Re: [R] plot to postscript orientation
Miruna Petrescu-Prahova wrote: Hi I am trying to save some plots in a postscript file. When I generate the plots in the main window, they appear correctly - their orientation is landscape (i.e., horizontal). However, when I open the .ps file with GSview, the whole page appears vertically, and the plot appears horizontally, which means that the plot is only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/default.ps ). I searched the R-help mailing list archive and found 2 suggestions: setting the width and height and setting horizontal = FALSE. I have tried setting the width and height but it makes no difference. I have also tried using horizontal = FALSE. This rotates and elongates the plot, but it is still displayed horizontally on a vertical page, and so only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps). I am not sure what is wrong. Plots are created with filled.contour. I guess this is a misconfiguration of your GSview. The plots are fine for me. Anyway, you might also want to set the argument paper=special in the postscript() call. Uwe Ligges Thanks Miruna Miruna Petrescu-Prahova Department of Sociology University of California, Irvine [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] plot to postscript orientation
Hi, My vanilla code works fine... See also attached .eps file (seperate email sent directly to you) r-rnorm(100) postscript(figure.eps) plot.ts(r) dev.off() Also this works ok as you have been told already: paper=special in the postscript() call. If you see my eps file wrongly then your GSVIEW setup is wrong. Choose Orientation Auto and under Options (bottom half) click-select-tick everything except Ignore DSC. That should do the trick... Costas Miruna Petrescu-Prahova wrote: Hi I am trying to save some plots in a postscript file. When I generate the plots in the main window, they appear correctly - their orientation is landscape (i.e., horizontal). However, when I open the .ps file with GSview, the whole page appears vertically, and the plot appears horizontally, which means that the plot is only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/default.ps https://webfiles.uci.edu/mpetresc/postscript.files/default.ps ). I searched the R-help mailing list archive and found 2 suggestions: setting the width and height and setting horizontal = FALSE. I have tried setting the width and height but it makes no difference. I have also tried using horizontal = FALSE. This rotates and elongates the plot, but it is still displayed horizontally on a vertical page, and so only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps ). I am not sure what is wrong. Plots are created with filled.contour. I guess this is a misconfiguration of your GSview. The plots are fine for me. Anyway, you might also want to set the argument paper=special in the postscript() call. Uwe Ligges Thanks Miruna Miruna Petrescu-Prahova Department of Sociology University of California, Irvine [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. --- Costas Vorlow Research Economist Eurobank EFG Division of Research Forecasting --- tel: +30-210-3337273 (ext 17273) fax: +30-210-3337687 P Think before you print. Disclaimer: This e-mail is confidential. If you are not the intended recipient, you should not copy it, re-transmit it, use it or disclose its contents, but should return it to the sender immediately and delete the copy from your system. EFG Eurobank Ergasias S.A. is not responsible for, nor endorses, any opinion, recommendation, conclusion, solicitation, offer or agreement or any information contained in this communication. EFG Eurobank Ergasias S.A. cannot accept any responsibility for the accuracy or completeness of this message as it has been transmitted over a public network. If you suspect that the message may have been intercepted or amended, please call the sender. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] problem with reading data files with different numbers oflines to skip
Hi Tom
It looks as if you are reading in genepix files. I believe the format for the
start lines includes a second line to say how many lines to skip. Something
like this, specifying 27 lines to skip:
ATF 1
27 43
Type=GenePix Results 1.4
DateTime=2003/11/14 17:18:30
If so here is a function I use to do what you want to do. If your files have a
different format then you need to modify how you set the number of lines to
skip.
# Preprocess the genepix files - strip off first header lines
dopix-function(genepixfiles, workingdir) {
pre-Pre
# Read in each genepix file, strip unwanted rows and write out again
for (pixfile in genepixfiles) {
pixfileout-paste(workingdir, pre, basename(pixfile), sep=)
secondline-read.table(pixfile, skip=1, nrows=1)
skiplines-as.numeric(secondline[1]) + 2
outdf-read.table(pixfile, header=T, skip=skiplines, sep=\t)
write.table(outdf, file=pixfileout, sep=\t, row.names=FALSE)
}
}
Regards
John Seers
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tom Cohen
Sent: 03 August 2007 13:04
To: r-help@stat.math.ethz.ch
Subject: Re: [R] problem with reading data files with different numbers oflines
to skip
Thanks to Ted and Gabor for your response.
I apology for not being clear with my previous description of the problem. I
tried with your suggestions using readLines but couldn't make it work. I now
explain the problem in more details and hope that you can help me out.
I have 30 data files, where some of them have 33 lines and the rests have 31
lines that I want to skip (examples below with bold text). That is, I only want
to keep the lines start from
Block Column Row Name ID
I read in the data files with a loop like below, the problem is how do I tell
the loop to skip 31 lines in some data files and 33 in the rests ?
for (i in 1:num.files) {
a-read.table(file=data[i],
,header=T,skip=31,sep='\t',na.strings=NA) }
Thanks for your help,
Tom
# 33 lines to skip
Type=GenePix Results 3 DateTime=2006/10/20
13:35:11Settings=
GalFile=G:\Avdelningar\viv\translational
immunologi\Peptide-arrays\Gal-files\742-human-pep2.galPixelSize=10
Wavelengths=635
ImageFiles=M:\Peptidearrays\061020\742-2.tif 1
NormalizationMethod=None NormalizationFactors=1
JpegImage=C:\Documents and Settings\Shahnaz Mahdavifar\Skrivbord\Human
pep,742\742-2.s1.jpgStdDev=Type 1
RatioFormulations=W1/W2 (635/)FeatureType=Circular
Barcode= BackgroundSubtraction=LocalFeature
ImageOrigin=560, 1360 JpegOrigin=1940, 3670
Creator=GenePix Pro 6.0.1.25 Scanner=GenePix 4000B [84948]
FocusPosition=0Temperature=30.2
LinesAveraged=1
Comment=PMTGain=600
ScanPower=100LaserPower=3.36
Filters=EmptyScanRegion=56,136,2123,6532
Supplier=Genetix Ltd. ArrayerSoftwareName=MicroArraying
ArrayerSoftwareVersion=QSoft XP Build 6450 (Revision 131)
Block Column Row Name ID X Y Dia. F635 Median F635 Mean1 1 1
IgG-human none 2390 4140 200 301 3171 2 1 PGDR_HUMAN (P09619)
AHASDEIYEIMQK 2630 4140 200 254 2501 3 1 ML1X_HUMAN (Q13585)
AIAHPVSDDSDLP 2860 4140 200 268 252
1000 more rows
# 31 lines to skip
ATF 1.029 41
Type=GenePix Results 3 DateTime=2006/10/20 13:05:20
Settings= GalFile=G:\Avdelningar\viv\translational
immunologi\Peptide-arrays\Gal-files\742-s2.gal PixelSize=10
Wavelengths=635
ImageFiles=M:\Peptidearrays\061020\742-4.tif 1
NormalizationMethod=None NormalizationFactors=1
JpegImage=C:\Documents and Settings\Shahnaz Mahdavifar\Skrivbord\Human
pep,742\742-4.s2.jpgStdDev=Type 1
RatioFormulations=W1/W2 (635/)FeatureType=Circular
Barcode= BackgroundSubtraction=LocalFeature
ImageOrigin=560, 1360 JpegOrigin=1950, 24310
Creator=GenePix Pro 6.0.1.25 Scanner=GenePix 4000B [84948]
FocusPosition=0
Temperature=28.49LinesAveraged=1
Comment=PMTGain=600ScanPower=100
LaserPower=3.32
Re: [R] Problem with making dll under Windows
Please check that you have installed a suitable environment (tools,
compiler etc.) as mentioned in the R Installation and Administration
manual. Öooks like your version of Perl is corrupted.
I got with your C program:
d:\aaaR CMD SHLIB dmypow.c
making dmypow.d from dmypow.c
gcc -It:/R/include -Wall -O3 -std=gnu99 -c dmypow.c -o dmypow.o
windres -I t:/R/include -i dmypow_res.rc -o dmypow_res.o
gcc -shared -s -o dmypow.dll dmypow.def dmypow.o dmypow_res.o
-Lt:/R/bin-lR
Uwe Ligges
Albrecht, Dr. Stefan (APEP) wrote:
Dear all,
I have problems to compile a DLL for Windows XP with R version 2.5.1
(2007-06-27).
See output below:
C:\AZ_DATEN\C, C++\BE_speedupR CMD SHLIB dmypow.c
Goto undefined subroutine DynaLoader::bootstrap_inherit at
C:\Programme\R\R-2.5
.1\share\perl/XSLoader.pm line 80.
Compilation failed in require at c:/Programme/Perl/lib/IO/Handle.pm line 262.
BEGIN failed--compilation aborted at c:/Programme/Perl/lib/IO/Handle.pm line
262
.
Compilation failed in require at c:/Programme/Perl/lib/IO/Seekable.pm line
101.
BEGIN failed--compilation aborted at c:/Programme/Perl/lib/IO/Seekable.pm
line 1
01.
Compilation failed in require at c:/Programme/Perl/lib/IO/File.pm line 133.
BEGIN failed--compilation aborted at c:/Programme/Perl/lib/IO/File.pm line
133.
Compilation failed in require at
C:\Programme\R\R-2.5.1\share\perl/FileHandle.pm
line 6.
Compilation failed in require at C:\Programme\R\R-2.5.1\share\perl/R/Utils.pm
li
ne 6.
BEGIN failed--compilation aborted at
C:\Programme\R\R-2.5.1\share\perl/R/Utils.p
m line 6.
Compilation failed in require at C:\Programme\R\R-2.5.1/bin/SHLIB line 24.
BEGIN failed--compilation aborted at C:\Programme\R\R-2.5.1/bin/SHLIB line 24.
The file DynaLoader.pm is in the same directory as, e.g. XSLoader.pm
The c-file itself is very simple:
#include Rinternals.h
#include math.h
SEXP mypow(SEXP lifeFund, SEXP bow)
{
int i;
double n;
n = length(lifeFund);
for (i=0; in; i++)
REAL(lifeFund)[i] = pow((i+1)/n,REAL(bow)[0]);
return(lifeFund);
}
Could anybody help, please?
With many thanks and best regards,
Stefan
Dr. Stefan Albrecht, CFA
Allianz Private Equity Partners GmbH
Königinstr. 19 | 80539 Munich | Germany
Phone: +49.(0)89.3800.18317
Fax: +49.(0)89.3800.818317
EMail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Web: www.apep.com http://www.apep.com/
Allianz Private Equity Partners GmbH | Geschäftsführung: Wan Ching Ang, Karl
Ralf Jung
Sitz der Gesellschaft: München | Registergericht: München HRB 126221 |
Ust-ID-Nr.: DE 813 264 786
[[alternative HTML version deleted]]
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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.
__
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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] How to properly finalize external pointers?
Dear R .Call() insiders,
Can someone enlighten me how to properly finalize external pointers in C code
(R-2.5.1 win)? What is the relation between R_ClearExternalPtr and the
finalizer set in R_RegisterCFinalizer?
I succeeded registering a finalizer that works when an R object containing an
external pointer is garbage collected. However, I have some difficulties
figuring out how to do that in an explicit closing function.
I observed that
- calling R_ClearExternalPtr does not trigger the finalizer and is dangerous
because it removes the pointer before the finalizer needs it at
garbage-collection-time (no finalization = memory leak)
- calling the finalizer directly ensures finalization but now the finalizer is
called twice (once again at garbage collection time, and I did not find
documentation how to unregister the finalizer)
- It works to delete the SEXP external pointer object but only if not calling
R_ClearExternalPtr (but why then do we need it?) Furthermore it is unfortunate
to delay freeing the external pointers memory if I know during runtime that it
can be done immediately.
Shouldn't R_ClearExternalPtr call the finalizer and then unregister it? (this
would also work when removing the SEXP external pointer object is difficult
because it was handed over to the closing function directly as a parameter)
Best regards
Jens Oehlschlägel
// C-code
static void rindex_finalize(SEXP extPtr){
pINT ptr = R_ExternalPtrAddr(extPtr);
if(ptr){
Free(ptr);
Rprintf(finalized\n);
}else{
Rprintf(nothing to finalize\n);
}
return;
}
SEXP rindex_open(
SEXP Sn
){
int i,n = INTEGER(Sn)[0];
pINT ptr = Calloc(sizeof(INT)*n, INT);
SEXP extPtr, ret;
for (i=0;in;i++){
ptr[i] = i;
}
extPtr = R_MakeExternalPtr(ptr, install(Rindex_extPtr), R_NilValue);
R_RegisterCFinalizer(extPtr, rindex_finalize);
PROTECT(ret = allocVector(VECSXP, 1));
SET_VECTOR_ELT(ret,0,extPtr);
UNPROTECT(1);
return ret;
}
SEXP rindex_close(
SEXP obj
){
int i, n= 10;
SEXP ret, extPtr=VECTOR_ELT(obj, 0);
pINT p, ptr = R_ExternalPtrAddr(extPtr);
PROTECT(ret = allocVector(INTSXP, n));
p = INTEGER(ret);
for (i=0;in;i++){
Rprintf(ptri=%d\n,ptr[i]);
p[i] = ptr[i];
}
/* this does finalize immediately but at next garbage collection again
rindex_finalize(extPtr);
*/
/* this must not called otherwise the pointer is gone at garbage collection
time
R_ClearExternalPtr(extPtr);
*/
/* this triggers the finalizer but only at next garbage collection */
SET_VECTOR_ELT(obj,0,R_NilValue);
UNPROTECT(1);
return ret;
}
# R-Code
initRindex - function(){
dyn.load(file.path(.libPaths(), rindex, libs, paste(rindex,
.Platform$dynlib.ext, sep = )))
}
doneRindex - function(){
dyn.unload(file.path(.libPaths(), rindex, libs, paste(rindex,
.Platform$dynlib.ext, sep = )))
}
openRindex - function(n=10){
.Call(rindex_open, as.integer(n))
}
closeRindex - function(extPtr){
.Call(rindex_close, extPtr)
}
if (FALSE){
# now try it
require(rindex)
initRindex()
extPtr - openRindex()
extPtr
extPtr2 - closeRindex(extPtr)
extPtr2
gc()
extPtr - openRindex()
extPtr2 - extPtr
extPtr2
rm(extPtr)
gc()
extPtr2
rm(extPtr2)
gc()
extPtr2
doneRindex()
}
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 5.1
year 2007
month 06
day27
svn rev42083
language R
version.string R version 2.5.1 (2007-06-27)
--
Pt! Schon vom neuen GMX MultiMessenger gehört?
Der kanns mit allen: http://www.gmx.net/de/go/multimessenger
__
R-help@stat.math.ethz.ch 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] Problem with making dll under Windows
Dear all,
I have problems to compile a DLL for Windows XP with R version 2.5.1
(2007-06-27).
See output below:
C:\AZ_DATEN\C, C++\BE_speedupR CMD SHLIB dmypow.c
Goto undefined subroutine DynaLoader::bootstrap_inherit at C:\Programme\R\R-2.5
.1\share\perl/XSLoader.pm line 80.
Compilation failed in require at c:/Programme/Perl/lib/IO/Handle.pm line 262.
BEGIN failed--compilation aborted at c:/Programme/Perl/lib/IO/Handle.pm line 262
.
Compilation failed in require at c:/Programme/Perl/lib/IO/Seekable.pm line 101.
BEGIN failed--compilation aborted at c:/Programme/Perl/lib/IO/Seekable.pm line 1
01.
Compilation failed in require at c:/Programme/Perl/lib/IO/File.pm line 133.
BEGIN failed--compilation aborted at c:/Programme/Perl/lib/IO/File.pm line 133.
Compilation failed in require at C:\Programme\R\R-2.5.1\share\perl/FileHandle.pm
line 6.
Compilation failed in require at C:\Programme\R\R-2.5.1\share\perl/R/Utils.pm li
ne 6.
BEGIN failed--compilation aborted at C:\Programme\R\R-2.5.1\share\perl/R/Utils.p
m line 6.
Compilation failed in require at C:\Programme\R\R-2.5.1/bin/SHLIB line 24.
BEGIN failed--compilation aborted at C:\Programme\R\R-2.5.1/bin/SHLIB line 24.
The file DynaLoader.pm is in the same directory as, e.g. XSLoader.pm
The c-file itself is very simple:
#include Rinternals.h
#include math.h
SEXP mypow(SEXP lifeFund, SEXP bow)
{
int i;
double n;
n = length(lifeFund);
for (i=0; in; i++)
REAL(lifeFund)[i] = pow((i+1)/n,REAL(bow)[0]);
return(lifeFund);
}
Could anybody help, please?
With many thanks and best regards,
Stefan
Dr. Stefan Albrecht, CFA
Allianz Private Equity Partners GmbH
Königinstr. 19 | 80539 Munich | Germany
Phone: +49.(0)89.3800.18317
Fax: +49.(0)89.3800.818317
EMail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Web: www.apep.com http://www.apep.com/
Allianz Private Equity Partners GmbH | Geschäftsführung: Wan Ching Ang, Karl
Ralf Jung
Sitz der Gesellschaft: München | Registergericht: München HRB 126221 |
Ust-ID-Nr.: DE 813 264 786
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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] problem with reading data files with different numbers of lines to skip
Thanks to Ted and Gabor for your response.
I apology for not being clear with my previous description of the problem. I
tried with your suggestions using readLines but couldn't make it work. I now
explain the problem in more details and hope that you can help me out.
