Re: [R] AIC extract and comparison
Lisa wrote: Hi, I need to fit models and use AIC method to campare the best fitted model manually. When i extract AIC by using extractAIC, it gave me the df and AIC values. Now the problem is, how can I compare the AIC values from two models? is there anyway to extract AIC with no df so that I can compare directly? Thank you! extractAIC(coxout) [1]1.000 1723.038 extractAIC(coxout)[2] Uwe [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] What are ties? Wilcox u-test
Hi, When I execute a Wilcox u-test on two variables I receive a warning : 'cannot compute exact p-value with ties' - What are ties? What does this mean for my data? - Is that a problem for significance testing? - is there a way to overcome this problem? I have different threads in this forum but it hard to find what the exact meaning of this warning message is. -- View this message in context: http://www.nabble.com/What-are-ties--Wilcox-u-test-tp16977232p16977232.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] What are ties? Wilcox u-test
Dirkheld wrote: Hi, When I execute a Wilcox u-test on two variables I receive a warning : 'cannot compute exact p-value with ties' - What are ties? What does this mean for my data? If you have two identical values in your data, these are called ties. Now the ranks are not unique anymore and hence exact p-values cannot be calculated. And since you do not know this, it might be worth to note that the Wilcoxon test also assumes a non-skewed distribution. - Is that a problem for significance testing? If there are just a few ties, you should not worry, but re-check how your data looks like. It is a warning, not an error message. - is there a way to overcome this problem? If you need to, use an appropriate test for your data. I have different threads in this forum but it hard to find what the exact meaning of this warning message is. Read some textbook? Uwe Ligges __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem installing packages
I cannot reproduce this, hence we need much more information in order to reproduce the problem. Which OS are we talking about? XP or Vista? If Vista: Are you running R with administrator privileges when trying to install the packages? Please do so (e.g. by right-clicking appropriately when starting R). Which version of R? (I guess 2.7.0 release from the paths given below) Which version of DBI (I guess it does not matter). Which CRAN mirror? (I guess it does not matter). Uwe Ligges Owe Jessen wrote: Hi, when I try installing new packages (in this case DBI) I run into the following problem: Paket 'DBI' erfolgreich ausgepackt und MD5 Summen abgeglichen Warnung: kann temporäre Installation 'C:\Programme\R\R-2.7.0\library\file5f906952\DBI' nicht nach 'Ý xlDÌú [EMAIL PROTECTED]' verschieben Has anybody any idea where these strange symbols come from? Thanks in advance, Owe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] What are ties? Wilcox u-test
On 30-Apr-08 07:47:56, Uwe Ligges wrote: Dirkheld wrote: Hi, When I execute a Wilcox u-test on two variables I receive a warning : 'cannot compute exact p-value with ties' - What are ties? What does this mean for my data? If you have two identical values in your data, these are called ties. Now the ranks are not unique anymore and hence exact p-values cannot be calculated. And since you do not know this, it might be worth to note that the Wilcoxon test also assumes a non-skewed distribution. For the sake of clarification, it should be emphasised that assumes a non-skewed distribution applies only to the paired two-sample case (signed-rank) or the single sample case. In this case the Wilcoxon test is in effect a test of symmetry. I think this is reasonably clear from ?wilcox.test. Dirkheld did not state that he was using the paired test, and may well simply have been comparing two samples (possibly of different sizes) of values of X and Y. When the Wilcoxon test is used to compare two samples of values which are not paired, it makes no assumption about the shape of the distribution, only that (as null hypothesis) the distribution from which X is sampled is the same as the distribution from which Y is sampled. It is, in effect, based on an estimate of P(X Y). In this respect, I think ?wilcox.test is misleading. While people commonly think that the Wilcoxon test (or its equivalent the Mann-Whitney U test) is a test of shift in location, this is only a special case of the class of alternatives (to the null hypothesis that the distributions are the same) to which the Wilcoxon (or Mann-Whitney) test is sensitive. In particular, the expected value of the Wilxoxon (or the Mann-Whitney) test statistic is a linear function of P(X Y). Hoping this helps, Ted. - Is that a problem for significance testing? If there are just a few ties, you should not worry, but re-check how your data looks like. It is a warning, not an error message. - is there a way to overcome this problem? If you need to, use an appropriate test for your data. I have different threads in this forum but it hard to find what the exact meaning of this warning message is. Read some textbook? Uwe Ligges __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 30-Apr-08 Time: 09:24:57 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combine Values into a Vector or List
Hello Jorge,
Sorry, my aim is to get each individual separately, so that if I input
A1 # the the result would be
1
This because I would like to use
lm.D - lm(y~A1+A1+A3...)
Thanks,
Diego
- Original Message
From: Jorge Ivan Velez [EMAIL PROTECTED]
To: Diego Culattoni [EMAIL PROTECTED]
Cc: R mailing list r-help@r-project.org
Sent: Tuesday, April 29, 2008 9:03:20 PM
Subject: Re: [R] Combine Values into a Vector or List
Hi Diego,
Try this:
z-As[A1]+As[A2]; names(z)-z
z
4
HTH,
Jorge
On Tue, Apr 29, 2008 at 2:57 PM, Diego Culattoni [EMAIL PROTECTED] wrote:
Thank you Jorge, what I want to have is
z - A1+A2
z
4
The problem is that A1, A2,... still unknown, so that I have the following error
A1
object A1 not found
Thank you in advance!
- Original Message
From: Jorge Ivan Velez [EMAIL PROTECTED]
To: Diego Culattoni [EMAIL PROTECTED]
Cc: R mailing list r-help@r-project.org
Sent: Tuesday, April 29, 2008 7:38:41 PM
Subject: Re: [R] Combine Values into a Vector or List
Hi Diego,
Is this what you want?
# Data set
set.seed(123)
x1-paste(A, 1:6, sep = )
x2- round(rgamma(6,2,1))
x3-paste(B, 1:6, sep = )
x4- round(rgamma(6,2,1))
data1 - data.frame(x1,x2,x3,x4)
data1
x1 x2 x3 x4
1 A1 1 B1 0
2 A2 3 B2 0
3 A3 0 B3 3
4 A4 2 B4 2
5 A5 4 B5 2
6 A6 2 B6 2
# A's
As=as.numeric(t(data1[,1:2])[-1,])
names(As)=paste('A',1:length(As),sep=)
As
A1 A2 A3 A4 A5 A6
1 3 0 2 4 2
# B's
Bs=as.numeric(t(data1[,3:4])[-1,])
names(Bs)=paste('B',1:length(Bs),sep=)
Bs
B1 B2 B3 B4 B5 B6
0 0 3 2 2 2
HTH,
Jorge
On Tue, Apr 29, 2008 at 1:20 PM, Diego Culattoni [EMAIL PROTECTED] wrote:
Hi Richard,
Thanks a lot! What I actually want to have
A1
4
A2
2
... and so on! Is this possible?
Thank you again :)!
- Original Message
From: [EMAIL PROTECTED] [EMAIL PROTECTED]
To: Diego Culattoni [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]
Sent: Monday, April 28, 2008 11:24:12 AM
Subject: Re: [R] Combine Values into a Vector or List
x1-paste(A, 1:6, sep = )
x2- round(rgamma(6,2,1))
x3-paste(B, 1:6, sep = )
x4- round(rgamma(6,2,1))
data1 - data.frame(x1,x2,x3,x4)
I would like to get
data2 - c(A1=4, A2=1, A3=0,...)
Is there any standard for such a case?
I presume that 4, 2, 0 are the first few values of x2. In which case, I
think that what you want is simply this:
names(x2) - x1
Regards,
Richie.
Mathematical Sciences Unit
HSL
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[R] randomForest weighting of variables and count data
Hello R-user! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and statistics beginner) I try to find the most important variables to divide my dataset as given in a categorical variable using randomForest. I was wondering if there is the possibility in randomForest to give different weights to the explaining variables and additonally if it makes a difference using count data? Thanks in advance Birgit Birgit Lemcke Institut für Systematische Botanik Zollikerstrasse 107 CH-8008 Zürich Switzerland Ph: +41 (0)44 634 8351 [EMAIL PROTECTED] 175 Jahre UZH «staunen.erleben.begreifen. Naturwissenschaft zum Anfassen.» MNF-Jubiläumsevent für gross und klein. 19. April 2008, 10.00 Uhr bis 02.00 Uhr Campus Irchel, Winterthurerstrasse 190, 8057 Zürich Weitere Informationen http://www.175jahre.uzh.ch/naturwissenschaft __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Summary statistics across factor levels
R users, I intention is to calculate some summary statistics across factor levels. I know that in Hmisc package there is a summary function which produces neat summary statistics when using cross option. I would like to produce similar output with N and Missing columns but produce a data.frame. Is there any built-in function for that? #example data install.packages(Hmisc) library(Hmisc) sek - seq(1, nrow(Indometh), 9) Indometh$time[sek] - NA Indometh$timeclass - factor(cut(Indometh$time, breaks=c(0,2,4,6,8,10))) Indometh with(Indometh, summary(conc ~ Subject + timeclass, method=cross)) #similar with aggregate and reshape but no N or Missing count i.mean - aggregate(Indometh$conc, list(Indometh$Subject, Indometh$timeclass), mean, na.rm=T) i.mean.rhsp - reshape(i.mean, v.names=x, idvar=Group.1, timevar=Group.2, direction=wide) i.mean.rhsp # N and missing columns needed Thanks, Lauri __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] missing values in document
No matter how I´ve tried o find a solution for this simple question, I can´t. Sorry for bothering with such a matter. I have an excel-files with some empty cells=missing values. How do I tell R that these should be NA´s? TRFLP1 -(read.table(file=S://SEDIM//Kokeilu//TRFLP1.txt,col.names= c(Dye_Sample Peak, Sample_File_Name, Size, Height, Area_in_Point, Area_in_BP, Data_Point, Begin_Point, Begin_BP, End_Point, End_BP, Width_in_Point, Width_in_BP, 1 ), header=F , dec = ,, )Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1743 did not have 14 elements I believe the error occurs becouse line 1743 has an empty cell. How do I read in the file without first checking for missing values and changing them to NAs myself? Thank you for you time, Monna Nygård _ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] + and - in RODBC : no longer considered factors
It is nothing to do with RODBC, which follows read.table here: % cat foo.txt x + - ... read.table(foo.txt, header=TRUE) x 1 0 2 0 and that uses type.convert(c(+, -)) [1] 0 0 type.convert(c(+, a)) [1] + a Levels: + a Whereas 2.6.2 did type.convert(c(+, -)) [1] + - Levels: + - The difference is related to a change to deciding in R (and not the OS) what a 'numeric field' is: o Parsing and scanning of numerical constants is now done by R's own C code. This ensures cross-platform consistency, and mitigates the effects of setting LC_NUMERIC (within base R it only applies to output -- packages may differ). The format accepted is more general than before and includes binary exponents in hexadecimal constants: see ?NumericConstants for details. There's a comment in the sources that numeric fields with no digits should perhaps be regarded as non-numeric, so this can easily be changed. On Wed, 30 Apr 2008, Dieter Menne wrote: I have a large Sweave report that reads data from a database file. Some of the columns are 1-character strings containing only +, - or NA. An example for such a table is shown below, and can be downloaded for easier testing from http://www.menne-biomed.de/uni/test.zip (For security reasons, the file is zipped) table test hp hp1 + a - + library(RODBC) channel = odbcConnectAccess(test.mdb) ret = sqlQuery(channel,select * from test) odbcClose(channel) str(ret) # 'data.frame': 2 obs. of 2 variables: # $ hp : num 0 0 # $ hp1: Factor w/ 2 levels +,a: 2 1 Note that the column hp with + and - only is read as numeric 0, but when there is only other character such as in hp1, the conversion occurs. In R 2.6.2 (or was it an earlier version of RODBC?), column hp was treated as factor. Is this a new feature I have to live with, or an ... ahem ... issue? I know that with as.is I can get around this, but it need a lot of explicit programming for the columns I don't want to be as.issed Disclaimer: -- Yes, I know I should have reported this earlier, but the problem of having to re-create the report came up today. -- Yes, I should have reported this on the windows/devel r-help or directly to the author (of RODBC; or base?), so I feel guilty in advance that this is the wrong list. -- Yes, I have read the NEWS, and could not find something related. -- Yes, I cannot rule out this is a user error. Dieter --- R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=Germ an_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RODBC_1.2-3 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot2: labels and breaks order does not match and I can't usescale_fill_identity
Mikhail, Have you tried sorting your dataframe according to the levels on the x-axis? HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Mikhail Spivakov Verzonden: dinsdag 29 april 2008 16:53 Aan: r-help@r-project.org Onderwerp: [R] ggplot2: labels and breaks order does not match and I can't usescale_fill_identity Hi, I'm plotting a bar chart like this: ggplot() + geom_bar(data=res,aes(fill=f1,x=f2,y=y),stat=identity,position=dodge ) f1 contains quite a few levels and the plot is really quite difficult to read when the order of bars on the graph and on the legend does not match. This problem has been discussed recently here: http://www.nabble.com/ggplot2---legend-for-fill-coulours-td16235166.html and the solution was to use scale_fill_identity to manually define the order of both the breaks and the labels. This is however unsuitable for me (at least in the unmodified form), as this is part of a script that does not know in advance how many levels there arae in f1. Is there a way round this problem? Many thanks Mikhail Spivakov Mikhail Spivakov PhD Postdoctoral Fellow EMBL/EBI Germany/UK [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Empty Set In a Set
On 29/04/2008 9:39 PM, Jason Q. McClintic wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Dear List: I'm looking for a form of the empty set such that if ES is said representation, ~ES %in% c(1,2,3) evaluates to TRUE. %in% is a vector operator, checking each element of ES and returning a vector result. It sounds like you want a subset test, i.e. to check that all the results are TRUE, all(ES %in% c(1,2,3)) which returns TRUE when ES is empty. Duncan Murdoch Thank you in advance for your assistance. Sincerely, Jason Q. McClintic - -- Jason Q McClintic UST MB 1945 2115 Summit Avenue St. Paul, MN 55105 [EMAIL PROTECTED] [EMAIL PROTECTED] It is insufficient to protect ourselves with laws, we must protect ourselves with mathematics.--Bruce Schneier -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iQEVAwUBSBfN5hMtGNvij6jtAQgx3gf7Bxmht6ODCjsvhuFPkW1QWC1ey/ygVW9m uuwNZVCz2hBNDSV2NktaOHe+hl3sEj4gmxv0Q6onf4Opg59o9OQ1EtaeY13S/ouk EIO2fERY7VQcFbqjr1SnhlXGfyjX5bLk0ipFlqd11R+yXzFxzbafDtfcfKP+sp59 CQ8uZ2wAshPgrN5ZHIrg8RpBEWUnjH19iS4vDr40IrYyVbFLSnT1XM+D3kaMHgtc oEi3wldigmSllX8KGVVp7DeXbEvUdrvsJgF1VLG/R8EFlMMHUVE1OD3d8SJ+y9Wh SuVqWcL+aFXqJvjpQsQaE/2ywk8mis+46EjX1zcYKHPyoIoeqv4OdQ== =tBx1 -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot2: labels and breaks order does not match and I can't use scale_fill_identity
The solution to this problem is in the mail below. I initially forgot to send a copy to the mailing list, and I'm doing it now for the record, in case someone bumps into this problem. Xavier Message original Sujet: Re: [R] ggplot2: labels and breaks order does not match and I can't use scale_fill_identity Date: Tue, 29 Apr 2008 17:29:13 +0200 De: Xavier Chardon [EMAIL PROTECTED] Répondre à :: [EMAIL PROTECTED] Pour :: Mikhail Spivakov [EMAIL PROTECTED] Références: [EMAIL PROTECTED] Hi, I had a similar problem. I don't know if the solution will apply to your case but you might want to give it a try. It consists in including the following line before the plot is created: res$f1 - factor(res$f1, levels = unique(res$f1) ) with f1 sorted in the order you want it to appear. Xavier Mikhail Spivakov a écrit : Hi, I'm plotting a bar chart like this: ggplot() + geom_bar(data=res,aes(fill=f1,x=f2,y=y),stat=identity,position=dodge) f1 contains quite a few levels and the plot is really quite difficult to read when the order of bars on the graph and on the legend does not match. This problem has been discussed recently here: http://www.nabble.com/ggplot2---legend-for-fill-coulours-td16235166.html and the solution was to use scale_fill_identity to manually define the order of both the breaks and the labels. This is however unsuitable for me (at least in the unmodified form), as this is part of a script that does not know in advance how many levels there arae in f1. Is there a way round this problem? Many thanks Mikhail Spivakov Mikhail Spivakov PhD Postdoctoral Fellow EMBL/EBI Germany/UK [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Xavier Chardon Thésard Institut de l'élevage / INRA Projet ACTA modélisation environnementale des systèmes bovins et porcins [EMAIL PROTECTED] [EMAIL PROTECTED] 02 23 48 50 91 -- Xavier Chardon Thésard Institut de l'élevage / INRA Projet ACTA modélisation environnementale des systèmes bovins et porcins [EMAIL PROTECTED] [EMAIL PROTECTED] 02 23 48 50 91 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] missing values in document
What exactly is on line 1743?
