Re: [R] gamm design matrices

[Jarrod Hadfield]

Hi Simon,

Sorry, I spoke too soon. I now have the basic spline code working but  
with `by' variables I get an error in smoothCon:


Error in ExtractData(object, data, knots) :
  'names' attribute [1] must be the same length as the vector [0]

 and a segfault with smooth.construct (see example code below). I  
think it is something to do with by.done, but although by.done is  
mentioned as an item/object/attribute in the details section of  
?smoothCon and the value section of ?smooth.construct, there seems to  
be no additional documentation so I'm not sure what by.done is or  
should be.


Any help would be gratefully received.

Cheers,

Jarrod


nt<-10
nid<-100

X<-matrix(rnorm(nt*nid),nid,nt)
beta<-sin(1:nt)
y<-X%*%beta+rnorm(nid)

index<-matrix(rep(1:nt,each=nid),nid, nt)

dat<-data.frame(y=y, X=X, index=index)

  smooth.spec.object<-interpret.gam(~s(index,k=10,by=X))$smooth.spec[[1]]

  sm<-smoothCon(smooth.spec.object,data=dat, knots=NULL,absorb.cons=TRUE)
Error in ExtractData(object, data, knots) :
  'names' attribute [1] must be the same length as the vector [0]

  sm<-smooth.construct(smooth.spec.object,data=dat, knots=NULL)
*** caught segfault ***






Quoting Simon Wood  on Mon, 03 Mar 2014 13:35:04 +:


Dear Jarrod,

I've only managed to have a very quick look at this, but I wonder if  
the difference is to do with identifiability constraints? It looks  
to me as if your smooth.construct call does not have sum to zero  
constraints applied to the smooth, but by default 'gamm' will impose  
these (even when the model has only one smooth). 'gamm' then  
includes an explicit intercept term, which would explain why the  
model matrix dimensions still look ok.


If you mimic gamm by calling smoothCon rather than smooth.construct  
and asking for constraints to be absorbed, and then add the model  
matrix column for the intercept back in, then it should be possible  
to get the model matrices to match.


best,

Simon

On 02/03/14 17:16, Jarrod Hadfield wrote:

Hi All,

I would like to fit a varying coefficient model using MCMCglmm. To do
this it is possible to reparameterise the smooth terms as a mixed model
as Simon Wood neatly explains in his book.

Given the original design matrix W and penalisation matrix S, I would
like to find the fixed (X) and random (Z) design matrices for the mixed
model parameteristaion. X are the columns of W for which S has zero
eigenvalues and Z is the random effect design matrix for which ZZ' =
W*S*^{-1}W* where W* is W with the fixed effect columns dropped and S*
is S with the fixed effect row/columns dropped.

Having e as the eigenvlaues of S* and L the associated eigenvectors then
Z  can be formed as W*LE^{-1}  where E = Diag(sqrt(e)).

However, obtaining W and S from mgcv's smooth.construct and applying the
above logic I can recover the X but not the Z that gamm is passing to
nlme. I have posted an example below.

I have dredged the mgcv code but to no avail to see why I get
differences. I want to fit the model to ordinal data, and I also have a
correlated random effect structure (through a pedigree) hence the need
to use MCMCglmm.

Any help would be greatly appreciated.

Cheers,

Jarrod




library(mgcv)

x<-rnorm(100)
y<-sin(x)+rnorm(100)

dat<-data.frame(y=y,x=x) # generate some data

smooth.spec.object<-interpret.gam(y~s(x,k=10))$smooth.spec[[1]]

sm<-smooth.construct(smooth.spec.object,data=dat, knots=NULL)

# get penalty matrix S = sm$S[[1]] and original design matrix W=sm$X

   Sed<-eigen(sm$S[[1]])
   Su<-Sed$vectors
   Sd<-Sed$values
   nonzeros <- which(Sd > sqrt(.Machine$double.eps))

   Xn<-sm$X[,-nonzeros]

   Zn<-sm$X%*%Su[,nonzeros]%*%diag(1/sqrt(Sd[nonzeros]))

# form X and Z

   m2.lme<-gamm(y~s(x,k=10), data=dat)

   Xo<-m2.lme$lme$data$X
   Zo<-m2.lme$lme$data$Xr

# fit gamm and extract X and Z used by lme

plot(Xo,Xn)  # OK
plot(Zo,Zn)  # not OK
















--
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603   http://people.bath.ac.uk/sw283






--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

Re: [R] gamm design matrices

[Jarrod Hadfield]

Hi Simon,

That's perfect - the matrices now agree.

Thanks,

Jarrod

Quoting Simon Wood  on Mon, 03 Mar 2014 13:35:04 +:


Dear Jarrod,

I've only managed to have a very quick look at this, but I wonder if  
the difference is to do with identifiability constraints? It looks  
to me as if your smooth.construct call does not have sum to zero  
constraints applied to the smooth, but by default 'gamm' will impose  
these (even when the model has only one smooth). 'gamm' then  
includes an explicit intercept term, which would explain why the  
model matrix dimensions still look ok.


If you mimic gamm by calling smoothCon rather than smooth.construct  
and asking for constraints to be absorbed, and then add the model  
matrix column for the intercept back in, then it should be possible  
to get the model matrices to match.


best,

Simon

On 02/03/14 17:16, Jarrod Hadfield wrote:

Hi All,

I would like to fit a varying coefficient model using MCMCglmm. To do
this it is possible to reparameterise the smooth terms as a mixed model
as Simon Wood neatly explains in his book.