I have 30 data files, where some of them have 33 lines and the rests have 31
lines that I want to skip (examples below with bold text). That is, I only want
to keep the lines start from
Block Column Row Name ID
I read in the data files with a loop like below, the problem is how do I tell
the loop to skip 31 lines in some data files and 33 in the rests ?
for (i in 1:num.files) {
a-read.table(file=data[i], ,header=T,skip=31,sep='\t',na.strings=NA) }
Thanks for your help,
Tom
# 33 lines to skip
Type=GenePix Results 3 DateTime=2006/10/20
13:35:11Settings=
GalFile=G:\Avdelningar\viv\translational
immunologi\Peptide-arrays\Gal-files\742-human-pep2.galPixelSize=10
Wavelengths=635
ImageFiles=M:\Peptidearrays\061020\742-2.tif 1
NormalizationMethod=None NormalizationFactors=1
JpegImage=C:\Documents and Settings\Shahnaz Mahdavifar\Skrivbord\Human
pep,742\742-2.s1.jpgStdDev=Type 1
RatioFormulations=W1/W2 (635/)FeatureType=Circular
Barcode= BackgroundSubtraction=LocalFeature
ImageOrigin=560, 1360 JpegOrigin=1940, 3670
Creator=GenePix Pro 6.0.1.25 Scanner=GenePix 4000B [84948]
FocusPosition=0Temperature=30.2
LinesAveraged=1
Comment=PMTGain=600
ScanPower=100LaserPower=3.36
Filters=EmptyScanRegion=56,136,2123,6532
Supplier=Genetix Ltd. ArrayerSoftwareName=MicroArraying
ArrayerSoftwareVersion=QSoft XP Build 6450 (Revision 131)
Block Column Row Name ID X Y Dia. F635 Median F635 Mean1 1 1
IgG-human none 2390 4140 200 301 3171 2 1 PGDR_HUMAN (P09619)
AHASDEIYEIMQK 2630 4140 200 254 2501 3 1 ML1X_HUMAN (Q13585)
AIAHPVSDDSDLP 2860 4140 200 268 252
1000 more rows
# 31 lines to skip
ATF 1.029 41
Type=GenePix Results 3 DateTime=2006/10/20 13:05:20
Settings= GalFile=G:\Avdelningar\viv\translational
immunologi\Peptide-arrays\Gal-files\742-s2.gal PixelSize=10
Wavelengths=635
ImageFiles=M:\Peptidearrays\061020\742-4.tif 1
NormalizationMethod=None NormalizationFactors=1
JpegImage=C:\Documents and Settings\Shahnaz Mahdavifar\Skrivbord\Human
pep,742\742-4.s2.jpgStdDev=Type 1
RatioFormulations=W1/W2 (635/)FeatureType=Circular
Barcode= BackgroundSubtraction=LocalFeature
ImageOrigin=560, 1360 JpegOrigin=1950, 24310
Creator=GenePix Pro 6.0.1.25 Scanner=GenePix 4000B [84948]
FocusPosition=0
Temperature=28.49LinesAveraged=1
Comment=PMTGain=600ScanPower=100
LaserPower=3.32Filters=Empty
ScanRegion=56,136,2113,6532 Supplier=
Block Column Row Name ID X Y Dia. F635 Median F635 Mean1 1 1
IgG-human none 2370 24780 200 133 1751 2 1 PGDR_HUMAN (P09619)
AHASDEIYEIMQK 2600 24780 200 120 1211 3 1 ML1X_HUMAN (Q13585)
AIAHPVSDDSDLP 2840 24780 200 120 118
1000 more rows
[EMAIL PROTECTED] skrev:
On 02-Aug-07 21:14:20, Tom Cohen wrote:
Dear List,
I have 30 data files with different numbers of lines (31 and 33) that
I want to skip before reading the files. If I use the skip option I can
only choose either to skip 31 or 33 lines. The data files with 31 lines
have no blank rows between the lines and the header row. How can I read
the files without manually checking which files have 31 respectively 33
lines ? The only text line I want to keep is the header.
Thamks for your help,
Tom
for (i in 1:num.files) {
a-read.table(file=data[i],
,header=T,skip=31,sep='\t',na.strings=NA)
}
Apologies, I misunderstood your description in my previous response
(I thought that the total number of lines in one of your files was
either 31 or 33, and you wanted to know which was which).
I now
Re: [R] [R-SIG-Finance] question on analyzing of correlation structure
I don't understand your question but there is a package called VARs
that may be helpful to you.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of liu lu
Sent: Friday, August 03, 2007 8:39 AM
To: [EMAIL PROTECTED]
Subject: [R-SIG-Finance] question on analyzing of correlation structure
I am currently working on an empirical analysis of the respective A and
B series in the three markets: X, Y, and Z. Suppose the correlation of
the A B series in market X shows a different pattern for the
significant short-run adjustment as the impulse reponse fuctions
indicate (Haan, Wouter J. den. 2000. The comovement between output and
prices. Journal of Monetary Economics 46:3-30.).
Could somebody share some ideas about any package can do the following:
(1) to work out the factors contributing the disparity; (2) to contrast
and highlight the difference.
Many thanks to your kind attention.
Wei-han Liu
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-- Subscriber-posting only.
-- If you want to post, subscribe first.
This is not an offer (or solicitation of an offer) to buy/se...{{dropped}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple table with frequency variable
Ok, then tapply() might be your friend: set.seed(1) b - rbinom(10,6,0.3) c - rbinom(10,6,0.9) w - trunc(runif(10)*3) b;c;w table(b, c) tapply(w, list(b, c), sum) Is this what you were looking for? /Johan G. Draisma skrev: Thanks Johan, I realize that I did not use the right example. I have a table with two factors, say b and c, and a third case weight variable, say w. Then I would like the table command to sum the weights w for each combination of i and j. For instance, with b - rbinom(10,6,0.3) c - rbinom(10,6,0.9) w - trunc(runif(10)*3) the command table(i,j) counts the occurrences of combinations (b,c). I am looking for a command like table(i,j,weight=w) that would print the sum of the w's for each combination. e.g. if the combination (2,5) occurs twice I would like to see the sum of the two weights in the table, instead of the count 2. Gerrit. on 02-Aug-2007 11:03 Johan Lindbäck said the following: Would it be ok with a matrix? i - 1:5; j - 1:2 li - length(i) lj - length(j) A - matrix(numeric(li * lj), nrow = li, dimnames = list(i, j)) for (r in 1:li) for (s in 1:lj) A[r, s] - 10*r + s A HTH /Johan G. Draisma skrev: Thank you Jim, Sorry, that I was not clear enough. Each case has a frequency variable N. so when tabulating combinations (i,j) they should be weighted with weight N. In this case I would like a command table(i,j,N) resulting in j i 1 2 1 11 12 2 21 22 ... 5 51 52 And I was looking for a table command that allows for a case weight variable. Gerrit. on 01-Aug-2007 22:38 jim holtman said the following: I am not exactly sure what you are asking for. I am assuming that you want a vector that represent the combinations that are given combinations that are present: N [1] 11 22 31 42 51 12 21 32 41 52 table(i,j) j i 1 2 1 1 1 2 1 1 3 1 1 4 1 1 5 1 1 z - table(i,j) which(z==1) [1] 1 2 3 4 5 6 7 8 9 10 which(z==1,arr.ind=T) row col 1 1 1 2 2 1 3 3 1 4 4 1 5 5 1 1 1 2 2 2 2 3 3 2 4 4 2 5 5 2 x - which(z==1,arr.ind=T) paste(rownames(z)[x[,'row']], colnames(z)[x[,'col']], sep='') [1] 11 21 31 41 51 12 22 32 42 52 On 8/1/07, G. Draisma [EMAIL PROTECTED] wrote: Hallo, Im trying to find out how to tabulate frequencies of factors when the data have a frequency variable. e,g: i-rep(1:5,2) j-rep(1:2,5) N-10*i+j table(i,j) gives a table of ones as each combination occurs only once. How does one get a table with the corresponding N's? Thanks! Gerrit. -- Gerrit Draisma Department of Public Health Erasmus MC, University Medical Center Rotterdam Room AE-103 P.O. Box 2040 3000 CA Rotterdam The Netherlands Phone: +31 10 4087124 Fax: +31 10 4638474 http://mgzlx4.erasmusmc.nl/pwp/?gdraisma __ R-help@stat.math.ethz.ch 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. -- O| Johan Lindbäck, Biostatistician /\| Uppsala Clinical Research Center | \_. SE-751 85 UPPSALA ~~ http://www.ucr.uu.se -- __ R-help@stat.math.ethz.ch 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] How to properly finalize external pointers?
On 8/3/2007 9:19 AM, Jens Oehlschlägel wrote:
Dear R .Call() insiders,
Can someone enlighten me how to properly finalize external pointers in C code
(R-2.5.1 win)? What is the relation between R_ClearExternalPtr and the
finalizer set in R_RegisterCFinalizer?
I succeeded registering a finalizer that works when an R object containing an
external pointer is garbage collected. However, I have some difficulties
figuring out how to do that in an explicit closing function.
I observed that
- calling R_ClearExternalPtr does not trigger the finalizer and is dangerous
because it removes the pointer before the finalizer needs it at
garbage-collection-time (no finalization = memory leak)
- calling the finalizer directly ensures finalization but now the finalizer
is called twice (once again at garbage collection time, and I did not find
documentation how to unregister the finalizer)
- It works to delete the SEXP external pointer object but only if not calling
R_ClearExternalPtr (but why then do we need it?) Furthermore it is
unfortunate to delay freeing the external pointers memory if I know during
runtime that it can be done immediately.
Shouldn't R_ClearExternalPtr call the finalizer and then unregister it? (this
would also work when removing the SEXP external pointer object is difficult
because it was handed over to the closing function directly as a parameter)
I think we want R_ClearExternalPtr to work even if the finalizer would
fail (e.g. to clean up when there was an error when trying to build the
external object).
So I'd suggest that when you want to get rid of an external object
immediately, you call the finalizer explicitly, then call
R_ClearExternalPtr. The documentation doesn't address the question of
whether this will clear the registered finalizer so I don't know if
you'll get a second call to the finalizer during garbage collection, but
even if you do, isn't it easy enough to do nothing when you see the null
ptr, as you do below?
By the way, questions about programming at this level are better asked
in the R-devel group.
Duncan Murdoch
Best regards
Jens Oehlschlägel
// C-code
static void rindex_finalize(SEXP extPtr){
pINT ptr = R_ExternalPtrAddr(extPtr);
if(ptr){
Free(ptr);
Rprintf(finalized\n);
}else{
Rprintf(nothing to finalize\n);
}
return;
}
SEXP rindex_open(
SEXP Sn
){
int i,n = INTEGER(Sn)[0];
pINT ptr = Calloc(sizeof(INT)*n, INT);
SEXP extPtr, ret;
for (i=0;in;i++){
ptr[i] = i;
}
extPtr = R_MakeExternalPtr(ptr, install(Rindex_extPtr), R_NilValue);
R_RegisterCFinalizer(extPtr, rindex_finalize);
PROTECT(ret = allocVector(VECSXP, 1));
SET_VECTOR_ELT(ret,0,extPtr);
UNPROTECT(1);
return ret;
}
SEXP rindex_close(
SEXP obj
){
int i, n= 10;
SEXP ret, extPtr=VECTOR_ELT(obj, 0);
pINT p, ptr = R_ExternalPtrAddr(extPtr);
PROTECT(ret = allocVector(INTSXP, n));
p = INTEGER(ret);
for (i=0;in;i++){
Rprintf(ptri=%d\n,ptr[i]);
p[i] = ptr[i];
}
/* this does finalize immediately but at next garbage collection again
rindex_finalize(extPtr);
*/
/* this must not called otherwise the pointer is gone at garbage collection
time
R_ClearExternalPtr(extPtr);
*/
/* this triggers the finalizer but only at next garbage collection */
SET_VECTOR_ELT(obj,0,R_NilValue);
UNPROTECT(1);
return ret;
}
# R-Code
initRindex - function(){
dyn.load(file.path(.libPaths(), rindex, libs, paste(rindex,
.Platform$dynlib.ext, sep = )))
}
doneRindex - function(){
dyn.unload(file.path(.libPaths(), rindex, libs, paste(rindex,
.Platform$dynlib.ext, sep = )))
}
openRindex - function(n=10){
.Call(rindex_open, as.integer(n))
}
closeRindex - function(extPtr){
.Call(rindex_close, extPtr)
}
if (FALSE){
# now try it
require(rindex)
initRindex()
extPtr - openRindex()
extPtr
extPtr2 - closeRindex(extPtr)
extPtr2
gc()
extPtr - openRindex()
extPtr2 - extPtr
extPtr2
rm(extPtr)
gc()
extPtr2
rm(extPtr2)
gc()
extPtr2
doneRindex()
}
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 5.1
year 2007
month 06
day27
svn rev42083
language R
version.string R version 2.5.1 (2007-06-27)
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
Re: [R] Streamlining Prcomp Data
Try this result - summary(prcomp(USArrests)) names(result) M - result$importance M[2,] The labels are the dimnames of the importance matrix. They only show up when the matrix is printed. If you wish, you can remove them with dimnames(M) - NULL. -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch 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] plot to postscript orientation
Do you have the Orientation menu set to 'Auto'? The effect described seems that if 'Rotate media' is selected, which it should not be. The files look fine to me in GSView 4.8 on Windows and other viewers on Linux. I agree with Uwe that it is a viewer issue (most reported postscript/PDF are). On Fri, 3 Aug 2007, John Kane wrote: I seem to see the same problem that Miruna gets just to confirm that it is not just her set-up. I'm using GSview4.8 if that helps --- Uwe Ligges [EMAIL PROTECTED] wrote: Miruna Petrescu-Prahova wrote: Hi I am trying to save some plots in a postscript file. When I generate the plots in the main window, they appear correctly - their orientation is landscape (i.e., horizontal). However, when I open the .ps file with GSview, the whole page appears vertically, and the plot appears horizontally, which means that the plot is only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/default.ps ). I searched the R-help mailing list archive and found 2 suggestions: setting the width and height and setting horizontal = FALSE. I have tried setting the width and height but it makes no difference. I have also tried using horizontal = FALSE. This rotates and elongates the plot, but it is still displayed horizontally on a vertical page, and so only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps). I am not sure what is wrong. Plots are created with filled.contour. I guess this is a misconfiguration of your GSview. The plots are fine for me. Anyway, you might also want to set the argument paper=special in the postscript() call. Uwe Ligges Thanks Miruna Miruna Petrescu-Prahova Department of Sociology University of California, Irvine [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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. -- 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 __ R-help@stat.math.ethz.ch 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] t-distribution
Look at the power.examp and run.power.examp functions in the
TeachingDemos package. Do these do what you want? If not you can look
at the code in them to see how to fill part of the area under the curve.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Nair,
Murlidharan T
Sent: Friday, August 03, 2007 8:46 AM
To: Stephen Tucker; r-help@stat.math.ethz.ch
Subject: Re: [R] t-distribution
I am trying to shade the critical regions for normal
distribution with different means and making overlaps of the
plots to explain Type I and Type II errors. I tried the
following. If I calculate the z score and as I did below, can
I use it to pick regions from the original data? I think I am
making mistake by calculating the z scores for d$x, can
someone explain the mistake I am making?
left- -1.96
right- 1.96
mu1-rnorm(10,20,5)
d-(density(mu1))
x.tmp-d$x
y.tmp-d$y
x-x.tmp
y-y.tmp
mu1z-(x.tmp-mean(x.tmp))/sd(x.tmp) # is it correct?
a-which(mu1z =left)
b-which(mu1z =right)
plot(x.tmp,y.tmp, type=l)
polygon(x=c(x.tmp[a],rev(x.tmp[a])),y=c(y.tmp[a],rep(0,length(
y.tmp[a]))
),col=gray90)
polygon(x=c(x.tmp[b],rev(x.tmp[b])),y=c(y.tmp[b],rep(0,length(
y.tmp[b]))
),col=gray90)
-Original Message-
From: Stephen Tucker [mailto:[EMAIL PROTECTED]
Sent: Thursday, August 02, 2007 3:11 PM
To: Nair, Murlidharan T; r-help@stat.math.ethz.ch
Subject: RE: [R] t-distribution
yes, or
p - seq(0.001,0.999,,1000)
x - qt(p,df=9)
y - dt(x,df=9)
plot(x,y,type=l)
f - function(x,y,...) {
polygon(x=c(x,rev(x)),y=c(y,rep(0,length(y))),...)
}
with(data.frame(x,y)[x = 2.3,],f(x,y,col=gray90))
with(data.frame(x,y)[x = -2.3,],f(x,y,col=gray90))
--- Nair, Murlidharan T [EMAIL PROTECTED] wrote:
I tried doing it this way.
left--2.3
right-2.3
p - seq(0.001,0.999,,1000)
x - qt(p,df=9)
y - dt(x,df=9)
plot(x,y,type=l)
x.tmp-x
y.tmp-y
a-which(x=left)
polygon(x=c(x.tmp[a],rev(x.tmp[a])),y=c(y.tmp[a],rep(0,length(
y.tmp[a]))
),col=gray90)
b-which(x=right)
polygon(x=c(x.tmp[b],rev(x.tmp[b])),y=c(y.tmp[b],rep(0,length(
y.tmp[b]))
),col=gray90)
Please let me know if I have made any mistakes.
Thanks ../Murli
-Original Message-
From: Richard M. Heiberger [mailto:[EMAIL PROTECTED]
Sent: Thu 8/2/2007 10:25 AM
To: Nair, Murlidharan T; Stephen Tucker; r-help@stat.math.ethz.ch
Subject: Re: [R] t-distribution
I believe you are looking for the functionality I have in the
norm.curve function in the HH package.
Download and install HH from CRAN and then look at
example(norm.curve)
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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.
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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] Re : change the names of all listed objects
On 8/3/2007 11:28 AM, justin bem wrote: It not too simple what ls return the variable that have been create in your environment even if you change their names, ls will not return a1 b1 ... The names attribute in OOP of an object is just an attribute and it is different with an instance of the object. ls() show instance But you can try this : a-10 ls() [1] a assign(paste(deparse(substitute(a)),1,sep=),a) # here I create a new instance with name # a1 and the same value than a rm(a) # In destroy the original. The use of deparse(substitute(a)) suggests you want to do this in a function, but then your rm() will only remove the local copy. Writing a gemeral purpose function for this is tricky, because it's not obvious what should happen in certain weird cases. For example: rename( c, collect ) to rename the c() function to collect(): should it really try to go into the base environment and delete the c object? That would be fairly disastrous if it succeeded. But if it found a c() function in the global environment, removing it from there might be sensible (maybe even if this rename request were executed from a function, rather than at the top level). Duncan Murdoch ls() [1] a1 Justin BEM BP 1917 Yaoundé Tél (237) 99597295 (237) 22040246 - Message d'origine De : Luca Laghi [EMAIL PROTECTED] À : r-help@stat.math.ethz.ch Envoyé le : Vendredi, 3 Août 2007, 15h23mn 01s Objet : [R] change the names of all listed objects Dear list members, I have created seven objects, from a to g, so that ls() gives me [1] a b c d e f g how can I automatically change their names in a1 b1 c1 d1 e1 f1 g1 It seems simple, ut it is driving me mad. Thank you very much for your help. Luca Laghi __ R-help@stat.math.ethz.ch 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. _ l [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Background color of symbols in xyplot
Dear R-users, I am using plot symbols given by pch=21:25 in a xyplot. The background color of these symbols can be defined by 'fill' in the panel argument, however I have a hard time to find how to define the same background color in the key. I tried different options like using the auto.key argument and modifying the par.settings, or using normal key argument plus 'fill', 'bg' or 'background'... nothing seems to do I want. What should I change in the following code to make it work ? key=list(space=bottom, points = list(pch = 21:25, col = 32, bg=15), text=list(mylegend)), Thank in advance Sebastien PS: cheng __ R-help@stat.math.ethz.ch 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] Saving an expression to a file
Dear Friends. I have a very long expression and I use function D to find its derivative, which will be even longer. I save the resulting expression in a variavle, say bbb. But when I tried to display bbb on the screen, the R screen is not long enough for me to view it. Is there a way to save the expression to a file? Best Wishes Yuchen Luo [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] t-distribution
Thanks, I figured it out after I realized my mistake here is the
corrected one. But I will certainly look at the teaching demos package.
left- -1.96
right- 1.96
mu1-rnorm(10,20,5)
d-(density(mu1))
x.tmp-d$x
y.tmp-d$y
x-x.tmp
y-y.tmp
x.int1-20 + (5*1.96)
x.int2-20 - (5*1.96)
a-which(x =x.int2)
b-which(x =x.int1)
plot(x.tmp,y.tmp, type=l)
polygon(x=c(x.tmp[a],rev(x.tmp[a])),y=c(y.tmp[a],rep(0,length(y.tmp[a]))
),col=gray90)
polygon(x=c(x.tmp[b],rev(x.tmp[b])),y=c(y.tmp[b],rep(0,length(y.tmp[b]))
),col=gray90)
-Original Message-
From: Greg Snow [mailto:[EMAIL PROTECTED]
Sent: Friday, August 03, 2007 11:01 AM
To: Nair, Murlidharan T; Stephen Tucker; r-help@stat.math.ethz.ch
Subject: RE: [R] t-distribution
Look at the power.examp and run.power.examp functions in the
TeachingDemos package. Do these do what you want? If not you can look
at the code in them to see how to fill part of the area under the curve.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Nair,
Murlidharan T
Sent: Friday, August 03, 2007 8:46 AM
To: Stephen Tucker; r-help@stat.math.ethz.ch
Subject: Re: [R] t-distribution
I am trying to shade the critical regions for normal
distribution with different means and making overlaps of the
plots to explain Type I and Type II errors. I tried the
following. If I calculate the z score and as I did below, can
I use it to pick regions from the original data? I think I am
making mistake by calculating the z scores for d$x, can
someone explain the mistake I am making?
left- -1.96
right- 1.96
mu1-rnorm(10,20,5)
d-(density(mu1))
x.tmp-d$x
y.tmp-d$y
x-x.tmp
y-y.tmp
mu1z-(x.tmp-mean(x.tmp))/sd(x.tmp) # is it correct?
a-which(mu1z =left)
b-which(mu1z =right)
plot(x.tmp,y.tmp, type=l)
polygon(x=c(x.tmp[a],rev(x.tmp[a])),y=c(y.tmp[a],rep(0,length(
y.tmp[a]))
),col=gray90)
polygon(x=c(x.tmp[b],rev(x.tmp[b])),y=c(y.tmp[b],rep(0,length(
y.tmp[b]))
),col=gray90)
-Original Message-
From: Stephen Tucker [mailto:[EMAIL PROTECTED]
Sent: Thursday, August 02, 2007 3:11 PM
To: Nair, Murlidharan T; r-help@stat.math.ethz.ch
Subject: RE: [R] t-distribution
yes, or
p - seq(0.001,0.999,,1000)
x - qt(p,df=9)
y - dt(x,df=9)
plot(x,y,type=l)
f - function(x,y,...) {
polygon(x=c(x,rev(x)),y=c(y,rep(0,length(y))),...)