Genuinely empty cells will probably read as NA anyway. Excel errors, prefixed #
in excel, will be read as comment markers and cause the remainder of the line
to be ignored. This often causes this kind of error.
Steve E
Monna Nygård [EMAIL PROTECTED] 30/04/2008 11:51:16
No matter how I´ve tried o find a solution for this simple question, I can´t.
Sorry for bothering with such a matter.
I have an excel-files with some empty cells=missing values. How do I tell R
that these should be NA´s?
TRFLP1 -(read.table(file=S://SEDIM//Kokeilu//TRFLP1.txt,col.names=
c(Dye_Sample Peak, Sample_File_Name, Size, Height, Area_in_Point,
Area_in_BP, Data_Point, Begin_Point, Begin_BP, End_Point, End_BP,
Width_in_Point, Width_in_BP, 1 ), header=F , dec = ,, )Error in
scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line
1743 did not have 14 elements
I believe the error occurs becouse line 1743 has an empty cell. How do I read
in the file without first checking for missing values and changing them to NAs
myself?
Thank you for you time,
Monna Nygård
_
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Re: [R] missing values in document
Monna Nygård wrote: No matter how I´ve tried o find a solution for this simple question, I can´t. Sorry for bothering with such a matter. I have an excel-files with some empty cells=missing values. How do I tell R that these should be NA´s? TRFLP1 -(read.table(file=S://SEDIM//Kokeilu//TRFLP1.txt,col.names= c(Dye_Sample Peak, Sample_File_Name, Size, Height, Area_in_Point, Area_in_BP, Data_Point, Begin_Point, Begin_BP, End_Point, End_BP, Width_in_Point, Width_in_BP, 1 ), header=F , dec = ,, )Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1743 did not have 14 elements I believe the error occurs becouse line 1743 has an empty cell. How do I read in the file without first checking for missing values and changing them to NAs myself? Hi Monna, read.table has an argument na.strings that allows you to specify what will be read as a missing value. Setting this to na.strings= should get you there. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] + and - in RODBC : no longer considered factors
Prof Brian Ripley ripley at stats.ox.ac.uk writes: It is nothing to do with RODBC, which follows read.table here: % cat foo.txt x + - ... read.table(foo.txt, header=TRUE) x 1 0 2 0 and that uses type.convert(c(+, -)) [1] 0 0 type.convert(c(+, a)) [1] + a Levels: + a Thank, Prof. Ripley, this makes sense as an explanation. So even a = type.convert(c(+, -),as.is=TRUE) str(a) # num [1:2] 0 0 does not help, because num bites first. Since the docs say convert it it to logical, integer, numeric or complex I would have expected this to be integer, but that's only of academic interest. So the only workaround to make the large old code base to work is get the old type.convert implementation and inject it. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] rmvbin
Hie all, Anyone with an idea on how to generate binary data using (rmvbin) taking into account covariates e.g age and gender. Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] fCopulae
Hello, Hela wrote : My problem in a few words is as folow: I used the fCopulae packages because i have 2 series which are already transformed in the uniform domain (the space of the copulas functions) and i estimated with type archmList() from 1 to 22, but i don't know their names:for exemple the type=4 is the Gumbel Copula...and for the others i can't have any idea about how can i find teir names explicitly? Please can you help me in this point? Thank you. Very Best Regards, Adnen CHOCKRI [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Summary statistics across factor levels
Try this: sek - seq(1, nrow(Indometh), 9) Indometh$time[sek] - NA Indometh$timeclass - factor(cut(Indometh$time, breaks=c(0,2,4,6,8,10))) x - summary(conc ~ Subject + timeclass, method=cross, data=Indometh) vec - x$S dim(vec) - attr(x, out.attrs)$dim dimnames(vec) - attr(x, out.attrs)$dimnames as.data.frame(vec) On Wed, Apr 30, 2008 at 7:27 AM, Lauri Nikkinen [EMAIL PROTECTED] wrote: R users, I intention is to calculate some summary statistics across factor levels. I know that in Hmisc package there is a summary function which produces neat summary statistics when using cross option. I would like to produce similar output with N and Missing columns but produce a data.frame. Is there any built-in function for that? #example data install.packages(Hmisc) library(Hmisc) sek - seq(1, nrow(Indometh), 9) Indometh$time[sek] - NA Indometh$timeclass - factor(cut(Indometh$time, breaks=c(0,2,4,6,8,10))) Indometh with(Indometh, summary(conc ~ Subject + timeclass, method=cross)) #similar with aggregate and reshape but no N or Missing count i.mean - aggregate(Indometh$conc, list(Indometh$Subject, Indometh$timeclass), mean, na.rm=T) i.mean.rhsp - reshape(i.mean, v.names=x, idvar=Group.1, timevar=Group.2, direction=wide) i.mean.rhsp # N and missing columns needed Thanks, Lauri __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] missing values in document
How are the 'empty' cell identified? It appears that you are using the default of read.table which says blanks are the delimiters. How are two or more empty cells identified? Can you output a CSV file so that you have commas as separators so you can identify the empty fields? On Wed, Apr 30, 2008 at 6:51 AM, Monna Nygård [EMAIL PROTECTED] wrote: No matter how I´ve tried o find a solution for this simple question, I can´t. Sorry for bothering with such a matter. I have an excel-files with some empty cells=missing values. How do I tell R that these should be NA´s? TRFLP1 -(read.table(file=S://SEDIM//Kokeilu//TRFLP1.txt,col.names= c(Dye_Sample Peak, Sample_File_Name, Size, Height, Area_in_Point, Area_in_BP, Data_Point, Begin_Point, Begin_BP, End_Point, End_BP, Width_in_Point, Width_in_BP, 1 ), header=F , dec = ,, )Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1743 did not have 14 elements I believe the error occurs becouse line 1743 has an empty cell. How do I read in the file without first checking for missing values and changing them to NAs myself? Thank you for you time, Monna Nygård _ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] fft: characteristic function to distribution
The characteristic function is the inverse Fourier transform of the distribution function. The characteristic function of a normaly distributed random variable is exp(-t^2/2). x=seq(-2,2,length=100) fft(pnorm(x),inverse=T)/length(x) exp(-x^2/2) Why aren't the inverse fft and the mentioned function the same? Thanks for help, Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Summary statistics across factor levels
Lauri Nikkinen wrote: R users, I intention is to calculate some summary statistics across factor levels. I know that in Hmisc package there is a summary function which produces neat summary statistics when using cross option. I would like to produce similar output with N and Missing columns but produce a data.frame. Is there any built-in function for that? Take a look at the Hmisc summarize function. #example data install.packages(Hmisc) library(Hmisc) sek - seq(1, nrow(Indometh), 9) Indometh$time[sek] - NA Indometh$timeclass - factor(cut(Indometh$time, breaks=c(0,2,4,6,8,10))) Indometh with(Indometh, summary(conc ~ Subject + timeclass, method=cross)) If using summary I suggest summary(conc ~ Subject + cut2(time, c(0,2,4,6,8,10)), data=Indometh, method='cross') Frank #similar with aggregate and reshape but no N or Missing count i.mean - aggregate(Indometh$conc, list(Indometh$Subject, Indometh$timeclass), mean, na.rm=T) i.mean.rhsp - reshape(i.mean, v.names=x, idvar=Group.1, timevar=Group.2, direction=wide) i.mean.rhsp # N and missing columns needed Thanks, Lauri __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Survival Regression with multiple records per subject
Dear R users! I reformulate the question with another example perhaps my question will be more clearly now. I have several subjects. One subject has multiple records. Only a starting point exists the end point is vague. Here is an example: itm ID exercise time 1.40186910 1 1.32439010 2 1.32439010 3 1.3810 4 1.34676110 5 1.31544111 6 1.33781220 1 1.31991520 2 1.35123521 3 itm is the covariate; ID is the subject Id; exercise indicates if the subject is dead=1 or alive=0 How can I allocate the multiple records to one subject (for example record 1-6 are part of subject with ID 1 record 7-9 are part of subject with ID2) and process a survival regression. the survRegData - survreg(formula=Surv(time,exercise)~itm, data=Data, dist=weibull) command doesn't take into account that multiple records are part of one subject. Many thanks! Fabian Hefner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] dlda scores
Dear Bioc, I am using the stat.diag.da function from sma package in R-2.7.0 to make class prediction in microarray dataset. I would like to retrive the not only the classification, but also the raw score assigned to each sample in order to be classified both in the training and in the validation set. how can I do that? thank you John [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Survival Regression with multiple records per subject
If 'itm' is a covariate with measurement error, then you could also have a look at the 'JM' package. I hope it helps. Best, Dimitris Dimitris Rizopoulos Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Fabian Hefner [EMAIL PROTECTED] To: 'Terry Therneau' [EMAIL PROTECTED] Cc: r-help@r-project.org Sent: Wednesday, April 30, 2008 1:25 PM Subject: [R] Survival Regression with multiple records per subject Dear R users! I reformulate the question with another example perhaps my question will be more clearly now. I have several subjects. One subject has multiple records. Only a starting point exists the end point is vague. Here is an example: itm ID exercise time 1.40186910 1 1.32439010 2 1.32439010 3 1.3810 4 1.34676110 5 1.31544111 6 1.33781220 1 1.31991520 2 1.35123521 3 itm is the covariate; ID is the subject Id; exercise indicates if the subject is dead=1 or alive=0 How can I allocate the multiple records to one subject (for example record 1-6 are part of subject with ID 1 record 7-9 are part of subject with ID2) and process a survival regression. the survRegData - survreg(formula=Surv(time,exercise)~itm, data=Data, dist=weibull) command doesn't take into account that multiple records are part of one subject. Many thanks! Fabian Hefner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do you test for consecutivity?
Charles C. Berry: Are the numbers 1:30 equiprobable?? If so, you can find the probability by direct enumeration. Or by a simple formula: * Probabilities of Consecutive Integers in Lotto * Author(s): Stanley P. Gudder and James N. Hagler * Source: Mathematics Magazine, Vol. 74, No. 3 (Jun., 2001), pp. 216-222 * Publisher: Mathematical Association of America * Stable URL: http://www.jstor.org/stable/2690723 -- Karl Ove Hufthammer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] c code working in linux and hanging in windows
Vidhu Choudhary vidhu.choudhary at gmail.com writes: Hi All, I am calling some c code from R. It successfully makes the dll and .so files. When I run .so in Linux is works prefect but hangs in windows. Though the dll loads but it never returns back from the c function Can you please suggest the possible cause of this thank you vidhu This isn't enough detail for us to work with (you might have gotten lucky and this problem would have rung a bell for someone, but I guess not). Therefore, you need to go back and do the hard stuff -- try to create a minimal example (you will often figure out the problem in the process), tell us what versions of R, compiler, OS you are using, etc etc etc ... Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Applying user function over a large matrix
Dear Folks
Thanks for all your replies and suggestions, I will be trying
out these suggestions today and let you know how it goes.
Please let me know if you can think of anything else to
resolve the issue.
Regards
Original message
Date: Tue, 29 Apr 2008 15:43:41 -0700
From: Bert Gunter [EMAIL PROTECTED]
Subject: Re: [R] Applying user function over a large matrix
To: 'Ray Brownrigg' [EMAIL PROTECTED],
r-help@r-project.org
Cc: 'Tony Plate' [EMAIL PROTECTED]
If you can(one dimensional only), try using lowess() instead.
Probably in a
for loop as Ray suggested.
loess() is more powerful and flexible, but you pay for it in
extra
complexity and time. Maybe in this case, it's not worth it.
-- Bert Gunter
Genentech
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On
Behalf Of Ray Brownrigg
Sent: Tuesday, April 29, 2008 3:19 PM
To: r-help@r-project.org
Cc: Tony Plate
Subject: Re: [R] Applying user function over a large matrix
In addition to Tony's suggestion, have a look at the
following sequence,
which
I suspect is because the call to apply will duplicate your
1.5GB matrix,
whereas the for loop doesn't [I stand to be corrected here].
x - matrix(runif(21), 21)
unix.time({res - numeric(ncol(x)); for(i in 1:length(res))
res[i] -
sum(x[, i])})
user system elapsed
0.079 0.000 0.079
unix.time(apply(x, 2, sum))
user system elapsed
0.100.010.11
x - matrix(runif(210), 21)
unix.time({res - numeric(ncol(x)); for(i in 1:length(res))
res[i] -
sum(x[, i])})
user system elapsed
0.791 0.010 0.801
unix.time(apply(x, 2, sum))
user system elapsed
1.096 0.011 1.107
x - matrix(runif(2100), 21)
unix.time({res - numeric(ncol(x)); for(i in 1:length(res))
res[i] -
sum(x[, i])})
user system elapsed
7.825 0.011 7.840
unix.time(apply(x, 2, sum))
user system elapsed
15.431 0.142 15.592
Also, preliminary checking using the top utility shows the
for loop requires
just over half the memory of the apply() call. This is on a
NetBSD system
with 2GB memory.