Given the original design matrix W and penalisation matrix S, I would
like to find the fixed (X) and random (Z) design matrices for the mixed
model parameteristaion. X are the columns of W for which S has zero
eigenvalues and Z is the random effect design matrix for which ZZ' =
W*S*^{-1}W* where W* is W with the fixed effect columns dropped and S*
is S with the fixed effect row/columns dropped.

Having e as the eigenvlaues of S* and L the associated eigenvectors then
Z  can be formed as W*LE^{-1}  where E = Diag(sqrt(e)).

However, obtaining W and S from mgcv's smooth.construct and applying the
above logic I can recover the X but not the Z that gamm is passing to
nlme. I have posted an example below.

I have dredged the mgcv code but to no avail to see why I get
differences. I want to fit the model to ordinal data, and I also have a
correlated random effect structure (through a pedigree) hence the need
to use MCMCglmm.

Any help would be greatly appreciated.

Cheers,

Jarrod




library(mgcv)

x<-rnorm(100)
y<-sin(x)+rnorm(100)

dat<-data.frame(y=y,x=x) # generate some data

smooth.spec.object<-interpret.gam(y~s(x,k=10))$smooth.spec[[1]]

sm<-smooth.construct(smooth.spec.object,data=dat, knots=NULL)

# get penalty matrix S = sm$S[[1]] and original design matrix W=sm$X

   Sed<-eigen(sm$S[[1]])
   Su<-Sed$vectors
   Sd<-Sed$values
   nonzeros <- which(Sd > sqrt(.Machine$double.eps))

   Xn<-sm$X[,-nonzeros]

   Zn<-sm$X%*%Su[,nonzeros]%*%diag(1/sqrt(Sd[nonzeros]))

# form X and Z

   m2.lme<-gamm(y~s(x,k=10), data=dat)

   Xo<-m2.lme$lme$data$X
   Zo<-m2.lme$lme$data$Xr

# fit gamm and extract X and Z used by lme

plot(Xo,Xn)  # OK
plot(Zo,Zn)  # not OK
















--
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603   http://people.bath.ac.uk/sw283






--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

[R] gamm design matrices

[Jarrod Hadfield]

Hi All,

I would like to fit a varying coefficient model using MCMCglmm. To do  
this it is possible to reparameterise the smooth terms as a mixed  
model as Simon Wood neatly explains in his book.


Given the original design matrix W and penalisation matrix S, I would  
like to find the fixed (X) and random (Z) design matrices for the  
mixed model parameteristaion. X are the columns of W for which S has  
zero eigenvalues and Z is the random effect design matrix for which  
ZZ' = W*S*^{-1}W* where W* is W with the fixed effect columns dropped  
and S* is S with the fixed effect row/columns dropped.


Having e as the eigenvlaues of S* and L the associated eigenvectors  
then Z  can be formed as W*LE^{-1}  where E = Diag(sqrt(e)).


However, obtaining W and S from mgcv's smooth.construct and applying  
the above logic I can recover the X but not the Z that gamm is passing  
to nlme. I have posted an example below.


I have dredged the mgcv code but to no avail to see why I get  
differences. I want to fit the model to ordinal data, and I also have  
a correlated random effect structure (through a pedigree) hence the  
need to use MCMCglmm.


Any help would be greatly appreciated.

Cheers,

Jarrod




library(mgcv)

x<-rnorm(100)
y<-sin(x)+rnorm(100)

dat<-data.frame(y=y,x=x) # generate some data

smooth.spec.object<-interpret.gam(y~s(x,k=10))$smooth.spec[[1]]

sm<-smooth.construct(smooth.spec.object,data=dat, knots=NULL)

# get penalty matrix S = sm$S[[1]] and original design matrix W=sm$X

   Sed<-eigen(sm$S[[1]])
   Su<-Sed$vectors
   Sd<-Sed$values
   nonzeros <- which(Sd > sqrt(.Machine$double.eps))

   Xn<-sm$X[,-nonzeros]

   Zn<-sm$X%*%Su[,nonzeros]%*%diag(1/sqrt(Sd[nonzeros]))

# form X and Z

   m2.lme<-gamm(y~s(x,k=10), data=dat)

   Xo<-m2.lme$lme$data$X
   Zo<-m2.lme$lme$data$Xr

# fit gamm and extract X and Z used by lme

plot(Xo,Xn)  # OK
plot(Zo,Zn)  # not OK













--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

Re: [R] Swaeve, Beamer and \alt

[Jarrod Hadfield]

Hi,

Unfortunately not, nor \begin{frame}[fragile], which does work with  
the uncover environment.


Cheers,

Jarrod
Quoting Uwe Ligges  on Sat, 09 Feb  
2013 18:45:39 +0100:





On 09.02.2013 17:00, Jarrod Hadfield wrote:

Hi,

I am having trouble getting \alt (or \altenv) to work with Schunk/Sinput
and was wondering if anybody had had success? With the slide

\begin{frame}[fragile]\frametitle{Basic R}
\alt<2>{
<>=
2+2
@
}{
<>=
2+2
@
}
\end{frame}

I get the error message:


! FancyVerb Error:
  Extraneous input `> 2+2 \end {Sinput} \end {Schunk} ' between
\begin{Sinput}[
] and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
}

which cannot be fixed using the fragile or containsverbatim options for
the frame.

Thanks for any help,


Jarrod




Untested: Does \begin{frame}[containsverbatim] help?

