Thanks very much Simon, that is super helpful.
Best,
Chris
On 25/3/20, 9:47 am, "Simon Wood" <simon.w...@bath.edu> wrote:
Hi Chris,
It's kind of a documentation glitch, a node is not supposed to be listed
as its own neighbour (it causes the diagonal entries in the penalty
matrix to be over-written by the wrong value). i.e. the neighbour list
should be.
NB <- list()
NB$'East Timor' <- c(2,15)
NB$Australia <- c(1,15)
NB$'Sri Lanka' <-c(12,16)
NB$Bangladesh <-c(12,13,16)
NB$Philippines <- c(6,11,14,15,17)
NB$Taiwan <- c(5,11)
NB$Thailand <- c(8,10,12,13,14,15)
NB$Vietnam <- c(7,10,11,14,15)
NB$`South Korea` <- c(11)
NB$Cambodia <- c(7,8)
NB$China <- c(5,6,8,9,14)
NB$India <- c(3,4,7,13,15,16)
NB$Myanmar <- c(4,7,12,16)
NB$Malaysia <- c(5,7,8,11,15)
NB$Indonesia <- c(1,2,5,7,8,12,14)
NB$HighSeas2 <- c(3,4,12,13)
NB$HighSeas1 <- c(5)
I've fixed the help page and had the smooth constructor ignore
auto-neighbours for the next release.
best,
Simon
On 18/03/2020 07:44, Wilcox, Chris (O&A, Hobart) wrote:
> Hi all,
>
> I am trying to fit a model with a markov random field smooth in
mgcv. I am having some trouble with getting it to run, and in particular I am
getting the message
>
> Error in initial.sp(w * x, S, off) : S[[1]] matrix is not +ve
definite.
>
> After reading everything I could find on mrf, it sounds like there
was a bug that was brought up with Simon Wood in 2012, due to differences
between windows and linux, with the linus machine stopping due to this error,
while windows was not. I have not been able to find much else on it. Any
suggestions would be much appreciated.
>
> There is reproducible code below.
>
> Thanks
>
> Chris
>
>
> library(mgcv)
>
> #create data
> Country <-
as.factor(c("Australia","Australia","Australia","Australia","Australia","Australia","Bangladesh","Bangladesh","Bangladesh",
>
"Bangladesh","Bangladesh","Bangladesh","Cambodia","Cambodia","Cambodia","Cambodia","Cambodia","Cambodia",
> "China","China","China","China","China","China","East Timor","East
Timor","East Timor",
> "East Timor","East Timor","East
Timor","HighSeas1","HighSeas1","HighSeas1","HighSeas1","HighSeas1","HighSeas1",
>
"HighSeas2","HighSeas2","HighSeas2","HighSeas2","HighSeas2","HighSeas2","China","China","China","China","China","China",
>
"India","India","India","India","India","India","Indonesia","Indonesia","Indonesia","Indonesia","Indonesia","Indonesia",
>
"Malaysia","Malaysia","Malaysia","Malaysia","Malaysia","Malaysia","Myanmar","Myanmar","Myanmar","Myanmar","Myanmar",
>
"Myanmar","Philippines","Philippines","Philippines","Philippines","Philippines","Philippines","South
Korea","South Korea",
> "South Korea","South Korea","South Korea","South
Korea","China","China","China","China","China","China",
> "Sri Lanka","Sri Lanka","Sri Lanka","Sri Lanka","Sri Lanka","Sri
Lanka","Taiwan","Taiwan","Taiwan","Taiwan",
>
"Taiwan","Taiwan","Thailand","Thailand","Thailand","Thailand","Thailand","Thailand","Vietnam","Vietnam","Vietnam","Vietnam",
> "Vietnam","Vietnam"))
>
> Count <-
c(0,0,3,5,1,5,0,0,0,0,0,1,0,0,0,0,0,3,0,0,2,1,0,6,0,0,0,1,0,0,0,1,0,0,0,0
>
,0,0,20,0,1,0,0,0,0,0,0,2,0,0,6,3,3,10,1,1,18,11,8,11,0,1,2,2,1,14,0,0,0,1,0,0
>
,0,0,4,3,9,16,0,0,3,0,0,1,0,0,1,0,0,0,0,0,33,18,8,16,0,0,0,0,0,2,0,1,14,6,8,2
> ,0,0,0,0,1,1)
>
> Data <- data.frame(Count,Country)
>
> #create neighbour matrix
> NB <- list()
> NB$'East Timor' <- c(1,2,15)
> NB$Australia <- c(1,2,15)
> NB$'Sri Lanka' <-c(3,12,16)
> NB$Bangladesh <-c(4,12,13,16)
> NB$Philippines <- c(5,6,11,14,15,17)
> NB$Taiwan <- c(5,6,11)
> NB$Thailand <- c(7,8,10,12,13,14,15)
> NB$Vietnam <- c(7,8,10,11,14,15)
> NB$`South Korea` <- c(9,11)
> NB$Cambodia <- c(7,8,10)
> NB$China <- c(5,6,8,9,11,14)
> NB$India <- c(3,4,7,12,13,15,16)
> NB$Myanmar <- c(4,7,12,13,16)
> NB$Malaysia <- c(5,7,8,11,14,15)
> NB$Indonesia <- c(1,2,5,7,8,12,14,15)
> NB$HighSeas2 <- c(3,4,12,13,16)
> NB$HighSeas1 <- c(5,17)
>
> #check levels and names match
> all.equal(sort(names(NB)), sort(levels(Data$Country)))
>
> #try fitting GAM
> m1 <- gam(Data$Count ~ s(Data$Country, bs = 'mrf', xt = list(nb =
NB)))
>
>
>
> ______________________________________________
> R-help@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.
--
Simon Wood, School of Mathematics, University of Bristol, BS8 1TW UK
https://people.maths.bris.ac.uk/~sw15190/
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