HTH,
Ray Brownrigg
On Wed, 30 Apr 2008, Tony Plate wrote:
It's quite possible that much of the time spent in loess()
is setting up
the data (i.e., the formula, terms, model.frame, etc.), and
that much of
that is repeated identically for each call to loess(). I
would suggest
looking at the code of loess() and work out what arguments
it is calling
simpleLoess() with, and then try calling
stats:::simpleLoess() directly.
(Of course you have to be careful with this because this is
not using the
published API).
-- Tony Plate
Sudipta Sarkar wrote:
Respected R experts,
I am trying to apply a user function that basically calls and
applies the R loess function from stat package over each time
series. I have a large matrix of size 21 X 900 and I need
to apply the loess for each column and hence I have
implemented this separate user function that applies loess
over each column and I am calling this function foo as
follows:
xc-apply(t,2,foo) where t is my 21 X 900 matrix and
loess. This is turning out to be a very slow process and I
need to repeat this step for 25-30 such large matrix chunks.
Is there any trick I can use to make this work faster?
Any help will be deeply appreciated.
Regards
Sudipta Sarkar PhD
Senior Analyst/Scientist
Lanworth Inc. (Formerly Forest One Inc.)
300 Park Blvd., Ste 425
Itasca, IL
Ph: 630-250-0468
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Sudipta Sarkar PhD
Senior Analyst/Scientist
Lanworth Inc. (Formerly Forest One Inc.)
300 Park Blvd., Ste 425
Itasca, IL
Ph: 630-250-0468
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Re: [R] Cross Spectrum Analysis
$names [1] freq spec coh phase kerneldf [7] bandwidth n.usedorig.nseriessnamesmethod [13] taper pad detrend demean $freq and $spec are used to plot the power spectrum. freq is the x-axis and spec is the y-axis. $coh is the squared coherency between the two signals in your case and I believe that this is also plotted against frequency. This is your correlation strength. Phase I haven't been able to figure out- I think that it is some sort of estimator for the phase shift. to get either phase or coherency plot add the plot.type argument to your plot command x - spectrum(yourdata, log=no) #this will plot it without a log scale I find it useful to look at both the no log plot and then the logscale plot (just remove the log=no) plot(x, plot.type=marginal) #this is the default type (the powerspectrum) plot(x, plot.type=phase) plot(x, plot.type=coherency) also just look at ?spectrum schumway is a good book - I think it is something like time series analysis with examples in R hope this helps stephen On Tue, Apr 29, 2008 at 8:54 PM, Maura E Monville [EMAIL PROTECTED] wrote: I am reading some documentation about Cross Spectrum Analysis as a technique to compare spectra. My understanding is that it estimates the correlation strength between quasi-periodic structures embedded in two signals. I believe it may be useful for my signals analysis. I was referred to the R functions that implement this type of analysis. I tried all the examples which generated a series of fancy plots. But I need to work on the numerical results. I have read that the following info is available through Cross Spectra analysis: *Cross-periodogram, Cross-Density, Quadrature-density, Cross-amplitude, Squared Coherency, Gain, and Phase Shift* I went through a couple of the two-series (bivariate) cross-spectrum analysis examples with R. I also printed out the attributes of the analysis (see the following). I cannot quite match the above quantities with the attributes/features output of cross-spectra analysis with R. I would greatly appreciate some explanation (which is what) and seeing some more worked out examples. attributes(mfdeaths.spc) $names [1] freq spec coh phase kerneldf [7] bandwidth n.usedorig.nseriessnamesmethod [13] taper pad detrend demean $class [1] spec Thank you so much. Yours Faithfully, -- Maura E.M [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Tab-delimited AOV summaries
Hello, I am trying to print out ANOVA summaries --- as returned by summary (aov(...))--- in tab-delimited format, either to a file or to the console, but so far I haven't been able to figure out a solution. My particular ANOVA has repeated measures, so it is an instance of class aovlist. Can anyone offer any suggestions? I am relatively new to R, so please forgive me if I am missing something obvious. Regards, -Chris Chris R. Sims Doctoral Student, Department of Cognitive Science Rensselaer Polytechnic Institute Troy, NY 12180 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] NumDeriv - derivatives of covariance matrix
Your calculation can be thought of as a function from R^m to R^(n*n),
and functions in numDeriv can be used to calculate a numerical
approximation to the derivative of the function. However, the functions
in numDeriv try to calculate accurate approximations, as opposed to
quick approximations like one might want in an optimization problem.
Given that you already have an analytic solution, I doubt that even a
quick approximation will be faster. You might better look at trying to
convert parts of your double loop into vector or matrix calculations, or
focusing on the fact that the matrix is symmetric.
Paul Gilbert
Daomeng Gao wrote:
Hello R-help,
I need to compute matrices of first derivatives of a covariance matrix C
with entries given by c_ij=theta*exp(-0.5* sum(eta*(x[i,]-x[j,])^2)), wrt to
elements of eta, a m-dimensional vector of parameters, given a n*m data
matrix x. So far, I have been computing matrices for each parameter (given
by par[index]) analytically, using the following
kmatder- function(x, par, index) {
## x: n*m matrix
## par: vector of parameters, m=length(par)=ncol(x)
## compute matrix of partial derivatives wrt parameter par[index]: Cder
= d C/d par[index]
theta-1
eta-par
n-nrow(x)
Cder-matrix(0,n,n)
for (i in 1:n) {
for (j in i:n) {
Cder[i,j]-(-0.5*((x[i,index]-x[j,index])^2))*theta*exp(-0.5*
sum(eta*(x[i,]-x[j,])^2))
}
}
Cder-0.5*(Cder+t(Cder))
Cder
}
I was wondering whether it might be possible to speed up things using
numDeriv (jacobian). If so, what would be the right way to implement a
suitable method ?
Cheers,
Gao Daomeng
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Re: [R] Calling R from C - part way there but need a push!
Maximillian Murphy wrote on 04/29/2008 11:19 AM:
Dear All,
I've read the manual on Writing R Extensions and in particular the
part on calling R from C. (Most of the manual is about calling C from
R, not the other way around.)
The good news is that I can now call _some_ R from C, specifically the R
functions which have C header files. However it isn't clear to me how
to call R functions that are written in R. I imagine that there is a
standard C function of the form
Call_r_from_C(package name, Rfunction name as a string, arg1, arg2,
...);
where arg1 etc are standardised ways of representing R data structures
in C. However I haven't been able to find such a function prototype in
the R include/*.h files. See footnote (1). Can you point me in the
right direction please? Is there a set of examples somewhere that I can
peruse?
Does R keep any state when being called from C? Should I think of it as
being a co-process, so I can make consecutive calls to it and expect it
to remember previous calls? I'm thinking of a sequence of calls such as
load library, load R code from a file of my own, set value of x,
make a call and read the values back into my C program?
Help is much appreciated.
I would recommend studying the examples found in the tests/Embedding
directory from the R sources. For instance, the following is from
RNamedCall.c:
/*
Call the function foo() with 3 arguments, 2 of which
are named.
foo(pch=+, id = 123, c(T,F))
Note that PrintValue() of the expression seg-faults.
We have to set the print name correctly.
*/
void
bar1()
{
SEXP fun, pch;
SEXP e;
PROTECT(e = allocVector(LANGSXP, 4));
fun = findFun(install(foo), R_GlobalEnv);
if(fun == R_NilValue) {
fprintf(stderr, No definition for function foo. Source foo.R and save
the session.\n);
UNPROTECT(1);
exit(1);
}
SETCAR(e, fun);
SETCADR(e, mkString(+));
SET_TAG(CDR(e), install(pch));
SETCADDR(e, ScalarInteger(123));
SET_TAG(CDR(CDR(e)), install(id));
pch = allocVector(LGLSXP, 2);
LOGICAL(pch)[0] = TRUE;
LOGICAL(pch)[1] = FALSE;
SETCADDDR(e, pch);
PrintValue(e);
eval(e, R_GlobalEnv);
SETCAR(e, install(foo));
PrintValue(e);
R_tryEval(e, R_GlobalEnv, NULL);
UNPROTECT(1);
}
Best,
Jeff
Regards, Max
(1) The most likely include file is Rinterface.h and within that the
most likely candidates seem to be:
extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);
extern void (*ptr_R_WriteConsole)(const char *, int);
extern void (*ptr_R_WriteConsoleEx)(const char *, int, int);
but it turns out that they assume that R is running the terminal and
these are requests to R to display or read from R's console. R isn't
acting as the back end being given work and returning answers.
(2) Googling calling r from c yields precisely five hits, most of
which just point back at the R extensions document with vague It's in
there somewhere's. I've looked!
(3) Leads suggested by help.search(C)
Foreign(base):
Foreign Function Interface Functions to make calls to compiled
code that has been loaded into R.
.Internal(base) Call an Internal Function
'.Internal' performs a call to an internal code which is built in
to the R interpreter.
Only true R wizards should even consider using this function, and
only R developers can add to the list of internal functions.
(Definitely not me!)
.Primitive(base)Call a Primitive Internal Function
The advantage of '.Primitive' over '.Internal' functions is the
potential efficiency of argument passing.
(4) R code that I have called successfully is that with prototypes
defined in e.g. include/R_ext/Applic.h
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Re: [R] + and - in RODBC : no longer considered factors
So the only workaround to make the large old code base to work is get the old type.convert implementation and inject it. That would be rather hard. Try R-patched (from tomorrow, say) instead. Note that in well over a month of testing no one else has reported this. On Wed, 30 Apr 2008, Dieter Menne wrote: Prof Brian Ripley ripley at stats.ox.ac.uk writes: It is nothing to do with RODBC, which follows read.table here: % cat foo.txt x + - ... read.table(foo.txt, header=TRUE) x 1 0 2 0 and that uses type.convert(c(+, -)) [1] 0 0 type.convert(c(+, a)) [1] + a Levels: + a Thank, Prof. Ripley, this makes sense as an explanation. So even a = type.convert(c(+, -),as.is=TRUE) str(a) # num [1:2] 0 0 does not help, because num bites first. Since the docs say convert it it to logical, integer, numeric or complex I would have expected this to be integer, but that's only of academic interest. So the only workaround to make the large old code base to work is get the old type.convert implementation and inject it. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Empty Set In a Set
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Exactly what I needed. Thanks to everyone who replied. Sincerely, Jason Q. McClintic - -- MIDN 1/C Jason Q McClintic Battalion Commander Naval ROTC Battalion University of Minnesota UST MB 1945 2115 Summit Avenue Saint Paul, MN 55105 [EMAIL PROTECTED] [EMAIL PROTECTED] (c) 763-442-3404 It is insufficient to protect ourselves with laws, we must protect ourselves with mathematics.--Bruce Schneier Duncan Murdoch wrote: | On 29/04/2008 9:39 PM, Jason Q. McClintic wrote: | Dear List: | | I'm looking for a form of the empty set such that if ES is said | representation, | | ~ES %in% c(1,2,3) | | evaluates to TRUE. | | %in% is a vector operator, checking each element of ES and returning a | vector result. It sounds like you want a subset test, i.e. to check | that all the results are TRUE, | | all(ES %in% c(1,2,3)) | | which returns TRUE when ES is empty. | | Duncan Murdoch | | Thank you in advance for your assistance. | | Sincerely, | | Jason Q. McClintic | __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iQEVAwUBSBiD6BMtGNvij6jtAQj+awf+KNXnXImjCi/x0V+pYZI+3A41Pf3yRbXo oV99Px/ymBjGjwO4q3rKnMZmJFNTr906MPziAgTKxVQ1tboJyGpF/KAhk8ASQhO0 JqxlpzlEMwVnfZlORgo9vOjmNyl5nGL4G5X8Q1Ta9HqrvovZk2MJooP7jg37uEJy CaSLmGQrFiqQjdrXpDEfkmThUYQaAcpAKQtJFo3BeC3qjFeF2h+fK9lrFEb2bNX+ jCKWIZbJSdFHsxR6rZrsExcyE6uv+WCgPMb0WW9LXYR03mGMmin6Sr/xcqW6jXKJ dzrXc6RmFlsgfdqg/afTYwk9CVzIyWjq9/4FT9+Muj7VKClnCYlMOA== =fxWV -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] wireframe - add data points
Hello all,
Im trying to add some data points to a wireframe. X an Y axis are independent
variables, Z axis is predicted probability. Id like to add the original data
points on which the predicted probabilities are based to the wireframe. Ive
followed some of the previous post on this but get stuck :
## first part yields the wireframe##
setwd(C:/Temp)
rnp - read.table(interact.csv,header=T,sep=;)
status -rnp[,1:1]
totalfrost - rnp[,2:2]
logtps - rnp[,3:3]
logpd - rnp[,4:4]
logwinterp - rnp[,5:5]
model -
glm(status~totalfrost+logtps+logpd+logwinterp+totalfrost*logtps+totalfrost*logwinterp,binomial)
abc -
expand.grid(totalfrost=seq(-1.9,3.6,by=0.25),logtps=seq(-3.3,1.1,by=0.25),logpd=seq(0.95,4.1,
by=0.25),logwinterp=seq(1.49,1.78, by=0.25))
abc$status -as.vector(predict(model,abc,type=response))
##below is the import of the original data together with their predicted
probabilities##
punten - read.table(probs.csv,header=T,sep=;)
x - punten[,1:1]
y - punten[,2:2]
z - punten[,3:3]
pts - data.frame(x=x,y=y,z=z)
##end import original data##
wireframe(status~totalfrost*logtps,abc,scales=list(arrows=TRUE),drape=TRUE,
screen =list (x=15, y=-50, z=-105), pts = pts,
panel.3d.wireframe =
function(x, y, z,
xlim, ylim, zlim,
xlim.scaled, ylim.scaled, zlim.scaled,
pts,
...) {
panel.3dwire(x = x, y = y, z = z,
xlim = xlim,
ylim = ylim,
zlim = zlim,
xlim.scaled = xlim.scaled,
ylim.scaled = ylim.scaled,
zlim.scaled = zlim.scaled,
...)
xx -
xlim.scaled[1] + diff(xlim.scaled) *
(pts$x - xlim[1]) / diff(xlim)
yy -
ylim.scaled[1] + diff(ylim.scaled) *
(pts$y - ylim[1]) / diff(ylim)
zz -
zlim.scaled[1] + diff(zlim.scaled) *
(pts$z - zlim[1]) / diff(zlim)
panel.3dscatter(x = xx,
y = yy,
z = zz,
xlim = xlim,
ylim = ylim,
zlim = zlim,
xlim.scaled = xlim.scaled,
ylim.scaled = ylim.scaled,
zlim.scaled = zlim.scaled,
...)