Best,
Uwe Ligges






--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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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.

[R] Swaeve, Beamer and \alt

[Jarrod Hadfield]

Hi,

I am having trouble getting \alt (or \altenv) to work with  
Schunk/Sinput and was wondering if anybody had had success? With the  
slide


\begin{frame}[fragile]\frametitle{Basic R}
\alt<2>{
<>=
2+2
@
}{
<>=
2+2
@
}
\end{frame}

I get the error message:


! FancyVerb Error:
  Extraneous input `> 2+2 \end {Sinput} \end {Schunk} ' between  
\begin{Sinput}[

] and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
}

which cannot be fixed using the fragile or containsverbatim options  
for the frame.


Thanks for any help,


Jarrod


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

Re: [R] [R-sig-ME] Question on overdispersion

[Jarrod Hadfield]

Hi Thierry + nameless,

It is not necessary to expand the binomial into Bernoulli trials (nor  
advisable if n and/or the binomial size are large). You can just fit  
observation-level random effects:


dataset$resid<-as.factor(1:dim(dataset)[1])

fit3 <- glmer(cbind(male_chick_no, female_chick_no) ~ 1+(1|FemaleID)+  
(1|resid), data = dataset, family = binomial)


gives the same answer as fit2

Cheers,

Jarrod






Quoting "ONKELINX, Thierry" :


Dear Nameless,

The quasi distribution can no longer be used in lme4 because a) the
results were not very reliable b) there is an alternative to model
overdispersion.

The alternative is to expand your dataset to bernoulli trials. Then add
a random effect with one level per observation. This random effect will
model additive overdisperion. The quasi distributions model
overdisperion multiplicative.

In the example below, the random effect of RowID has 0 variance. Hence
no overdispersion.

dataset <- data.frame(
male_chick_no = c(2,4,1,0,3,5,2),
female_chick_no=c(1,0,3,3,1,0,2),
FemaleID=c("A","A","B","B","C","D","E"))

longFormat <- do.call(rbind, lapply(seq_len(nrow(dataset)), function(i){
with(dataset, data.frame(Sex = c(rep("M", male_chick_no[i]),
rep("F", female_chick_no[i])), FemaleID = FemaleID[i]))
}))
longFormat$FemaleID <- factor(longFormat$FemaleID)
longFormat$RowID <- factor(seq_len(nrow(longFormat)))
longFormat$Male <- longFormat$Sex == "M"

library(lme4)
fit1 <- glmer(Male ~ (1|FemaleID), data = longFormat, family = binomial)
fit2 <- glmer(Male ~ (1|FemaleID) + (1|RowID), data = longFormat, family
= binomial)
anova(fit1, fit2)

Best regards,

Thierry

PS sig-mixed-models is a better mailinglist for this kind of questions.



ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium

Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium

tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey



-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] Namens cct663
Verzonden: vrijdag 19 november 2010 5:39
Aan: r-help@r-project.org
Onderwerp: [R] Question on overdispersion


I have a few questions relating to overdispersion in a sex
ratio data set that I am working with (note that I already
have an analysis with GLMMs for fixed effects, this is just
to estimate dispersion). The response variable is binomial
because nestlings can only be male or female. I have samples of
1-5 nestlings from each nest (individuals within a nest are
not independent, so the response variable is the ratio of
sons to daughters) and some females have multiple nests in
the data set (so I need to include female identity as a
random effect).

Here is an example of what the three vectors used in the
model look like (the real data set is much bigger, just to
illustrate what I'm talking
about):

male_chick_no=c(2,4,1,0,3,5,2)
female_chick_no=c(1,0,3,3,1,0,2)
FemaleID=c(A,A,B,B,C,D,E)

My first question relates to coding the test in R. I received
this suggested R syntax from a reviewer:

SexRatio = cbind(male_chick_no, female_chick_no)

Model <- lmer(SexRatio ~ 1 +(1|FemaleID), family = quasibinomial)

But when I try to use this in R I get the error: "Error in
glmer(formula = ratio ~ 1 + (1 | femid), family =
quasibinomial) : "quasi" families cannot be used in glmer".

I've tried playing around with some other mixed model
functions but can't seem to find one that will provide an
estimate of dispersion and allow me to include my random effect.

Is there some other function I should be using? Or is there a
different syntax that I should use for lmer?

My second question is more general: I understand that with
binomial data overdispersion suggests that the observed data
have a greater variance than expected given binomial errors
(in my case this means that more nests would be all male/all
female than expected if sex is random). So with binomial
errors the expected estimate of dispersion is 1, if I find
that dispersion is > 1 it suggests that my data are
overdispersed. My question is, how much greater than 1 should
that number be to conclude that the data are overdispersed?
Is there a rule of thumb or does it just depend on the dataset?

I was thinking of doing a randomization test with the same
structure (nest size and female id) as my real data set but
with sex ratio of each ne

[R] unexpected behaviour with sparse.model.matrix

[Jarrod Hadfield]

Hi,

I'm trying to get sparse.model.matrix to retain unused levels. I can't  
seem to get this working through the most obvious routes such as  
specifying drop.unused.levels = FALSE in the model.frame or trying to  
pass all levels in xlev,which is an argument to sparse.model.matrix  
(see code below).


Any help would be gratefully received.

