Re: [R] R CMD BATCH command
On Tue, 5 Jun 2007, Peter Dalgaard wrote: Austin, Peter wrote: The version of R on our unix system has been updated to version 2.5.0. When I type the following command at the unix prompt: 'R CMD BATCH filename' I receive the following error message: Error in Sys.unsetenv(R_BATCH) : 'Sys.unsetenv' is not available on this system Execution halted. 'R CMD BATCH filename' used to work with the prior version of R that I had installed (version 2.2.0). Is there something that I need to modify for it to work now? Thanks, Peter A similar problem was found on an old version of Solaris and discussed on this very list on May 14 (use the list archive and look for the thread started by Simon Penel). This could be similar to your problem (but you omitted to tell us what system you were on). And that problem has been fixed in R-patched, so please try R-patched. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] correspondence analysis
Hello, I am new to R and I have a question about the difference between correspondence analysis in R and SPSS. This is the input table I am working with (4 products and 18 attributes): mytable 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 1 15 11 20 4 14 7 1 2 1 4 12 12 17 19 11 20 9 10 2 19 18 14 14 16 4 14 11 11 15 22 19 22 16 21 19 15 16 3 16 13 10 9 15 4 10 7 11 13 18 17 14 14 16 16 13 11 4 21 18 16 14 20 6 12 14 14 17 23 20 19 18 21 18 19 18 I found the function corresp() in the package MASS, but the results are different from the output in SPSS. Also, I don't understand the coordinates; in the biplot I cannot find a -2 limit for example from the first product on any of the x axes. Rresult - corresp(mytable, nf=2) Rresult First canonical correlation(s): 0.20823373 0.04840434 Row scores: [,1][,2] 1 -2.0838424 0.01237391 2 0.4901559 1.51190922 3 0.4463375 -0.72631884 4 0.4946202 -0.87620237 Column scores: [,1][,2] 1 -0.29870621 -0.32282847 2 0.04851042 0.73570925 3 -1.79584803 0.04537505 4 1.10904141 1.21563470 5 -0.35048140 -1.28883782 6 -1.80044987 -1.99532989 7 1.96987033 1.89925225 8 1.59225423 -0.42249233 9 1.96534193 -2.01733348 10 1.29641406 -0.67857429 11 0.33216906 0.05071065 12 0.12620111 -0.30281237 13 -0.59997905 1.90985228 14 -1.18972391 -0.46697874 15 0.34099302 0.55835672 16 -1.07356465 0.44743219 17 0.32569239 -1.21741819 18 0.07133121 0.20777127 Thank you for your patience. am [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rJava installation under linux: configuration failed
Which java have you installed? ( java -version ) You need a Sun Java and better is a 1.5 series Java, JGR seems to have some problem with the new 1.6 series. And you need the JDK, not the JRE. You can google how to do those installations on suse linux. Stefan Original Message Subject: [R] rJava installation under linux: configuration failed From: zhihua li [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Date: 05.06.2007 19:55 Hi netter, Recently I was trying to install rJava. The operating system is suse 10.0, and the R versionis 2.5.0. Following the instructions of R Wiki for rJava, I did configuration first: R CMD javareconf and then it showed a series of information, from what it seems that java is in the system and the configuration succeeded. Then I tried to install rJava: install.packages(rJava) following which rJava was downloaded and being installed, but during the last test step it said: can't complie a simple JNL program. Configuration Failed! Did I do something wrong? Or there's something I should do that I didn't? Thanks a lot! Sincerely Yours: Zhihua Li __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.472 / Virus Database: 269.8.9/834 - Release Date: 05.06.2007 14:38 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] multiple plot in odfWeave
Hello Max,
Thanks for your help.
So, I changed the = with
carte2, echo = FALSE, results=XML, fig = TRUE=
So , now I can open the output file .odt, but it plot only the last map
and not all the maps.
But on the R graphics window, i can see the several maps overwrite each
other.
Maybe there is something wrong in my loop?