})
This yields me the following errors :
Warning messages:
1: In Ops.factor(pts$x, xlim[1]) : - not meaningful for factors
2: In Ops.factor(pts$y, ylim[1]) : - not meaningful for factors
3: In Ops.factor(pts$z, zlim[1]) : - not meaningful for factors
Any idea about what is wrong and what to do about it?
Thanks!
Diederi
Diederik Strubbe
Evolutionary Ecology Group
Department of Biology, University of Antwerp
Universiteitsplein 1
B-2610 Antwerp, Belgium
http://webhost.ua.ac.be/deco
tel : 32 3 820 23 85
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Re: [R] fft: characteristic function to distribution
On Wed, 30 Apr 2008, Thomas Steiner wrote: The characteristic function is the inverse Fourier transform of the distribution function. The characteristic function of a normaly distributed random variable is exp(-t^2/2). The fft is a discrete Fourier transforn, not a continuous one. Further in each case where the normalizing constants are placed and the units of frequecy differ from source to source. ?fft has references to exactly what it computes: please consult them. x=seq(-2,2,length=100) fft(pnorm(x),inverse=T)/length(x) exp(-x^2/2) Why aren't the inverse fft and the mentioned function the same? Thanks for help, Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Test its performace on new data of a established neural network or SVM model
Hi: I have already using the MLInterface to train and build a neural network model and SVM model to clustering a set of data. Now I have a new set of data. I need use these established NN model and SVM to cluster these new data without retraining it. I am aware that I can use predict command to do this in a linear regressing model. Should I use predict command to do it? Is there any other way to do this? Weihsin Wang Department of bioinformatics ITRI, Taiwan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem installing packages
Owe Jessen schrieb: Hi, when I try installing new packages (in this case DBI) I run into the following problem: Paket 'DBI' erfolgreich ausgepackt und MD5 Summen abgeglichen Warnung: kann temporäre Installation 'C:\Programme\R\R-2.7.0\library\file5f906952\DBI' nicht nach 'Ý xlDÌú [EMAIL PROTECTED]' verschieben Has anybody any idea where these strange symbols come from? Thanks in advance, Owe Excuse me for not giving much detail: The OS is Win XP SP2, R is 2.7.0, DBI is 0.2-4, the mirror was Göttingen, but I had similar problems with Zürich. A rough translation of the warning is: Package 'DBI' successfully extracted and MD5 sums successfully checked. Warning: cannot move temporary installation 'C:\Programme\R\R-2.7.0\library\file5f906952\DBI' to 'Ý xlDÌú [EMAIL PROTECTED]'. The cryptic part is not constant when i repeat the installation, another example is 'Ý xlÔu [EMAIL PROTECTED]' or 'Ý xlÈ/w [EMAIL PROTECTED]'. I hope this makes a bit more sense. TIA Owe -- Owe Jessen Diplom-Volkswirt Von-der-Horst-Str. 9 24118 Kiel [EMAIL PROTECTED] http://www.econinfo.de __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] error with lme within a loop
Dear R users,
I want to conduct a small simulation study and I have to use the lme
function in a loop to save the restricted log likelihood.
However, for one simulated data set the lme function gives this error
Error en lme.formula(yboot ~ X[, -1], data = data.fr, random = Z.block) :
nlminb problem, convergence error code = 1
message = singular convergence (7)
and then, the simulation stops. I would like to skip this
simulated data, and then continue with the loop, but I cannot find
the way of doing this. I am using R2.6.2.
Can anybody tell me if I can write a condition to avoid the problematic data?
I Have also obtained similar errors
Error en lme.formula(yboot ~ X[, -1], data = data.fr, random = Z.block) :
nlminb problem, convergence error code = 1
message = false convergence (8)
My data can be reproduced as follows
library(splines)
library(nlme)
x-c(rep(1993:2007,9))
barrio-factor(c(rep(1:9,rep(15,9
xl-min(x)-0.1
xr-max(x)+0.1
ndx-4
bdeg-3
pord-2
dx - (xr-xl)/ndx
knots - seq(xl-bdeg*dx, xr+bdeg*dx, by=dx)
B-spline.des(knots,x,bdeg+1,0*x)$design
m=ncol(B)
D=diff(diag(m),differences=pord)
P=t(D)%*%D
P.svd=svd(t(D)%*%D)
U=(P.svd$u)[,1:(m-pord)]
d=(P.svd$d)[1:(m-pord)]
Delta=diag(1/sqrt(d))
Z=B%*%U%*%Delta
X=NULL
for(i in 0:(pord-1)){X=cbind(X,x^i)}
### This X and Z matrix are the matrices in the mixed model
representation of a spline
n-nrow(X)
Id- factor(rep(1,n))
Z.block-list(list(Id=pdIdent(~Z-1)),list(barrio=pdIdent(~1)))
Z.block-unlist(Z.block,recursive=FALSE)
fijos2-c(-326.9178203,0.1645375 )
ef.spline-c(-0.2214524, -0.1649163, -0.1649163, 0.8878776, -0.2214524)
set.seed(48)
ef.error-rnorm(135,0,sqrt(0.03073974))
where
ef.spline are standardized random effects, and errores are the residuals.
My loop looks like this
B-1000
y.boot-array(0,c(nrow(Z),B))
log.comp-array(0,B)
while(iB){
i-i+1
spline-sample(ef.spline,size=ncol(Z),replace=T)
errores-sample(ef.error,size=nrow(Z),replace=T)
y.boot[,i]-X%*%fijos2+Z%*%spline+errores
yboot-y.boot[,i]
data.fr - groupedData( yboot ~ X[,-1] |Id ,data =
data.frame(yboot,X,Z,barrio))
log.comp[i]-lme(yboot~X[,-1],data=data.fr,random=Z.block)$logLik
}
The idea is to add a condition in the loop such that
if(condition..) {i-i-1}
and then substitute the problematic data by a new one,
Many thanks,
Tomas Goicoa
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[R] checking whether a file is empty
Hi, Is there a way to check whether a file is empty in R. I did the customary searches, but did not find anything. Please cc me on any reply. Thanks, Faheem. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] checking whether a file is empty
What is wrong with file.create(foo) [1] TRUE file.info(foo)$size [1] 0 file.remove(foo) ? I really wonder what searches you did: help.search(file) come up with file.info. On Wed, 30 Apr 2008, Faheem Mitha wrote: Is there a way to check whether a file is empty in R. I did the customary searches, but did not find anything. Please cc me on any reply. Thanks, Faheem. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] checking whether a file is empty
On Wed, 30 Apr 2008, Prof Brian Ripley wrote: What is wrong with file.create(foo) [1] TRUE file.info(foo)$size [1] 0 file.remove(foo) ? Thanks, that works for me. I really wonder what searches you did: help.search(file) come up with file.info. I did a Google search for R check file empty, R check file size and similar. Then I tried one of those R specific searches you can find on the web. Then I did a help.search(empty). Probably not the best search term. It didn't occur to me to search for file. Faheem. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] wireframe - add data points
On 4/30/08, Strubbe Diederik [EMAIL PROTECTED] wrote:
Hello all,
I'm trying to add some data points to a wireframe. X an Y axis are
independent variables, Z axis is predicted probability. I'd like to add the
original data points on which the predicted probabilities are based to the
wireframe. I've followed some of the previous post on this but get stuck :
## first part yields the wireframe##
setwd(C:/Temp)
rnp - read.table(interact.csv,header=T,sep=;)
status -rnp[,1:1]
totalfrost - rnp[,2:2]
logtps - rnp[,3:3]
logpd - rnp[,4:4]
logwinterp - rnp[,5:5]
model -
glm(status~totalfrost+logtps+logpd+logwinterp+totalfrost*logtps+totalfrost*logwinterp,binomial)
abc -
expand.grid(totalfrost=seq(-1.9,3.6,by=0.25),logtps=seq(-3.3,1.1,by=0.25),logpd=seq(0.95,4.1,
by=0.25),logwinterp=seq(1.49,1.78, by=0.25))
abc$status -as.vector(predict(model,abc,type=response))
##below is the import of the original data together with their predicted
probabilities##
punten - read.table(probs.csv,header=T,sep=;)
x - punten[,1:1]
y - punten[,2:2]
z - punten[,3:3]
pts - data.frame(x=x,y=y,z=z)
##end import original data##
wireframe(status~totalfrost*logtps,abc,scales=list(arrows=TRUE),drape=TRUE,
screen =list (x=15, y=-50, z=-105), pts = pts,
panel.3d.wireframe =
function(x, y, z,
xlim, ylim, zlim,
xlim.scaled, ylim.scaled, zlim.scaled,
pts,
...) {
panel.3dwire(x = x, y = y, z = z,
xlim = xlim,
ylim = ylim,
zlim = zlim,
xlim.scaled = xlim.scaled,
ylim.scaled = ylim.scaled,
zlim.scaled = zlim.scaled,
...)
xx -
xlim.scaled[1] + diff(xlim.scaled) *
(pts$x - xlim[1]) / diff(xlim)
yy -
ylim.scaled[1] + diff(ylim.scaled) *
(pts$y - ylim[1]) / diff(ylim)
zz -
zlim.scaled[1] + diff(zlim.scaled) *
(pts$z - zlim[1]) / diff(zlim)
panel.3dscatter(x = xx,
y = yy,
z = zz,
xlim = xlim,
ylim = ylim,
zlim = zlim,
xlim.scaled = xlim.scaled,
ylim.scaled = ylim.scaled,
zlim.scaled = zlim.scaled,
...)
})
This yields me the following errors :
Warning messages:
1: In Ops.factor(pts$x, xlim[1]) : - not meaningful for factors
2: In Ops.factor(pts$y, ylim[1]) : - not meaningful for factors
3: In Ops.factor(pts$z, zlim[1]) : - not meaningful for factors
Any idea about what is wrong and what to do about it?
Without access to the data, my only guess is that pty$x etc. are
factors. Can you show us tthe output of str(pts)?
-Deepayan
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Re: [R] checking whether a file is empty
Hi Faheem, Also, you could try in www.rseek.org and RSiteSearch(your.topic.here). HTH, Jorge On Wed, Apr 30, 2008 at 11:53 AM, Faheem Mitha [EMAIL PROTECTED] wrote: On Wed, 30 Apr 2008, Prof Brian Ripley wrote: What is wrong with file.create(foo) [1] TRUE file.info(foo)$size [1] 0 file.remove(foo) ? Thanks, that works for me. I really wonder what searches you did: help.search(file) come up with file.info. I did a Google search for R check file empty, R check file size and similar. Then I tried one of those R specific searches you can find on the web. Then I did a help.search(empty). Probably not the best search term. It didn't occur to me to search for file. Faheem. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem installing packages
The first message makes sense, but unfortunately if we cannot reproduce it, we cannot help. The issue appears to be that your OS is garbling file names. Is this is a translation back from German? The original would appear to be unable to move temporary installation '...' to '...' Could you try a recent R-patched build? There is a possibility that one of two fixes might have fixed this too. On Wed, 30 Apr 2008, Owe Jessen wrote: Owe Jessen schrieb: Hi, when I try installing new packages (in this case DBI) I run into the following problem: Paket 'DBI' erfolgreich ausgepackt und MD5 Summen abgeglichen Warnung: kann temporäre Installation 'C:\Programme\R\R-2.7.0\library\file5f906952\DBI' nicht nach 'Ý xlDÌú [EMAIL PROTECTED]' verschieben Has anybody any idea where these strange symbols come from? Thanks in advance, Owe Excuse me for not giving much detail: The OS is Win XP SP2, R is 2.7.0, DBI is 0.2-4, the mirror was Göttingen, but I had similar problems with Zürich. A rough translation of the warning is: Package 'DBI' successfully extracted and MD5 sums successfully checked. Warning: cannot move temporary installation 'C:\Programme\R\R-2.7.0\library\file5f906952\DBI' to 'Ý xlDÌú [EMAIL PROTECTED]'. The cryptic part is not constant when i repeat the installation, another example is 'Ý xlÔu [EMAIL PROTECTED]' or 'Ý xlÈ/w [EMAIL PROTECTED]'. I hope this makes a bit more sense. TIA Owe -- Owe Jessen Diplom-Volkswirt Von-der-Horst-Str. 9 24118 Kiel [EMAIL PROTECTED] http://www.econinfo.de __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] checking whether a file is empty
help(file.info). /Henrik On Wed, Apr 30, 2008 at 5:33 PM, Faheem Mitha [EMAIL PROTECTED] wrote: Hi, Is there a way to check whether a file is empty in R. I did the customary searches, but did not find anything. Please cc me on any reply. Thanks, Faheem. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] checking whether a file is empty
On Wed, Apr 30, 2008 at 11:33:01AM -0400, Faheem Mitha wrote: Is there a way to check whether a file is empty in R. I did the customary searches, but did not find anything. Please cc me on any reply. Empty file have, by definition, a size of zero, so here's one way: system(touch /tmp/faheem) file.info(/tmp/faheem)$size == 0 [1] TRUE Hth, Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] randomForest interaction detection
I've been using the randomForest package and getting very useful results for some time now. I have a question pertaining to variable interactions. Since, unlike CART, no single tree representative of the solution is available, I was wondering if there was some way of discerning / identifying potential interactions in the data. I'll sometimes produce 2-way partial dependence plots but I select variables for these plots somewhat arbitrarily (i.e. without prior suggestion of interaction). On Breimans website he mentions an experimental approach to identify interactions. I know this has come up before, a couple years ago, and Andy Liaw noted it was not implemented in part due to its experimental nature. I was wondering if anyone had a suggestion for detecting interactions using the randomForest package (In an analogous manner to Breimans' suggestion or another approach). Many Thanks, Joe Retzer [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] predict.glm newdata
You could just say: yhat=predict(reg1,x2) the function predict will assing x2 to 'newdata' by default. thanks Daniel Malter wrote: Hi, could it be the newdata argument? When I run predict with the newdata argument, I get an error message - a different one though. The second reason might be that your dataset is named df, which is defined as a function an may produce problems. Try renaming the dataset. yhat=predict(reg1,newdata=x2) x1=seq(1:100) r.norm1=rnorm(100,0,20) x1=r.norm1+x1 x2=x1*2 r.norm2=rnorm(200,0,20) x2=r.norm2+x2 reg1=glm(y1~x1,binomial) yhat=predict(reg1) ##prediction works fine yhat=predict(reg1,newdata=x2) ##gives error message because of newdata Error in eval(predvars, data, env) : numeric 'envir' arg not of length one yhat=predict(reg1,data=x2) ##works fine ##using offset ofst=rep(0.5,100) reg1=glm(y1~x1,binomial,offset=ofst) yhat=predict(reg1) yhat1=predict(reg1,newdata=x2) ##gives error message yhat2=predict(reg1,data=x2) ##works fine - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Tom Guston Gesendet: Friday, April 04, 2008 1:29 PM An: r-help@r-project.org Betreff: [R] predict.glm newdata Hi all - I'm stumped by the following mdl - glm(resp ~ . , data = df, family=binomial, offset = ofst) WORKS yhat - predict(mdl) WORKS yhat - predict(mdl,newdata = df) FAILS Error in drop(X[, piv, drop = FALSE] %*% beta[piv]) : subscript out of bounds I've tried without offset, quoting binomial. The offset variable ofst IS in df. Previous postings indicate possible names(df) problems (renaming factor levels?) but I'm using the same data.frame for the newdata option. Thank you in advance for any pointers. Tom. _ Going green? See the top 12 foods to eat organic. 1N1653A [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/predict.glm---newdata-tp16501614p16986751.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] sudden problem with script
Hi, First off, please understand that I am not a frequent R user. I am trying to use a script generated by another program in R for a certain analysis. I have used the script successfully in the past. Recently, when trying to load the script, I receive a warning message: package 'nls' has been merged with 'stats'. As a result, program R does not do the analysis. Does anyone have any idea how to fix this sudden problem? I have not done anything differently between my successful analyses and the current attempts. Any advice would be greatly appreciated. Thanks Dan _ =en-US?ocid=TAG_APRIL [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sudden problem with script