Cheers,

Jarrod


fac<-factor(rep(1:10,10), levels=1:100)
mf<-model.frame(~fac, drop.unused.levels = TRUE)
mf2<-model.frame(~fac, drop.unused.levels = FALSE)

dim(model.matrix(~fac, mf))
dim(model.matrix(~fac, mf2))
dim(model.matrix(~fac, xlev=list(fac=1:10)))
dim(model.matrix(~fac, xlev=list(fac=1:100)))

dim(sparse.model.matrix(~fac, mf))
dim(sparse.model.matrix(~fac, mf2))
dim(sparse.model.matrix(~fac, xlev=list(fac=1:10)))
dim(sparse.model.matrix(~fac, xlev=list(fac=1:100)))

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
__
R-help@r-project.org mailing list
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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.

Re: [R] [Rd] R CMD build wiped my computer

[Jarrod Hadfield]

Hi Marc,

Thanks for the info on recovery - most of it can pieced together from  
backups but a quick, cheap and easy method of recovery would have been  
nicer.


My main concern is that this could happen again and that the "bug" is  
not limited to R 2.9. I would think that an accidental carriage return  
at the end of a file name (even a temporary one) would be a reasonably  
common phenomenon (I'm surprised I hadn't done it before).


Cheers,

Jarrod



On 28 Jul 2010, at 14:04, Marc Schwartz wrote:


Jarrod,

Noting your exchange with Martin, Martin brings up a point that  
certainly I missed, which is that somehow the tilde ('~') character  
got into the chain of events. As Martin noted, on Linuxen/Unixen  
(including OSX), the tilde, when used in the context of file name  
globbing, refers to your home directory. Thus, a command such as:


 ls ~

will list the files in your home directory. Similarly:

 rm ~

will remove the files there as well. If the -rf argument is added,  
then the deletion becomes recursive through that directory tree,  
which appears to be the case here.


I am unclear, as Martin appears to be, as to the steps that caused  
this to happen. That may yet be related in some fashion to Duncan's  
hypothesis.


That being said, the use of the tilde character as a suffix to  
denote that a file is a backup version, is not limited to Fedora or  
Linux, for that matter. It is quite common for many text editors  
(eg. Emacs) to use this. As a result, it is also common for many  
applications to ignore files that have a tilde suffix.


Based upon your follow up posts to the original thread, it would  
seem that you do not have any backups. The default ext3 file system  
that is used on modern Linuxen, by design, makes it a bit more  
difficult to recover deleted files. This is due to the unlinking of  
file metadata at the file system data structure level, as opposed to  
simply marking the file as deleted in the directory structures, as  
happens on Windows.


There is a utility called ext3undel (http://projects.izzysoft.de/trac/ext3undel 
), which is a wrapper of sorts to other undelete utilities such as  
PhotoRec and foremost. I have not used it/them, so cannot speak from  
personal experience. Thus it would be a good idea to engage in some  
reviews of the documentation and perhaps other online resources  
before proceeding. The other consideration is the Catch-22 of not  
copying anything new to your existing HD, for fear of overwriting  
the lost files with new data. So you would need to consider an  
approach of downloading these utilities via another computer and  
then running them on the computer in question from other media, such  
as a CD/DVD or USB HD.


A more expensive option would be to use a professional data recovery  
service, where you would have to consider the cost of recovery  
versus your lost time. One option would be Kroll OnTrack UK (http://www.ontrackdatarecovery.co.uk/ 
). I happen to live about a quarter mile from their world HQ here in  
a suburb of Minneapolis. I have not used them myself, but others  
that I know have, with good success. Again, this comes at a  
potentially substantial monetary cost.


The key is that if you have any hope to recover the deleted files,  
you not copy anything new onto the hard drive in the mean time.  
Doing so will decrease the possibility of file recovery to near 0.


As Duncan noted, there is great empathy with your situation. We have  
all gone through this at one time or another. In my case, it was  
perhaps 20+ years ago, but as a result, I am quite anal retentive  
about having backups, which I have done for some time on my systems,  
hourly.


HTH,

Marc Schwartz


On Jul 28, 2010, at 5:55 AM, Jarrod Hadfield wrote:


Hi Martin,

I think this is the most likely reason given that the name in the  
DESCRIPTION file does NOT have a version number. Even so, it is  
very easy to misname a file and then delete it/change its name (as  
I've done here) and I hope current versions of R would not cause  
this problem. Perhaps Fedora should not use ~ as its back up file  
suffixes?


Cheers,

Jarrod


On 28 Jul 2010, at 11:41, Martin Maechler wrote:


Jarrod Hadfield 
 on Tue, 27 Jul 2010 21:37:09 +0100 writes:



Hi, I ran R (version 2.9.0) CMD build under root in
Fedora (9). When it tried to remove "junk files" it
removed EVERYTHING in my local account! (See below).



Can anyone tell me what happened,


the culprit may lay here:

* removing junk files
unlink MCMCglmm_2.05/R/   residuals.MCMCglmm.R
~


where it seems that someone (you?) have added a newline
in the filname, so instead of
'residuals.MCMCglmm.R~'
you got

'residuals.MCMCglmm.R
~'

and the unlink / rm  command interpreted '~' as your home
directory.

But I can hardly believe it.
This seems explanation seems a bit doubtful to me.. ...


and even more importantly if I can I rest

Re: [R] [Rd] R CMD build wiped my computer

[Jarrod Hadfield]

Hi Martin,

I think this is the most likely reason given that the name in the  
DESCRIPTION file does NOT have a version number. Even so, it is very  
easy to misname a file and then delete it/change its name (as I've  
done here) and I hope current versions of R would not cause this  
problem. Perhaps Fedora should not use ~ as its back up file suffixes?