}
with(data.frame(x,y)[x = 2.3,],f(x,y,col=gray90))
with(data.frame(x,y)[x = -2.3,],f(x,y,col=gray90))
--- Nair, Murlidharan T [EMAIL PROTECTED] wrote:
I tried doing it this way.
left--2.3
right-2.3
p - seq(0.001,0.999,,1000)
x - qt(p,df=9)
y - dt(x,df=9)
plot(x,y,type=l)
x.tmp-x
y.tmp-y
a-which(x=left)
polygon(x=c(x.tmp[a],rev(x.tmp[a])),y=c(y.tmp[a],rep(0,length(
y.tmp[a]))
),col=gray90)
b-which(x=right)
polygon(x=c(x.tmp[b],rev(x.tmp[b])),y=c(y.tmp[b],rep(0,length(
y.tmp[b]))
),col=gray90)
Please let me know if I have made any mistakes.
Thanks ../Murli
-Original Message-
From: Richard M. Heiberger [mailto:[EMAIL PROTECTED]
Sent: Thu 8/2/2007 10:25 AM
To: Nair, Murlidharan T; Stephen Tucker; r-help@stat.math.ethz.ch
Subject: Re: [R] t-distribution
I believe you are looking for the functionality I have in the
norm.curve function in the HH package.
Download and install HH from CRAN and then look at
example(norm.curve)
__
__
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Check out tonight's top picks on Yahoo! TV.
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R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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 the names of all listed objects
On 8/3/2007 10:23 AM, Luca Laghi wrote:
Dear list members,
I have created seven objects, from a to g, so that ls() gives me
[1] a b c d e f g
how can I automatically change their names in
a1 b1 c1 d1 e1 f1 g1
It seems simple, ut it is driving me mad.
R doesn't have a rename operation, so you need to copy the objects and
then delete the original. For example:
# create a vector of the names of your objects
namelist - letters[1:7]
for (i in seq_along(namelist)) {
oldname - namelist[i]
# compute a new name from the old one
newname - paste(oldname, 1, sep=)
# create a variable with the new name
assign(newname, get(oldname))
# delete the old object
rm(list=oldname)
}
The code above should work in simple cases where you run it in the
console and it works on objects in the global workspace. If you want to
write a function to do this things get more complicated, because you
want to make the assignment in the same place the function found the
original.
There are quicker ways (using mget() and apply()), but they'd really
just be doing the same as the above in a less clear way.
Duncan Murdoch
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[R] question about logistic models (AIC)
Dear fellow R-ussers, I have a question about the Akaike Information Criterion in the R output. Normally you would want it to be as small as possible, yet when i check up the information in my study books, the AIC is usually displayed as a negative number. In the exercises it is given as - AIC . R displays it as a positive number, does this mean that a large AIC gives a small - AIC , so the bigger the better? Kind regards, Tom. Tom Willems CODA-CERVA-VAR Department of Virology Epizootic Diseases Section Groeselenberg 99 B-1180 Ukkel Tel.: +32 2 3790522 Fax: +32 2 3790666 E-mail: [EMAIL PROTECTED] www.var.fgov.be Disclaimer: click here [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] t-distribution
I am trying to shade the critical regions for normal distribution with
different means and making overlaps of the plots to explain Type I and
Type II errors. I tried the following. If I calculate the z score and as
I did below, can I use it to pick regions from the original data? I
think I am making mistake by calculating the z scores for d$x, can
someone explain the mistake I am making?
left- -1.96
right- 1.96
mu1-rnorm(10,20,5)
d-(density(mu1))
x.tmp-d$x
y.tmp-d$y
x-x.tmp
y-y.tmp
mu1z-(x.tmp-mean(x.tmp))/sd(x.tmp) # is it correct?
a-which(mu1z =left)
b-which(mu1z =right)
plot(x.tmp,y.tmp, type=l)
polygon(x=c(x.tmp[a],rev(x.tmp[a])),y=c(y.tmp[a],rep(0,length(y.tmp[a]))
),col=gray90)
polygon(x=c(x.tmp[b],rev(x.tmp[b])),y=c(y.tmp[b],rep(0,length(y.tmp[b]))
),col=gray90)
-Original Message-
From: Stephen Tucker [mailto:[EMAIL PROTECTED]
Sent: Thursday, August 02, 2007 3:11 PM
To: Nair, Murlidharan T; r-help@stat.math.ethz.ch
Subject: RE: [R] t-distribution
yes, or
p - seq(0.001,0.999,,1000)
x - qt(p,df=9)
y - dt(x,df=9)
plot(x,y,type=l)
f - function(x,y,...) {
polygon(x=c(x,rev(x)),y=c(y,rep(0,length(y))),...)
}
with(data.frame(x,y)[x = 2.3,],f(x,y,col=gray90))
with(data.frame(x,y)[x = -2.3,],f(x,y,col=gray90))
--- Nair, Murlidharan T [EMAIL PROTECTED] wrote:
I tried doing it this way.
left--2.3
right-2.3
p - seq(0.001,0.999,,1000)
x - qt(p,df=9)
y - dt(x,df=9)
plot(x,y,type=l)
x.tmp-x
y.tmp-y
a-which(x=left)
polygon(x=c(x.tmp[a],rev(x.tmp[a])),y=c(y.tmp[a],rep(0,length(y.tmp[a]))
),col=gray90)
b-which(x=right)
polygon(x=c(x.tmp[b],rev(x.tmp[b])),y=c(y.tmp[b],rep(0,length(y.tmp[b]))
),col=gray90)
Please let me know if I have made any mistakes.
Thanks ../Murli
-Original Message-
From: Richard M. Heiberger [mailto:[EMAIL PROTECTED]
Sent: Thu 8/2/2007 10:25 AM
To: Nair, Murlidharan T; Stephen Tucker; r-help@stat.math.ethz.ch
Subject: Re: [R] t-distribution
I believe you are looking for the functionality I have
in the norm.curve function in the HH package.
Download and install HH from CRAN and then look at
example(norm.curve)
Ready for the edge of your seat?
Check out tonight's top picks on Yahoo! TV.
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Re: [R] Background color of symbols in xyplot
On 8/2/07, Sébastien [EMAIL PROTECTED] wrote: Dear R-users, I am using plot symbols given by pch=21:25 in a xyplot. The background color of these symbols can be defined by 'fill' in the panel argument, however I have a hard time to find how to define the same background color in the key. I tried different options like using the auto.key argument and modifying the par.settings, or using normal key argument plus 'fill', 'bg' or 'background'... nothing seems to do I want. What should I change in the following code to make it work ? key=list(space=bottom, points = list(pch = 21:25, col = 32, bg=15), text=list(mylegend)), For starters, upgrade to the latest version of R and lattice. -Deepayan __ R-help@stat.math.ethz.ch 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] Saving an expression to a file
Maybe use the sink() function -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Yuchen Luo Sent: Thursday, August 02, 2007 10:17 PM To: r-help@stat.math.ethz.ch Subject: [R] Saving an expression to a file Dear Friends. I have a very long expression and I use function D to find its derivative, which will be even longer. I save the resulting expression in a variavle, say bbb. But when I tried to display bbb on the screen, the R screen is not long enough for me to view it. Is there a way to save the expression to a file? Best Wishes Yuchen Luo [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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 the names of all listed objects
On Fri, 2007-08-03 at 16:23 +0200, Luca Laghi wrote:
Dear list members,
I have created seven objects, from a to g, so that ls() gives me
[1] a b c d e f g
how can I automatically change their names in
a1 b1 c1 d1 e1 f1 g1
It seems simple, ut it is driving me mad.
Thank you very much for your help.
Luca Laghi
Try this:
ls()
character(0)
# Create the 7 objects
for (i in seq(7)) assign(letters[i], i)
ls()
[1] a b c d e f g i
# Just get the objects we want
MyObj - ls(pattern = ^[a-g]$)
MyObj
[1] a b c d e f g
# Rename to new and delete old
for (i in MyObj)
{
assign(paste(i, 1, sep = ), get(i))
rm(list = i)
}
ls()
[1] a1b1c1d1e1f1g1i
[9] MyObj
See ?assign and ?get
You could encapsulate the above in a function, but need to be cautious
relative to environments and the old to new naming schema.
HTH,
Marc Schwartz
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Re: [R] Problem with making dll under Windows
Dear all,
Now everything is fine. Thanks a lot for your responses.
After the first attempts did not work, I moved some perl files into the
C:\Programme\R\R-2.5.1\share\perl
folder.
However, also this did not help either.
Finally, after you emails, I (re)installed R, Rtools and Perl (and removed
cygwin and DevC++ before) and so the R CMD SHLIB is now working.
I am not fully aware, what was exactly going wrong, but I guess the PATH names
did make some trouble, but this might not have been the only reason.
Best regards,
Stefan Albrecht
Dr. Stefan Albrecht, CFA
Allianz Private Equity Partners GmbH
Königinstr. 19 | 80539 Munich | Germany
Phone: +49.(0)89.3800.18317
Fax: +49.(0)89.3800.818317
EMail: [EMAIL PROTECTED]
Web: www.apep.com
Allianz Private Equity Partners GmbH | Geschäftsführung: Wan Ching Ang, Karl
Ralf Jung
Sitz der Gesellschaft: München | Registergericht: München HRB 126221 |
Ust-ID-Nr.: DE 813 264 786
-Ursprüngliche Nachricht-
Von: Uwe Ligges [mailto:[EMAIL PROTECTED]
Gesendet: Friday, August 03, 2007 15:10
An: Albrecht, Dr. Stefan (APEP)
Cc: r-help@stat.math.ethz.ch
Betreff: Re: [R] Problem with making dll under Windows
Please check that you have installed a suitable environment (tools,
compiler etc.) as mentioned in the R Installation and Administration
manual. Öooks like your version of Perl is corrupted.
I got with your C program:
d:\aaaR CMD SHLIB dmypow.c
making dmypow.d from dmypow.c
gcc -It:/R/include -Wall -O3 -std=gnu99 -c dmypow.c -o dmypow.o
windres -I t:/R/include -i dmypow_res.rc -o dmypow_res.o
gcc -shared -s -o dmypow.dll dmypow.def dmypow.o dmypow_res.o
-Lt:/R/bin-lR
Uwe Ligges
Albrecht, Dr. Stefan (APEP) wrote:
Dear all,
I have problems to compile a DLL for Windows XP with R version 2.5.1
(2007-06-27).
See output below:
C:\AZ_DATEN\C, C++\BE_speedupR CMD SHLIB dmypow.c
Goto undefined subroutine DynaLoader::bootstrap_inherit at
C:\Programme\R\R-2.5
.1\share\perl/XSLoader.pm line 80.
Compilation failed in require at c:/Programme/Perl/lib/IO/Handle.pm line 262.
BEGIN failed--compilation aborted at c:/Programme/Perl/lib/IO/Handle.pm line
262
.
Compilation failed in require at c:/Programme/Perl/lib/IO/Seekable.pm line
101.
BEGIN failed--compilation aborted at c:/Programme/Perl/lib/IO/Seekable.pm
line 1
01.
Compilation failed in require at c:/Programme/Perl/lib/IO/File.pm line 133.
BEGIN failed--compilation aborted at c:/Programme/Perl/lib/IO/File.pm line
133.
Compilation failed in require at
C:\Programme\R\R-2.5.1\share\perl/FileHandle.pm
line 6.
Compilation failed in require at C:\Programme\R\R-2.5.1\share\perl/R/Utils.pm
li
ne 6.
BEGIN failed--compilation aborted at
C:\Programme\R\R-2.5.1\share\perl/R/Utils.p
m line 6.
Compilation failed in require at C:\Programme\R\R-2.5.1/bin/SHLIB line 24.
BEGIN failed--compilation aborted at C:\Programme\R\R-2.5.1/bin/SHLIB line 24.
The file DynaLoader.pm is in the same directory as, e.g. XSLoader.pm
The c-file itself is very simple:
#include Rinternals.h
#include math.h
SEXP mypow(SEXP lifeFund, SEXP bow)
{
int i;
double n;
n = length(lifeFund);
for (i=0; in; i++)
REAL(lifeFund)[i] = pow((i+1)/n,REAL(bow)[0]);
return(lifeFund);
}
Could anybody help, please?
With many thanks and best regards,
Stefan
Dr. Stefan Albrecht, CFA
Allianz Private Equity Partners GmbH
Königinstr. 19 | 80539 Munich | Germany
Phone: +49.(0)89.3800.18317
Fax: +49.(0)89.3800.818317
EMail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Web: www.apep.com http://www.apep.com/
Allianz Private Equity Partners GmbH | Geschäftsführung: Wan Ching Ang, Karl
Ralf Jung
Sitz der Gesellschaft: München | Registergericht: München HRB 126221 |
Ust-ID-Nr.: DE 813 264 786
[[alternative HTML version deleted]]
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Re: [R] Saving an expression to a file
See ?save Also you might be able to use the Ryacas package to simplify your derivative. See Simplify in 5.5 of: http://ryacas.googlecode.com/svn/trunk/inst/doc/Ryacas.pdf More info at: http://code.google.com/p/ryacas/ On 8/2/07, Yuchen Luo [EMAIL PROTECTED] wrote: Dear Friends. I have a very long expression and I use function D to find its derivative, which will be even longer. I save the resulting expression in a variavle, say bbb. But when I tried to display bbb on the screen, the R screen is not long enough for me to view it. Is there a way to save the expression to a file? Best Wishes Yuchen Luo [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] question about logistic models (AIC)
Tom: That's a good question. AIC, as i'm sure you know, is usually calculated as 2k-2ln(L), where k is the number of free parameters in the model, and L is the log-likelihood of the model. The goal of AIC--and the reason one normally tries to select a model with minimal AIC--is to minimize what's referred to as the Kullback-Leibler distance between the distribution of your data's density from the theoretical true theoretical density as defined by the model. More concisely, the AIC is an index of the amount of information regarding your data that is lost when your model is used to describe it. To get back to your question, I can't say without a little more information why the AIC's your referring to are negative (but perhaps it's an issue of using the log-likelihood instead of the negative log- likelihood), but my first instinct is that it doesn't matter. I would go with the AIC that is closest to zero. I hope that helps. Kyle H. Ambert Graduate Student, Dept. Behavioral Neuroscience Oregon Health Science University [EMAIL PROTECTED] On Aug 3, 2007, at 8:41 AM, Tom Willems wrote: Dear fellow R-ussers, I have a question about the Akaike Information Criterion in the R output. Normally you would want it to be as small as possible, yet when i check up the information in my study books, the AIC is usually displayed as a negative number. In the exercises it is given as - AIC . R displays it as a positive number, does this mean that a large AIC gives a small - AIC , so the bigger the better? Kind regards, Tom. Tom Willems CODA-CERVA-VAR Department of Virology Epizootic Diseases Section Groeselenberg 99 B-1180 Ukkel Tel.: +32 2 3790522 Fax: +32 2 3790666 E-mail: [EMAIL PROTECTED] www.var.fgov.be Disclaimer: click here [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Functional data analysis
Hi, Does anyone know if exist a library or a method to perform functional logistic regression in R? I have the FDA package, but I think it makes possible to do at most functional linear regression with the fRegress routine, not logistic regression. Is there such a thing like fGLM from S+FDA library for Splus? Thanks, Maurizio __ R-help@stat.math.ethz.ch 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] plot to postscript orientation
I seem to see the same problem that Miruna gets just to confirm that it is not just her set-up. I'm using GSview4.8 if that helps --- Uwe Ligges [EMAIL PROTECTED] wrote: Miruna Petrescu-Prahova wrote: Hi I am trying to save some plots in a postscript file. When I generate the plots in the main window, they appear correctly - their orientation is landscape (i.e., horizontal). However, when I open the .ps file with GSview, the whole page appears vertically, and the plot appears horizontally, which means that the plot is only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/default.ps ). I searched the R-help mailing list archive and found 2 suggestions: setting the width and height and setting horizontal = FALSE. I have tried setting the width and height but it makes no difference. I have also tried using horizontal = FALSE. This rotates and elongates the plot, but it is still displayed horizontally on a vertical page, and so only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps). I am not sure what is wrong. Plots are created with filled.contour. I guess this is a misconfiguration of your GSview. The plots are fine for me. Anyway, you might also want to set the argument paper=special in the postscript() call. Uwe Ligges Thanks Miruna Miruna Petrescu-Prahova Department of Sociology University of California, Irvine [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] two plots super-impose
It's not clear exactly what you want, but you may want to look at the layout function, or the subplot function in the TeachingDemos package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Thursday, August 02, 2007 12:07 PM To: R-help@stat.math.ethz.ch Subject: [R] two plots super-impose Dear R users, I used plot(x,y) to draw a scatter plot. I need to add another smaller histogram on the same plot I just had. However when I used hist(y), the histogram was on another page. Any suggestion? Best Regards, Philip [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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 the names of all listed objects
Dear list members, I have created seven objects, from a to g, so that ls() gives me [1] a b c d e f g how can I automatically change their names in a1 b1 c1 d1 e1 f1 g1 It seems simple, ut it is driving me mad. Thank you very much for your help. Luca Laghi __ R-help@stat.math.ethz.ch 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] problem with reading data files with different numbers of lines to skip
Please read the last line of every message
to r-help:
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
We don't know what you did.