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of daniel guertin Sent: Wednesday, April 30, 2008 9:59 AM To: r-help@r-project.org Subject: [R] sudden problem with script Hi, First off, please understand that I am not a frequent R user. I am trying to use a script generated by another program in R for a certain analysis. I have used the script successfully in the past. Recently, when trying to load the script, I receive a warning message: package 'nls' has been merged with 'stats'. As a result, program R does not do the analysis. Does anyone have any idea how to fix this sudden problem? I have not done anything differently between my successful analyses and the current attempts. Any advice would be greatly appreciated. Thanks Dan My crystal ball is malfunctioning, so from way over here it is hard to see your code. Without seeing the script it is speculation, but the script likely has a reference to the package nls in a library statement. Something like library(nls) You can change that to library(stats) and the script will likely run. But again, this is pure speculation. Dan Daniel Nordlund Bothell, WA USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Bug? in summary( ) function base package
There seems to be an error in the summary() function when applied to ts class objects. The results of a call to summary( ), on the R ts data set USAccDeaths , reports the wrong value for Max. The value reported by the summary function is 11320. The max( ) function returns the correct value 11317, the July 1993 value. Coercing the data to a data.frame and calling summary returns the correct max value. A search of R -help found a post in 2007 that mentioned a problem but attributed it to rounding errors. But this is too large a difference to account for a simple rounding error. Has anyone else encountered the problem? Is there a workaround? R version 2.6.2 Patched (2008-02-08 r44394) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. data(USAccDeaths) summary(USAccDeaths) Min. 1st Qu. MedianMean 3rd Qu.Max. 68928089872887899323 11320 max(USAccDeaths) [1] 11317 USAccDeaths Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 1973 9007 8106 8928 9137 10017 10826 11317 10744 9713 9938 9161 8927 1974 7750 6981 8038 8422 8714 9512 10120 9823 8743 9129 8710 8680 1975 8162 7306 8124 7870 9387 9556 10093 9620 8285 8466 8160 8034 1976 7717 7461 7767 7925 8623 8945 10078 9179 8037 8488 7874 8647 1977 7792 6957 7726 8106 8890 9299 10625 9302 8314 8850 8265 8796 1978 7836 6892 7791 8192 9115 9434 10484 9827 9110 9070 8633 9240 dat1-as.data.frame(USAccDeaths) summary(dat1) x Min. : 6892 1st Qu.: 8089 Median : 8728 Mean : 8789 3rd Qu.: 9323 Max. :11317 Thanks, R Saba __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bug? in summary( ) function base package
On Wed, Apr 30, 2008 at 1:06 PM, Richard Saba [EMAIL PROTECTED] wrote: There seems to be an error in the summary() function when applied to ts class objects. The results of a call to summary( ), on the R ts data set USAccDeaths , reports the wrong value for Max. The value reported by the summary function is 11320. The max( ) function returns the correct value 11317, the July 1993 value. Coercing the data to a data.frame and calling summary returns the correct max value. A search of R -help found a post in 2007 that mentioned a problem but attributed it to rounding errors. But this is too large a difference to account for a simple rounding error. Notice that all the numbers in : summary(USAccDeaths) Min. 1st Qu. MedianMean 3rd Qu.Max. 68928089872887899323 11320 have four significant digits and then carefully read the documentation for the digits argument of summary. That should suggest both the cause and a solution. Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ordering a factor in boxplot output
I'm sure I'm missing something obvious in the documentation... I'm generating a boxplot boxplot(CleanValue~ApptCategory*ReportingCode,data=newfile) where ApptCategory is a factor with possible values (New,Established) Problem is, the output orders those factors alphabetically, and I'd really rather see New come first. I'm apparently confused by the reorder function because somehow my attempts to apply it have resulted in reversing the labelling (so now the established boxes are labelled as new). What am I missing? Thanks. -- View this message in context: http://www.nabble.com/ordering-a-factor-in-boxplot-output-tp16989073p16989073.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Use of recordPlot
My impression of the plot recording in windows was that it was a quick tool to be useful, but not a high priority. Trying to keep track of 50 plots (and using different plot windows) is pushing it beyond its original intention. I expect that he core people have higher priorities, so may not even want to look at it for a while. If you want to be able to scroll through 50 or so plots made by a script, I would suggest using the pdf device (or postscript) to write them all to a file, then open the file and use pgup/pgdn to scroll through the graphs. This is a couple of extra steps, but I think it will work better for you at this point. From: Beck, Kenneth (STP) [mailto:[EMAIL PROTECTED] Sent: Mon 4/28/2008 8:53 AM To: Greg Snow; r-help@r-project.org Subject: RE: [R] Use of recordPlot Thanks for the clarification, this helps a lot, expecially your comment about source is real. I will stop my effort to save the graphs permanently, the scripts don't take long to generate. But the end of your response hits on the key issue: when I create several graphs, I would like to be able to use PgUp/PgDn or some other keystroke to easily scroll through them all in sequence. One of my scripts now creates 30+ graphs, and to view them I have to mouse to the list of graphics devices and pick off the list. Your last comment indicates you can set it up to quick page through lists of graphs. I just tried adding options(graphics.record=TRUE); to my code, and I now find the .SavedPlots variable in the work space, but I was hoping to use replayPlot(.SavedPlots) or something like that to be able to scroll through the plots, but it does not seem to work. Why do I not get anything when I ask for help (?.SavedPlots)? Does this variable contain only those plots for which I call recordPlot? At times it seems yes (e.g. only a few plots), but then later it seemed to contain all that were generated by the script (nearly 50). When I pick Previous/Next Plot or use PgUp/PgDn when viewing a graphcis Device, the title bar stays on the latest graphics Device number, though the graph itself may change. But then on further PgUp, I see only the layout, not the graph. When I use commands in the console to attempt to show graphs, I get a warning suggesting the graph was saved in an older format, but I have the latest R installed (2.6.2): .SavedPlots[2] or replayPlot(.SavedPlots[2]) Warning message: In replayPlot(x) : loading snapshot from pre-2.0.0 R version Is there a simple command or series of commands to add to the script to enable scrolling through all plots generated by that script? Or maybe something at the beginning with something else at the end?? Thanks for your help... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Greg Snow Sent: Tuesday, April 22, 2008 10:43 AM To: Beck, Kenneth (STP); r-help@r-project.org Subject: Re: [R] Use of recordPlot You seem to be confusing several issues. First, being object oriented does not mean that it matches C++ syntax or that every object is guarenteed to have specific methods. What lead you to think that a recordedplot would have a metafile method? Nothing else has that method, and the only function I find with metafile is the win.metafile graphics device. The difference between SavedPlots and recordedPlot is the same as the difference between flock and sheep when talking about a flock of sheep. A recordedPlot object is a single plot, a SavedPlots object is a group of recordedPlot objects (not the plural vs. singular). Look at the help for objects or ls (?ls) and look at the 'all.names' argument to see how to find .SavedPlots R does not use object.method for method dispatch, trying that is confusing the parser and that is why you get an error. Try method(object) instead. Also recognize that R follows the philosophy of Source is Real. For what you are trying to do, it will probably work better to write a script or function that creates your plots, then rerun the code when you want the plots again. The current mechanism is useful for a quick paging through plots, but was not meant for much more. -- 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 Beck, Kenneth (STP) Sent: Monday, April 21, 2008 4:10 PM To: r-help@r-project.org Subject: [R] Use of recordPlot I am trying to save plots that I create using calls to windows() folowed by multiple calls to plot to place several plots on a page. I want to store the plots as variables to be able to recall them later. The documentation states: Recorded plot histories are of class SavedPlots. They have a print method, and a subset method. As the individual plots are of class recordedplot they can be replayed by printing them: see recordPlot. The active plot history is stored in variable
[R] Aggregate() questions
Dear all -- I have a data frame containing data related to heat gain through windows. The general form is ... Key ProfAIAC many other numeric columns AAA0.7 AAA 10.6 AAA0 .66 AAA 20 .45 (more AAA rows) (then AAB rows) 'Key' identifies the physical configuration ... rows with a given Key contain data for same window under various conditions. I want to add a column IAC0 containing, for each Key, the mean IAC of all rows with ProfA == 0. The general approach I think I need is approximately (the following is not known to run) -- 1) XS-subset( X, ProfA .01) to get the ProfA == 0 rows. This could be done implicitly as part of step 2, I suppose. 2) X0-aggregate( XS[,IAC], by=list( Key=XS$Key), mean) 3) XF-merge( X, X0, by=Key) 4) Change new col name to IAC0 (see Question 2). Question 1: Is this a reasonable way to solve my problem? Question 2: The aggregate() result has 2 columns: Key and x. Can the name of the mean column be specified (short of renaming after the fact)? All the aggregate() examples (e.g. in help()) elegantly produce the right result with nicely named columns etc. I can't seem to make things work so smoothly. Thanks! Chip Barnaby - Chip Barnaby [EMAIL PROTECTED] Vice President of Research Wrightsoft Corp. 781-862-8719 x118 voice 131 Hartwell Ave 781-861-2058 fax Lexington, MA 02421 www.wrightsoft.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Survival Regression with multiple records per subject
Em Qua 30 Abr 2008, Fabian Hefner escreveu: Here is an example: itm ID exercise time 1.401869 1 0 1 1.324390 1 0 2 1.324390 1 0 3 1.38 1 0 4 1.346761 1 0 5 1.315441 1 1 6 1.337812 2 0 1 1.319915 2 0 2 1.351235 2 1 3 itm is the covariate; ID is the subject Id; exercise indicates if the subject is dead=1 or alive=0 How can I allocate the multiple records to one subject (for example record 1-6 are part of subject with ID 1 record 7-9 are part of subject with ID2) and process a survival regression. Hi, If I got it, the time must be converted to time to death, your table must be: itm ID exercise time to death 1.31544111 6 1.35123521 3 The problem is your itm covariate, may be it must be converted to de difference between the first value and the last value. Inte Ronaldo -- Send lawyers, guns and money... -- Lyrics from a Warren Zevon song -- Prof. Ronaldo Reis Júnior | .''`. UNIMONTES/Depto. Biologia Geral/Lab. de Biologia Computacional | : :' : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia | `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil | `- Fone: (38) 3229-8187 | [EMAIL PROTECTED] | [EMAIL PROTECTED] | http://www.ppgcb.unimontes.br/ | ICQ#: 5692561 | LinuxUser#: 205366 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Aggregate() questions
If I understand your question: x$IAC0 - with(x, ave(IAC, list(ProfA, Key), FUN = mean)) On Wed, Apr 30, 2008 at 3:52 PM, Chip Barnaby [EMAIL PROTECTED] wrote: Dear all -- I have a data frame containing data related to heat gain through windows. The general form is ... Key ProfAIAC many other numeric columns AAA0.7 AAA 10.6 AAA0 .66 AAA 20 .45 (more AAA rows) (then AAB rows) 'Key' identifies the physical configuration ... rows with a given Key contain data for same window under various conditions. I want to add a column IAC0 containing, for each Key, the mean IAC of all rows with ProfA == 0. The general approach I think I need is approximately (the following is not known to run) -- 1) XS-subset( X, ProfA .01) to get the ProfA == 0 rows. This could be done implicitly as part of step 2, I suppose. 2) X0-aggregate( XS[,IAC], by=list( Key=XS$Key), mean) 3) XF-merge( X, X0, by=Key) 4) Change new col name to IAC0 (see Question 2). Question 1: Is this a reasonable way to solve my problem? Question 2: The aggregate() result has 2 columns: Key and x. Can the name of the mean column be specified (short of renaming after the fact)? All the aggregate() examples (e.g. in help()) elegantly produce the right result with nicely named columns etc. I can't seem to make things work so smoothly. Thanks! Chip Barnaby - Chip Barnaby [EMAIL PROTECTED] Vice President of Research Wrightsoft Corp. 781-862-8719 x118 voice 131 Hartwell Ave 781-861-2058 fax Lexington, MA 02421 www.wrightsoft.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R isn't finding tcltk
On a x86 machine operating under Gentoo Linux, I'm having persistent difficulty in getting R version 2.6.1 (the latest available through Gentoo's portage system) to use tcltk. The R command library(tcltk) elicits the following response: Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error in library(tcltk) : .First.lib failed for 'tcltk' After first encountering this problem, I took the following steps: 1. Made sure that installed programs include dev-lang/tcl, dev-tcltk/mysqltcl, dev-tcltk/otcl, dev-tcltk/tcl-debug, dev-tcltk/tcldom, dev-tcltk/tcllib, dev-tcltk/tclperl, dev-tcltk/tclpython, dev-tcltk/tclreadline, dev-tcltk/tclxml, and dev-tcltk/tclxml-expat. 2. Verified that tcltk was installed by writing a little file hello.tcl, running the command tclsh hello.tcl, and observing that the output was correct. 3. Removed R by doing emerge -C R. 4. Set a tcltk USE flag for R by appending the line dev-lang/R tcltk to my /etc/portage/package.use file. 5. Reinstalled R by doing emerge R Then I started R and again tried library(tcltk). The response was exactly the same before. I would be very grateful for your suggestions for solving this problem. Best regards, John -- John P. Burkett Department of Environmental and Natural Resource Economics and Department of Economics University of Rhode Island Kingston, RI 02881-0808 USA phone (401) 874-9195 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to stop buffering of cat
Hi All, My R code takes very long time to finish the processing. I want to see at what stage the script is running. So I wrote some output messages using cat. But instead of displaying the cat messages at different stages they are buffered and displayed in the end when entire processing is done. Can you please suggest how to stop this buffering or some alternative way to display messages Thank you Vidhu [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to stop buffering of cat
If you're using Rgui under Windows, see FAQ 7.1: 7.1 When using Rgui the output to the console seems to be delayed. This is deliberate: the console output is buffered ... (the FAQ says how to turn it off -- it's a menu item). Vidhu Choudhary wrote: Hi All, My R code takes very long time to finish the processing. I want to see at what stage the script is running. So I wrote some output messages using cat. But instead of displaying the cat messages at different stages they are buffered and displayed in the end when entire processing is done. Can you please suggest how to stop this buffering or some alternative way to display messages Thank you Vidhu [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to stop buffering of cat
On Wed, 30 Apr 2008, Vidhu Choudhary wrote: Hi All, My R code takes very long time to finish the processing. I want to see at what stage the script is running. So I wrote some output messages using cat. But instead of displaying the cat messages at different stages they are buffered and displayed in the end when entire processing is done. Can you please suggest how to stop this buffering or some alternative way to display messages By reading the R for Windows FAQ?? 7.1 When using Rgui the output to the console seems to be delayed. Thank you Vidhu [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Why R is 200 times slower than Matlab ?