Cheers,

Jarrod


On 28 Jul 2010, at 11:41, Martin Maechler wrote:


Jarrod Hadfield 
   on Tue, 27 Jul 2010 21:37:09 +0100 writes:



Hi, I ran R (version 2.9.0) CMD build under root in
Fedora (9). When it tried to remove "junk files" it
removed EVERYTHING in my local account! (See below).



Can anyone tell me what happened,


the culprit may lay here:

* removing junk files
unlink MCMCglmm_2.05/R/   residuals.MCMCglmm.R
~


where it seems that someone (you?) have added a newline
in the filname, so instead of
'residuals.MCMCglmm.R~'
you got

'residuals.MCMCglmm.R
~'

and the unlink / rm  command interpreted '~' as your home
directory.

But I can hardly believe it.
This seems explanation seems a bit doubtful to me.. ...


and even more importantly if I can I restore what was lost.


well, you just get it from the backup. You do daily backups, do
you?

Regards,
Martin Maechler, ETH Zurich


Panickingly,



Jarrod



[jar...@localhost AManal]$ R CMD build MCMCglmm_2.05
* checking for file 'MCMCglmm_2.05/DESCRIPTION' ... OK
* preparing 'MCMCglmm_2.05':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package ?MCMCglmm? ...
** libs
g++ -m64 -I/usr/include/R  -I/usr/local/include-fpic  -O2 -g - 
pipe

-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c MCMCglmm.cc -o
MCMCglmm.o
MCMCglmm.cc: In function ?void MCMCglmm(double*, double*, double*,
int*, int*, int*, int*, int*, int*, double*, int*, int*, double*,
int*, int*, double*, double*, int*, int*, int*, int*, int*, int*,
int*, int*, int*, int*, double*, double*, double*, int*, int*, int*,
int*, double*, double*, double*, int*, double*, bool*, double*,
double*, int*, int*, int*, int*, int*, double*, int*, int*, int*,
double*, double*, double*, int*, int*, double*, int*, int*, int*,
int*, double*, double*, double*, double*)?:
MCMCglmm.cc:228: warning: ?pvLS? may be used uninitialized in this  
function
MCMCglmm.cc:227: warning: ?pvLL? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?Lrv? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?pmuL? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?pvL? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?LambdaX? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?bv_tmp? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?bv? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?A? may be used uninitialized in this  
function
MCMCglmm.cc:86: warning: ?dimG? may be used uninitialized in this  
function

MCMCglmm.cc:228: warning: ?AlphainvS? may be used uninitialized in
this function
MCMCglmm.cc:227: warning: ?AlphainvL? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphalocation_tmp? may be used
uninitialized in this function
MCMCglmm.cc:225: warning: ?alphalocation? may be used uninitialized  
in

this function
MCMCglmm.cc:225: warning: ?alphazstar? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphapred? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphaastar? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?muAlpha? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?Alphainv? may be used uninitialized in  
this

function
MCMCglmm.cc:225: warning: ?tXalpha? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?Xalpha? may be used uninitialized in  
this function

MCMCglmm.cc:225: warning: ?linky_orig? may be used uninitialized in
this function
MCMCglmm.cc:228: warning: ?tYKrinvYS? may be used uninitialized in
this function
MCMCglmm.cc:228: warning: ?LambdaS? may be used uninitialized in  
this function

MCMCglmm.cc:227: warning: ?tYKrinvYL? may be used uninitialized in
this function
MCMCglmm.cc:227: warning: ?LambdaLU? may be used uninitialized in  
this

function
MCMCglmm.cc:225: warning: ?tYKrinvY? may be used uninitialized in  
this

function
MCMCglmm.cc:225: warning: ?tYKrinv? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?ILY? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?tY? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?Y? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?I? may be used uninitialized in this  
function
MCMCglmm.cc:228: warning: ?alphaS? may be used uninitializ

Re: [R] R CMD build wiped my computer

[Jarrod Hadfield]

Hi,

Thanks for your responses. Although a wrist slapping for not keeping  
updated with R/Fedora may be warranted,  I find it quite terrifying  
that by simply having a version number in a directory name R went on  
to try and erase everything on the computer! Thank god I wasn't logged  
in as root.


Anyway, the more pressing issue is what I can do about this. My main  
concern is recovering those changes that were made to the package  
prior to its deletion. Luckily, just before running R CMD build I ran  
R CMD install under root (hence my belief I had ran R CMD build under  
root). I also have an open terminal for which the current package is  
loaded (and working I think). My question is how and how much can be  
recovered from this - having the C/C++ code would be particularly  
useful.


Cheers,

Jarrod


On 27 Jul 2010, at 22:53, Duncan Murdoch wrote:


On 27/07/2010 4:39 PM, Jarrod Hadfield wrote:

Hi,
I ran R (version 2.9.0) CMD build under root in Fedora (9). When it
tried to remove "junk files" it removed EVERYTHING in my local
account! (See below).
Can anyone tell me what happened, and even more importantly if I  
can I

restore what was lost.


You did several things you shouldn't have done.  Don't run as root  
unless you need to do what root can do.  R CMD build shouldn't need  
special permissions, so it shouldn't be run as root.  (Actually, it  
looks as though you didn't run as root: you got a number of  
"permissions denied" messages.)


And don't run obsolete versions of R.  There have been a lot of bug  
fixes since 2.9.0; you should take advantage of them.