On 8/3/07, Tom Cohen [EMAIL PROTECTED] wrote:
Thanks to Ted and Gabor for your response.
I apology for not being clear with my previous description of the problem. I
tried with your suggestions using readLines but couldn't make it work. I now
explain the problem in more details and hope that you can help me out.
I have 30 data files, where some of them have 33 lines and the rests have
31 lines that I want to skip (examples below with bold text). That is, I only
want to keep the lines start from
Block Column Row Name ID
I read in the data files with a loop like below, the problem is how do I
tell the loop to skip 31 lines in some data files and 33 in the rests ?
for (i in 1:num.files) {
a-read.table(file=data[i], ,header=T,skip=31,sep='\t',na.strings=NA) }
Thanks for your help,
Tom
# 33 lines to skip
Type=GenePix Results 3 DateTime=2006/10/20
13:35:11Settings=
GalFile=G:\Avdelningar\viv\translational
immunologi\Peptide-arrays\Gal-files\742-human-pep2.galPixelSize=10
Wavelengths=635
ImageFiles=M:\Peptidearrays\061020\742-2.tif 1
NormalizationMethod=None NormalizationFactors=1
JpegImage=C:\Documents and Settings\Shahnaz Mahdavifar\Skrivbord\Human
pep,742\742-2.s1.jpgStdDev=Type 1
RatioFormulations=W1/W2 (635/)FeatureType=Circular
Barcode= BackgroundSubtraction=LocalFeature
ImageOrigin=560, 1360 JpegOrigin=1940, 3670
Creator=GenePix Pro 6.0.1.25 Scanner=GenePix 4000B
[84948]FocusPosition=0Temperature=30.2
LinesAveraged=1
Comment=PMTGain=600
ScanPower=100LaserPower=3.36
Filters=EmptyScanRegion=56,136,2123,6532
Supplier=Genetix Ltd. ArrayerSoftwareName=MicroArraying
ArrayerSoftwareVersion=QSoft XP Build 6450 (Revision 131)
Block Column Row Name ID X Y Dia. F635 Median F635 Mean1 1
1 IgG-human none 2390 4140 200 301 3171 2 1 PGDR_HUMAN
(P09619) AHASDEIYEIMQK 2630 4140 200 254 2501 3 1 ML1X_HUMAN
(Q13585) AIAHPVSDDSDLP 2860 4140 200 268 252
1000 more rows
# 31 lines to skip
ATF 1.029 41
Type=GenePix Results 3 DateTime=2006/10/20 13:05:20
Settings= GalFile=G:\Avdelningar\viv\translational
immunologi\Peptide-arrays\Gal-files\742-s2.gal PixelSize=10
Wavelengths=635
ImageFiles=M:\Peptidearrays\061020\742-4.tif 1
NormalizationMethod=None NormalizationFactors=1
JpegImage=C:\Documents and Settings\Shahnaz Mahdavifar\Skrivbord\Human
pep,742\742-4.s2.jpgStdDev=Type 1
RatioFormulations=W1/W2 (635/)FeatureType=Circular
Barcode= BackgroundSubtraction=LocalFeature
ImageOrigin=560, 1360 JpegOrigin=1950, 24310
Creator=GenePix Pro 6.0.1.25 Scanner=GenePix 4000B
[84948]FocusPosition=0
Temperature=28.49LinesAveraged=1
Comment=PMTGain=600ScanPower=100
LaserPower=3.32Filters=Empty
ScanRegion=56,136,2113,6532 Supplier=
Block Column Row Name ID X Y Dia. F635 Median F635 Mean1 1
1 IgG-human none 2370 24780 200 133 1751 2 1 PGDR_HUMAN
(P09619) AHASDEIYEIMQK 2600 24780 200 120 1211 3 1 ML1X_HUMAN
(Q13585) AIAHPVSDDSDLP 2840 24780 200 120 118
1000 more rows
[EMAIL PROTECTED] skrev:
On 02-Aug-07 21:14:20, Tom Cohen wrote:
Dear List,
I have 30 data files with different numbers of lines (31 and 33) that
I want to skip before reading the files. If I use the skip option I can
only choose either to skip 31 or 33 lines. The data files with 31 lines
have no blank rows between the lines and the header row. How can I read
the files without manually checking which files have 31 respectively 33
lines ? The only text line I want to keep is the header.
Thamks for your help,
Tom
for (i in 1:num.files) {
[R] 'font' argument in text function unevaluated
R-help, I have a plot in which I use the following: text(1 , 2, expression(61*degree ~ paste(N)), font = 2) but the expression(61*degree ~ paste(N)) will not come out in font = 2. However cex=2 will work. What is the problem? Thanks in advance. version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 5.1 year 2007 month 06 day27 svn rev42083 language R version.string R version 2.5.1 (2007-06-27) __ R-help@stat.math.ethz.ch 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] Sourcing commands but delaying their execution
Colleagues: I have encountered the following situation: SERIES OF COMMANDS source(File1) MORE COMMANDS source(File2) Optimally, I would like File1 and File2 to be merged into a single file (FileMerged). However, if I wrote the following: SERIES OF COMMANDS source(FileMerged) MORE COMMANDS I encounter an error: the File2 portion of FileMerged contains commands that cannot be executed properly until MORE COMMANDS are executed. Similarly, sourcing FileMerged after MORE COMMANDS does not work because MORE COMMANDS requires the information from the File1 portion of FileMerged. I am looking for a means to source FileMerged but not execute some of the commands immediately. Functionally this would look like: SERIES OF COMMANDS source(FileMerged)# but withhold execution of some of the commands MORE COMMANDS COMMAND TO EXECUTE THE WITHHELD COMMANDS Does R offer some option to accomplish this? Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.com __ R-help@stat.math.ethz.ch 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] useR! 2008
We are happy to announce that the R user conference useR! 2008 is scheduled for August 12-14, 2008, and will take place at the University of Dortmund. As for the predecessor conferences, the program will consist of two parts: invited lectures and user-contributed sessions (abstract submission will be available online starting from December 2007). Prior to the conference, there will be tutorials on R (proposals for tutorials should be sent before 2007-10-31). INVITED LECTURES Invited speakers will include Peter Bühlmann, John Fox, Kurt Hornik, Gary King, Duncan Murdoch, Jean Thioulouse, Graham J. Williams, and Keith Worsley. USER-CONTRIBUTED SESSIONS The sessions will be a platform to bring together R users, contributors, package maintainers and developers in the S spirit that `users are developers'. People from different fields will show us how they solve problems with R in fascinating applications. The sessions are organized by members of the program committee, including Micah Altman, Roger Bivand, Peter Dalgaard, Jan de Leeuw, Ramón Díaz-Uriarte, Spencer Graves, Leonhard Held, Torsten Hothorn, François Husson, Christian Kleiber, Friedrich Leisch, Andy Liaw, Martin Mächler, Kate Mullen, Ei-ji Nakama, Thomas Petzold, Martin Theus, and Heather Turner. The program will cover topics such as * Applied Statistics Biostatistics * Bayesian Statistics * Bioinformatics * Chemometrics and Computational Physics * Data Mining * Econometrics Finance * Environmetrics Ecological Modeling * High Performance Computing * Machine Learning * Marketing Business Analytics * Psychometrics * Robust Statistics * Sensometrics * Spatial Statistics * Statistics in the Social and Political Sciences * Teaching * Visualization Graphics * and many more. PRE-CONFERENCE TUTORIALS Before the official program, half-day tutorials will be offered on Monday, August 11th. We invite R users to submit proposals for three hour tutorials on special topics on R. The proposals should give a brief description of the tutorial, including goals, detailed outline, justification why the tutorial is important, background knowledge required and potential attendees. The proposals should be sent before 2007-10-31 to [EMAIL PROTECTED] A web page offering more information on the `useR!' conference is available at http://www.R-project.org/useR-2008 ABOUT DORTMUND In the past, Dortmund was famous for coal, steel and the beer industry - quite typical for a city in the Ruhrgebiet. Today, Dortmund evolves to a city with high tech industry, exhibitions and service companies. Dortmund's football (i.e. soccer) club is world famous and attracts roughly 8 people on a regular basis. IMPORTANT DATES 2007-10-31: submission deadline of tutorial proposals 2007-12-01: start of registration 2007-12-01: start of online abstract submission 2008-03-31: early registration deadline: 2008-03-31: submission deadline of abstracts 2008-05-15: notification of acceptance 2008-05-31: regular registration deadline 2008-07-25: registration deadline We hope to meet you in Dortmund! The conference committee: Uwe Ligges (conference), Achim Zeileis (program), Claus Weihs, Gerd Kopp (local organization), Friedrich Leisch, Torsten Hothorn ___ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@stat.math.ethz.ch 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] How to properly finalize external pointers?
On Fri, 3 Aug 2007, Duncan Murdoch wrote: On 8/3/2007 9:19 AM, Jens Oehlschlägel wrote: Dear R .Call() insiders, Can someone enlighten me how to properly finalize external pointers in C code (R-2.5.1 win)? What is the relation between R_ClearExternalPtr and the finalizer set in R_RegisterCFinalizer? I succeeded registering a finalizer that works when an R object containing an external pointer is garbage collected. However, I have some difficulties figuring out how to do that in an explicit closing function. I observed that - calling R_ClearExternalPtr does not trigger the finalizer and is dangerous because it removes the pointer before the finalizer needs it at garbage-collection-time (no finalization = memory leak) - calling the finalizer directly ensures finalization but now the finalizer is called twice (once again at garbage collection time, and I did not find documentation how to unregister the finalizer) - It works to delete the SEXP external pointer object but only if not calling R_ClearExternalPtr (but why then do we need it?) Furthermore it is unfortunate to delay freeing the external pointers memory if I know during runtime that it can be done immediately. Shouldn't R_ClearExternalPtr call the finalizer and then unregister it? (this would also work when removing the SEXP external pointer object is difficult because it was handed over to the closing function directly as a parameter) I think we want R_ClearExternalPtr to work even if the finalizer would fail (e.g. to clean up when there was an error when trying to build the external object). So I'd suggest that when you want to get rid of an external object immediately, you call the finalizer explicitly, then call R_ClearExternalPtr. The documentation doesn't address the question of whether this will clear the registered finalizer so I don't know if you'll get a second call to the finalizer during garbage collection, but even if you do, isn't it easy enough to do nothing when you see the null ptr, as you do below? You will get a further finalizer call at GC, and I know of no way to unregister finalizers. So make sure the finalizer does nothing the second time. The way connections are handled in R-devel provides an example (although it is work in progress). Another possibility is to call the GC yourself if you know there are a lot of objects to clear up. By the way, questions about programming at this level are better asked in the R-devel group. Indeed. [...] -- 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__ R-help@stat.math.ethz.ch 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] Re : change the names of all listed objects
It not too simple what ls return the variable that have been create in your environment even if you change their names, ls will not return a1 b1 ... The names attribute in OOP of an object is just an attribute and it is different with an instance of the object. ls() show instance But you can try this : a-10 ls() [1] a assign(paste(deparse(substitute(a)),1,sep=),a) # here I create a new instance with name # a1 and the same value than a rm(a) # In destroy the original. ls() [1] a1 Justin BEM BP 1917 Yaoundé Tél (237) 99597295 (237) 22040246 - Message d'origine De : Luca Laghi [EMAIL PROTECTED] À : r-help@stat.math.ethz.ch Envoyé le : Vendredi, 3 Août 2007, 15h23mn 01s Objet : [R] change the names of all listed objects Dear list members, I have created seven objects, from a to g, so that ls() gives me [1] a b c d e f g how can I automatically change their names in a1 b1 c1 d1 e1 f1 g1 It seems simple, ut it is driving me mad. Thank you very much for your help. Luca Laghi __ R-help@stat.math.ethz.ch 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. _ l [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] question about logistic models (AIC)
Tom Willems Tom.Willems at var.fgov.be writes: I have a question about the Akaike Information Criterion in the R output. Normally you would want it to be as small as possible, yet when i check up the information in my study books, the AIC is usually displayed as a negative number. In the exercises it is given as - AIC . R displays it as a positive number, does this mean that a large AIC gives a small - AIC , so the bigger the better? I don't know about your books, but confirm that smaller AIC is better. AIC is usually positive (likelihood is between 0 and 1, therefore log-likelihood is negative, therefore -2L + 2k is positive), although continuous probability densities or neglected normalization coefficients can lead to negative AICs -- but smaller (more negative, if AIC0) is still better. Ben Bolker __ R-help@stat.math.ethz.ch 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] Sourcing commands but delaying their execution
While I don't use such a workflow, one option would be to place the
series of commands in a function, and then run that as appropriate.
do.initialisation - function() {
...
}
do.cleanup - function() {
}
Best wishes,
Mark
On 03/08/07, Dennis Fisher [EMAIL PROTECTED] wrote:
Colleagues:
I have encountered the following situation:
SERIES OF COMMANDS
source(File1)
MORE COMMANDS
source(File2)
Optimally, I would like File1 and File2 to be merged into a single
file (FileMerged). However, if I wrote the following:
SERIES OF COMMANDS
source(FileMerged)
MORE COMMANDS
I encounter an error: the File2 portion of FileMerged contains
commands that cannot be executed properly until MORE COMMANDS are
executed. Similarly, sourcing FileMerged after MORE COMMANDS does
not work because MORE COMMANDS requires the information from the
File1 portion of FileMerged.
I am looking for a means to source FileMerged but not execute some of
the commands immediately. Functionally this would look like:
SERIES OF COMMANDS
source(FileMerged)# but withhold execution of some of the
commands
MORE COMMANDS
COMMAND TO EXECUTE THE WITHHELD COMMANDS
Does R offer some option to accomplish this?
Dennis
Dennis Fisher MD
P (The P Less Than Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
__
R-help@stat.math.ethz.ch 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.
__
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For more information please visit http://www.messagelabs.com/email
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--
Dr. Mark Wardle
Clinical research fellow and specialist registrar, Neurology
Cardiff, UK
__
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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] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name (FileName instead of Filename) which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers I'll be tracking down such a bug soon too. Is there any options() setting, or debug technique that will flag data frame column extractions that reference a non-existent column? It seems to me that the [.data.frame extractor used to throw an error if given a mis-spelled variable name, and I still see lines of code in [.data.frame such as if (any(is.na(cols))) stop(undefined columns selected) In R 2.5.1 a NULL is silently returned. foo - data.frame(Filename = c(a, b)) foo[, FileName] NULL Has something changed so that the code lines if (any(is.na(cols))) stop(undefined columns selected) in [.data.frame no longer work properly (if I am understanding the intention properly)? If not, could [.data.frame check an options() variable setting (say warn.undefined.colnames) and throw a warning if a non-existent column name is referenced? sessionInfo() R version 2.5.1 (2007-06-27) powerpc-apple-darwin8.9.1 locale: en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: plotrix lme4 Matrix lattice 2.2-3 0.99875-4 0.999375-0 0.16-2 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -Original Message- From: [EMAIL PROTECTED] on behalf of Johnstone, Alice Sent: Wed 8/1/2007 7:20 PM To: [EMAIL PROTECTED] Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame For interest sake, I have found out why I wasn't getting my expected results when using read.AnnotatedDataFrame Turns out the error was made in the ReadAffy command, where I specified the filenames to be read from my AnnotatedDataFrame object. There was a typo error with a capital N ($FileName) rather than lowercase n ($Filename) as in my target file..whoops. However this meant the filename argument was ignored without the error message(!) and instead of using the information in the AnnotatedDataFrame object (which included filenames, but not alphabetically) it read the .cel files in alphabetical order from the working directory - hence the wrong file was given the wrong label (given by the order of Annotated object) and my comparisons were confused without being obvious as to why or where. Our solution: specify that filename is as.character so assignment of file to target is correct(after correcting $Filename) now that using read.AnnotatedDataFrame rather than readphenoData. Data-ReadAffy(filenames=as.character(pData(pd)$Filename),phenoData=pd) Hurrah! It may be beneficial to others, that if the filename argument isn't specified, that filenames are read from the phenoData object if included here. Thanks! -Original Message- From: Martin Morgan [mailto:[EMAIL PROTECTED] Sent: Thursday, 26 July 2007 11:49 a.m. To: Johnstone, Alice Cc: [EMAIL PROTECTED] Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame Hi Alice -- Johnstone, Alice [EMAIL PROTECTED] writes: Using R2.5.0 and Bioconductor I have been following code to analysis Affymetrix expression data: 2 treatments vs control. The original code was run last year and used the read.phenoData command, however with the newer version I get the error message Warning messages: read.phenoData is deprecated, use read.AnnotatedDataFrame instead The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead I use the read.AnnotatedDataFrame command, but when it comes to the end of the analysis the comparison of the treatment to the controls gets mixed up compared to what you get using the original read.phenoData ie it looks like the 3 groups get labelled wrong and so the comparisons are different (but they can still be matched up). My questions are, 1) do you need to set up your target file differently when using read.AnnotatedDataFrame - what is the standard format? I can't quite tell where things are going wrong for you, so it would help if you can narrow down where the problem occurs. I think read.AnnotatedDataFrame should be comparable to read.phenoData. Does pData(pd) look right? What about pData(Data) and pData(eset.rma) ? It's not important but pData(pd)$Target is the same as pd$Target. Since the analysis is on eset.rma, it probably makes sense to use the pData from there to construct your design matrix
Re: [R] question about logistic models (AIC)
On 03-Aug-07 16:42:33, Kyle. wrote: Tom: That's a good question. AIC, as i'm sure you know, is usually calculated as 2k-2ln(L), where k is the number of free parameters in the model, and L is the log-likelihood of the model. The goal of AIC--and the reason one normally tries to select a model with minimal AIC--is to minimize what's referred to as the Kullback-Leibler distance between the distribution of your data's density from the theoretical true theoretical density as defined by the model. More concisely, the AIC is an index of the amount of information regarding your data that is lost when your model is used to describe it. To get back to your question, I can't say without a little more information why the AIC's your referring to are negative (but perhaps it's an issue of using the log-likelihood instead of the negative log- likelihood), but my first instinct is that it doesn't matter. I would go with the AIC that is closest to zero. I hope that helps. That could be wrong! Don't forget that ln(L) is indeterminate to within an additive constant (for given data), so one man's negative AIC could be another mans positive AIC -- but if each compared their AICs with different models (the same different models for each) then they should get the same *difference* of AIC. The correct approach is to compare AICs on the basis of algebraic difference: AIC1 - AIC2 in comparing Model1 with Model2. If this is positive then Model2 is better than Model1 (on the AIC criterion). Taking the AIC that is closest to zero would be the wrong way round for negative AICs. Ted. On Aug 3, 2007, at 8:41 AM, Tom Willems wrote: Dear fellow R-ussers, I have a question about the Akaike Information Criterion in the R output. Normally you would want it to be as small as possible, yet when i check up the information in my study books, the AIC is usually displayed as a negative number. In the exercises it is given as - AIC . R displays it as a positive number, does this mean that a large AIC gives a small - AIC , so the bigger the better? Kind regards, Tom. Tom Willems CODA-CERVA-VAR Department of Virology Epizootic Diseases Section Groeselenberg 99 B-1180 Ukkel Tel.: +32 2 3790522 Fax: +32 2 3790666 E-mail: [EMAIL PROTECTED] www.var.fgov.be E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 03-Aug-07 Time: 18:31:51 -- XFMail -- __ R-help@stat.math.ethz.ch 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] question about logistic models (AIC)
Ah. Very good point. I stand corrected. ---Kyle. [EMAIL PROTECTED] 08/03/07 10:32 AM On 03-Aug-07 16:42:33, Kyle. wrote: Tom: That's a good question. AIC, as i'm sure you know, is usually calculated as 2k-2ln(L), where k is the number of free parameters in the model, and L is the log-likelihood of the model. The goal of AIC--and the reason one normally tries to select a model with minimal AIC--is to minimize what's referred to as the Kullback-Leibler distance between the distribution of your data's density from the theoretical true theoretical density as defined by the model. More concisely, the AIC is an index of the amount of information regarding your data that is lost when your model is used to describe it. To get back to your question, I can't say without a little more information why the AIC's your referring to are negative (but perhaps it's an issue of using the log-likelihood instead of the negative log- likelihood), but my first instinct is that it doesn't matter. I would go with the AIC that is closest to zero. I hope that helps. That could be wrong! Don't forget that ln(L) is indeterminate to within an additive constant (for given data), so one man's negative AIC could be another mans positive AIC -- but if each compared their AICs with different models (the same different models for each) then they should get the same *difference* of AIC. The correct approach is to compare AICs on the basis of algebraic difference: AIC1 - AIC2 in comparing Model1 with Model2. If this is positive then Model2 is better than Model1 (on the AIC criterion). Taking the AIC that is closest to zero would be the wrong way round for negative AICs. Ted. On Aug 3, 2007, at 8:41 AM, Tom Willems wrote: Dear fellow R-ussers, I have a question about the Akaike Information Criterion in the R output. Normally you would want it to be as small as possible, yet when i check up the information in my study books, the AIC is usually displayed as a negative number. In the exercises it is given as - AIC . R displays it as a positive number, does this mean that a large AIC gives a small - AIC , so the bigger the better? Kind regards, Tom. Tom Willems CODA-CERVA-VAR Department of Virology Epizootic Diseases Section Groeselenberg 99 B-1180 Ukkel Tel.: +32 2 3790522 Fax: +32 2 3790666 E-mail: [EMAIL PROTECTED] www.var.fgov.be E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 03-Aug-07 Time: 18:31:51 -- XFMail -- __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Sourcing commands but delaying their execution
Merged file can become:
... current file1 contents ...
