[R-sig-Geo] Fwd: dimensions do not match

Thu Apr 10 14:15:31 CEST 2008

Yes that's it.
It works perfectly with my variable "column" for data column name :

as.formula(paste(column,"~",1))

Thank you all.

Mathieu

--------

2008/4/10, Jon Olav Skoien <j.skoien at geo.uu.nl>:
> Hi,
>
>  I think Mathieu wanted to know how to create formula strings from variable
> names. The function "as.formula" should be able to do what he is looking
> for.
>
>  as.formula(paste(names(meuse)[4],"~",names(meuse)[6]) )
>
>  is an alternative way of calling a function with the formula zinc~dist,
> knowing that these are the 4th and 6th column respectively:
>
>  library(automap)
>  data(meuse)
>  coordinates(meuse) =~ x+y
>  names(meuse)
>  v1 =
> autofitVariogram(as.formula(paste(names(meuse)[4],"~",names(meuse)[6])
> ), meuse)
>  v1
>  v2 = autofitVariogram(zinc~dist,meuse)
>  v2
>
>  Cheers,
>  Jon
>
>
>  Paul Hiemstra wrote:
>
> > Hi mathieu,
> >
> > I'm not sure if I understand what your last question is. Why do you want
> to modify "z~1" if z is your data column name? If you want "variable~1" to
> work you need to change your column name to variable.
> >
> > cheers,
> > Paul
> >
> > mathieu grelier wrote:
> >
> >
> > > Hi,
> > > Yes, autokrige deals with duplicates.
> > > But I found there were two problems, and the first come from the way
> > > autokrige calls the krige function from gstat.
> > > Edzer, you gave the answer : it was necessary to specify "nmax=30" in
> the call.
> > > Automap doesn't do it and adding this argument to the call remove the
> > > "memory.c" problem.
> > >
> > > The second problem (dimensions do not match) comes from the formula
> > > parameter for the krige function.
> > > If your data column is z, and you want to perform ordinary kriging,
> > > you have to specify z~1.
> > > In my case, I only know the data column name at execution time as it
> > > is a parameter in my script.
> > > And I must admit that I didn't achieve to find the right code to pass
> > > this parameter to the formula argument.
> > > Basically "variable~1" doesn't work and I don't know why exactly.
> > > It was my code that was wrong and if I use hard code to give the
> > > formula argument to the autokrige call, it works fine.
> > >
> > > So last question is :
> > > -how can I modify "z~1" in the krige formula to be able to use my data
> > > column parameter??
> > >
> > > Thanks
> > > Mathieu
> > >
> > >
> > >
> > >
> > >
> > > 2008/4/7, Edzer Pebesma <edzer.pebesma at uni-muenster.de>:
> > >
> > >
> > > > The following worked for me, although I didn't understand the result:
> > > >
> > > >  > zd = zerodist(sitesR)
> > > >  > kriging_result = krige(valeur~1, sitesR[-zd[,1],], mask_SG, vgm(1,
> "Exp",
> > > > 300), nmax = 30)
> > > >
> > > >  of course arbitrarily throwing away the first of each location-paired
> > > > point, choosing an nmax, and some nonsense variogram.
> > > >
> > > >  Please keep r-sig-geo in the mail loop.
> > > >
> > > >  --
> > > >  Edzer
> > > >
> > > >  mathieu grelier wrote:
> > > >
> > > >
> > > >
> > > > > Ok,
> > > > > I've just tried to use zerodist before calling the autoKrige
> function
> > > > > but the error remains the same (memory_c...).
> > > > > Did you manage to perform the local kriging? You said there was
> still an
> > > > >
> > > > >
> > > > error.
> > > >
> > > >
> > > > > I forward this message to the author of automap.
> > > > > I don't know if automap can handle this situation.
> > > > > Paul, please could you give us an answer about last question from
> edzer?
> > > > >
> > > > > Thanks
> > > > > Mathieu
> > > > >
> > > > > ---------- Forwarded message ----------
> > > > > From: Edzer Pebesma <edzer.pebesma at uni-muenster.de>
> > > > > Date: 7 avr. 2008 12:42
> > > > > Subject: Re: [R-sig-Geo] dimensions do not match
> > > > > To: mathieu grelier <greliermathieu at gmail.com>,
> > > > >
> > > > >
> > > > r-sig-geo at stat.math.ethz.ch
> > > >
> > > >
> > > > > Thanks Mathieu, for sending me the data off-line.
> > > > >
> > > > >  If you have a massive data set, you should use kriging within a
> local
> > > > > neighbourhood to prevent forming and inverting a covariance matrix
> of
> > > > > 4.3 Gb (24067 records, squared, times 8 bytes per double). You may