You should have known those two.  One thing you might not have known  
is that it's a bad idea to name a package with the version number in  
the directory name.  I don't think this will cause a lot of trouble  
with current versions of R, but it won't work.  Apparently in 2.9.0  
it caused  a lot of trouble.


Basically you need to restore from your backup.  If you don't have  
one, you just learned how important Davidson's laws of computing are:


The First Law: Back it up.

The Second Law:  Do it now.

It may not sound like it, but I am sympathetic.

Duncan Murdoch



Panickingly,
Jarrod
[jar...@localhost AManal]$ R CMD build MCMCglmm_2.05
* checking for file 'MCMCglmm_2.05/DESCRIPTION' ... OK
* preparing 'MCMCglmm_2.05':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package ?MCMCglmm? ...
** libs
g++ -m64 -I/usr/include/R  -I/usr/local/include-fpic  -O2 -g - 
pipe

-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c MCMCglmm.cc -o
MCMCglmm.o
MCMCglmm.cc: In function ?void MCMCglmm(double*, double*, double*,
int*, int*, int*, int*, int*, int*, double*, int*, int*, double*,
int*, int*, double*, double*, int*, int*, int*, int*, int*, int*,
int*, int*, int*, int*, double*, double*, double*, int*, int*, int*,
int*, double*, double*, double*, int*, double*, bool*, double*,
double*, int*, int*, int*, int*, int*, double*, int*, int*, int*,
double*, double*, double*, int*, int*, double*, int*, int*, int*,
int*, double*, double*, double*, double*)?:
MCMCglmm.cc:228: warning: ?pvLS? may be used uninitialized in this  
function
MCMCglmm.cc:227: warning: ?pvLL? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?Lrv? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?pmuL? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?pvL? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?LambdaX? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?bv_tmp? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?bv? may be used uninitialized in this  
function
MCMCglmm.cc:225: warning: ?A? may be used uninitialized in this  
function
MCMCglmm.cc:86: warning: ?dimG? may be used uninitialized in this  
function

MCMCglmm.cc:228: warning: ?AlphainvS? may be used uninitialized in
this function
MCMCglmm.cc:227: warning: ?AlphainvL? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphalocation_tmp? may be used
uninitialized in this function
MCMCglmm.cc:225: warning: ?alphalocation? may be used uninitialized  
in

this function
MCMCglmm.cc:225: warning: ?alphazstar? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphapred? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphaastar? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?muAlpha? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?Alphainv? may be used uninitialized in  
this

function
MCMCglmm.cc:225: warning: ?tXalpha? may be used uninitialized in  
this function
MCMCglmm.cc:225: warning: ?Xalpha? may be used uninitialized i

[R] R CMD build wiped my computer

[Jarrod Hadfield]

Hi,

I ran R (version 2.9.0) CMD build under root in Fedora (9). When it
tried to remove "junk files" it removed EVERYTHING in my local
account! (See below).

Can anyone tell me what happened, and even more importantly if I can I
restore what was lost.

Panickingly,

Jarrod

[jar...@localhost AManal]$ R CMD build MCMCglmm_2.05
* checking for file 'MCMCglmm_2.05/DESCRIPTION' ... OK
* preparing 'MCMCglmm_2.05':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package ?MCMCglmm? ...
** libs
g++ -m64 -I/usr/include/R  -I/usr/local/include-fpic  -O2 -g -pipe
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c MCMCglmm.cc -o
MCMCglmm.o
MCMCglmm.cc: In function ?void MCMCglmm(double*, double*, double*,
int*, int*, int*, int*, int*, int*, double*, int*, int*, double*,
int*, int*, double*, double*, int*, int*, int*, int*, int*, int*,
int*, int*, int*, int*, double*, double*, double*, int*, int*, int*,
int*, double*, double*, double*, int*, double*, bool*, double*,
double*, int*, int*, int*, int*, int*, double*, int*, int*, int*,
double*, double*, double*, int*, int*, double*, int*, int*, int*,
int*, double*, double*, double*, double*)?:
MCMCglmm.cc:228: warning: ?pvLS? may be used uninitialized in this function
MCMCglmm.cc:227: warning: ?pvLL? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?Lrv? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?pmuL? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?pvL? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?LambdaX? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?bv_tmp? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?bv? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?A? may be used uninitialized in this function
MCMCglmm.cc:86: warning: ?dimG? may be used uninitialized in this function
MCMCglmm.cc:228: warning: ?AlphainvS? may be used uninitialized in
this function
MCMCglmm.cc:227: warning: ?AlphainvL? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphalocation_tmp? may be used
uninitialized in this function
MCMCglmm.cc:225: warning: ?alphalocation? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphazstar? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphapred? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?alphaastar? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?muAlpha? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?Alphainv? may be used uninitialized in this
function
MCMCglmm.cc:225: warning: ?tXalpha? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?Xalpha? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?linky_orig? may be used uninitialized in
this function
MCMCglmm.cc:228: warning: ?tYKrinvYS? may be used uninitialized in
this function
MCMCglmm.cc:228: warning: ?LambdaS? may be used uninitialized in this function
MCMCglmm.cc:227: warning: ?tYKrinvYL? may be used uninitialized in
this function
MCMCglmm.cc:227: warning: ?LambdaLU? may be used uninitialized in this
function
MCMCglmm.cc:225: warning: ?tYKrinvY? may be used uninitialized in this
function
MCMCglmm.cc:225: warning: ?tYKrinv? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?ILY? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?tY? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?Y? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?I? may be used uninitialized in this function
MCMCglmm.cc:228: warning: ?alphaS? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?alphaMME? may be used uninitialized in this
function
MCMCglmm.cc:225: warning: ?alphaM? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?XtmKRinv? may be used uninitialized in this
function
MCMCglmm.cc:227: warning: ?alphaL? may be used uninitialized in this function
MCMCglmm.cc:227: warning: ?L? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?alphaastar_tmp? may be used uninitialized
in this function
MCMCglmm.cc:225: warning: ?dev? may be used uninitialized in this function
MCMCglmm.cc:225: warning: ?astar_tmp? may be used uninitialized in
this function
MCMCglmm.cc:225: warning: ?Worig? may be used uninitialized in this function
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include-fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_add.c -o cs_add.o
gcc -m64 -std=gnu99 -I/usr/include/R  -I/usr/local/include-fpic
-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c
cs_addR.