I am switching from Matlab to R, but I found that R is 200 times slower than
matlab.
Since I am newbie to R, I must be missing some important programming tips.
Please help me out on this.
Here is the function:
## make the full pair-wise permutation of a vector
## input_fc=c(1,2,3);
## output_fc=(
1 1 1 2 2 2 3 3 3
1 2 3 1 2 3 1 2 3
);
grw_permute = function(input_fc){
fc_vector = input_fc
index = 1
k = length(fc_vector)
fc_matrix = matrix(0,2,k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] = fc_vector[i]
fc_matrix[index+1] = fc_vector[j]
index = index+2
}
}
return(fc_matrix)
}
For an input vector of size 300. It took R 2.17 seconds to run.
But the same code in matlab only needs 0.01 seconds to run.
Am I missing sth in R.. Is there a away to optimize. ???
Thanks
--
Zhandong Liu
Genomics and Computational Biology
University of Pennsylvania
616 BRB II/III, 421 Curie Boulevard
University of Pennsylvania School of Medicine
Philadelphia, PA 19104-6160
[[alternative HTML version deleted]]
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Re: [R] R isn't finding tcltk
John P. Burkett wrote: On a x86 machine operating under Gentoo Linux, I'm having persistent difficulty in getting R version 2.6.1 (the latest available through Gentoo's portage system) to use tcltk. The R command library(tcltk) elicits the following response: Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error in library(tcltk) : .First.lib failed for 'tcltk' Hmm, so Gentoo's all-singing all-dancing build system is helping you install an obsolescent version incorrectly? Can't you try building from plain sources? In particulat the output from the configure step should be informative. Usually, it is a -devel package that is missing, e.g. on Fedora you need not only tk-8.4.17-2.fc8 tcl-8.4.17-1.fc8 but also tk-devel-8.4.17-2.fc8 tcl-devel-8.4.17-1.fc8 -pd After first encountering this problem, I took the following steps: 1. Made sure that installed programs include dev-lang/tcl, dev-tcltk/mysqltcl, dev-tcltk/otcl, dev-tcltk/tcl-debug, dev-tcltk/tcldom, dev-tcltk/tcllib, dev-tcltk/tclperl, dev-tcltk/tclpython, dev-tcltk/tclreadline, dev-tcltk/tclxml, and dev-tcltk/tclxml-expat. 2. Verified that tcltk was installed by writing a little file hello.tcl, running the command tclsh hello.tcl, and observing that the output was correct. 3. Removed R by doing emerge -C R. 4. Set a tcltk USE flag for R by appending the line dev-lang/R tcltk to my /etc/portage/package.use file. 5. Reinstalled R by doing emerge R Then I started R and again tried library(tcltk). The response was exactly the same before. I would be very grateful for your suggestions for solving this problem. Best regards, John -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to fit parametric survival model using counting process data
Hi, I was trying to fit a parametric survival model with Weibull distribution on counting process type of data (NOT interval censor data), but the survreg(Surv(T1,T2,event)~x,data,dist=weibull) did not seem to work. Anyone can help me with that? Thanks, Rachel Memorial Sloan-Kettering Cancer Center -- View this message in context: http://www.nabble.com/How-to-fit-parametric-survival-model-using-counting-process-data-tp16990348p16990348.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
Hi, ZD,
Your comment about speed is too general. Here is a benchmark
comparison among several languages and HTH.
http://www.sciviews.org/benchmark/index.html
On Wed, Apr 30, 2008 at 4:15 PM, Zhandong Liu
[EMAIL PROTECTED] wrote:
I am switching from Matlab to R, but I found that R is 200 times slower than
matlab.
Since I am newbie to R, I must be missing some important programming tips.
Please help me out on this.
Here is the function:
## make the full pair-wise permutation of a vector
## input_fc=c(1,2,3);
## output_fc=(
1 1 1 2 2 2 3 3 3
1 2 3 1 2 3 1 2 3
);
grw_permute = function(input_fc){
fc_vector = input_fc
index = 1
k = length(fc_vector)
fc_matrix = matrix(0,2,k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] = fc_vector[i]
fc_matrix[index+1] = fc_vector[j]
index = index+2
}
}
return(fc_matrix)
}
For an input vector of size 300. It took R 2.17 seconds to run.
But the same code in matlab only needs 0.01 seconds to run.
Am I missing sth in R.. Is there a away to optimize. ???
Thanks
--
Zhandong Liu
Genomics and Computational Biology
University of Pennsylvania
616 BRB II/III, 421 Curie Boulevard
University of Pennsylvania School of Medicine
Philadelphia, PA 19104-6160
[[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.
--
===
WenSui Liu
ChoicePoint Precision Marketing
Phone: 678-893-9457
Email : [EMAIL PROTECTED]
Blog : statcompute.spaces.live.com
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[R] Getting variable names from as.matrix
Hi all, I'm running a multidimensional scaling model on data that are first transformed into a similarity matrix using the program daisy in the cluster package. If I already provide the similarity matrix, the plotting routine will give me the variable names on the plot itself. But, it seems that when I use the daisy program to create the similarity matrix, I can't get the program to give me variable names on the plot. Here is the input ## Sammon's MDS country.demog - read.csv(~/Desktop/country.demog.csv) ## daisy requires loading the cluster package. It will calculate standardized Eculidean distances country.demog.dist - daisy(country.demog,metric=euclidean,stand=TRUE) ## The following line calculates the ordinal MDS country.mds - sammon(dist(country.demog.dist), k=2) ## The following lines create the MDS map using country names. It also places horizontal and vertical lines for reference. plot(country.mds$points,type=n) text(country.mds$points, labels = as.character(country.demog$country)) abline(h=0) abline(v=0) Thanks for any advice, David -- === David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706 email: dkaplan at education dot wisc dot edu homepage: http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm Phone: 608-262-0836 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
I would rather not comment on matlab (where is
your matlab code by the way?), but your function
could be simplified a bit:
grw.permute - function(v) {
cbind( rep(v, each=length(v)), rep(v, length(v)) )
}
system.time(tmp - f( 1:300))
user system elapsed
0.020 0.000 0.019
This is on my quite busy 4 years old laptop
Best,
Gabor
On Wed, Apr 30, 2008 at 04:15:46PM -0400, Zhandong Liu wrote:
I am switching from Matlab to R, but I found that R is 200 times slower than
matlab.
Since I am newbie to R, I must be missing some important programming tips.
[...]
--
Csardi Gabor [EMAIL PROTECTED]UNIL DGM
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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] arcsine transformation
I have been trying to preform both a bartlett's test and an arcsine transformation on some average percentage data. I've tried inputting it different ways and I keep getting the same error message: head(workingdata) DYAD BEFORE AFTER 1 BG-FL 4.606772 5.787520 2 BG-LL 5.467503 7.847395 3 AD-MV 5.333735 11.107380 4 MM-FL 5.578708 12.063500 5 MM-MV 2.037605 6.415303 6 MM-RM 6.158885 11.911080 bartlett.test(BEFORE ~ AFTER) Error in bartlett.test.default(c(4.606772, 5.467503, 5.333735, 5.578708, : there must be at least 2 observations in each group asin(BEFORE) [1] NaN NaN NaN NaN NaN NaN NaN Warning message: In asin(BEFORE) : NaNs produced I'm at a loss here and I would greatly appreciate any guidance that could be given me. Thank you! -- Claire Sheller Department of Anthropology Tulane University New Orleans, LA 70118 615-210-9129 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
You just have to use the right functions: is this fast enough
system.time(x - expand.grid(1:300, 1:300))
user system elapsed
0.000.010.01
On Wed, Apr 30, 2008 at 4:15 PM, Zhandong Liu
[EMAIL PROTECTED] wrote:
I am switching from Matlab to R, but I found that R is 200 times slower than
matlab.
Since I am newbie to R, I must be missing some important programming tips.
Please help me out on this.
Here is the function:
## make the full pair-wise permutation of a vector
## input_fc=c(1,2,3);
## output_fc=(
1 1 1 2 2 2 3 3 3
1 2 3 1 2 3 1 2 3
);
grw_permute = function(input_fc){
fc_vector = input_fc
index = 1
k = length(fc_vector)
fc_matrix = matrix(0,2,k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] = fc_vector[i]
fc_matrix[index+1] = fc_vector[j]
index = index+2
}
}
return(fc_matrix)
}
For an input vector of size 300. It took R 2.17 seconds to run.
But the same code in matlab only needs 0.01 seconds to run.
Am I missing sth in R.. Is there a away to optimize. ???
Thanks
--
Zhandong Liu
Genomics and Computational Biology
University of Pennsylvania
616 BRB II/III, 421 Curie Boulevard
University of Pennsylvania School of Medicine
Philadelphia, PA 19104-6160
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] Bug? in summary( ) function base package
Richard Saba [EMAIL PROTECTED] wrote: There seems to be an error in the summary() function when applied to ts class objects. The results of a call to summary( ), on the R ts data set USAccDeaths , reports the wrong value for Max. The value reported by the summary function is 11320. The max( ) function returns the correct value 11317, the July 1993 value. Coercing the data to a data.frame and calling summary returns the correct max value. A search of R -help found a post in 2007 that mentioned a problem but attributed it to rounding errors. But this is too large a difference to account for a simple rounding error. Has anyone else encountered the problem? Is there a workaround? A documented feature of summary() is that it rounds values. In doing so, it may print meaningless digits and thus give the appearance of more precision than is really represented. -- Mike Prager, NOAA, Beaufort, NC * Opinions expressed are personal and not represented otherwise. * Any use of tradenames does not constitute a NOAA endorsement. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
Zhandong Liu wrote:
I am switching from Matlab to R, but I found that R is 200 times slower than
matlab.
Since I am newbie to R, I must be missing some important programming tips.
The most important tip I would give you is to use the vectorized nature
of R whenever possible. This helps avoid messy indexing and 'for' loops.
Look at the following 3 functions. Yours, Gabor's, and my own (which I
was about to post when I saw Gabor's nice solution, and is basically the
same).
Also see the system timings after the definitions.
grw_permute - function(input_fc){
fc_vector - input_fc
index - 1
k - length(fc_vector)
fc_matrix - matrix(0, 2, k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] - fc_vector[i]
fc_matrix[index+1] - fc_vector[j]
index - index + 2
}
}
return(fc_matrix)
}
grw.permute2 - function(v) {
cbind( rep(v, each=length(v)), rep(v, length(v)) )
}
grw_permute3 - function(input_fc) {
matrix(c(rep(input_fc, each = length(input_fc)),
rep.int(input_fc, times = length(input_fc))),
nrow = 2, byrow = TRUE)
}
system.time(p1 - grw_permute(1:300))
user system elapsed
1.548 0.064 2.341
system.time(p2 - grw_permute2(1:300))
user system elapsed
0.009 0.001 0.010
system.time(p3 - grw_permute3(1:300))
user system elapsed
0.008 0.002 0.010
Erik Iverson
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Re: [R] Why R is 200 times slower than Matlab ?
But please consider that this benchmark is five years old, and i believe that R has changed quite a lot since version 1.9. Gabor On Wed, Apr 30, 2008 at 04:21:51PM -0400, Wensui Liu wrote: Hi, ZD, Your comment about speed is too general. Here is a benchmark comparison among several languages and HTH. http://www.sciviews.org/benchmark/index.html [...] -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
Zhandong Liu wrote:
I am switching from Matlab to R, but I found that R is 200 times slower than
matlab.
Since I am newbie to R, I must be missing some important programming tips.
Please help me out on this.
Here is the function:
## make the full pair-wise permutation of a vector
## input_fc=c(1,2,3);
## output_fc=(
1 1 1 2 2 2 3 3 3
1 2 3 1 2 3 1 2 3
);
grw_permute = function(input_fc){
fc_vector = input_fc
index = 1
k = length(fc_vector)
fc_matrix = matrix(0,2,k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] = fc_vector[i]
fc_matrix[index+1] = fc_vector[j]
index = index+2
}
}
return(fc_matrix)
}
For an input vector of size 300. It took R 2.17 seconds to run.
But the same code in matlab only needs 0.01 seconds to run.
Am I missing sth in R.. Is there a away to optimize. ???
Thanks
This is pretty characteristic. With R, you really don't want nested
loops doing single-element accessing (if you have better things to do
with 2.16 seconds of our life). You will usually find that this sort of
problem is handled either using vectorized operations at a higher level,
or pushed into C code which is dynamically loaded. For the particular
problem, notice that the same result is obtained with
system.time(rbind(rep(1:300,300),rep(1:300,each=300)))
user system elapsed
0.041 0.006 0.050
or even (OK, so it's transposed)
system.time(expand.grid(1:300,1:300))
user system elapsed
0.027 0.011 0.040
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] ordering a factor in boxplot output
One option is to set the order in newfile:
newfile$ApptCategory - factor(newfile$ApptCategory,
levels=c('New','Established'))
Of course, this will then affect the order for other things associated
with ApptCategory, but that is probably what you want.
HTH ...
Peter Alspach
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tubin
Sent: Thursday, 1 May 2008 6:40 a.m.
To: r-help@r-project.org
Subject: [R] ordering a factor in boxplot output
I'm sure I'm missing something obvious in the documentation...
I'm generating a boxplot
boxplot(CleanValue~ApptCategory*ReportingCode,data=newfile)
where ApptCategory is a factor with possible values
(New,Established)
Problem is, the output orders those factors alphabetically,
and I'd really rather see New come first. I'm apparently
confused by the reorder function because somehow my
attempts to apply it have resulted in reversing the labelling
(so now the established boxes are labelled as new).
What am I missing? Thanks.
--
View this message in context:
http://www.nabble.com/ordering-a-factor-in-boxplot-output-tp16
989073p16989073.html
Sent from the R help mailing list archive at Nabble.com.
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[R] Fwd: Why R is 200 times slower than Matlab ?
This is what I refer to as ab uno disce omnes-thinking:
-- from one example all is revealed -- but this is the antithesis
of statistical thinking.
Here is an example function, others can probably do better.
On a vector of length 300 it takes .018 seconds on my aging
G5 ppc mac:
pears - function(x){
n - length(x)
A - combos(n,2)
rbind(x[A[1,]],x[A[2,]])
}
This is actually a (shameless) advertisement for the function
combos in my quantreg package which uses a slightly fancy
algorithm to order the n choose p indices as, say produced
by base R's combn() in such a way that adjacent columns
differ by only one element.
