Dear Z and Nikolaus, Thank you for your help. Here is my R codes:>data("MunichBnd")>N <- length(MunichBnd); n <- N*5 >dat <- data.frame(x1 = runif(n, -3, 3),id = as.factor(rep(names(MunichBnd), length.out = n))) >dat$sp <- with(dat, sort(runif(N, -2, 2), decreasing = TRUE)[id]) >dat$re_poi <- with(dat, rpois(N, 10)[id]) >dat$y_poi <- with(dat, 1.5 + sin(x1) + sp + re_poi + rpois(n, 10)) >b_poi <- bayesx(y_poi ~ sx(x1) + sx(id, bs = "mrf", map = MunichBnd) + sx(id, bs = "re"), method = "MCMC", data = dat, family='poisson')Warning message: running command '"C:/Users/ChongS/Documents/R/win-library/3.1/BayesXsrc/libs/x64/BayesX.exe" C:/Users/ChongS/AppData/Local/Temp/RtmpqMhw3Z/bayesx/bayesx.estim.input.prg' had status 3 If I run the model using family='gaussian', it doesn't have problem. b_poi <- bayesx(y_poi ~ sx(x1) + sx(id, bs = "mrf", map = MunichBnd) + sx(id, bs = "re"), method = "MCMC", data = dat, family='gaussian') Kind regards, Shanley -----Original Message----- From: Achim Zeileis [mailto:Achim.Zeileis at uibk.ac.at] Sent: Wednesday, 4 February 2015 8:20 PM To: Shanley Chong Cc: r-help at r-project.org; Nikolaus.Umlauf at uibk.ac.at Subject: Re: [R] R2BayesX Shanley:> I am trying to run STAR logistic/binomial model using R2BayesX . A > warning message came up every time when i included a random effect, > bs='re', (unstructured spatial effect) into the model. The warning > message is : Warning message: running command > '"C:/Users/ChongS/Documents/R/win-library/3.1/BayesXsrc/libs/x64/BayesX.exe" > C:/Users/ChongS/AppData/Local/Temp/RtmpCW8QY9/bayesx33/bayesx.estim.input.prg' > had status 5I haven't seen this problem before. Maybe you can provide "commented, minimal, self-contained, reproducible code" (as the posting guide asks)? I'm also cc'ing the package maintainer (Nikolaus Umlauf) as he might be able to give more insight. Best, Z> The model is fine when i just ran the model using mrf, bs='mrf', (structured spatial effect). > > And when i tried to run STAR using family=Gaussian (response is normally distributed) with structured and unstructured spatial effect, it is fine too. > > Can anyone please help? > > Regards, > > Shanley > > > _____________________________________________________________________ > This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. > Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy. > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >_____________________________________________________________________ This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy. _____________________________________________________________________ This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy.
Shanley, thanks for the example.> Thank you for your help. > Here is my R codes: > >> data("MunichBnd") > >> N <- length(MunichBnd); n <- N*5 >> dat <- data.frame(x1 = runif(n, -3, 3),id = as.factor(rep(names(MunichBnd), length.out = n))) >> dat$sp <- with(dat, sort(runif(N, -2, 2), decreasing = TRUE)[id]) >> dat$re_poi <- with(dat, rpois(N, 10)[id]) >> dat$y_poi <- with(dat, 1.5 + sin(x1) + sp + re_poi + rpois(n, 10)) >> b_poi <- bayesx(y_poi ~ sx(x1) + sx(id, bs = "mrf", map = MunichBnd) + sx(id, bs = "re"), method = "MCMC", data = dat, family='poisson') > > Warning message: > running command '"C:/Users/ChongS/Documents/R/win-library/3.1/BayesXsrc/libs/x64/BayesX.exe" C:/Users/ChongS/AppData/Local/Temp/RtmpqMhw3Z/bayesx/bayesx.estim.input.prg' had status 3 > > If I run the model using family='gaussian', it doesn't have problem. > b_poi <- bayesx(y_poi ~ sx(x1) + sx(id, bs = "mrf", map = MunichBnd) + sx(id, bs = "re"), method = "MCMC", data = dat, family='gaussian')This appears to be a problem in BayesX for combination of bs="re", method="MCMC" and family="poisson". If at least one of these is changed, everything works. An even simpler example is: set.seed(1) d <- data.frame(y = rpois(1000, 5)) d$x <- rep(1:100, each = 10) Then: bayesx(y ~ sx(x, bs = "re"), data = d, method = "MCMC", family = "poisson") ## -> problem processing BayesX! whereas bayesx(y ~ sx(x), data = d, method = "MCMC", family = "poisson") bayesx(y ~ sx(x, bs = "re"), data = d, method = "REML", family = "poisson") bayesx(y ~ sx(x, bs = "re"), data = d, method = "MCMC", family = "gaussian") are all ok. Niki has contacted the original BayesX authors who might be able to give more insight. For the moment, I would recommend to use method="REML". Best, Z> Kind regards, > Shanley > > > -----Original Message----- > From: Achim Zeileis [mailto:Achim.Zeileis at uibk.ac.at] > Sent: Wednesday, 4 February 2015 8:20 PM > To: Shanley Chong > Cc: r-help at r-project.org; Nikolaus.Umlauf at uibk.ac.at > Subject: Re: [R] R2BayesX > > Shanley: > >> I am trying to run STAR logistic/binomial model using R2BayesX . A >> warning message came up every time when i included a random effect, >> bs='re', (unstructured spatial effect) into the model. The warning >> message is : Warning message: running command >> '"C:/Users/ChongS/Documents/R/win-library/3.1/BayesXsrc/libs/x64/BayesX.exe" >> C:/Users/ChongS/AppData/Local/Temp/RtmpCW8QY9/bayesx33/bayesx.estim.input.prg' >> had status 5 > > I haven't seen this problem before. Maybe you can provide "commented, minimal, self-contained, reproducible code" (as the posting guide asks)? > > I'm also cc'ing the package maintainer (Nikolaus Umlauf) as he might be able to give more insight. > > Best, > Z > >> The model is fine when