f - function() {
... current file 2 contents ...
}
and then source that followed by running your middle code
followed by running f().
Of course, you may need to make some changes in the body
of f due to the changed scoping that this introduces.
On 8/3/07, Dennis Fisher [EMAIL PROTECTED] wrote:
Colleagues:
I have encountered the following situation:
SERIES OF COMMANDS
source(File1)
MORE COMMANDS
source(File2)
Optimally, I would like File1 and File2 to be merged into a single
file (FileMerged). However, if I wrote the following:
SERIES OF COMMANDS
source(FileMerged)
MORE COMMANDS
I encounter an error: the File2 portion of FileMerged contains
commands that cannot be executed properly until MORE COMMANDS are
executed. Similarly, sourcing FileMerged after MORE COMMANDS does
not work because MORE COMMANDS requires the information from the
File1 portion of FileMerged.
I am looking for a means to source FileMerged but not execute some of
the commands immediately. Functionally this would look like:
SERIES OF COMMANDS
source(FileMerged)# but withhold execution of some of the
commands
MORE COMMANDS
COMMAND TO EXECUTE THE WITHHELD COMMANDS
Does R offer some option to accomplish this?
Dennis
Dennis Fisher MD
P (The P Less Than Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
__
R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] FW: Selecting undefined column of a data frame (was [BioC]read.phenoData vs read.AnnotatedDataFrame)
I see now that for my example
foo - data.frame(Filename = c(a, b))
foo[, FileName]
NULL
the issue is in this clause of the
[.data.frame extractor.
The lines
if (drop length(y) == 1L)
return(.subset2(y, 1L))
return the NULL result just before the
error check
cols - names(y)
if (any(is.na(cols)))
stop(undefined columns selected)
is performed.
Is this intended behaviour, or has a logical
bug crept into the [.data.frame extractor?
if (missing(i)) {
if (missing(j) drop length(x) == 1L)
return(.subset2(x, 1L))
y - if (missing(j))
x
else .subset(x, j)
if (drop length(y) == 1L)
return(.subset2(y, 1L)) ## This returns a result before undefined
columns check is done. Is this intended?
cols - names(y)
if (any(is.na(cols)))
stop(undefined columns selected)
if (any(duplicated(cols)))
names(y) - make.unique(cols)
nrow - .row_names_info(x, 2L)
if (drop !mdrop nrow == 1L)
return(structure(y, class = NULL, row.names = NULL))
else return(structure(y, class = oldClass(x), row.names =
.row_names_info(x,
0L)))
}
sessionInfo()
R version 2.5.1 (2007-06-27)
powerpc-apple-darwin8.9.1
locale:
en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
plotrix lme4 Matrix lattice
2.2-3 0.99875-4 0.999375-0 0.16-2
Should this discussion move to R-devel?
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
-Original Message-
From: [EMAIL PROTECTED] on behalf of Steven McKinney
Sent: Fri 8/3/2007 10:37 AM
To: r-help@stat.math.ethz.ch
Subject: [R] FW: Selecting undefined column of a data frame (was
[BioC]read.phenoData vs read.AnnotatedDataFrame)
Hi all,
What are current methods people use in R to identify
mis-spelled column names when selecting columns
from a data frame?
Alice Johnson recently tackled this issue
(see [BioC] posting below).
Due to a mis-spelled column name (FileName
instead of Filename) which produced no warning,
Alice spent a fair amount of time tracking down
this bug. With my fumbling fingers I'll be tracking
down such a bug soon too.
Is there any options() setting, or debug technique
that will flag data frame column extractions that
reference a non-existent column? It seems to me
that the [.data.frame extractor used to throw an
error if given a mis-spelled variable name, and I
still see lines of code in [.data.frame such as
if (any(is.na(cols)))
stop(undefined columns selected)
In R 2.5.1 a NULL is silently returned.
foo - data.frame(Filename = c(a, b))
foo[, FileName]
NULL
Has something changed so that the code lines
if (any(is.na(cols)))
stop(undefined columns selected)
in [.data.frame no longer work properly (if
I am understanding the intention properly)?
If not, could [.data.frame check an
options() variable setting (say
warn.undefined.colnames) and throw a warning
if a non-existent column name is referenced?
sessionInfo()
R version 2.5.1 (2007-06-27)
powerpc-apple-darwin8.9.1
locale:
en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
plotrix lme4 Matrix lattice
2.2-3 0.99875-4 0.999375-0 0.16-2
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
-Original Message-
From: [EMAIL PROTECTED] on behalf of Johnstone, Alice
Sent: Wed 8/1/2007 7:20 PM
To: [EMAIL PROTECTED]
Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame
For interest sake, I have found out why I wasn't getting my expected
results when using read.AnnotatedDataFrame
Turns out the error was made in the ReadAffy command, where I specified
the filenames to be read from my AnnotatedDataFrame object. There was a
typo error with a capital N ($FileName) rather than lowercase n
($Filename) as in my target file..whoops. However this meant the
filename argument was ignored without the error message(!) and instead
of using the information in the AnnotatedDataFrame object (which
included filenames, but not alphabetically) it read the .cel files in
alphabetical order from the working directory - hence the wrong file was
given the wrong label (given by the order of
Re: [R] Background color of symbols in xyplot
Thank you very much for your help. I have installed the latest versions of R and lattice are installed, and now the 'fill' argument (instead of bg) gives me what I want. [EMAIL PROTECTED] a écrit : On 8/2/07, Sébastien [EMAIL PROTECTED] wrote: Dear R-users, I am using plot symbols given by pch=21:25 in a xyplot. The background color of these symbols can be defined by 'fill' in the panel argument, however I have a hard time to find how to define the same background color in the key. I tried different options like using the auto.key argument and modifying the par.settings, or using normal key argument plus 'fill', 'bg' or 'background'... nothing seems to do I want. What should I change in the following code to make it work ? key=list(space=bottom, points = list(pch = 21:25, col = 32, bg=15), text=list(mylegend)), For starters, upgrade to the latest version of R and lattice. -Deepayan [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] lme and aov
I have a mixed balanced ANOVA design with a between-subject factor (Grp) and a within-subject factor (Rsp). When I tried the following two commands which I thought are equivalent, fit.lme - lme(Beta ~ Grp*Rsp, random = ~1|Subj, Model); fit.aov - aov(Beta ~ Rsp*Grp+Error(Subj/Rsp)+Grp, Model); I got totally different results. What did I do wrong? Thanks, Gang __ R-help@stat.math.ethz.ch 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] plot to postscript orientation
I don't know about for Miruna but it does not work for me. I tried postscript (figure.eps, paper=letter) http://ca.geocities.com/jrkrideau/R/eps.figure.pdf postscript(figure.eps, paper=special, width=5, height=4) with similaar same results. Interstingly enough figure.eps imports completely into Word but rotated 90 degrees as Miruna noted. Where are you finding the Options for Auto? I don't see them. john --- Vorlow Constantinos [EMAIL PROTECTED] wrote: Hi, My vanilla code works fine... See also attached .eps file (seperate email sent directly to you) r-rnorm(100) postscript(figure.eps) plot.ts(r) dev.off() Also this works ok as you have been told already: paper=special in the postscript() call. If you see my eps file wrongly then your GSVIEW setup is wrong. Choose Orientation Auto and under Options (bottom half) click-select-tick everything except Ignore DSC. That should do the trick... Costas Miruna Petrescu-Prahova wrote: Hi I am trying to save some plots in a postscript file. When I generate the plots in the main window, they appear correctly - their orientation is landscape (i.e., horizontal). However, when I open the .ps file with GSview, the whole page appears vertically, and the plot appears horizontally, which means that the plot is only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/default.ps https://webfiles.uci.edu/mpetresc/postscript.files/default.ps ). I searched the R-help mailing list archive and found 2 suggestions: setting the width and height and setting horizontal = FALSE. I have tried setting the width and height but it makes no difference. I have also tried using horizontal = FALSE. This rotates and elongates the plot, but it is still displayed horizontally on a vertical page, and so only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps ). I am not sure what is wrong. Plots are created with filled.contour. I guess this is a misconfiguration of your GSview. The plots are fine for me. Anyway, you might also want to set the argument paper=special in the postscript() call. Uwe Ligges Thanks Miruna Miruna Petrescu-Prahova Department of Sociology University of California, Irvine [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. --- Costas Vorlow Research Economist Eurobank EFG Division of Research Forecasting --- tel: +30-210-3337273 (ext 17273) fax: +30-210-3337687 P Think before you print. Disclaimer: This e-mail is confidential. If you are not the intended recipient, you should not copy it, re-transmit it, use it or disclose its contents, but should return it to the sender immediately and delete the copy from your system. EFG Eurobank Ergasias S.A. is not responsible for, nor endorses, any opinion, recommendation, conclusion, solicitation, offer or agreement or any information contained in this communication. EFG Eurobank Ergasias S.A. cannot accept any responsibility for the accuracy or completeness of this message as it has been transmitted over a public network. If you suspect that the message may have been intercepted or amended, please call the sender. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] plot to postscript orientation
None of the suggestions work for me, either. I see Costas's plot just like mine, i.e., incorrectly. I tried modifying the Orientation to Auto, selecting all the Options, and using paper=special. It does not work. I am using GSView 4.8 under Windows. Miruna - Original Message - From: John Kane [EMAIL PROTECTED] To: Vorlow Constantinos [EMAIL PROTECTED]; [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Friday, August 03, 2007 11:40 AM Subject: Re: [R] plot to postscript orientation I don't know about for Miruna but it does not work for me. I tried postscript (figure.eps, paper=letter) http://ca.geocities.com/jrkrideau/R/eps.figure.pdf postscript(figure.eps, paper=special, width=5, height=4) with similaar same results. Interstingly enough figure.eps imports completely into Word but rotated 90 degrees as Miruna noted. Where are you finding the Options for Auto? I don't see them. john --- Vorlow Constantinos [EMAIL PROTECTED] wrote: Hi, My vanilla code works fine... See also attached .eps file (seperate email sent directly to you) r-rnorm(100) postscript(figure.eps) plot.ts(r) dev.off() Also this works ok as you have been told already: paper=special in the postscript() call. If you see my eps file wrongly then your GSVIEW setup is wrong. Choose Orientation Auto and under Options (bottom half) click-select-tick everything except Ignore DSC. That should do the trick... Costas Miruna Petrescu-Prahova wrote: Hi I am trying to save some plots in a postscript file. When I generate the plots in the main window, they appear correctly - their orientation is landscape (i.e., horizontal). However, when I open the .ps file with GSview, the whole page appears vertically, and the plot appears horizontally, which means that the plot is only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/default.ps https://webfiles.uci.edu/mpetresc/postscript.files/default.ps ). I searched the R-help mailing list archive and found 2 suggestions: setting the width and height and setting horizontal = FALSE. I have tried setting the width and height but it makes no difference. I have also tried using horizontal = FALSE. This rotates and elongates the plot, but it is still displayed horizontally on a vertical page, and so only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps ). I am not sure what is wrong. Plots are created with filled.contour. I guess this is a misconfiguration of your GSview. The plots are fine for me. Anyway, you might also want to set the argument paper=special in the postscript() call. Uwe Ligges Thanks Miruna Miruna Petrescu-Prahova Department of Sociology University of California, Irvine [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. --- Costas Vorlow Research Economist Eurobank EFG Division of Research Forecasting --- tel: +30-210-3337273 (ext 17273) fax: +30-210-3337687 P Think before you print. Disclaimer: This e-mail is confidential. If you are not the intended recipient, you should not copy it, re-transmit it, use it or disclose its contents, but should return it to the sender immediately and delete the copy from your system. EFG Eurobank Ergasias S.A. is not responsible for, nor endorses, any opinion, recommendation, conclusion, solicitation, offer or agreement or any information contained in this communication. EFG Eurobank Ergasias S.A. cannot accept any responsibility for the accuracy or completeness of this message as it has been transmitted over a public network. If you suspect that the message may have been intercepted or amended, please call the sender. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. Ask a question on any topic and get answers from real people. Go to __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
Re: [R] Sourcing commands but delaying their execution
Here's one possibility:
The file garbage.R has
x - rnorm(100)
print(summary(x))
You can do:
cmds - parse(file=garbage.R, n=NA)
and when you want to execute those commands, do
eval(cmds)
Andy
From: Dennis Fisher
Colleagues:
I have encountered the following situation:
SERIES OF COMMANDS
source(File1)
MORE COMMANDS
source(File2)
Optimally, I would like File1 and File2 to be merged into a single
file (FileMerged). However, if I wrote the following:
SERIES OF COMMANDS
source(FileMerged)
MORE COMMANDS
I encounter an error: the File2 portion of FileMerged contains
commands that cannot be executed properly until MORE COMMANDS are
executed. Similarly, sourcing FileMerged after MORE COMMANDS does
not work because MORE COMMANDS requires the information from the
File1 portion of FileMerged.
I am looking for a means to source FileMerged but not execute
some of
the commands immediately. Functionally this would look like:
SERIES OF COMMANDS
source(FileMerged)# but withhold execution of
some of the commands
MORE COMMANDS
COMMAND TO EXECUTE THE WITHHELD COMMANDS
Does R offer some option to accomplish this?
Dennis
Dennis Fisher MD
P (The P Less Than Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
__
R-help@stat.math.ethz.ch 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.