PS. Isn't there a better way to do the indexing on the last line?
url:www.econ.uiuc.edu/~rogerRoger Koenker
email[EMAIL PROTECTED]Department of Economics
vox: 217-333-4558University of Illinois
fax: 217-244-6678Champaign, IL 61820
On Apr 30, 2008, at 3:15 PM, Zhandong Liu wrote:
I am switching from Matlab to R, but I found that R is 200 times
slower than
matlab.
Since I am newbie to R, I must be missing some important programming
tips.
Please help me out on this.
Here is the function:
## make the full pair-wise permutation of a vector
## input_fc=c(1,2,3);
## output_fc=(
1 1 1 2 2 2 3 3 3
1 2 3 1 2 3 1 2 3
);
grw_permute = function(input_fc){
fc_vector = input_fc
index = 1
k = length(fc_vector)
fc_matrix = matrix(0,2,k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] = fc_vector[i]
fc_matrix[index+1] = fc_vector[j]
index = index+2
}
}
return(fc_matrix)
}
For an input vector of size 300. It took R 2.17 seconds to run.
But the same code in matlab only needs 0.01 seconds to run.
Am I missing sth in R.. Is there a away to optimize. ???
Thanks
--
Zhandong Liu
Genomics and Computational Biology
University of Pennsylvania
616 BRB II/III, 421 Curie Boulevard
University of Pennsylvania School of Medicine
Philadelphia, PA 19104-6160
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] arcsine transformation
Perhaps you need with(workingdata, asin(BEFORE)) or asin(workingdata$BEFORE) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ On Apr 30, 2008, at 4:52 PM, Claire Sheller wrote: I have been trying to preform both a bartlett's test and an arcsine transformation on some average percentage data. I've tried inputting it different ways and I keep getting the same error message: head(workingdata) DYAD BEFORE AFTER 1 BG-FL 4.606772 5.787520 2 BG-LL 5.467503 7.847395 3 AD-MV 5.333735 11.107380 4 MM-FL 5.578708 12.063500 5 MM-MV 2.037605 6.415303 6 MM-RM 6.158885 11.911080 bartlett.test(BEFORE ~ AFTER) Error in bartlett.test.default(c(4.606772, 5.467503, 5.333735, 5.578708, : there must be at least 2 observations in each group asin(BEFORE) [1] NaN NaN NaN NaN NaN NaN NaN Warning message: In asin(BEFORE) : NaNs produced I'm at a loss here and I would greatly appreciate any guidance that could be given me. Thank you! -- Claire Sheller Department of Anthropology Tulane University New Orleans, LA 70118 615-210-9129 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
On Thu, 01 May 2008, Zhandong Liu wrote:
I am switching from Matlab to R, but I found that R is 200 times slower
than matlab.
Since I am newbie to R, I must be missing some important programming tips.
Please help me out on this.
Here is the function:
## make the full pair-wise permutation of a vector
## input_fc=c(1,2,3);
## output_fc=(
1 1 1 2 2 2 3 3 3
1 2 3 1 2 3 1 2 3
);
grw_permute = function(input_fc){
fc_vector = input_fc
index = 1
k = length(fc_vector)
fc_matrix = matrix(0,2,k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] = fc_vector[i]
fc_matrix[index+1] = fc_vector[j]
index = index+2
}
}
return(fc_matrix)
}
For an input vector of size 300. It took R 2.17 seconds to run.
But the same code in matlab only needs 0.01 seconds to run.
I am not a MATLAB user, but I suspect it wasn't the same code that produced
an answer in MATLAB, but you don't provide your MATLAB code, nor do you
specify what version of R, of MATLAB, or what hardware and OS you are using.
I get {NetBSD, R version 2.6.0 (2007-10-03), Core 2 Duo, 3.x GHz}:
input_fc - sample(1:600)
unix.time(a1 - grw_permute(input_fc))
user system elapsed
3.279 -0.001 3.280
unix.time({n - length(input_fc); a2 - matrix(c(rep(input_fc, each=n),
rep(input_fc, n)), 2, n*n, byrow = T)})
user system elapsed
0.019 0.020 0.040
all.equal(a1, a2)
[1] TRUE
A sample of length 300 took less than 1 second using your grw_permute() (so
your OS may be making a difference as well).
Am I missing sth in R.. Is there a away to optimize. ???
Yes. Loops are not efficient in R.
Thanks
HTH,
Ray Brownrigg
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and provide commented, minimal, self-contained, reproducible code.
[R] Lattice book
Dear all, I haven't seen this mentioned and presumably Dr. Deepayan Sarkar is too polite to advertise! I just received a flyer from Springer: A new book on Lattice released today!! http://www.springer.com/statistics/computational/book/978-0-387-75968-5?cm_mmc=NBA-_-Apr-08_UK_1753460-_-product-_-978-0-387-75968-5 http://www.amazon.co.uk/exec/obidos/ASIN/0387759689/ref=ord_cart_shr?%5Fencoding=UTF8m=A3P5ROKL5A1OLE Well done and many congratulations. My order is being processed as we speak! Best wishes, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
This is the missing Matlab code:
function[fc_matrix]=grw_permute(fc_vector)
n=length(fc_vector);
fc_matrix=zeros(2,n^2);
index=1;
for i=1:n
for j=1:n
fc_matrix(index)=fc_vector(i);
fc_matrix(index+1)=fc_vector(j);
index=index+2;
end
end
On Wed, Apr 30, 2008 at 4:47 PM, Ray Brownrigg [EMAIL PROTECTED]
wrote:
On Thu, 01 May 2008, Zhandong Liu wrote:
I am switching from Matlab to R, but I found that R is 200 times slower
than matlab.
Since I am newbie to R, I must be missing some important programming
tips.
Please help me out on this.
Here is the function:
## make the full pair-wise permutation of a vector
## input_fc=c(1,2,3);
## output_fc=(
1 1 1 2 2 2 3 3 3
1 2 3 1 2 3 1 2 3
);
grw_permute = function(input_fc){
fc_vector = input_fc
index = 1
k = length(fc_vector)
fc_matrix = matrix(0,2,k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] = fc_vector[i]
fc_matrix[index+1] = fc_vector[j]
index = index+2
}
}
return(fc_matrix)
}
For an input vector of size 300. It took R 2.17 seconds to run.
But the same code in matlab only needs 0.01 seconds to run.
I am not a MATLAB user, but I suspect it wasn't the same code that
produced
an answer in MATLAB, but you don't provide your MATLAB code, nor do you
specify what version of R, of MATLAB, or what hardware and OS you are
using.
I get {NetBSD, R version 2.6.0 (2007-10-03), Core 2 Duo, 3.x GHz}:
input_fc - sample(1:600)
unix.time(a1 - grw_permute(input_fc))
user system elapsed
3.279 -0.001 3.280
unix.time({n - length(input_fc); a2 - matrix(c(rep(input_fc, each=n),
rep(input_fc, n)), 2, n*n, byrow = T)})
user system elapsed
0.019 0.020 0.040
all.equal(a1, a2)
[1] TRUE
A sample of length 300 took less than 1 second using your grw_permute()
(so
your OS may be making a difference as well).
Am I missing sth in R.. Is there a away to optimize. ???
Yes. Loops are not efficient in R.
Thanks
HTH,
Ray Brownrigg
--
Zhandong Liu
Genomics and Computational Biology
University of Pennsylvania
616 BRB II/III, 421 Curie Boulevard
University of Pennsylvania School of Medicine
Philadelphia, PA 19104-6160
[[alternative HTML version deleted]]
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Re: [R] Why R is 200 times slower than Matlab ?
Ah, so the code is quite similar in MATLAB (and the *algorithm* is the
same :-) ).
The Important programming tip is that when converting from MATLAB to R, you
shouldn't just 'translate' from MATLAB code to R code, you must reconsider
the problem in the context of the R environment. This is very much like
translating poetry, where the result should really be a poem in the target
language, not just an accurate word-for-word (or even sentence-for-sentence)
translation.
Ray
On Thu, 01 May 2008, you wrote:
This is the missing Matlab code:
function[fc_matrix]=grw_permute(fc_vector)
n=length(fc_vector);
fc_matrix=zeros(2,n^2);
index=1;
for i=1:n
for j=1:n
fc_matrix(index)=fc_vector(i);
fc_matrix(index+1)=fc_vector(j);
index=index+2;
end
end
On Wed, Apr 30, 2008 at 4:47 PM, Ray Brownrigg
[EMAIL PROTECTED]
wrote:
On Thu, 01 May 2008, Zhandong Liu wrote:
I am switching from Matlab to R, but I found that R is 200 times slower
than matlab.
Since I am newbie to R, I must be missing some important programming
tips.
Please help me out on this.
Here is the function:
## make the full pair-wise permutation of a vector
## input_fc=c(1,2,3);
## output_fc=(
1 1 1 2 2 2 3 3 3
1 2 3 1 2 3 1 2 3
);
grw_permute = function(input_fc){
fc_vector = input_fc
index = 1
k = length(fc_vector)
fc_matrix = matrix(0,2,k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] = fc_vector[i]
fc_matrix[index+1] = fc_vector[j]
index = index+2
}
}
return(fc_matrix)
}
For an input vector of size 300. It took R 2.17 seconds to run.
But the same code in matlab only needs 0.01 seconds to run.
I am not a MATLAB user, but I suspect it wasn't the same code that
produced
an answer in MATLAB, but you don't provide your MATLAB code, nor do you
specify what version of R, of MATLAB, or what hardware and OS you are
using.
I get {NetBSD, R version 2.6.0 (2007-10-03), Core 2 Duo, 3.x GHz}:
input_fc - sample(1:600)
unix.time(a1 - grw_permute(input_fc))
user system elapsed
3.279 -0.001 3.280
unix.time({n - length(input_fc); a2 - matrix(c(rep(input_fc, each=n),
rep(input_fc, n)), 2, n*n, byrow = T)})
user system elapsed
0.019 0.020 0.040
all.equal(a1, a2)
[1] TRUE
A sample of length 300 took less than 1 second using your grw_permute()
(so
your OS may be making a difference as well).
Am I missing sth in R.. Is there a away to optimize. ???
Yes. Loops are not efficient in R.
Thanks
HTH,
Ray Brownrigg
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[R] why my code is not computing significance level and power correctly
I am trying to compare Levene,bartlett, count5 tests for a random normal sample for the significance level and power, the problem seems bug free but with obvious wrong result, anyone can help, I send the R code as attachment. Thanks http://www.nabble.com/file/p16992744/758%2Bproject 758+project -- View this message in context: http://www.nabble.com/why-my-code-is-not-computing-significance-level-and-power-correctly-tp16992744p16992744.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] efficiency profiling? (was: Why R is 200 times slower than Matlab ?)
This has been an interesting discussion, and brings up two questions for me: Is there a good collection of hints/suggestions for R language idoms in terms of efficiency? For instance I read not to use for-loops, so I used apply only to later read that apply is internally implemented as a for so nothing gained here. Warnings about pitfalls (such as nested loops), hints, suggestions would be great. The second question - is there some sort of profiling tool available that would make it easy to recognize where the script is spending most of its time? Might be especially useful for newbies like me. Thanks all, Esmail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Spell a grand slam in this game where word skill meets World Series. Get in the game. 08 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Lattice book
Actually it's been out for a couple of weeks now at least. I just finished my first reading of it, and I must say it was spectacular. Congratulations Deepayan, the book gave me exactly the kind of lattice knowledge I needed, and then some. The graphics are really impressive and good illustrations of what lattice can do, and I found the writing very clear, with the complexity increasing at just the right speed. I definitely recommend it to anyone who wants to learn how to use lattice, at any level they desire. Ok, I guess I better stop now. Happy reading Mark! Haris Skiadas Department of Mathematics and Computer Science Hanover College On Apr 30, 2008, at 4:51 PM, Mark Wardle wrote: Dear all, I haven't seen this mentioned and presumably Dr. Deepayan Sarkar is too polite to advertise! I just received a flyer from Springer: A new book on Lattice released today!! http://www.springer.com/statistics/computational/book/ 978-0-387-75968-5?cm_mmc=NBA-_-Apr-08_UK_1753460-_-product- _-978-0-387-75968-5 http://www.amazon.co.uk/exec/obidos/ASIN/0387759689/ ref=ord_cart_shr?%5Fencoding=UTF8m=A3P5ROKL5A1OLE Well done and many congratulations. My order is being processed as we speak! Best wishes, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] arcsine transformation
On 4/30/2008 4:52 PM, Claire Sheller wrote: I have been trying to preform both a bartlett's test and an arcsine transformation on some average percentage data. I've tried inputting it different ways and I keep getting the same error message: head(workingdata) DYAD BEFORE AFTER 1 BG-FL 4.606772 5.787520 2 BG-LL 5.467503 7.847395 3 AD-MV 5.333735 11.107380 4 MM-FL 5.578708 12.063500 5 MM-MV 2.037605 6.415303 6 MM-RM 6.158885 11.911080 bartlett.test(BEFORE ~ AFTER) Error in bartlett.test.default(c(4.606772, 5.467503, 5.333735, 5.578708, : there must be at least 2 observations in each group bartlett.test() expects the second argument to be a vector or factor object giving the group for the corresponding elements of x. You seem to have paired samples instead. asin(BEFORE) [1] NaN NaN NaN NaN NaN NaN NaN Warning message: In asin(BEFORE) : NaNs produced You might divide the values by 100 prior to asin(). I'm at a loss here and I would greatly appreciate any guidance that could be given me. Thank you! -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why R is 200 times slower than Matlab ?
Aside from optiming your code by making use of R functions
that use C underneath as much as possible the big difference
between R and Matlab is Matlab's just-in-time compilation of
code. When that was introduced in Matlab huge speedups of
Matlab programs were noticeable.
For R, there is a new package on CRAN, jit, that
aims to provide similar speedups.
On Wed, Apr 30, 2008 at 4:15 PM, Zhandong Liu
[EMAIL PROTECTED] wrote:
I am switching from Matlab to R, but I found that R is 200 times slower than
matlab.
Since I am newbie to R, I must be missing some important programming tips.
Please help me out on this.
Here is the function:
## make the full pair-wise permutation of a vector
## input_fc=c(1,2,3);
## output_fc=(
1 1 1 2 2 2 3 3 3
1 2 3 1 2 3 1 2 3
);
grw_permute = function(input_fc){
fc_vector = input_fc
index = 1
k = length(fc_vector)
fc_matrix = matrix(0,2,k^2)
for(i in 1:k){
for(j in 1:k){
fc_matrix[index] = fc_vector[i]
fc_matrix[index+1] = fc_vector[j]
index = index+2
}
}
return(fc_matrix)
}
For an input vector of size 300. It took R 2.17 seconds to run.
But the same code in matlab only needs 0.01 seconds to run.
Am I missing sth in R.. Is there a away to optimize. ???
