date:20050928

[R] need suggestion about building formual

2005-09-28 Thread Simple

hi,
I'm an newbie for R,I want do some fitting in R.

I wander if it is possible to write a few of equations but only one formual 
when fitting 

Currently,My problem is,in R, is there methods combination a few equations 
into one formual?
For example, 
y=f1(k);
k=f2(t);
t=f3(x);
although it is certain that the can be equations turn into one formual as 
y~f(x),but write such a complexity string make me painful.

I have searched the web and found out there were only examples with one 
formual.any suggestion? 

I hope that I have omit something.

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[R] gfortran Makefile for cygwin

2005-09-28 Thread Joel Bremson

Hi all,

I'm porting a package that I've worked on for OS X to Cygwin/Windows.

This package requires a Makefile. My question is, how can I find out
(or what is), the link command?

Here is the OS X Makefile:


RLIB_LOC=${R_HOME}

F90_FILES=\
class_data_frame.f90 \
class_old_dbest.f90 \
class_cm_data.f90 \
class_cm.f90 \
class_bgw.f90 \
class_cm_mle.f90 \
cme.f90


FORTRAN_FILES=\
dgletc.f \
dglfgb.f\
dglfg.f\
dmdc.f\
mecdf.f


%.o: %.f90
gfortran -c -g $

%.o: %.f
gfortran -c -g $

bpkg.so: $(F90_FILES:%.f90=%.o) $(FORTRAN_FILES:%.f=%.o)
gcc -Wall -bundle -flat_namespace -undefined suppress -L/sw/lib
-L/usr/local/lib -o $@ $^ \
-L$(RLIB_LOC)/lib -lR

###EOF

The -L lib dirs are not correct. On a *nix platform I would do something
like this

sh -x R CMD SHLIB ...

to get at the R internal link information but I can't get that to work on
Cygwin.

Regards,

Joel


--
Joel Bremson
Graduate Student
Institute for Transportation Studies - UC Davis
http://etrans.blogspot.com

[[alternative HTML version deleted]]

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Re: [R] scatterplot3d + density() + polygon(color)

2005-09-28 Thread Uwe Ligges

klebyn wrote:
 Hi R Users,
 
 How to use the function polygon()
 together with the package scatterplot3d?
 
 I am trying to color below of the curves
 defined for the function density().
 
 I tried to use the site: R GRAPH GALLERY
 as tutorial.
 
 I tried to adapt the example of this page:
 [figure]:
 http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=30
 
 [code]:
 http://addictedtor.free.fr/graphiques/sources/source_30.R
 
 to my case but I do not obtain success.
 
 Somebody could give a tip to me, please?
 
 I am thankful anticipatedly.
 
 Cleber Borges
 
 
 
 #My code test
 ##
 library(scatterplot3d)
 x=c(0.4, -1.2, .8, -.7, 0)
 
 d1 = density(x[1],bw=1.2, from=-3.0,  to=3.0  )
 d2 = density(x[2],bw=0.8, from=-3.0,  to=3.0  )
 d3 = density(x[3],bw=0.6, from=-2.5,  to=2.5  )
 d4 = density(x[4],bw=0.5, from=-2.0,  to=2.0  )
 d5 = density(x[5],bw=0.3, from=-1.5,  to=1.5  )
 
 sx = c(d1$x,d2$x,d3$x,d4$x,d5$x)
 sy = c(d1$y,d2$y,d3$y,d4$y,d5$y)
 sz = c(rep(0.1,512),rep(0.2,512),rep(0.3,512),rep(0.4,512),rep(0.5,512))
 
 scatterplot3d(x=sx,y=sz,z=sy,type='l')
 ##
 
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Example:

 library(scatterplot3d)

 x - c(0.4, -1.2, .8, -.7, 0)
 d - vector(length = length(x), mode = list)
 d[[1]] - density(x[1], bw = 1.2, from = -3.0, to = 3.0)
 d[[2]] - density(x[2], bw = 0.8, from = -3.0, to = 3.0)
 d[[3]] - density(x[3], bw = 0.6, from = -2.5, to = 2.5)
 d[[4]] - density(x[4], bw = 0.5, from = -2.0, to = 2.0)
 d[[5]] - density(x[5], bw = 0.3, from = -1.5, to = 1.5)

 x - lapply(d, [[, x)
 y - lapply(d, [[, y)
 z - lapply(seq(0.1, 0.5, 0.1), rep, each = 512)

 sx - unlist(x)
 sy - unlist(y)
 sz - unlist(z)

 s3d - scatterplot3d(x = sx, y = sz, z = sy, type = n)
 for(i in rev(seq(along=d))){
 s3d_coords - s3d$xyz.convert(x[[i]], z[[i]], y[[i]])
 polygon(s3d_coords, col = i, border = black)
 }


Uwe Ligges

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Re: [R] gfortran Makefile for cygwin

2005-09-28 Thread Uwe Ligges

Joel Bremson wrote:

 Hi all,
 
 I'm porting a package that I've worked on for OS X to Cygwin/Windows.

Cygwin is not supported.

Please use MinGW's compilers, the tools and import from MkRules, as the 
manuals indicate. See other packages' Makefile.win files as examples.

Messages regarding development seem to be more appropriate for the 
R-devel list.
[Please move it there for follow-ups.]