--
Notice: This e-mail message, together with any attachments,...{{dropped}}
__
R-help@stat.math.ethz.ch 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] plot to postscript orientation-update
Follow-up I seem to have manged to get the eps file to work using: postscript(C:/temp/figure.eps, horizontal=F, paper=special, height=8, width=8, pointsize=12) Exactly why I'm not sure since I just copied some old code that I had used a year or so ago. --- Vorlow Constantinos [EMAIL PROTECTED] wrote: Hi, My vanilla code works fine... See also attached .eps file (seperate email sent directly to you) r-rnorm(100) postscript(figure.eps) plot.ts(r) dev.off() Also this works ok as you have been told already: paper=special in the postscript() call. If you see my eps file wrongly then your GSVIEW setup is wrong. Choose Orientation Auto and under Options (bottom half) click-select-tick everything except Ignore DSC. That should do the trick... Costas Miruna Petrescu-Prahova wrote: Hi I am trying to save some plots in a postscript file. When I generate the plots in the main window, they appear correctly - their orientation is landscape (i.e., horizontal). However, when I open the .ps file with GSview, the whole page appears vertically, and the plot appears horizontally, which means that the plot is only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/default.ps https://webfiles.uci.edu/mpetresc/postscript.files/default.ps ). I searched the R-help mailing list archive and found 2 suggestions: setting the width and height and setting horizontal = FALSE. I have tried setting the width and height but it makes no difference. I have also tried using horizontal = FALSE. This rotates and elongates the plot, but it is still displayed horizontally on a vertical page, and so only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps ). I am not sure what is wrong. Plots are created with filled.contour. I guess this is a misconfiguration of your GSview. The plots are fine for me. Anyway, you might also want to set the argument paper=special in the postscript() call. Uwe Ligges Thanks Miruna Miruna Petrescu-Prahova Department of Sociology University of California, Irvine [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. --- Costas Vorlow Research Economist Eurobank EFG Division of Research Forecasting --- tel: +30-210-3337273 (ext 17273) fax: +30-210-3337687 P Think before you print. Disclaimer: This e-mail is confidential. If you are not the intended recipient, you should not copy it, re-transmit it, use it or disclose its contents, but should return it to the sender immediately and delete the copy from your system. EFG Eurobank Ergasias S.A. is not responsible for, nor endorses, any opinion, recommendation, conclusion, solicitation, offer or agreement or any information contained in this communication. EFG Eurobank Ergasias S.A. cannot accept any responsibility for the accuracy or completeness of this message as it has been transmitted over a public network. If you suspect that the message may have been intercepted or amended, please call the sender. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Rmetrics and log returns
Hi all. How do I compute a Monday Open to Friday Close weekly return in Rmetrics from daily data? Thanks! John [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
You are reading the wrong part of the code for your argument list: foo[FileName] Error in `[.data.frame`(foo, FileName) : undefined columns selected [.data.frame is one of the most complex functions in R, and does many different things depending on which arguments are supplied. On Fri, 3 Aug 2007, Steven McKinney wrote: Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name (FileName instead of Filename) which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers I'll be tracking down such a bug soon too. Is there any options() setting, or debug technique that will flag data frame column extractions that reference a non-existent column? It seems to me that the [.data.frame extractor used to throw an error if given a mis-spelled variable name, and I still see lines of code in [.data.frame such as if (any(is.na(cols))) stop(undefined columns selected) In R 2.5.1 a NULL is silently returned. foo - data.frame(Filename = c(a, b)) foo[, FileName] NULL Has something changed so that the code lines if (any(is.na(cols))) stop(undefined columns selected) in [.data.frame no longer work properly (if I am understanding the intention properly)? If not, could [.data.frame check an options() variable setting (say warn.undefined.colnames) and throw a warning if a non-existent column name is referenced? sessionInfo() R version 2.5.1 (2007-06-27) powerpc-apple-darwin8.9.1 locale: en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: plotrix lme4 Matrix lattice 2.2-3 0.99875-4 0.999375-0 0.16-2 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -Original Message- From: [EMAIL PROTECTED] on behalf of Johnstone, Alice Sent: Wed 8/1/2007 7:20 PM To: [EMAIL PROTECTED] Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame For interest sake, I have found out why I wasn't getting my expected results when using read.AnnotatedDataFrame Turns out the error was made in the ReadAffy command, where I specified the filenames to be read from my AnnotatedDataFrame object. There was a typo error with a capital N ($FileName) rather than lowercase n ($Filename) as in my target file..whoops. However this meant the filename argument was ignored without the error message(!) and instead of using the information in the AnnotatedDataFrame object (which included filenames, but not alphabetically) it read the .cel files in alphabetical order from the working directory - hence the wrong file was given the wrong label (given by the order of Annotated object) and my comparisons were confused without being obvious as to why or where. Our solution: specify that filename is as.character so assignment of file to target is correct(after correcting $Filename) now that using read.AnnotatedDataFrame rather than readphenoData. Data-ReadAffy(filenames=as.character(pData(pd)$Filename),phenoData=pd) Hurrah! It may be beneficial to others, that if the filename argument isn't specified, that filenames are read from the phenoData object if included here. Thanks! -Original Message- From: Martin Morgan [mailto:[EMAIL PROTECTED] Sent: Thursday, 26 July 2007 11:49 a.m. To: Johnstone, Alice Cc: [EMAIL PROTECTED] Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame Hi Alice -- Johnstone, Alice [EMAIL PROTECTED] writes: Using R2.5.0 and Bioconductor I have been following code to analysis Affymetrix expression data: 2 treatments vs control. The original code was run last year and used the read.phenoData command, however with the newer version I get the error message Warning messages: read.phenoData is deprecated, use read.AnnotatedDataFrame instead The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead I use the read.AnnotatedDataFrame command, but when it comes to the end of the analysis the comparison of the treatment to the controls gets mixed up compared to what you get using the original read.phenoData ie it looks like the 3 groups get labelled wrong and so the comparisons are different (but they can still be matched up). My questions are, 1) do you need to set up your target file differently when using read.AnnotatedDataFrame - what is the standard format? I can't quite tell where things are going wrong for you, so it would help if you can narrow
Re: [R] plot to postscript orientation-update
Well, it seems that having a square page works...If you modify the width or height so that they are not equal, it goes back to the same problem. I guess this is good enough for now. Miruna - Original Message - From: John Kane [EMAIL PROTECTED] To: Vorlow Constantinos [EMAIL PROTECTED]; [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Friday, August 03, 2007 11:52 AM Subject: Re: [R] plot to postscript orientation-update Follow-up I seem to have manged to get the eps file to work using: postscript(C:/temp/figure.eps, horizontal=F, paper=special, height=8, width=8, pointsize=12) Exactly why I'm not sure since I just copied some old code that I had used a year or so ago. --- Vorlow Constantinos [EMAIL PROTECTED] wrote: Hi, My vanilla code works fine... See also attached .eps file (seperate email sent directly to you) r-rnorm(100) postscript(figure.eps) plot.ts(r) dev.off() Also this works ok as you have been told already: paper=special in the postscript() call. If you see my eps file wrongly then your GSVIEW setup is wrong. Choose Orientation Auto and under Options (bottom half) click-select-tick everything except Ignore DSC. That should do the trick... Costas Miruna Petrescu-Prahova wrote: Hi I am trying to save some plots in a postscript file. When I generate the plots in the main window, they appear correctly - their orientation is landscape (i.e., horizontal). However, when I open the .ps file with GSview, the whole page appears vertically, and the plot appears horizontally, which means that the plot is only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/default.ps https://webfiles.uci.edu/mpetresc/postscript.files/default.ps ). I searched the R-help mailing list archive and found 2 suggestions: setting the width and height and setting horizontal = FALSE. I have tried setting the width and height but it makes no difference. I have also tried using horizontal = FALSE. This rotates and elongates the plot, but it is still displayed horizontally on a vertical page, and so only partially visible (example here https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps https://webfiles.uci.edu/mpetresc/postscript.files/horiz.false.ps ). I am not sure what is wrong. Plots are created with filled.contour. I guess this is a misconfiguration of your GSview. The plots are fine for me. Anyway, you might also want to set the argument paper=special in the postscript() call. Uwe Ligges Thanks Miruna Miruna Petrescu-Prahova Department of Sociology University of California, Irvine [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. --- Costas Vorlow Research Economist Eurobank EFG Division of Research Forecasting --- tel: +30-210-3337273 (ext 17273) fax: +30-210-3337687 P Think before you print. Disclaimer: This e-mail is confidential. If you are not the intended recipient, you should not copy it, re-transmit it, use it or disclose its contents, but should return it to the sender immediately and delete the copy from your system. EFG Eurobank Ergasias S.A. is not responsible for, nor endorses, any opinion, recommendation, conclusion, solicitation, offer or agreement or any information contained in this communication. EFG Eurobank Ergasias S.A. cannot accept any responsibility for the accuracy or completeness of this message as it has been transmitted over a public network. If you suspect that the message may have been intercepted or amended, please call the sender. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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. Ask a question on any topic and get answers from real people. Go to __ R-help@stat.math.ethz.ch 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] lme and aov
Gang Chen wrote: I have a mixed balanced ANOVA design with a between-subject factor (Grp) and a within-subject factor (Rsp). When I tried the following two commands which I thought are equivalent, fit.lme - lme(Beta ~ Grp*Rsp, random = ~1|Subj, Model); fit.aov - aov(Beta ~ Rsp*Grp+Error(Subj/Rsp)+Grp, Model); I got totally different results. What did I do wrong? Except for not telling us what your data are and what you mean by totally different? One model has a random interaction between Subj and Rsp, the other does not. This may make a difference, unless the interaction term is aliased with the residual error. If your data are unbalanced, aov is not guaranteed to give meaningful results. -pd __ R-help@stat.math.ethz.ch 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] Sourcing commands but delaying their execution
On 8/3/2007 3:01 PM, Liaw, Andy wrote:
Here's one possibility:
The file garbage.R has
x - rnorm(100)
print(summary(x))
You can do:
cmds - parse(file=garbage.R, n=NA)
and when you want to execute those commands, do
eval(cmds)
And since it's Friday afternoon, I'll suggest something that allows the
commands to be broken into two parts and executed separately (but which
is ridiculous overkill for this problem):
Put
x - rnorm(100)
divider
print(summary(x))
into your file, then
cmds - parse(file=garbage.R, n=NA)
as in Andy's suggestion. Then find the dividing line using
divider - which(unlist(lapply(cmds, deparse)) == divider)
and then
part_one - 1:(divider-1)
part_two - (divider+1):length(cmds)
Finally, execute as
eval(cmds[part_one])
MORE_COMMANDS
eval(cmds[part_two])
Duncan Murdoch
Andy
From: Dennis Fisher
Colleagues:
I have encountered the following situation:
SERIES OF COMMANDS
source(File1)
MORE COMMANDS
source(File2)
Optimally, I would like File1 and File2 to be merged into a single
file (FileMerged). However, if I wrote the following:
SERIES OF COMMANDS
source(FileMerged)
MORE COMMANDS
I encounter an error: the File2 portion of FileMerged contains
commands that cannot be executed properly until MORE COMMANDS are
executed. Similarly, sourcing FileMerged after MORE COMMANDS does
not work because MORE COMMANDS requires the information from the
File1 portion of FileMerged.
I am looking for a means to source FileMerged but not execute
some of
the commands immediately. Functionally this would look like:
SERIES OF COMMANDS
source(FileMerged)# but withhold execution of
some of the commands
MORE COMMANDS
COMMAND TO EXECUTE THE WITHHELD COMMANDS
Does R offer some option to accomplish this?
Dennis
Dennis Fisher MD
P (The P Less Than Company)
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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-help@stat.math.ethz.ch 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] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
Thanks Prof Ripley,
I used double indexing (if I understand the doc correctly)
so my call was
foo[, FileName]
I traced through each line of `[.data.frame`
following the sequence of commands executed
for my call.
In the code section
if (missing(i)) {
if (missing(j) drop length(x) == 1L)
return(.subset2(x, 1L))
y - if (missing(j))
x
else .subset(x, j)
if (drop length(y) == 1L)
return(.subset2(y, 1L)) ## This returns a result before undefined
columns check is done. Is this intended?
cols - names(y)
if (any(is.na(cols)))
stop(undefined columns selected)
if (any(duplicated(cols)))
names(y) - make.unique(cols)
nrow - .row_names_info(x, 2L)
if (drop !mdrop nrow == 1L)
return(structure(y, class = NULL, row.names = NULL))
else return(structure(y, class = oldClass(x), row.names =
.row_names_info(x,
0L)))
}
the return happened after execution of
if (drop length(y) == 1L)
return(.subset2(y, 1L))
before the check on column names.
Shouldn't the check on column names
cols - names(y)
if (any(is.na(cols)))
stop(undefined columns selected)
occur before
if (drop length(y) == 1L)
return(.subset2(y, 1L))
rather than after?
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: Fri 8/3/2007 12:25 PM
To: Steven McKinney
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] FW: Selecting undefined column of a data frame (was [BioC]
read.phenoData vs read.AnnotatedDataFrame)
You are reading the wrong part of the code for your argument list:
foo[FileName]
Error in `[.data.frame`(foo, FileName) : undefined columns selected
[.data.frame is one of the most complex functions in R, and does many
different things depending on which arguments are supplied.
On Fri, 3 Aug 2007, Steven McKinney wrote:
Hi all,
What are current methods people use in R to identify
mis-spelled column names when selecting columns
from a data frame?
Alice Johnson recently tackled this issue
(see [BioC] posting below).
Due to a mis-spelled column name (FileName
instead of Filename) which produced no warning,
Alice spent a fair amount of time tracking down
this bug. With my fumbling fingers I'll be tracking
down such a bug soon too.
Is there any options() setting, or debug technique
that will flag data frame column extractions that
reference a non-existent column? It seems to me
that the [.data.frame extractor used to throw an
error if given a mis-spelled variable name, and I
still see lines of code in [.data.frame such as
if (any(is.na(cols)))
stop(undefined columns selected)
In R 2.5.1 a NULL is silently returned.
foo - data.frame(Filename = c(a, b))
foo[, FileName]
NULL
Has something changed so that the code lines
if (any(is.na(cols)))
stop(undefined columns selected)
in [.data.frame no longer work properly (if
I am understanding the intention properly)?
If not, could [.data.frame check an
options() variable setting (say
warn.undefined.colnames) and throw a warning
if a non-existent column name is referenced?
sessionInfo()
R version 2.5.1 (2007-06-27)
powerpc-apple-darwin8.9.1
locale:
en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
plotrix lme4 Matrix lattice
2.2-3 0.99875-4 0.999375-0 0.16-2
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
-Original Message-
From: [EMAIL PROTECTED] on behalf of Johnstone, Alice
Sent: Wed 8/1/2007 7:20 PM
To: [EMAIL PROTECTED]
Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame
For interest sake, I have found out why I wasn't getting my expected
results when using read.AnnotatedDataFrame
Turns out the error was made in the ReadAffy command, where I specified
the filenames to be read from my AnnotatedDataFrame object. There was a
typo error with a capital N ($FileName) rather than lowercase n
($Filename) as in my target file..whoops. However this meant the
filename argument was ignored without the error message(!) and instead
of using the information in the AnnotatedDataFrame object (which
included filenames, but not alphabetically) it read the .cel files in
alphabetical order from the working directory - hence the wrong file was
given the wrong label (given by the order of Annotated object) and my
comparisons were confused without being obvious as to why or where.
Our solution: specify that filename is as.character so assignment
Re: [R] lme and aov
Thanks for the response! It is indeed a balanced design. The results are different in the sense all the F tests for main effects are not the same. Do you mean that a random interaction is modeled in the aov command? If so, what would be an equivalent command of aov to the one with lme? Thanks, Gang On Aug 3, 2007, at 3:52 PM, Peter Dalgaard wrote: Gang Chen wrote: I have a mixed balanced ANOVA design with a between-subject factor (Grp) and a within-subject factor (Rsp). When I tried the following two commands which I thought are equivalent, fit.lme - lme(Beta ~ Grp*Rsp, random = ~1|Subj, Model); fit.aov - aov(Beta ~ Rsp*Grp+Error(Subj/Rsp)+Grp, Model); I got totally different results. What did I do wrong? Except for not telling us what your data are and what you mean by totally different? One model has a random interaction between Subj and Rsp, the other does not. This may make a difference, unless the interaction term is aliased with the residual error. If your data are unbalanced, aov is not guaranteed to give meaningful results. -pd __ R-help@stat.math.ethz.ch 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] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
I've since seen your followup a more detailed explanation may help. The path through the code for your argument list does not go where you quoted, and there is a reason for it. Generally when you extract in R and ask for an non-existent index you get NA or NULL as the result (and no warning), e.g. y - list(x=1, y=2) y[[z]] NULL Because data frames 'must' have (column) names, they are a partial exception and when the result is a data frame you get an error if it would contain undefined columns. But in the case of foo[, FileName], the result is a single column and so will not have a name: there seems no reason to be different from foo[[FileName]] NULL foo$FileName NULL which similarly select a single column. At one time they were different in R, for no documented reason. On Fri, 3 Aug 2007, Prof Brian Ripley wrote: You are reading the wrong part of the code for your argument list: foo[FileName] Error in `[.data.frame`(foo, FileName) : undefined columns selected [.data.frame is one of the most complex functions in R, and does many different things depending on which arguments are supplied. On Fri, 3 Aug 2007, Steven McKinney wrote: Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name (FileName instead of Filename) which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers I'll be tracking down such a bug soon too. Is there any options() setting, or debug technique that will flag data frame column extractions that reference a non-existent column? It seems to me that the [.data.frame extractor used to throw an error if given a mis-spelled variable name, and I still see lines of code in [.data.frame such as if (any(is.na(cols))) stop(undefined columns selected) In R 2.5.1 a NULL is silently returned. foo - data.frame(Filename = c(a, b)) foo[, FileName] NULL Has something changed so that the code lines if (any(is.na(cols))) stop(undefined columns selected) in [.data.frame no longer work properly (if I am understanding the intention properly)? If not, could [.data.frame check an options() variable setting (say warn.undefined.colnames) and throw a warning if a non-existent column name is referenced? sessionInfo() R version 2.5.1 (2007-06-27) powerpc-apple-darwin8.9.1 locale: en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: plotrix lme4 Matrix lattice 2.2-3 0.99875-4 0.999375-0 0.16-2 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -Original Message- From: [EMAIL PROTECTED] on behalf of Johnstone, Alice Sent: Wed 8/1/2007 7:20 PM To: [EMAIL PROTECTED] Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame For interest sake, I have found out why I wasn't getting my expected results when using read.AnnotatedDataFrame Turns out the error was made in the ReadAffy command, where I specified the filenames to be read from my AnnotatedDataFrame object. There was a typo error with a capital N ($FileName) rather than lowercase n ($Filename) as in my target file..whoops. However this meant the filename argument was ignored without the error message(!) and instead of using the information in the AnnotatedDataFrame object (which included filenames, but not alphabetically) it read the .cel files in alphabetical order from the working directory - hence the wrong file was given the wrong label (given by the order of Annotated object) and my comparisons were confused without being obvious as to why or where. Our solution: specify that filename is as.character so assignment of file to target is correct(after correcting $Filename) now that using read.AnnotatedDataFrame rather than readphenoData. Data-ReadAffy(filenames=as.character(pData(pd)$Filename),phenoData=pd) Hurrah! It may be beneficial to others, that if the filename argument isn't specified, that filenames are read from the phenoData object if included here. Thanks! -Original Message- From: Martin Morgan [mailto:[EMAIL PROTECTED] Sent: Thursday, 26 July 2007 11:49 a.m. To: Johnstone, Alice Cc: [EMAIL PROTECTED] Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame Hi Alice -- Johnstone, Alice [EMAIL PROTECTED] writes: Using R2.5.0 and Bioconductor I have been following code to analysis Affymetrix expression data: 2 treatments vs
Re: [R] lme and aov
Gang: I think what Peter is asking for is for you to put some of your output in an email. If the values of the fixed effects are the same across models, but the F-tests are different, then there is a whole other thread we will point you to for an explanation. (I don't presume to speak for other people, btw, and I'm happy to stand corrected) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gang Chen Sent: Friday, August 03, 2007 4:01 PM To: Peter Dalgaard Cc: r-help@stat.math.ethz.ch Subject: Re: [R] lme and aov Thanks for the response! It is indeed a balanced design. The results are different in the sense all the F tests for main effects are not the same. Do you mean that a random interaction is modeled in the aov command? If so, what would be an equivalent command of aov to the one with lme? Thanks, Gang On Aug 3, 2007, at 3:52 PM, Peter Dalgaard wrote: Gang Chen wrote: I have a mixed balanced ANOVA design with a between-subject factor (Grp) and a within-subject factor (Rsp). When I tried the following two commands which I thought are equivalent, fit.lme - lme(Beta ~ Grp*Rsp, random = ~1|Subj, Model); fit.aov - aov(Beta ~ Rsp*Grp+Error(Subj/Rsp)+Grp, Model); I got totally different results. What did I do wrong? Except for not telling us what your data are and what you mean by totally different? One model has a random interaction between Subj and Rsp, the other does not. This may make a difference, unless the interaction term is aliased with the residual error. If your data are unbalanced, aov is not guaranteed to give meaningful results. -pd __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: Fri 8/3/2007 1:05 PM
To: Steven McKinney
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] FW: Selecting undefined column of a data frame (was [BioC]
read.phenoData vs read.AnnotatedDataFrame)
I've since seen your followup a more detailed explanation may help.
