscleRagged$startingValues
  >
  > ## Not run:
  > ##D # run with winbugs
  > ##D source("getInits.R")
  > ##D require(R2WinBUGS)
  > ##D muscleResult = bugs(muscleRagged$ragged, getInits, parameters.to.save = names(getInits()),
  > ##D model.file="model.bug", n.chain=3, n.iter=1000, n.burnin=100, n.thin=10,
  > ##D program="winbugs", working.directory=getwd())
  > ##D
  > ##D # a jags example
  > ##D require(R2jags)
  > ##D muscleResultJags = jags(
  > ##D muscleRagged$ragged, getInits, parameters.to.save = names(getInits()),
  > ##D model.file="model.bug", n.chain=3, n.iter=1000,
  > ##D n.burnin=100, n.thin=10,
  > ##D working.directory=getwd())
  > ##D
  > ##D
  > ## End(Not run)
  >
  > data(muscleResult)
  >
  > muscleParams = restoreParams(muscleResult, muscleRagged$ragged)
  > summaryChain(muscleParams)
  $scalars
  mean pval sd 0.5% 2.5%
  intercept -1.2655386 0.04074074 0.70100674 -2.94760500 -2.6941250
  betaobservations 0.2042404 0.00000000 0.02727729 0.13012150 0.1528450
  SDStrip 1.0388256 0.00000000 0.42350395 0.04037235 0.1175025
  5% 50% 95% 97.5% 99.5%
  intercept -2.45860 -1.28350 -0.086362 0.109909 0.3621930
  betaobservations 0.15690 0.20535 0.247320 0.254960 0.2655375
  SDStrip 0.17223 1.05600 1.653100 1.749325 2.0074250
  
  $betas
  mean pval sd 0.5% 2.5% 5% 50%
  betaobservations 0.2042404 0 0.02727729 0.1301215 0.152845 0.1569 0.20535
  95% 97.5% 99.5%
  betaobservations 0.24732 0.25496 0.2655375
  
  $RStrip
  mean pval sd 0.5% 2.5% 5% 50%
  S01 1.54992198 0.03333333 0.8868596 -0.1768250 -0.0246500 0.057724 1.544250
  S02 0.88417575 0.10740741 0.6983241 -0.9088650 -0.4244050 -0.155650 0.899500
  S03 -0.23390863 0.34814815 0.5914435 -1.9491715 -1.4687375 -1.262370 -0.190000
  S04 0.45283408 0.25925926 0.6843783 -1.1793696 -0.9058150 -0.669500 0.413550
  S05 0.60819344 0.24444444 0.7703025 -1.0634295 -0.6081000 -0.483135 0.533250
  S06 0.31592178 0.35925926 0.7376788 -1.3591490 -0.8759830 -0.731970 0.223750
  S07 -0.70460736 0.20740741 0.8126383 -3.1227065 -2.6569750 -2.265800 -0.547250
  S08 -0.25441374 0.35555556 0.7577606 -2.3061895 -1.7302175 -1.537680 -0.196500
  S09 -0.38743685 0.28148148 0.7355054 -2.6393470 -1.6964750 -1.560860 -0.329050
  S10 -0.68585621 0.21111111 0.8439765 -3.0587025 -2.5834400 -2.250790 -0.690900
  S11 -0.71912356 0.18518519 0.7478093 -2.7717245 -2.2527500 -1.901530 -0.714300
  S12 -0.71231756 0.18148148 0.7869166 -2.8318810 -2.2392250 -1.950660 -0.678975
  S13 -0.31868543 0.34814815 0.8149412 -2.7769955 -2.0222575 -1.699450 -0.256350
  S14 -0.48697259 0.28148148 0.8044144 -2.9784650 -2.2049950 -1.932700 -0.387950
  S15 -0.97838181 0.10740741 0.8504277 -3.2020285 -2.7934550 -2.502000 -0.857500
  S16 0.84256284 0.12592593 0.6946001 -0.5053900 -0.2942450 -0.152550 0.836100
  S17 0.64807114 0.19259259 0.7215709 -0.7991797 -0.5750000 -0.310640 0.548200
  S18 1.07191081 0.08888889 0.8276582 -0.8455955 -0.3352975 -0.115320 1.016500