Re: [R] mcmcglmm starting value example

[Jarrod Hadfield]

Dear Ping,

It is not possible to pass starting values for the fixed effects. It  
doesn't make much sense to give starting values for the fixed effects  
because they can be Gibbs sampled in a single pass conditional on the  
latent variables and the (co)variance components - after a single  
iteration they would "forget" their starting values.  The cut points  
in an ordinal model are a different matter. At the moment I do not  
allow user defined starting values for the cut points, but agree that  
it may be useful. I am about to release an update that allows spline  
fitting in MCMCglmm. If it is starting values for the cut points  
you're really after I can add that in before I release?


Cheers,

Jarrod


On 29 Mar 2010, at 22:06, ping chen wrote:


Hi R-users:

Can anyone give an example of giving starting values for MCMCglmm?
I can't find any anywhere.
I have 1 random effect (physicians, and there are 50 of them)
and family="ordinal"．

How can I specify starting values for my fixed effects? It doesn't  
seem to have the option to do so.


Thanks, Ping







--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

[R] plotmath

[Jarrod Hadfield]

Hi,

I want to have a legend that is a mixture of numbers and symbols, and  
have found no way of achieving this.


For example, if I want theta="x" or theta=2 this is easily achieved.

plot(0, xlab=expression(paste(theta, "= x")))
plot(0, xlab=expression(paste(theta, "= 2")))

However, if x is some numeric variable and I want to plot theta=x, how  
is this done?


Thanks for any help,

Jarrod


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

Re: [R] change attributes of all data.frame elements

[Jarrod Hadfield]

Hi Philipp,

# Sorry - perhaps I wasn't being very clear. For example, creating the  
data frame:


df<-data.frame(y=rnorm(100), x=array(1:100))

# gives 2 elements, the last of which has a dim attribute

lapply(df, dim)

# I would like some way of changing the dim attribute to NULL for all  
elements.


Thanks,

Jarrod




I was wondering whether there was an easy way to change the attributes
of all elements in a data.frame (rather than looping through  
elements)?


Specifically, I would like to set the "dim" attributes to NULL


Maybe I just don't really understand what you are after. The elements
of a data.frame are vectors so by definition they only have one
dimension. Furthermore, they are required to be the same length -
otherwise it wouldn't be a proper data.frame, anymore.

So I guess you really want to accomplish something I didn't quite
grasp. Could you give an example?

cu
Philipp

--
Dr. Philipp Pagel
Lehrstuhl f?r Genomorientierte Bioinformatik
Technische Universit?t M?nchen
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany
http://mips.gsf.de/staff/pagel


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
__
R-help@r-project.org mailing list
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.

[R] change attributes of all data.frame elements

[Jarrod Hadfield]

Hi,

I was wondering whether there was an easy way to change the attributes  
of all elements in a data.frame (rather than looping through elements)?


Specifically, I would like to set the "dim" attributes to NULL

Thanks for any help,

Jarrod



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

Re: [R] generalized mixed model + mcmcsamp

[Jarrod Hadfield]

Hi Thomas/Ben,

This model ca be MCMCed using MCMCglmm by specifying  
"multinomial2" (i.e. binomial) in the family argument.  MCMCglmm by  
default, fits a residual in the linear model to soak up extra-binomial  
variation, which is similar in motivation to quasi models.


Cheers,

Jarrod








Hi,

I have fitted a generalized linear mixed effects model using lmer  
(library lme4), and the family = quasibinomial. I have tried to obtain  
a MCMC sample, but on calling mcmcsamp(model1, 1000) I get the  
following error which I don't understand at all:


Error in .local(object, n, verbose, ...) : Update not yet written

traceback() delivers:

4: .Call(mer_MCMCsamp, ans, object)
3: .local(object, n, verbose, ...)
2: mcmcsamp(model1, n = 1000, verbose = FALSE)
1: mcmcsamp(model1, n = 1000, verbose = FALSE)


which again doesn't particularly help me.

R is 2.8.1 under Windows, lme4 clean installed just today. Before the  
model is fitted I just read in data, and transform some variables. No  
other library is loaded.


Any ideas ?

thanks,
Thomas 


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

[R] model.matrix and missing values

[Jarrod Hadfield]

Hi,

Does anyone know an easy way of retaining rows in a model.matrix where  
missing values are present in the predictors.  Ideally I'd be able to  
retain these rows as zeros.


Thanks,

Jarrod



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

[R] uppercase greek and plotmath

[Jarrod Hadfield]

Hi,

I cant seem to get some uppercase greek symbols (e.g. Delta) using   
plotmath.  I'm on version R 2.7.0 (2008-04-22) Fedora Core 7 (34   
bit).  I have installed a whole heap of fonts, but still no luck, and  
any help would be appreciated.