The path through the code for your argument list does not go where you
quoted, and there is a reason for it.
Using a copy of [.data.frame with browser() I have traced
the flow of execution. (My copy with the browser command is at the end
of this email)
foo[, FileName]
Called from: `[.data.frame`(foo, , FileName)
Browse[1] n
debug: mdrop - missing(drop)
Browse[1] n
debug: Narg - nargs() - (!mdrop)
Browse[1] n
debug: if (Narg 3) {
if (!mdrop)
warning(drop argument will be ignored)
if (missing(i))
return(x)
if (is.matrix(i))
return(as.matrix(x)[i])
y - NextMethod([)
cols - names(y)
if (!is.null(cols) any(is.na(cols)))
stop(undefined columns selected)
if (any(duplicated(cols)))
names(y) - make.unique(cols)
return(structure(y, class = oldClass(x), row.names = .row_names_info(x,
0L)))
}
Browse[1] n
debug: if (missing(i)) {
if (missing(j) drop length(x) == 1L)
return(.subset2(x, 1L))
y - if (missing(j))
x
else .subset(x, j)
if (drop length(y) == 1L)
return(.subset2(y, 1L))
cols - names(y)
if (any(is.na(cols)))
stop(undefined columns selected)
if (any(duplicated(cols)))
names(y) - make.unique(cols)
nrow - .row_names_info(x, 2L)
if (drop !mdrop nrow == 1L)
return(structure(y, class = NULL, row.names = NULL))
else return(structure(y, class = oldClass(x), row.names =
.row_names_info(x,
0L)))
}
Browse[1] n
debug: if (missing(j) drop length(x) == 1L) return(.subset2(x,
1L))
Browse[1] n
debug: y - if (missing(j)) x else .subset(x, j)
Browse[1] n
debug: if (drop length(y) == 1L) return(.subset2(y, 1L))
Browse[1] n
NULL
So `[.data.frame` is exiting after executing
+ if (drop length(y) == 1L)
+ return(.subset2(y, 1L)) ## This returns a result before undefined
columns check is done. Is this intended?
Couldn't the error check
+ cols - names(y)
+ if (any(is.na(cols)))
+ stop(undefined columns selected)
be done before the above return()?
What would break if the error check on column names was done
before returning a NULL result due to incorrect column name spelling?
Why should
foo[, FileName]
NULL
differ from
foo[seq(nrow(foo)), FileName]
Error in `[.data.frame`(foo, seq(nrow(foo)), FileName) :
undefined columns selected
Thank you for your explanations.
Generally when you extract in R and ask for an non-existent index you get
NA or NULL as the result (and no warning), e.g.
y - list(x=1, y=2)
y[[z]]
NULL
Because data frames 'must' have (column) names, they are a partial
exception and when the result is a data frame you get an error if it would
contain undefined columns.
But in the case of foo[, FileName], the result is a single column and so
will not have a name: there seems no reason to be different from
foo[[FileName]]
NULL
foo$FileName
NULL
which similarly select a single column. At one time they were different
in R, for no documented reason.
On Fri, 3 Aug 2007, Prof Brian Ripley wrote:
You are reading the wrong part of the code for your argument list:
foo[FileName]
Error in `[.data.frame`(foo, FileName) : undefined columns selected
[.data.frame is one of the most complex functions in R, and does many
different things depending on which arguments are supplied.
On Fri, 3 Aug 2007, Steven McKinney wrote:
Hi all,
What are current methods people use in R to identify
mis-spelled column names when selecting columns
from a data frame?
Alice Johnson recently tackled this issue
(see [BioC] posting below).
Due to a mis-spelled column name (FileName
instead of Filename) which produced no warning,
Alice spent a fair amount of time tracking down
this bug. With my fumbling fingers I'll be tracking
down such a bug soon too.
Is there any options() setting, or debug technique
that will flag data frame column extractions that
reference a non-existent column? It seems to me
that the [.data.frame extractor used to throw an
error if given a mis-spelled variable name, and I
still see lines of code in [.data.frame such as
if (any(is.na(cols)))
stop(undefined columns selected)
In R 2.5.1 a NULL is silently returned.
foo - data.frame(Filename = c(a, b))
foo[, FileName]
NULL
Has something changed so that the code lines
if (any(is.na(cols)))
Re: [R] lme and aov
Gang Chen wrote: Thanks a lot for clarification! I just started to learn programming in R for a week, and wanted to try a simple mixed design of balanced ANOVA with a between-subject factor (Grp) and a within-subject factor (Rsp), but I'm not sure whether I'm modeling the data correctly with either of the command lines. Here is the result. Any help would be highly appreciated. fit.lme - lme(Beta ~ Grp*Rsp, random = ~1|Subj, Model); summary(fit.lme) Linear mixed-effects model fit by REML Data: Model AIC BIClogLik 233.732 251.9454 -108.8660 Random effects: Formula: ~1 | Subj (Intercept) Residual StdDev:1.800246 0.3779612 Fixed effects: Beta ~ Grp * Rsp Value Std.Error DFt-value p-value (Intercept) 1.1551502 0.5101839 36 2.2641837 0.0297 GrpB-1.1561248 0.7215090 36 -1.6023706 0.1178 GrpC-1.2345321 0.7215090 36 -1.7110417 0.0957 RspB-0.0563077 0.1482486 36 -0.3798196 0.7063 GrpB:RspB -0.3739339 0.2096551 36 -1.7835665 0.0829 GrpC:RspB0.3452539 0.2096551 36 1.6467705 0.1083 Correlation: (Intr) GrpB GrpC RspB GrB:RB GrpB -0.707 GrpC -0.707 0.500 RspB -0.145 0.103 0.103 GrpB:RspB 0.103 -0.145 -0.073 -0.707 GrpC:RspB 0.103 -0.073 -0.145 -0.707 0.500 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -1.72266114 -0.41242552 0.02994094 0.41348767 1.72323563 Number of Observations: 78 Number of Groups: 39 fit.aov - aov(Beta ~ Rsp*Grp+Error(Subj/Rsp)+Grp, Model); fit.aov Call: aov(formula = Beta ~ Rsp * Grp + Error(Subj/Rsp) + Grp, data = Model) Grand Mean: 0.3253307 Stratum 1: Subj Terms: Grp Sum of Squares 5.191404 Deg. of Freedom1 1 out of 2 effects not estimable Estimated effects are balanced Stratum 2: Subj:Rsp Terms: Rsp Sum of Squares 7.060585e-05 Deg. of Freedom1 2 out of 3 effects not estimable Estimated effects are balanced Stratum 3: Within Terms: Rsp Grp Rsp:Grp Residuals Sum of Squares0.33428 36.96518 1.50105 227.49594 Deg. of Freedom 1 2 270 Residual standard error: 1.802760 Estimated effects may be unbalanced This looks odd. It is a standard split-plot layout, right? 3 groups of 13 subjects, each measured with two kinds of Rsp = 3x13x2 = 78 observations. In that case you shouldn't see the same effect allocated to multiple error strata. I suspect you forgot to declare Subj as factor. Also: summary(fit.aov) is nicer, and anova(fit.lme) should be informative. __ R-help@stat.math.ethz.ch 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] lme and aov
Thanks a lot for clarification! I just started to learn programming in R for a week, and wanted to try a simple mixed design of balanced ANOVA with a between-subject factor (Grp) and a within-subject factor (Rsp), but I'm not sure whether I'm modeling the data correctly with either of the command lines. Here is the result. Any help would be highly appreciated. fit.lme - lme(Beta ~ Grp*Rsp, random = ~1|Subj, Model); summary(fit.lme) Linear mixed-effects model fit by REML Data: Model AIC BIClogLik 233.732 251.9454 -108.8660 Random effects: Formula: ~1 | Subj (Intercept) Residual StdDev:1.800246 0.3779612 Fixed effects: Beta ~ Grp * Rsp Value Std.Error DFt-value p-value (Intercept) 1.1551502 0.5101839 36 2.2641837 0.0297 GrpB-1.1561248 0.7215090 36 -1.6023706 0.1178 GrpC-1.2345321 0.7215090 36 -1.7110417 0.0957 RspB-0.0563077 0.1482486 36 -0.3798196 0.7063 GrpB:RspB -0.3739339 0.2096551 36 -1.7835665 0.0829 GrpC:RspB0.3452539 0.2096551 36 1.6467705 0.1083 Correlation: (Intr) GrpB GrpC RspB GrB:RB GrpB -0.707 GrpC -0.707 0.500 RspB -0.145 0.103 0.103 GrpB:RspB 0.103 -0.145 -0.073 -0.707 GrpC:RspB 0.103 -0.073 -0.145 -0.707 0.500 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -1.72266114 -0.41242552 0.02994094 0.41348767 1.72323563 Number of Observations: 78 Number of Groups: 39 fit.aov - aov(Beta ~ Rsp*Grp+Error(Subj/Rsp)+Grp, Model); fit.aov Call: aov(formula = Beta ~ Rsp * Grp + Error(Subj/Rsp) + Grp, data = Model) Grand Mean: 0.3253307 Stratum 1: Subj Terms: Grp Sum of Squares 5.191404 Deg. of Freedom1 1 out of 2 effects not estimable Estimated effects are balanced Stratum 2: Subj:Rsp Terms: Rsp Sum of Squares 7.060585e-05 Deg. of Freedom1 2 out of 3 effects not estimable Estimated effects are balanced Stratum 3: Within Terms: Rsp Grp Rsp:Grp Residuals Sum of Squares0.33428 36.96518 1.50105 227.49594 Deg. of Freedom 1 2 270 Residual standard error: 1.802760 Estimated effects may be unbalanced Thanks, Gang On Aug 3, 2007, at 4:09 PM, Doran, Harold wrote: Gang: I think what Peter is asking for is for you to put some of your output in an email. If the values of the fixed effects are the same across models, but the F-tests are different, then there is a whole other thread we will point you to for an explanation. (I don't presume to speak for other people, btw, and I'm happy to stand corrected) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gang Chen Sent: Friday, August 03, 2007 4:01 PM To: Peter Dalgaard Cc: r-help@stat.math.ethz.ch Subject: Re: [R] lme and aov Thanks for the response! It is indeed a balanced design. The results are different in the sense all the F tests for main effects are not the same. Do you mean that a random interaction is modeled in the aov command? If so, what would be an equivalent command of aov to the one with lme? Thanks, Gang On Aug 3, 2007, at 3:52 PM, Peter Dalgaard wrote: Gang Chen wrote: I have a mixed balanced ANOVA design with a between-subject factor (Grp) and a within-subject factor (Rsp). When I tried the following two commands which I thought are equivalent, fit.lme - lme(Beta ~ Grp*Rsp, random = ~1|Subj, Model); fit.aov - aov(Beta ~ Rsp*Grp+Error(Subj/Rsp)+Grp, Model); I got totally different results. What did I do wrong? Except for not telling us what your data are and what you mean by totally different? One model has a random interaction between Subj and Rsp, the other does not. This may make a difference, unless the interaction term is aliased with the residual error. If your data are unbalanced, aov is not guaranteed to give meaningful results. -pd __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] lme and aov
This looks odd. It is a standard split-plot layout, right? 3 groups of 13 subjects, each measured with two kinds of Rsp = 3x13x2 = 78 observations. Yes, that is right. In that case you shouldn't see the same effect allocated to multiple error strata. I suspect you forgot to declare Subj as factor. This is exactly the problem I had: Model$Subj was not a factor! Now they converge. A lesson well learned. Thanks a lot for the help, Gang On Aug 3, 2007, at 4:53 PM, Peter Dalgaard wrote: Gang Chen wrote: Thanks a lot for clarification! I just started to learn programming in R for a week, and wanted to try a simple mixed design of balanced ANOVA with a between-subject factor (Grp) and a within-subject factor (Rsp), but I'm not sure whether I'm modeling the data correctly with either of the command lines. Here is the result. Any help would be highly appreciated. fit.lme - lme(Beta ~ Grp*Rsp, random = ~1|Subj, Model); summary(fit.lme) Linear mixed-effects model fit by REML Data: Model AIC BIClogLik 233.732 251.9454 -108.8660 Random effects: Formula: ~1 | Subj (Intercept) Residual StdDev:1.800246 0.3779612 Fixed effects: Beta ~ Grp * Rsp Value Std.Error DFt-value p-value (Intercept) 1.1551502 0.5101839 36 2.2641837 0.0297 GrpB-1.1561248 0.7215090 36 -1.6023706 0.1178 GrpC-1.2345321 0.7215090 36 -1.7110417 0.0957 RspB-0.0563077 0.1482486 36 -0.3798196 0.7063 GrpB:RspB -0.3739339 0.2096551 36 -1.7835665 0.0829 GrpC:RspB0.3452539 0.2096551 36 1.6467705 0.1083 Correlation: (Intr) GrpB GrpC RspB GrB:RB GrpB -0.707 GrpC -0.707 0.500 RspB -0.145 0.103 0.103 GrpB:RspB 0.103 -0.145 -0.073 -0.707 GrpC:RspB 0.103 -0.073 -0.145 -0.707 0.500 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -1.72266114 -0.41242552 0.02994094 0.41348767 1.72323563 Number of Observations: 78 Number of Groups: 39 fit.aov - aov(Beta ~ Rsp*Grp+Error(Subj/Rsp)+Grp, Model); fit.aov Call: aov(formula = Beta ~ Rsp * Grp + Error(Subj/Rsp) + Grp, data = Model) Grand Mean: 0.3253307 Stratum 1: Subj Terms: Grp Sum of Squares 5.191404 Deg. of Freedom1 1 out of 2 effects not estimable Estimated effects are balanced Stratum 2: Subj:Rsp Terms: Rsp Sum of Squares 7.060585e-05 Deg. of Freedom1 2 out of 3 effects not estimable Estimated effects are balanced Stratum 3: Within Terms: Rsp Grp Rsp:Grp Residuals Sum of Squares0.33428 36.96518 1.50105 227.49594 Deg. of Freedom 1 2 270 Residual standard error: 1.802760 Estimated effects may be unbalanced __ R-help@stat.math.ethz.ch 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] a mixed effects model with collinear parameters.
Hi all, I have the following unbalanced data set : F1-rep(F1,29) F2-rep(F2,83) F3-rep(F3,18) F4-rep(F4,11) F5-rep(F5,25) F6-rep(F6,10) all.fac-c(F1,F2,F3,F4,F5,F6) batch1-rep(B1,29) batch2-rep(B2,83) batch3-rep(B2,18) batch4-rep(B1,11) batch5-rep(B2,25) batch6-rep(B2,10) batch-c(batch1,batch2,batch3,batch4,batch5,batch6) sample0[batch == B1]-rnorm(length(sample0[batch == B1]),5,1) sample0[batch == B2]-rnorm(length(sample0[batch == B2]),2,1) dataA - data.frame(samples = sample0, batches=factor(batch), soil=factor(all.fac)) dataA$soil - relevel(dataA$soil,ref=F2) X-matrix XX-t(X)%*%X solve(XX) Error in solve.default(XX) : system is computationally singular: reciprocal condition number = 3.74708e-18 Meaning there is collinearity between predictors. (F1 and B1) and (F4 and B1) I have tried a mixed effects model. amod - lme(fixed = samples ~ soil, random = ~ 1|batches, dataA, method=ML) summary(amod) Linear mixed-effects model fit by maximum likelihood Data: dataA AIC BIClogLik 507.0955 532.4594 -245.5478 Random effects: Formula: ~1 | batches (Intercept) Residual StdDev: 2.02532e-05 0.9764997 Fixed effects: samples ~ soil Value Std.Error DF t-value p-value (Intercept) 2.1540927 0.1090599 169 19.751470 0. soilF1 3.1223796 0.2143260 169 14.568363 0. soilF3 -0.2070161 0.2583386 169 -0.801336 0.4241 soilF4 2.7412508 0.3188104 169 8.598372 0. soilF5 -0.1668292 0.2266767 169 -0.735979 0.4628 soilF6 -0.2522510 0.3325879 169 -0.758449 0.4492 Correlation: (Intr) soilF1 soilF3 soilF4 soilF5 soilF1 -0.509 soilF3 -0.422 0.215 soilF4 -0.342 0.174 0.144 soilF5 -0.481 0.245 0.203 0.165 soilF6 -0.328 0.167 0.138 0.112 0.158 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -3.02335670 -0.59885469 0.03137624 0.65601671 3.71106690 Number of Observations: 176 Number of Groups: 2 ranef(amod) (Intercept) B1 5.944455e-23 B2 1.795242e-23 The fixed effects part seems to be right, should I just ignore the random effects part ? __ R-help@stat.math.ethz.ch 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] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
What would break is that three methods for doing the same thing would give different answers. Please do have the courtesy to actually read the detailed explanation you are given. Sorry Prof. Ripley, I am attempting to read carefully, as this issue has deeper coding/debugging implications, and as you point out, [.data.frame is one of the most complex functions in R so please bear with me. This change in behaviour has taken away a side-effect debugging tool, discussed below. On Fri, 3 Aug 2007, Steven McKinney wrote: -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Fri 8/3/2007 1:05 PM To: Steven McKinney Cc: r-help@stat.math.ethz.ch Subject: Re: [R] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame) I've since seen your followup a more detailed explanation may help. The path through the code for your argument list does not go where you quoted, and there is a reason for it. Generally when you extract in R and ask for an non-existent index you get NA or NULL as the result (and no warning), e.g. y - list(x=1, y=2) y[[z]] NULL Because data frames 'must' have (column) names, they are a partial exception and when the result is a data frame you get an error if it would contain undefined columns. But in the case of foo[, FileName], the result is a single column and so will not have a name: there seems no reason to be different from foo[[FileName]] NULL foo$FileName NULL which similarly select a single column. At one time they were different in R, for no documented reason. This difference provided a side-effect debugging tool, in that where bar - foo[, FileName] used to throw an error, alerting as to a typo, it now does not. Having been burned by NULL results due to typos in code lines using the $ extractor such as bar - foo$FileName I learned to use bar - foo[, FileName] to help cut down on typo bugs. With the ubiquity of camelCase object names, this is a constant typing bug hazard. I am wondering what to do now to double check spelling when accessing columns of a dataframe. If [.data.frame stays as is, can a debug mechanism be implemented in R that forces strict adherence to existing list names in debug mode? This would also help debug typos in camelCase names when using the $ and [[ extractors and accessors. Are there other debugging tools already in R that can help point out such camelCase list element name typos? On Fri, 3 Aug 2007, Prof Brian Ripley wrote: You are reading the wrong part of the code for your argument list: foo[FileName] Error in `[.data.frame`(foo, FileName) : undefined columns selected [.data.frame is one of the most complex functions in R, and does many different things depending on which arguments are supplied. On Fri, 3 Aug 2007, Steven McKinney wrote: Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name (FileName instead of Filename) which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers I'll be tracking down such a bug soon too. Is there any options() setting, or debug technique that will flag data frame column extractions that reference a non-existent column? It seems to me that the [.data.frame extractor used to throw an error if given a mis-spelled variable name, and I still see lines of code in [.data.frame such as if (any(is.na(cols))) stop(undefined columns selected) In R 2.5.1 a NULL is silently returned. foo - data.frame(Filename = c(a, b)) foo[, FileName] NULL Has something changed so that the code lines if (any(is.na(cols))) stop(undefined columns selected) in [.data.frame no longer work properly (if I am understanding the intention properly)? If not, could [.data.frame check an options() variable setting (say warn.undefined.colnames) and throw a warning if a non-existent column name is referenced? sessionInfo() R version 2.5.1 (2007-06-27) powerpc-apple-darwin8.9.1 locale: en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: plotrix lme4 Matrix lattice 2.2-3 0.99875-4 0.999375-0 0.16-2 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -- Brian D. Ripley,
Re: [R] FW: Selecting undefined column of a data frame (was [BioC]read.phenoData vs read.AnnotatedDataFrame)
I suspect you'll get some creative answers, but if all you're worried about is whether a column exists before you do something with it, what's wrong with: nm - ... ## a character vector of names if(!all(nm %in% names(yourdata))) ## complain else ## do something I think this is called defensive programming. Bert Gunter Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Steven McKinney Sent: Friday, August 03, 2007 10:38 AM To: r-help@stat.math.ethz.ch Subject: [R] FW: Selecting undefined column of a data frame (was [BioC]read.phenoData vs read.AnnotatedDataFrame) Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name (FileName instead of Filename) which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers I'll be tracking down such a bug soon too. Is there any options() setting, or debug technique that will flag data frame column extractions that reference a non-existent column? It seems to me that the [.data.frame extractor used to throw an error if given a mis-spelled variable name, and I still see lines of code in [.data.frame such as if (any(is.na(cols))) stop(undefined columns selected) In R 2.5.1 a NULL is silently returned. foo - data.frame(Filename = c(a, b)) foo[, FileName] NULL Has something changed so that the code lines if (any(is.na(cols))) stop(undefined columns selected) in [.data.frame no longer work properly (if I am understanding the intention properly)? If not, could [.data.frame check an options() variable setting (say warn.undefined.colnames) and throw a warning if a non-existent column name is referenced? sessionInfo() R version 2.5.1 (2007-06-27) powerpc-apple-darwin8.9.1 locale: en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: plotrix lme4 Matrix lattice 2.2-3 0.99875-4 0.999375-0 0.16-2 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -Original Message- From: [EMAIL PROTECTED] on behalf of Johnstone, Alice Sent: Wed 8/1/2007 7:20 PM To: [EMAIL PROTECTED] Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame For interest sake, I have found out why I wasn't getting my expected results when using read.AnnotatedDataFrame Turns out the error was made in the ReadAffy command, where I specified the filenames to be read from my AnnotatedDataFrame object. There was a typo error with a capital N ($FileName) rather than lowercase n ($Filename) as in my target file..whoops. However this meant the filename argument was ignored without the error message(!) and instead of using the information in the AnnotatedDataFrame object (which included filenames, but not alphabetically) it read the .cel files in alphabetical order from the working directory - hence the wrong file was given the wrong label (given by the order of Annotated object) and my comparisons were confused without being obvious as to why or where. Our solution: specify that filename is as.character so assignment of file to target is correct(after correcting $Filename) now that using read.AnnotatedDataFrame rather than readphenoData. Data-ReadAffy(filenames=as.character(pData(pd)$Filename),phenoData=pd) Hurrah! It may be beneficial to others, that if the filename argument isn't specified, that filenames are read from the phenoData object if included here. Thanks! -Original Message- From: Martin Morgan [mailto:[EMAIL PROTECTED] Sent: Thursday, 26 July 2007 11:49 a.m. To: Johnstone, Alice Cc: [EMAIL PROTECTED] Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame Hi Alice -- Johnstone, Alice [EMAIL PROTECTED] writes: Using R2.5.0 and Bioconductor I have been following code to analysis Affymetrix expression data: 2 treatments vs control. The original code was run last year and used the read.phenoData command, however with the newer version I get the error message Warning messages: read.phenoData is deprecated, use read.AnnotatedDataFrame instead The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead I use the read.AnnotatedDataFrame command, but when it comes to the end of the analysis the comparison of the treatment to the controls gets mixed up compared to what you get using the original read.phenoData ie it looks like the 3 groups get labelled wrong and so the comparisons are different (but they can still be matched up).