  S19 -0.59925374 0.20000000 0.7733523 -2.6562050 -2.2800750 -1.992600 -0.499850
  S20 -0.06239375 0.48148148 0.7080924 -1.6509095 -1.5234050 -1.339950 -0.019600
  S21 0.06676470 0.45925926 0.6311687 -1.5596288 -1.1945400 -0.964500 0.050350
  95% 97.5% 99.5%
  S01 2.9949900 3.2311500 3.5329890
  S02 1.9720450 2.2462605 2.6260415
  S03 0.7350450 0.8952500 1.1674910
  S04 1.5997700 1.7665375 2.0766735
  S05 2.1246900 2.3195575 2.5335875
  S06 1.5991900 1.9545075 2.5328225
  S07 0.3115500 0.5566500 0.9338500
  S08 1.0257300 1.3488825 1.9590830
  S09 0.7478450 1.0226500 1.7744205
  S10 0.6188800 0.8003152 1.0993755
  S11 0.3735000 0.6804675 0.9901384
  S12 0.4988500 0.6529947 1.0567460
  S13 0.9844800 1.3630475 1.5559440
  S14 0.6935000 0.8611075 1.4026265
  S15 0.1796335 0.3359150 0.5011000
  S16 2.0183800 2.0802900 2.3114275
  S17 1.9229700 2.1993862 2.6873200
  S18 2.4969750 2.6700415 3.4282300
  S19 0.6090200 0.7528225 1.1546985
  S20 1.0645500 1.2481600 2.0552690
  S21 1.1254000 1.2890550 1.9970190
  
  $FittedRStrip
  mean pval sd 0.5% 2.5% 5% 50%
  S01 0.2843833 0.35555556 0.9352313 -1.792905 -1.385450 -1.23780 0.31130
  S02 -0.3813629 0.35555556 0.8957498 -2.529095 -2.017550 -1.75560 -0.31270
  S03 -1.4994473 0.02592593 0.7867285 -3.470145 -3.112875 -2.82725 -1.46700
  S04 -0.8127046 0.12962963 0.7189631 -2.589780 -2.174950 -1.99675 -0.84455
  S05 -0.6573452 0.19259259 0.7658188 -2.335315 -1.995350 -1.79865 -0.62335
  S06 -0.9496169 0.09259259 0.7858372 -2.968710 -2.660275 -2.35600 -0.92520
  S07 -1.9701460 0.04074074 1.1473757 -5.392215 -4.274800 -4.05355 -1.83900
  S08 -1.5199524 0.04814815 0.8693870 -3.685370 -3.237650 -2.97615 -1.44250
  S09 -1.6529755 0.03333333 0.9538261 -4.157025 -3.608650 -3.31420 -1.60650
  S10 -1.9513948 0.04074074 1.0556197 -5.075270 -4.124600 -3.53905 -1.92500
  S11 -1.9846622 0.01111111 0.9322485 -4.258000 -3.833750 -3.46500 -1.93450
  S12 -1.9778562 0.02962963 1.1309717 -4.446620 -4.105350 -3.89935 -1.82350
  S13 -1.5842241 0.06296296 1.0543192 -4.128115 -3.705625 -3.53825 -1.57350
  S14 -1.7525112 0.05185185 1.0703809 -5.199205 -3.855150 -3.55950 -1.69900
  S15 -2.2439204 0.01851852 1.1667545 -4.950170 -4.571850 -4.28945 -2.22900
  S16 -0.4229758 0.31111111 0.8814157 -2.722620 -2.170275 -1.91445 -0.37980
  S17 -0.6174675 0.28518519 0.9230020 -3.132810 -2.621875 -2.11805 -0.60655
  S18 -0.1936278 0.38888889 0.8546320 -2.075205 -1.859850 -1.49365 -0.22885
  S19 -1.8647924 0.05555556 1.1403275 -4.461565 -4.224875 -3.80615 -1.78400
  S20 -1.3279324 0.09259259 1.0079839 -4.004515 -3.344100 -3.01325 -1.32000
  S21 -1.1987739 0.08518519 0.9083019 -3.594535 -3.242025 -2.80675 -1.22700
  95% 97.5% 99.5%
  S01 1.8397500 2.09522500 2.2832800
  S02 1.0476000 1.36715000 2.1566450
  S03 -0.1134550 -0.00046025 0.4915020
  S04 0.3144900 0.57624250 0.9059075
  S05 0.6854700 0.84702500 1.3936200
  S06 0.2206050 0.40609750 0.7693275