i just ran the model using mrf, bs='mrf', (structured spatial effect). >> >> And when i tried to run STAR using family=Gaussian (response is normally distributed) with structured and unstructured spatial effect, it is fine too. >> >> Can anyone please help? >> >> Regards, >> >> Shanley >> >> >> _____________________________________________________________________ >> This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. >> Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy. >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > > _____________________________________________________________________ > This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. > Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy. > > _____________________________________________________________________ > This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. > Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >
Many thanks Z and Nikolaus! Much appreciated! Have a great weekend! Kind regards, Shanley -----Original Message----- From: Achim Zeileis [mailto:Achim.Zeileis at uibk.ac.at] Sent: Thursday, 5 February 2015 8:01 PM To: Shanley Chong Cc: r-help at r-project.org; Nikolaus.Umlauf at uibk.ac.at Subject: Re: [R] R2BayesX Shanley, thanks for the example.> Thank you for your help. > Here is my R codes: > >> data("MunichBnd") > >> N <- length(MunichBnd); n <- N*5 >> dat <- data.frame(x1 = runif(n, -3, 3),id = >> as.factor(rep(names(MunichBnd), length.out = n))) dat$sp <- with(dat, >> sort(runif(N, -2, 2), decreasing = TRUE)[id]) dat$re_poi <- with(dat, >> rpois(N, 10)[id]) dat$y_poi <- with(dat, 1.5 + sin(x1) + sp + re_poi >> + rpois(n, 10)) b_poi <- bayesx(y_poi ~ sx(x1) + sx(id, bs = "mrf", >> map = MunichBnd) + sx(id, bs = "re"), method = "MCMC", data = dat, >> family='poisson') > > Warning message: > running command > '"C:/Users/ChongS/Documents/R/win-library/3.1/BayesXsrc/libs/x64/Bayes > X.exe" > C:/Users/ChongS/AppData/Local/Temp/RtmpqMhw3Z/bayesx/bayesx.estim.inpu > t.prg' had status 3 > > If I run the model using family='gaussian', it doesn't have problem. > b_poi <- bayesx(y_poi ~ sx(x1) + sx(id, bs = "mrf", map = MunichBnd) + sx(id, bs = "re"), method = "MCMC", data = dat, family='gaussian')This appears to be a problem in BayesX for combination of bs="re", method="MCMC" and family="poisson". If at least one of these is changed, everything works. An even simpler example is: set.seed(1) d <- data.frame(y = rpois(1000, 5)) d$x <- rep(1:100, each = 10) Then: bayesx(y ~ sx(x, bs = "re"), data = d, method = "MCMC", family = "poisson") ## -> problem processing BayesX! whereas bayesx(y ~ sx(x), data = d, method = "MCMC", family = "poisson") bayesx(y ~ sx(x, bs = "re"), data = d, method = "REML", family = "poisson") bayesx(y ~ sx(x, bs = "re"), data = d, method = "MCMC", family = "gaussian") are all ok. Niki has contacted the original BayesX authors who might be able to give more insight. For the moment, I would recommend to use method="REML". Best, Z> Kind regards, > Shanley > > > -----Original Message----- > From: Achim Zeileis [mailto:Achim.Zeileis at uibk.ac.at] > Sent: Wednesday, 4 February 2015 8:20 PM > To: Shanley Chong > Cc: r-help at r-project.org; Nikolaus.Umlauf at uibk.ac.at > Subject: Re: [R] R2BayesX > > Shanley: > >> I am trying to run STAR logistic/binomial model using R2BayesX . A >> warning message came up every time when i included a random effect, >> bs='re', (unstructured spatial effect) into the model. The warning >> message is : Warning message: running command >> '"C:/Users/ChongS/Documents/R/win-library/3.1/BayesXsrc/libs/x64/BayesX.exe" >> C:/Users/ChongS/AppData/Local/Temp/RtmpCW8QY9/bayesx33/bayesx.estim.input.prg' >> had status 5 > > I haven't seen this problem before. Maybe you can provide "commented, minimal, self-contained, reproducible code" (as the posting guide asks)? > > I'm also cc'ing the package maintainer (Nikolaus Umlauf) as he might be able to give more insight. > > Best, > Z > >> The model is fine when i just ran the model using mrf, bs='mrf', (structured spatial effect). >> >> And when i tried to run STAR using family=Gaussian (response is normally distributed) with structured and unstructured spatial effect, it is fine too. >> >> Can anyone please help? >> >> Regards, >> >> Shanley >> >> >> _____________________________________________________________________ >> This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. >> Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy. >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > > _____________________________________________________________________ > This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. > Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy. > > _____________________________________________________________________ > This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. > Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >_____________________________________________________________________ This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy. _____________________________________________________________________ This email has been scanned for the Sydney & South Western Sydney Local Health Districts by the MessageLabs Email Security System. Sydney & South Western Sydney Local Health Districts regularly monitor email and attachments to ensure compliance with the NSW Ministry of Health's Electronic Messaging Policy.