 Cheers,

Jarrod


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

__
R-help@r-project.org mailing list
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.

Re: [R] linking C/C++ external libraries.

[Jarrod Hadfield]

Hi Dirk,

ldd is not bringing up csparse which suggests that it is a linking  
problem.  For liking I used both the SHLIB and INSTALL comands using - 
L (see below), but both generate the same problem.

Cheers,

Jarrod

[EMAIL PROTECTED] ~]$ R CMD SHLIB ~/Work/AManal2/src/SStest.cc -L/ 
home/jarrod/My_Programs/SuiteSparse/CSparse/Lib -lcsparse
g++ -I/usr/lib/R/include -I/usr/lib/R/include  -I/usr/local/ 
include-fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 - 
fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 - 
march=i386 -mtune=generic -fasynchronous-unwind-tables -c /home/ 
jarrod/Work/AManal2/src/SStest.cc -o /home/jarrod/Work/AManal2/src/ 
SStest.o
/home/jarrod/Work/AManal2/src/SStest.cc: In function ‘void SStest 
(int*, int*, double*, int*, int*)’:
/home/jarrod/Work/AManal2/src/SStest.cc:18: warning: unused variable  
‘iA’
/home/jarrod/Work/AManal2/src/SStest.cc:19: warning: unused variable  
‘pA’
/home/jarrod/Work/AManal2/src/SStest.cc:20: warning: unused variable  
‘xA’
g++ -shared -L/usr/local/lib -o /home/jarrod/Work/AManal2/src/ 
SStest.so /home/jarrod/Work/AManal2/src/SStest.o -L/home/jarrod/ 
My_Programs/SuiteSparse/CSparse/Lib -lcsparse  -L/usr/lib/R/lib -lR

 >dyn.load("~/Work/AManal2/src/SStest.so")
Error in dyn.load("~/Work/AManal2/src/SStest.so") :
   unable to load shared library '/home/jarrod/Work/AManal2/src/ 
SStest.so':
   /home/jarrod/Work/AManal2/src/SStest.so: undefined symbol:  
_Z10cs_spalloci


[EMAIL PROTECTED] ~]$ R CMD INSTALL -l ~/Desktop  ~/Work/AManal2
* Installing *source* package 'AManal' ...
** libs
g++ -I/usr/lib/R/include -I/usr/lib/R/include -I/home/jarrod/ 
My_Programs/SuiteSparse/CSparse/Include -I/usr/local/include- 
fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack- 
protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic - 
fasynchronous-unwind-tables -c SStest.cc -o SStest.o
SStest.cc: In function ‘void SStest(int*, int*, double*, int*, int*) 
’:
SStest.cc:18: warning: unused variable ‘iA’
SStest.cc:19: warning: unused variable ‘pA’
SStest.cc:20: warning: unused variable ‘xA’
g++ -shared -L/usr/local/lib -o AManal.so SStest.o -L/home/jarrod/ 
My_Programs/SuiteSparse/CSparse/Lib -lcsparse  -L/usr/lib/R/lib -lR
** R
** data
** preparing package for lazy loading
** help
  >>> Building/Updating help pages for package 'AManal'
  Formats: text html latex example
** building package indices ...
* DONE (AManal)

library("AManal", lib.loc="~/Desktop")
Error in dyn.load(file, ...) :
   unable to load shared library '/home/jarrod/Desktop/AManal/libs/ 
AManal.so':
   /home/jarrod/Desktop/AManal/libs/AManal.so: undefined symbol:  
_Z10cs_spalloci
Error: package/namespace load failed for 'AManal'

On 3 Dec 2007, at 16:57, Dirk Eddelbuettel wrote:

>
> On 3 December 2007 at 14:54, Jarrod Hadfield wrote:
> | I'm trying to load some C++ code using dyn.load but I'm getting
> | unresolved symbols associated with some external libraries
> | (CSparse).  I gather this is something to do with linking as the the
> | code compiles fine.  However, I've passed
> |
> | -L/home/jarrod/My_Programs/SuiteSparse/CSparse/Lib -lcsparse
> |
> | to the complier (g++), either directly using R CMD SHLIB or as
> | PKG_LIBS in a Makevars file, and I cannot resolve the problem.  I'm
> | working with R 2.6.0 on fedora 6
> |
> | Any help would be appreciated.
>
> Can you show us your error message upon load?  What does ldd say  
> when pointed
> at your package's library?  How exactly is the linking done?
>
> Compare all that to a working library such as eg Matrix. That may  
> provide
> further clues.
>
> Hth, Dirk
>
> -- 
> Three out of two people have difficulties with fractions.
>


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[R] linking C/C++ external libraries.

[Jarrod Hadfield]

Hi Everyone,

I'm trying to load some C++ code using dyn.load but I'm getting  
unresolved symbols associated with some external libraries  
(CSparse).  I gather this is something to do with linking as the the  
code compiles fine.  However, I've passed

-L/home/jarrod/My_Programs/SuiteSparse/CSparse/Lib -lcsparse

to the complier (g++), either directly using R CMD SHLIB or as  
PKG_LIBS in a Makevars file, and I cannot resolve the problem.  I'm  
working with R 2.6.0 on fedora 6

Any help would be appreciated.

Thanks,

Jarrod

__
R-help@r-project.org mailing list
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.