  S07 -0.0912150 0.15297500 0.5283185
  S08 -0.0385945 0.16038500 0.4286980
  S09 -0.0973070 0.12896750 0.8124975
  S10 -0.0973375 0.04467425 0.5151385
  S11 -0.5521200 -0.16512250 0.2273673
  S12 -0.1306650 0.03379175 0.4698875
  S13 0.0957815 0.49388000 1.1230440
  S14 -0.0419790 0.27019250 0.4259840
  S15 -0.3269450 -0.07050375 0.1745775
  S16 1.0624500 1.39042500 1.7414450
  S17 0.7634650 0.99061750 1.5403200
  S18 1.3081000 1.40712500 1.8402850
  S19 0.1248135 0.32123000 0.8894485
  S20 0.2558300 0.42157000 1.5143000
  S21 0.2581700 0.53922250 0.9853340
  
  > checkChain(muscleParams)
  >
  >
  >
  > # a spatial example
  > ## Not run:
  > ##D library(diseasemapping)
  > ##D
  > ##D data(popdata)
  > ##D data(casedata)
  > ##D
  > ##D model = getRates(casedata, popdata, ~age*sex)
  > ##D ontario = getSMR(popdata, model, casedata)
  > ##D ontario = ontario@data[,c("CSDUID","observed","logExpected")]
  > ##D
  > ##D library(spdep)
  > ##D popDataAdjMat = poly2nb(popdata,row.names=as.character(popdata[["CSDUID"]]))
  > ## End(Not run)
  >
  > data(popDataAdjMat)
  > data(ontario)
  >
  > forBugs = glmmBUGS(formula=observed + logExpected ~ 1,
  + effects="CSDUID", family="poisson", spatial=popDataAdjMat,
  + spatialEffect="CSDUID",
  + data=ontario)
  iteration 1
  iteration 2
  iteration 3
  iteration 4
  iteration 5
  iteration 6
  iteration 7
  iteration 8
  iteration 9
  iteration 10
  >
  > startingValues = forBugs$startingValues
  >
  > source("getInits.R")
  >
  > ## Not run:
  > ##D library(R2WinBUGS)
  > ##D ontarioResult = bugs(forBugs$ragged, getInits,
  > ##D parameters.to.save = names(getInits()),
  > ##D model.file="model.bug", n.chain=3, n.iter=50, n.burnin=10, n.thin=2,
  > ##D program="winbugs", debug=T,working.directory=getwd())
  > ## End(Not run)
  >
  > data(ontarioResult)
  >
  > ontarioParams = restoreParams(ontarioResult, forBugs$ragged)
  >
  > ontarioSummary = summaryChain(ontarioParams)
  >
  > # posterior probability of having 10x excess risk
  > postProb = apply(ontarioParams$FittedRCSDUID, 3, function(x) mean(x>log(10)) )
  > hist(postProb)
  >
  > ## Not run:
  > ##D
  > ##D ontario = mergeBugsData(popdata, ontarioSummary)
  > ##D
  > ##D spplot(ontario, "FittedRateCSDUID.mean")
  > ##D
  > ##D
  > ##D ontario = mergeBugsData(ontario, postProb, newcol="postProb", by.x="CSDUID")
  > ##D spplot(ontario, "postProb")
  > ##D
  > ##D
  > ##D
  > ## End(Not run)
  >
  > # geostatistical example
  >
  > ## Not run:
  > ##D library(geoRglm)
  > ##D data(rongelap)
  > ## End(Not run)
  > rongelap= read.table(url("http://www.leg.ufpr.br/lib/exe/fetch.php/pessoais:paulojus:mbgbook:datasets:rongelap.txt"),header=TRUE)
  Warning in open.connection(file, "rt") :
  unable to connect to 'www.leg.ufpr.br' on port 80.
  Error in open.connection(file, "rt") : cannot open the connection
  Calls: read.table -> open -> open.connection
  Execution halted