Re: [R] ROC curve in R
On Thursday 26 July 2007 10:45, Frank E Harrell Jr wrote:
Dylan Beaudette wrote:
On Thursday 26 July 2007 06:01, Frank E Harrell Jr wrote:
Note that even though the ROC curve as a whole is an interesting
'statistic' (its area is a linear translation of the
Wilcoxon-Mann-Whitney-Somers-Goodman-Kruskal rank correlation
statistics), each individual point on it is an improper scoring rule,
i.e., a rule that is optimized by fitting an inappropriate model. Using
curves to select cutoffs is a low-precision and arbitrary operation, and
the cutoffs do not replicate from study to study. Probably the worst
problem with drawing an ROC curve is that it tempts analysts to try to
find cutoffs where none really exist, and it makes analysts ignore the
whole field of decision theory.
Frank Harrell
Frank,
This thread has caught may attention for a couple reasons, possibly
related to my novice-level experience.
1. in a logistic regression study, where i am predicting the probability
of the response being 1 (for example) - there exists a continuum of
probability values - and a finite number of {1,0} realities when i either
look within the original data set, or with a new 'verification' data set.
I understand that drawing a line through the probabilities returned from
the logistic regression is a loss of information, but there are times
when a 'hard' decision requiring prediction of {1,0} is required. I have
found that the ROCR package (not necessarily the ROC Curve) can be useful
in identifying the probability cutoff where accuracy is maximized. Is
this an unreasonable way of using logistic regression as a predictor?
Thanks for the detailed response Frank. My follow-up questions are below:
Logistic regression (with suitable attention to not assuming linearity
and to avoiding overfitting) is a great way to estimate P[Y=1]. Given
good predicted P[Y=1] and utilities (losses, costs) for incorrect
positive and negative decisions, an optimal decision is one that
optimizes expected utility. The ROC curve does not play a direct role
in this regard.
Ok.
If per-subject utilities are not available, the analyst
may make various assumptions about utilities (including the unreasonable
but often used assumption that utilities do not vary over subjects) to
find a cutoff on P[Y=1].
Can you elaborate on what exactly a per-subject utility is? In my case, I am
trying to predict the occurance of specific soil features based on two
predictor variables: 1 continuous, the other categorical. Thus far my
evaluation of how well this method works is based on how often I can
correctly predict (a categorical) quality.
A very nice feature of P[Y=1] is that error
probabilities are self-contained. For example if P[Y=1] = .02 for a
single subject and you predict Y=0, the probability of an error is .02
by definition. One doesn't need to compute an overall error probability
over the whole distribution of subjects' risks. If the cost of a false
negative is C, the expected cost is .02*C in this example.
Interesting. The hang-up that I am having is that I need to predict from
{O,1}, as the direct users of this information are not currently interested
in in raw probabilities. As far as I know, in order to predict a class from a
probability I need use a cutoff... How else can I accomplish this without
imposing a cutoff on the entire dataset? One thought, identify a cutoff for
each level of the categorical predictor term in the model... (?)
2. The ROC curve can be a helpful way of communicating false positives /
false negatives to other users who are less familiar with the output and
interpretation of logistic regression.
What is more useful than that is a rigorous calibration curve estimate
to demonstrate the faithfulness of predicted P[Y=1] and a histogram
showing the distribution of predicted P[Y=1]
Ok. I can make that histogram - how would one go about making the 'rigorous
calibration curve' ? Note that I have a training set, from which the model is
built, and a smaller testing set for evaluation.
. Models that put a lot of
predictions near 0 or 1 are the most discriminating. Calibration curves
and risk distributions are easier to explain than ROC curves.
By 'risk discrimination' do you mean said histogram ?
Too often
a statistician will solve for a cutoff on P[Y=1], imposing her own
utility function without querying any subjects.
in this case I have picked a cutoff that resulted in the smallest number of
incorrectly classified observations , or highest kappa / tau statistics --
the results were very close.
3. I have been using the area under the ROC Curve, kendall's tau, and
cohen's kappa to evaluate the accuracy of a logistic regression based
prediction, the last two statistics based on a some probability cutoff
identified before hand.
ROC area (equiv. to Wilcoxon-Mann-Whitney and Somers' Dxy rank
correlation
[R] extracting dispersion parameter from quasipoisson lmer model
Hi, I would like to obtain the dispersion parameter for a quasipoisson model for later use in calculating QAIC values for model comparison.Can anyone suggest a method of how to go about doing this? The idea I have now is that I could use the residual deviance divided by the residual degrees of freedom to obtain the dispersion parameter. The residual deviance is available in the summary output for the lmer model. The problem with this idea is that the residual degrees of freedom is not directly available. I have been assuming that the estimated/approximate DF can be obtained through the formula listed below, and then subsequently used to obtain the dispersion parameter as described above. Is this correct? samp.m4 - mcmcsamp(m4, n = 1000) print(summary(samp.m4)) (eDF - mean(samp.m4[,deviance]) - deviance(m4, REML=FALSE)) # potentially useful approximate DF? However, rather than going through this roundabout, there appears to be an easier way to obtain the dispersion parameter. I have noted that the 'quasibinomial' produces a dispersion parameter in the model output, but the 'quasipoisson' output does not contain this useful number. Given that each of my models is fit by lmer with a quasipoisson distribution, the program must be internally calculating the dispersion parameter as it runs. Perhaps there is a way to obtain this number directly since I assume it has already been calculated? Can somone who has experience with this code provide some advice on whether this is possible and how I might manage to do this? Thank you for your time, Wayne Hallstrom 403-370-3832 - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Opening a script with the R editor via file association (on Windows)
Is there an easy way to open an R script file in the R Editor found in more recent versions of R on Windows via a file association? I am looking for functionality akin to how the .ssc file extension works for S-Plus: upon double-clicking on a .R file, Rgui.exe starts up and loads the script file in the R Editor. As far as I can tell, Rgui.exe does not have a command line option to load a file (so associating .R with Rgui.exe %1 won't work). I can get Windows to start Rgui.exe when I double-click on a script file, but that's about it. I also don't see any way to have Rgui.exe evaluate an expression provided on the command line (which would allow file.edit(%1)). I also thought about creating a custom .First calling 'file.edit' in a batch file, but then I'd have to start R, load the .First file, then quit and restart R, so that's out. Is there an easy way to do this without resorting to some other R GUI? Thanks, Chris Green Christopher G. Green (cggreen AT stat.washington.edu) Doctoral Candidate Department of Statistics, Box 354322, Seattle, WA, 98195-4322, U.S.A. http://www.stat.washington.edu/cggreen/ __ R-help@stat.math.ethz.ch 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] Sorting data for multiple regressions
So I am trying to perform a robust regression (fastmcd in the robust
package) on a dataset and I want to perform individual regressions based
on the groups within the data. We have over 300 sites and we want to
perform a regression based on the day of week and the hour for every
site. I was wondering if anyone knows of a 'by' command similar to the
one used in SAS that automatically groups the data for the regressions.
If not, does anyone have any tips on how to split the data into smaller
sets and then perform the regression on each set. I am new to R, so I
don't know all of the common work arounds and such. At the moment the
only method I can think of is to split the data using condition
statements and manually running the regression on each set. Thanks or
your help
-Paul
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] FW: Selecting undefined column of a data frame (was [BioC]read.phenoData vs read.AnnotatedDataFrame)
Hi Bert, -Original Message- From: Bert Gunter [mailto:[EMAIL PROTECTED] Sent: Fri 8/3/2007 3:19 PM To: Steven McKinney; r-help@stat.math.ethz.ch Subject: RE: [R] FW: Selecting undefined column of a data frame (was [BioC]read.phenoData vs read.AnnotatedDataFrame) I suspect you'll get some creative answers, but if all you're worried about is whether a column exists before you do something with it, what's wrong with: nm - ... ## a character vector of names if(!all(nm %in% names(yourdata))) ## complain else ## do something I think this is called defensive programming. This is a good example of good defensive programming. I do indeed check variable/object names whenever obtaining them from an external source (user input, file input, a list in code). I was able to practice a defensive programming style in the past by using bar - foo[, FileName] instead of bar - foo$FileName but this has changed recently, so I need to figure out some other mechanisms. R is such a productive language, but this change will lead many of us to chase elusive typos that used to get revealed. I'm hoping that some kind of explicit data frame variable checking mechanism might be introduced since we've lost this one. It would also be great to have such a mechanism to help catch list access and extraction errors. Why should foo$FileName always quietly return NULL? I'm not sure why the following incongruity is okay. foo - matrix(1:4, nrow = 2) dimnames(foo) - list(NULL, c(a, b)) bar - foo[, A] Error: subscript out of bounds foo.df - as.data.frame(foo) foo.df a b 1 1 3 2 2 4 bar - foo.df[, A] bar NULL It is a lot of extra typing to wrap every command in extra code, but more of that will need to happen going forward. Steve McKinney Bert Gunter Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Steven McKinney Sent: Friday, August 03, 2007 10:38 AM To: r-help@stat.math.ethz.ch Subject: [R] FW: Selecting undefined column of a data frame (was [BioC]read.phenoData vs read.AnnotatedDataFrame) Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name (FileName instead of Filename) which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers I'll be tracking down such a bug soon too. Is there any options() setting, or debug technique that will flag data frame column extractions that reference a non-existent column? It seems to me that the [.data.frame extractor used to throw an error if given a mis-spelled variable name, and I still see lines of code in [.data.frame such as if (any(is.na(cols))) stop(undefined columns selected) In R 2.5.1 a NULL is silently returned. foo - data.frame(Filename = c(a, b)) foo[, FileName] NULL Has something changed so that the code lines if (any(is.na(cols))) stop(undefined columns selected) in [.data.frame no longer work properly (if I am understanding the intention properly)? If not, could [.data.frame check an options() variable setting (say warn.undefined.colnames) and throw a warning if a non-existent column name is referenced? sessionInfo() R version 2.5.1 (2007-06-27) powerpc-apple-darwin8.9.1 locale: en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: plotrix lme4 Matrix lattice 2.2-3 0.99875-4 0.999375-0 0.16-2 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -Original Message- From: [EMAIL PROTECTED] on behalf of Johnstone, Alice Sent: Wed 8/1/2007 7:20 PM To: [EMAIL PROTECTED] Subject: Re: [BioC] read.phenoData vs read.AnnotatedDataFrame For interest sake, I have found out why I wasn't getting my expected results when using read.AnnotatedDataFrame Turns out the error was made in the ReadAffy command, where I specified the filenames to be read from my AnnotatedDataFrame object. There was a typo error with a capital N ($FileName) rather than lowercase n ($Filename) as in my target file..whoops. However this meant the filename argument was ignored without the error message(!) and instead of using the information in the AnnotatedDataFrame object (which included filenames, but not alphabetically) it read the .cel files in alphabetical order from the working directory - hence the wrong file was given the wrong label
Re: [R] Opening a script with the R editor via file association (on Windows)
On 03/08/2007 7:16 PM, Christopher Green wrote: Is there an easy way to open an R script file in the R Editor found in more recent versions of R on Windows via a file association? I am looking for functionality akin to how the .ssc file extension works for S-Plus: upon double-clicking on a .R file, Rgui.exe starts up and loads the script file in the R Editor. As far as I can tell, Rgui.exe does not have a command line option to load a file (so associating .R with Rgui.exe %1 won't work). I can get Windows to start Rgui.exe when I double-click on a script file, but that's about it. I also don't see any way to have Rgui.exe evaluate an expression provided on the command line (which would allow file.edit(%1)). I also thought about creating a custom .First calling 'file.edit' in a batch file, but then I'd have to start R, load the .First file, then quit and restart R, so that's out. Is there an easy way to do this without resorting to some other R GUI? Easy? Not sure. But the following works: Set up the association as F:\R\R-2.5.1\bin\Rgui.exe --args %1 (with obvious modifications to the path) and put this line in your RHOME/etc/Rprofile.site file: utils::file.edit(commandArgs(TRUE)) You could make things more sophisticated if you don't want a blank edit window to open in case you're not using this shortcut. Duncan Murdoch __ R-help@stat.math.ethz.ch 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] ggplot2 qplot and add
On 8/2/07, Emilio Gagliardi [EMAIL PROTECTED] wrote: Hi Thierry and Hadley, Thanks for your help! I got it working almost 100% to what I want. My last questions are simple I think ;) 1) How can I pass a label to colour and assign the color at the same time? The auto-selection of colors is awesome for learning, but makes it harder to see some patterns. I'm not sure what you mean? Could you provide an example? 2) in regards to 1), where can I find a list of the possible values that can be passed to colour=? I've seen in some examples gray50 but when I try it, it doesn't come out gray50, it just prints that as the label. For example, in my case, I could have 4 colors with 4 different shades of each. Or maybe I can use word length and gray scale, and make longer words darker, etc... I will try and explain this more in the book - but there's a difference between mapping and setting. In qplot values are always mapped (this is usually what you want - you want to specify the raw values and have them automatically mapped to sensible visual properties). If you manually add on geoms you can map or set: * mapping: + geom_point(aes(colour = Treatment A)) * setting: + geom_point(colour = green) Note in the second case, the colour must be a valid R colour. Hadley __ R-help@stat.math.ethz.ch 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] request
I want to calculate the commulative sum of any numeric vector with the following command but this following command does not work comsum My question is , how we can calculate the commulative sum of any numeric vector with above command Thanks Zahid Khan Lecturer in Statistics Department of Mathematics Hazara University Mansehra. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] request
?cumsum --- zahid khan [EMAIL PROTECTED] wrote: I want to calculate the commulative sum of any numeric vector with the following command but this following command does not work comsum My question is , how we can calculate the commulative sum of any numeric vector with above command Thanks Zahid Khan Lecturer in Statistics Department of Mathematics Hazara University Mansehra. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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-help@stat.math.ethz.ch 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] Sorting data for multiple regressions
Well, R has a by() function that does what you want, and its help page contains an example of doing regression by group. (There are other ways.) On Fri, 3 Aug 2007, Paul Young wrote: So I am trying to perform a robust regression (fastmcd in the robust package) on a dataset and I want to perform individual regressions based fastmcd does not do regression ... or I would have adapted the ?by example to show you. on the groups within the data. We have over 300 sites and we want to perform a regression based on the day of week and the hour for every site. I was wondering if anyone knows of a 'by' command similar to the one used in SAS that automatically groups the data for the regressions. If not, does anyone have any tips on how to split the data into smaller sets and then perform the regression on each set. I am new to R, so I don't know all of the common work arounds and such. At the moment the only method I can think of is to split the data using condition statements and manually running the regression on each set. Thanks or your help -Paul -- 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 __ R-help@stat.math.ethz.ch 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.