Uwe Ligges


 This package requires a Makefile. My question is, how can I find out
 (or what is), the link command?
 
 Here is the OS X Makefile:
 
 
 RLIB_LOC=${R_HOME}
 
 F90_FILES=\
 class_data_frame.f90 \
 class_old_dbest.f90 \
 class_cm_data.f90 \
 class_cm.f90 \
 class_bgw.f90 \
 class_cm_mle.f90 \
 cme.f90
 
 
 FORTRAN_FILES=\
 dgletc.f \
 dglfgb.f\
 dglfg.f\
 dmdc.f\
 mecdf.f
 
 
 %.o: %.f90
 gfortran -c -g $
 
 %.o: %.f
 gfortran -c -g $
 
 bpkg.so: $(F90_FILES:%.f90=%.o) $(FORTRAN_FILES:%.f=%.o)
 gcc -Wall -bundle -flat_namespace -undefined suppress -L/sw/lib
 -L/usr/local/lib -o $@ $^ \
 -L$(RLIB_LOC)/lib -lR
 
 ###EOF
 
 The -L lib dirs are not correct. On a *nix platform I would do something
 like this
 
 sh -x R CMD SHLIB ...
 
 to get at the R internal link information but I can't get that to work on
 Cygwin.
 
 Regards,
 
 Joel
 
 
 --
 Joel Bremson
 Graduate Student
 Institute for Transportation Studies - UC Davis
 http://etrans.blogspot.com
 
   [[alternative HTML version deleted]]
 
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Re: [R] Question on lm(): When does R-squared come out as NA?

2005-09-28 Thread Prof Brian Ripley

I've not seen a reply to this, nor ever seen it.
Please make a reproducible example available (do see the posting guide).

On Sun, 25 Sep 2005, Ajay Narottam Shah wrote:

 I have a situation with a large dataset (3000+ observations), where
 I'm doing lags as regressors, where I get:

 Call:
 lm(formula = rj ~ rM + rM.1 + rM.2 + rM.3 + rM.4)

 Residuals:
 1990-06-04 1994-11-14 1998-08-21 2002-03-13 2005-09-15
  -5.64672   -0.59596   -0.041430.554128.18229

 Coefficients:
 Estimate Std. Error t value Pr(|t|)
 (Intercept) -0.003297   0.017603  -0.1870.851
 rM   0.845169   0.010522  80.322   2e-16 ***
 rM.1 0.116330   0.010692  10.880   2e-16 ***
 rM.2 0.002044   0.010686   0.1910.848
 rM.3 0.013181   0.010692   1.2330.218
 rM.4 0.009587   0.010525   0.9110.362
 ---
 Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

 Residual standard error: 1.044 on 3532 degrees of freedom
 Multiple R-Squared:NA,Adjusted R-squared:NA
 F-statistic:NA on 5 and 3532 DF,  p-value: NA


 rM.1, rM.2, etc. are lagged values of rM. The OLS seems fine in every
 respect, except that there is an NA as the multiple R-squared. I will
 be happy to give sample data to someone curious about what is going
 on. I wondered if this was a well-known pathology. The way I know it,
 if the data allows computation of (X'X)^{-1}, one can compute the R2.

 -- 
 Ajay Shah   Consultant
 [EMAIL PROTECTED]  Department of Economic Affairs
 http://www.mayin.org/ajayshah   Ministry of Finance, New Delhi

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-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [R] R CMD build produces tar error under FreeBSD 5.4

2005-09-28 Thread Prof Brian Ripley

On Tue, 27 Sep 2005, Eric van Gyzen wrote:

On Sun, Sep 25, 2005 at 12:07:02PM +0100, Prof Brian Ripley wrote:
On Sun, 25 Sep 2005, Andrew Robinson wrote:

Hi R-helpers,

I am trying to build a package under FreeBSD 5.4-RELEASE #0 using R
Version 2.1.1.

I have constructed a package using package.skeleton(), when I try

$ R CMD build foo
* checking for file 'foo/DESCRIPTION' ... OK
* preparing 'foo':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* removing junk files
tar: Option -L is not permitted in mode -x
Error: cannot open file 'foo/DESCRIPTION' for reading

foo/DESCRIPTION exists and the permissions are correct. The same
command works under Linux Fedora 2. The man pages on each OS imply
that tar differs across the two platforms. Does anyone have any
thoughts on a work-around?

No, because R does not use tar -L (which is to do with tape lengths on GNU
tar).

It does use tar chf and tar xhf. The h modifier would appear to be
applicable only to dumps, so at a wild guess the error message means -h is
not permitted. Try replacing xhf by xf.

FreeBSD = 5.3 uses bsdtar. Previous versions used GNU tar.

In bsdtar, -h is a synonym for -L, and -L means:

-L (c and r mode only) All symbolic links will be followed. Nor-
mally, symbolic links are archived as such. With this option,
the target of the link will be archived instead.

The man page for bsdtar doesn't indicate an option to dereference
symlinks during extraction. :(

Thanks for the confirmation (which I had managed to find from

http://www.freebsd.org/cgi/man.cgi?query=tarapropos=0sektion=0manpath=FreeBSD+5.4-RELEASE+and+Portsformat=html

). R does not need xh here, and I have changed it in 2.2.0-beta.

I do suggest you submit a bug report on the incorrect error message,
though, which should refer to the option used, not one that is not used.

--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595

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