> try
> > > > > to convince the author of automap to take care of this,
> automatically.
> > > > >
> > > > >  When applying local kriging to your data set, I get the error
> message:
> > > > >
> > > > >  > k = krige(valeur~1,sitesR,mask_SG,vgm(1,
> "Exp",300),
> > > > >
> > > > >
> > > > nmax=30)
> > > >
> > > >
> > > > >  [using ordinary kriging]
> > > > >
> > > > >  "chfactor.c", line 130: singular matrix in function LDLfactor()
> > > > >  Error in predict.gstat(g, newdata = newdata, block = block, nsim =
> nsim,
> > > > >
> > > > >
> > > > :
> > > >
> > > >
> > > > >  LDLfactor
> > > > >
> > > > >  which is usually, and in this case as well, due to duplicate
> > > > >
> > > > >
> > > > observations, try
> > > >
> > > >
> > > > >  > zerodist(sitesR)
> > > > >
> > > > >  Does automap take care of them, and if yes how?
> > > > >  --
> > > > >  Edzer
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >  mathieu grelier wrote:
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > > Ok, this is the data I use and the commands.
> > > > > > It is really weird because I use R CMD within grass and I can't
> > > > > > reproduce exactly the same error message when I follow the
> commands
> > > > > > directly in R.
> > > > > > This is the message I get now :
> > > > > >
> > > > > > "memory.c", line 57: can't allocate memory in function m_get()
> > > > > > Error in predict.gstat(g, newdata = newdata, block = block, nsim =
> nsim,
> > > > > >
> > > > > >
> > > > >
> > > >  :
> > > >
> > > >
> > > > >
> > > > > >      m_get
> > > > > >
> > > > > > But, I already had this memory error when working on big datasets.
> > > > > > In the same way, I looked on the archives to see if this memory
> > > > > > problem could be solved and I didn't find anything.
> > > > > >
> > > > > > Do you know it?
> > > > > > Thanks.
> > > > > >
> > > > > > Mathieu
> > > > > >
> > > > > >
> > > > > > 2008/4/6, Edzer Pebesma <edzer.pebesma at uni-muenster.de>:
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > > Please send me the data as a .RData R data file, along with the
> steps
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > that
> > > >
> > > >
> > > > >
> > > > > >
> > > > > > > led to the error message.
> > > > > > >  --
> > > > > > >  Edzer
> > > > > > >
> > > > > > >  mathieu grelier wrote:
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > > A question about a problem already described in this list (
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> https://stat.ethz.ch/pipermail/r-sig-geo/2006-July/001160.html),
> > > >
> > > >
> > > > >
> > > > > >
> > > > > > > but I
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > > didn't find any answer.
> > > > > > > > I am trying to achieve ordinary kriging using gstat (via the
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > autokrige
> > > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > > > package) in GRASS with a big dataset (24067 points).
> > > > > > > >
> > > > > > > > After the program removes duplicate data, I get the following
> same
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > error :
> > > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > > > "Error : dimensions do not match: locations 39916 and data
> 24067"
> > > > > > > > I don't have any NAs apparently.
> > > > > > > > Checking logfile, I could see that the error is occurring in
> the
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > krige
> > > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > > > function.
> > > > > > > >
> > > > > > > > Is there a known way to fix this problem?
> > > > > > > > Maybe I can send my data, but I don't send it for now to the
> list as
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > its
> > > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > > > weight is ~1Mo.
> > > > > > > >
> > > > > > > > Thanks
> > > > > > > > Mathieu
> > > > > > > >
> > > > > > > >     [[alternative HTML version deleted]]
> > > > > > > >
> > > > > > > >
> _______________________________________________
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> > > > > > > > R-sig-Geo at stat.math.ethz.ch
> > > > > > > >
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