Thanks
--
Zhandong Liu
Genomics and Computational Biology
University of Pennsylvania
616 BRB II/III, 421 Curie Boulevard
University of Pennsylvania School of Medicine
Philadelphia, PA 19104-6160
[[alternative HTML version deleted]]
__
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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] Why R is 200 times slower than Matlab ?
On Wed, Apr 30, 2008 at 6:27 PM, Gabor Grothendieck [EMAIL PROTECTED] wrote: Aside from optiming your code by making use of R functions that use C underneath as much as possible the big difference between R and Matlab is Matlab's just-in-time compilation of code. When that was introduced in Matlab huge speedups of Matlab programs were noticeable. For R, there is a new package on CRAN, jit, that aims to provide similar speedups. http://www.milbo.users.sonic.net/ra/index.html Great! I just found out about ra. In Python I love psyco and I guess I will test ra soon. Thanks, N.- -- http://arhuaco.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] efficiency profiling? (was: Why R is 200 times slower than Matlab ?)
On Wed, Apr 30, 2008 at 06:59:38PM -0400, esmail bonakdarian wrote:
This has been an interesting discussion, and brings up two questions
for me:
Is there a good collection of hints/suggestions for R language idoms in terms
of efficiency? For instance I read not to use for-loops, so I used apply only
to
later read that apply is internally implemented as a for so nothing gained
here. Warnings about pitfalls (such as nested loops), hints, suggestions would
be great.
Personally i like {l,t,}apply better, 1) it is more readable,
2) it takes two minutes to change it to par{L,S,}apply and then
it runs in parallel.
The second question - is there some sort of profiling tool available that
would
make it easy to recognize where the script is spending most of its time? Might
be especially useful for newbies like me.
See ?Rprof
G.
[...]
--
Csardi Gabor [EMAIL PROTECTED]UNIL DGM
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Re: [R] efficiency profiling?
On 30/04/2008 6:59 PM, esmail bonakdarian wrote: This has been an interesting discussion, and brings up two questions for me: Is there a good collection of hints/suggestions for R language idoms in terms of efficiency? For instance I read not to use for-loops, so I used apply only to later read that apply is internally implemented as a for so nothing gained here. Warnings about pitfalls (such as nested loops), hints, suggestions would be great. The second question - is there some sort of profiling tool available that would make it easy to recognize where the script is spending most of its time? Might be especially useful for newbies like me. See ?Rprof for the tool. For the tips, I think you just need to hang around here a while. I don't know of a nice collection (but I'm sure there are several.) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] efficiency profiling?
See ?Rprof for the tool. For the tips, I think you just need to hang around here a while. I don't know of a nice collection (but I'm sure there are several.) Duncan Murdoch Hi, thanks .. several folks pointed me to Rprof, I'll take a look. Yes, I have been reading the list, the amount of messages per day is simply amazing, I can hardly keep up. Do most of you read this on the web or get it as digest? I am getting them as individual e-mails (thank god for filters) ... :-) Esmail _ Back to work after babyhow do you know when youre ready? 5797498ocid=T067MSN40A0701A [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] efficiency profiling?
On 30/04/2008 7:47 PM, esmail bonakdarian wrote: See ?Rprof for the tool. For the tips, I think you just need to hang around here a while. I don't know of a nice collection (but I'm sure there are several.) Duncan Murdoch Hi, thanks .. several folks pointed me to Rprof, I'll take a look. Yes, I have been reading the list, the amount of messages per day is simply amazing, I can hardly keep up. Do most of you read this on the web or get it as digest? I am getting them as individual e-mails (thank god for filters) ... :-) I think most read as email, but a substantial minority read it on the web. You really do need filters. Personally, I scan the subject lines, and read about 1 in 10 threads. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using the sink() function in a for-look
hi all,
i wanted to use the sink function to sequentially output regression
summaries within a for-loop. i must have something wrong somewhere (or be
using the sink function incorrectly), but can anyone help?
the code I am using is:
where data.x is a data.frame of independents, and data.y is a data.frame of
dependents.
for (i in 1:length(data.y)){
taxa.i - names(data.y[i])
jpeg(file=paste(taxa.i,.multiple.regress.residuals.1.RAW.jpeg,sep=),
quality=90, width=1000, height=1000)
par(mfrow=c(2,2), lwd=0.5, mar=c(3,4,3,1), bty=o, oma=c(0,3,2,0))
attach(data.x)
mult.reg.raw.i - lm(data.y[,i] ~ CURRENT + LITTER + PERCURR + SUBST)
plot(mult.reg.raw.i, ask=FALSE)
mtext(names(data.y[i]), side=3, line=-1.5, adj=0.48, cex=0.75,
outer=TRUE)
dev.off()
sink(mulptiple regression - summary RAW.txt, append=TRUE)
summary(mult.reg.raw.i)
sink()
}
cheers,
tony
__
tony dell
department of marine and tropical biology james cook university townsville,
qld 4811 australia
[p] 07 47815751 or 47814520
[e] [EMAIL PROTECTED]
[skype] anphony
Checked by AVG.
6:27 PM
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Re: [R] efficiency profiling?
On Wed, Apr 30, 2008 at 4:33 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: On 30/04/2008 6:59 PM, esmail bonakdarian wrote: snip Is there a good collection of hints/suggestions for R language idoms in terms of efficiency? snip See ?Rprof for the tool. For the tips, I think you just need to hang around here a while. I don't know of a nice collection (but I'm sure there are several.) Duncan Murdoch ;-) here's one: https://stat.ethz.ch/pipermail/r-help/2005-October/080991.html Kingsford Jones __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: efficient code - yet another question
The code I sent before had some typos, here is the corrected one:
pca.nipals - function(X, ncomp, iter = 50, toler = sqrt(.Machine$double.eps))
# X...data matrix, ncomp...number of components,
# iter...maximal number of iterations per component,
# toler...precision tolerance for calculation of components
{
Xh - scale(X, center = TRUE, scale = FALSE)
nr - 0
T - NULL; P - NULL # matrix of scores and loadings
for (h in 1:ncomp)
{
th - Xh[, 1]
ende - FALSE
while (!ende)
{
nr - nr + 1
ph - t(crossprod(th, Xh) * as.vector(1 /
crossprod(th)))
ph - ph * as.vector(1/sqrt(crossprod(ph)))
thnew - t(tcrossprod(t(ph), Xh) *
as.vector(1/(crossprod(ph
prec - crossprod(th-thnew)
th - thnew
if (prec = (toler^2)) ende - TRUE
if (iter = nr) ende - TRUE # didn't converge
}
Xh - Xh - tcrossprod(th)
T - cbind(T, th); P - cbind(P, ph)
nr - 0
}
list(T = T, P = P)
}
Thanks again
-- Forwarded message --
From: steven wilson [EMAIL PROTECTED]
Date: Wed, Apr 30, 2008 at 11:56 PM
Subject: efficient code - yet another question
To: r-help@r-project.org
Dear list members;
The code given below corresponds to the PCA-NIPALS (principal
component analysis) algorithm adapted from the nipals function in the
package chemometrics. The reason for using NIPALS instead of SVD is
the ability of this algorithm to handle missing values, but that's a
different story. I've been trying to find a way to improve (if
possible) the efficiency of the code, especially when the number of
components to calculate is higher than 100. I've been working with a
data set of 500 rows x 700 variables. The code gets really slow when
the number of PC to calculate is for example 600 (why that number of
components?because I need them to detect outliers using another
algorithm). In my old laptop running Win XP and R 2.7.0 (1GB RAM) it
takes around 6 or 7 minutes. That shouldn't be a problem for one
analysis, but when cross-validation is added the time increases
severely.Although there are several examples on the R help list
giving some with 'hints' to improve effciency the truth is that I
don't know (or I can't see it) the part of the code that can be
improved (but it is clear that the bottle neck is the for and while
loops). I would really appreciate any ideas/comments/etc...
Thanks
#
pca.nipals - function(X, ncomp, iter = 50, toler = sqrt(.Machine$double.eps))
# X...data matrix, ncomp...number of components,
# iter...maximal number of iterations per component,
# toler...precision tolerance for calculation of components
{
Xh - scale(X, center = TRUE, scale = FALSE)
nr - 0
T - NULL; P - NULL # matrix of scores and loadings
for (h in 1:ncomp)
{
th - Xh[, 1]
ende - FALSE
while (!ende)
{
nr - nr + 1
ph - t(crossprod(th, Xh) * as.vector(1 /
crossprod(th)))
ph - ph * as.vector(1/sqrt(crossprod(ph)))
thnew - t(tcrossprod(t(ph), Xh) *
as.vector(1/(crossprod(ph
prec - crossprod(th-thnew)
th - thnew
if (prec = (tol^2)) ende - TRUE
if (it = nr) ende - TRUE # didn't converge
}
Xh - Xh - tcrossprod(th)
T - cbind(T, th); P - cbind(P, ph)
nr - 0
}
list(T = T, P = P)
}
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Re: [R] using the sink() function in a for-look
On 1/05/2008, at 2:32 PM, Tony Dell wrote:
hi all,
i wanted to use the sink function to sequentially output regression
summaries within a for-loop. i must have something wrong somewhere
(or be
using the sink function incorrectly), but can anyone help?
snip
You need to ***print*** the output you want to see.
Typing ``x'' in an interactive environment causes the value of
x to be printed. But in a non-interactive environment (inside
a function such as source() or a for loop) it doesn't, and
you need to say ``print(x)''.
Trap for young players.
cheers,
Rolf Turner
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
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[R] (no subject)
hi all,
i wanted to use the sink function to sequentially output regression
summaries within a for-loop. i must have something wrong somewhere (or be
using the sink function incorrectly), but can anyone help?
the code I am using is:
where data.x is a data.frame of independents, and data.y is a data.frame of
dependents.
for (i in 1:length(data.y)){
taxa.i - names(data.y[i])
jpeg(file=paste(taxa.i,.multiple.regress.residuals.1.RAW.jpeg,sep=),
quality=90, width=1000, height=1000)
par(mfrow=c(2,2), lwd=0.5, mar=c(3,4,3,1), bty=o, oma=c(0,3,2,0))
attach(data.x)
mult.reg.raw.i - lm(data.y[,i] ~ CURRENT + LITTER + PERCURR + SUBST)
plot(mult.reg.raw.i, ask=FALSE)
mtext(names(data.y[i]), side=3, line=-1.5, adj=0.48, cex=0.75,
outer=TRUE)
dev.off()
sink(mulptiple regression - summary RAW.txt, append=TRUE)
summary(mult.reg.raw.i)
sink()
}
cheers,
tony
__
tony dell
department of marine and tropical biology
james cook university
townsville, qld 4811 australia
[p] 07 47815751 or 47814520
[e] [EMAIL PROTECTED]
[skype] anphony
Checked by AVG.
6:27 PM
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[R] Forecasting observations in ARFIMA
I would like to compute the next 15 observations for an ARFIMA(2,1,0) model along with confidence intervals. Can someone provide code? Many thanks. Jill [[elided Yahoo spam]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] efficient code - yet another question
Dear list members;
The code given below corresponds to the PCA-NIPALS (principal
component analysis) algorithm adapted from the nipals function in the
package chemometrics. The reason for using NIPALS instead of SVD is
the ability of this algorithm to handle missing values, but that's a
different story. I've been trying to find a way to improve (if
possible) the efficiency of the code, especially when the number of
components to calculate is higher than 100. I've been working with a
data set of 500 rows x 700 variables. The code gets really slow when
the number of PC to calculate is for example 600 (why that number of
components?because I need them to detect outliers using another
algorithm). In my old laptop running Win XP and R 2.7.0 (1GB RAM) it
takes around 6 or 7 minutes. That shouldn't be a problem for one
analysis, but when cross-validation is added the time increases
severely.Although there are several examples on the R help list
giving some with 'hints' to improve effciency the truth is that I
don't know (or I can't see it) the part of the code that can be
improved (but it is clear that the bottle neck is the for and while
loops). I would really appreciate any ideas/comments/etc...
Thanks
#
pca.nipals - function(X, ncomp, iter = 50, toler = sqrt(.Machine$double.eps))
# X...data matrix, ncomp...number of components,
# iter...maximal number of iterations per component,
# toler...precision tolerance for calculation of components
{
Xh - scale(X, center = TRUE, scale = FALSE)
nr - 0
T - NULL; P - NULL # matrix of scores and loadings
for (h in 1:ncomp)
{
th - Xh[, 1]
ende - FALSE
while (!ende)
{
nr - nr + 1
ph - t(crossprod(th, Xh) * as.vector(1 /
crossprod(th)))
ph - ph * as.vector(1/sqrt(crossprod(ph)))
thnew - t(tcrossprod(t(ph), Xh) *
as.vector(1/(crossprod(ph
prec - crossprod(th-thnew)
th - thnew
if (prec = (tol^2)) ende - TRUE
if (it = nr) ende - TRUE # didn't converge
}
Xh - Xh - tcrossprod(th)
T - cbind(T, th); P - cbind(P, ph)
nr - 0
}
list(T = T, P = P)
}
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Re: [R] using the sink() function in a for-look
Tony Dell [EMAIL PROTECTED] [Thu, May 01, 2008 at 04:32:23AM CEST]:
hi all,
i wanted to use the sink function to sequentially output regression
summaries within a for-loop. i must have something wrong somewhere (or be
using the sink function incorrectly), but can anyone help?
the code I am using is:
Please use code and data which is reproducible for us. As we don't have
access to your data, we'd have to construct some of our own.
This code, however, has the same effect:
for (i in 1:100) {
sink(./sometext.txt, append=TRUE)
summary(rnorm(80))
sink()}
When you do the following:
for (i in 1:100) {
summary(rnorm(80))}
what output do you get?
And all this output is redirected to your file by sink(), so it works
as expected.
--
Johannes Hüsing There is something fascinating about science.
One gets such wholesale returns of conjecture
mailto:[EMAIL PROTECTED] from such a trifling investment of fact.
http://derwisch.wikidot.com (Mark Twain, Life on the Mississippi)
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Re: [R] using the sink() function in a for-look
bingo. thanks Ralph.
__
tony dell
department of marine and tropical biology
james cook university
townsville, qld 4811 australia
[p] 07 47815751 or 47814520
[e] [EMAIL PROTECTED]
[skype] anphony
-Original Message-
From: Rolf Turner [mailto:[EMAIL PROTECTED]
Sent: Thursday, 1 May 2008 1:20 PM
To: Tony Dell
Cc: r-help@r-project.org
Subject: Re: [R] using the sink() function in a for-look
On 1/05/2008, at 2:32 PM, Tony Dell wrote:
hi all,
i wanted to use the sink function to sequentially output regression
summaries within a for-loop. i must have something wrong somewhere (or
be using the sink function incorrectly), but can anyone help?
snip
You need to ***print*** the output you want to see.
Typing ``x'' in an interactive environment causes the value of x to be
printed. But in a non-interactive environment (inside a function such as
source() or a for loop) it doesn't, and you need to say ``print(x)''.
Trap for young players.
cheers,
Rolf Turner
##
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