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.zeil...@uibk.ac.at]
Sent: Wednesday, 4 February 2015 8:20 PM
To: Shanley Chong
Cc: r-help@r-project.org; nikolaus.uml...@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
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