I attached to this message a file with 2 projects, on different points
to map foreach projects
Thanks,
Laurence
here is the code:
Connection, echo = FALSE, results=XML =
library(RMySQL)
library(maps)
library(mapdata)
library(spmaps)
library(grid)
library(plotrix)
drv - dbDriver(MySQL)
con - dbConnect(drv, user=user, password=, dbname=Aquagenome,
host=toulouse.inra.fr, client.flag=CLIENT\_MULTI\_STATEMENTS)
@
Liste des projets:
carte2, echo = FALSE, results=XML, fig = TRUE=
lp - dbSendQuery(con, SELECT nom FROM projets)
projets - fetch(lp)
nbr=dim(projets)[1]
for (i in 1:nbr)
{
monprojet=(projets)[i,1]
myquery=paste(SELECT s.longitude, s.latitude, o.orgashort FROM
organisme o JOIN scientist s ON o.codeorga=s.codeorga JOIN partenaire p
ON p.codescientist=s.codescientist JOIN projets ON
projets.codeproj=p.codeproj WHERE projets.nom LIKE \',monprojet,\'
ORDER BY s.longitude, sep=)
rs - dbSendQuery(con, myquery)
df - fetch(rs)
map(database=world, xlim=c(-15,40),ylim=c(27,71), fill=TRUE,
col=#CC)
points(df$longitude,df$latitude, col=red, pch=16)
spread.labels(df$longitude,df$latitude,df$orgashort,0,bg=#CC,
border=TRUE, cex=0.8, xpad=0.5, ypad=0.8, font=6)
}
@
toto
Here is the result of the sessionInfo()
sessionInfo()
R version 2.5.0 (2007-04-23)
i686-pc-linux-gnu
locale:
[EMAIL PROTECTED];LC_NUMERIC=C;[EMAIL PROTECTED];[EMAIL PROTECTED];[EMAIL
PROTECTED];[EMAIL PROTECTED];[EMAIL
PROTECTED];LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL
PROTECTED];LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets
[7] methods base
other attached packages:
plotrix spmaps sp mapdata maps RMySQL DBI odfWeave
2.2 0.1-4 0.9-13 2.0-20 2.0-36 0.5-11 0.2-3 0.4.9
lattice
0.15-4
Kuhn, Max a écrit :
Laurence,
I haven't seen any issues like this. Can you:
1. Send the results of sessionInfo()
2. Try using carte2, echo = FALSE, results= xml, fig = TRUE=. It
sounds like the text being written to the xml file is not valid xml.
This could be the case if results != xml.
3. If that doesn't work, send me a data object and the odt file so
that I can try to reproduce the error?
Max
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Re: [R] odfTable
Great,
I will waiting for the new version... with the nice documentation!
thank you,
Laurence.
Kuhn, Max a écrit :
Sarah and Laurence,
A few comments:
1. The default background color for columns is horrible. I've changed
to white it in the upcoming version.
2. In the next version (in 1-2 weeks), I have a fairly long document
that goes into much more detail about the specific styles that can be
changed and examples.
3. To simply Sarah's approach, add the style definition via
setStyleDefs(existingStyles) as suggested. Then, just before making the
table, simply use
current - getStyles()
currrent$header - newStyle1
setStyles(current)
then produce the table. Unless I'm not understanding what you want,
you shouldn't need to use tableStyles.
If anyone wants the new version while I finish a few of the
documentation pages, send me an email off-list and I'll send it to you.
Thanks,
Max
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Re: [R] rJava installation under linux: configuration failed
On Wed, 6 Jun 2007, Stefan Grosse wrote: Which java have you installed? ( java -version ) You need a Sun Java and better is a 1.5 series Java, JGR seems to have some problem with the new 1.6 series. And you need the JDK, not the JRE. Precautionary note: the '1.5 series Java' (aka Java 5) does not work with JNI (and hence rJava) on some platforms, including AMD64 Linux. You can google how to do those installations on suse linux. It can be tricky, especially if you need a later Java than your OS version supports. Stefan Original Message Subject: [R] rJava installation under linux: configuration failed From: zhihua li [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Date: 05.06.2007 19:55 Hi netter, Recently I was trying to install rJava. The operating system is suse 10.0, and the R versionis 2.5.0. Following the instructions of R Wiki for rJava, I did configuration first: R CMD javareconf and then it showed a series of information, from what it seems that java is in the system and the configuration succeeded. Then I tried to install rJava: install.packages(rJava) following which rJava was downloaded and being installed, but during the last test step it said: can't complie a simple JNL program. Configuration Failed! Did I do something wrong? Or there's something I should do that I didn't? Thanks a lot! Sincerely Yours: Zhihua Li __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.472 / Virus Database: 269.8.9/834 - Release Date: 05.06.2007 14:38 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] spgrass6 and aggregation
Dear all, I am exporting grass map into R thanks to the very useful spgrass6 package. library(spgrass6) # I have 3 map I am working with a MASK map of a specific area. # 1) a landuse map landuse-readRAST6(landuse_mapname_in_grass) # 2) a catchment map which divide the area in several catchements catchment-readRAST6(catchement_mapname_in_grass) # 3) a precipitation map precipitation-readRAST6(precipitation_mapname_in_grass) # then I would like to sum the precipitation spatialy over each catchment and landuse. So, first I cbind all maps with cbind MAP-cbind(Dear all, __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rJava installation under linux: configuration failed
Precautionary note: the '1.5 series Java' (aka Java 5) does not work with JNI (and hence rJava) on some platforms, including AMD64 Linux. You can google how to do those installations on suse linux. It can be tricky, especially if you need a later Java than your OS version supports. Since the Suse Version is 10.0 there is an installation repository provided by Suse: http://download.opensuse.org/distribution/SL-10.0-OSS/inst-source-java/ you can add that via Yast and this should then provide Java 5 JDK. (provided that you are on the correct platform ...) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] opening vignetten
Dear R-Users, I have a quite stupid question. I load the GO-package with the command require(GO). Now I want to read the corresponding vignetten but I forgot the command for opening it. Please help me, Corinna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Svar: Re: help with simple R-question
thanks, that works great!! just have another thing...i the same area What if the class is list instead of array, how can you name the first unrecognized column? Rina John Kane [EMAIL PROTECTED] 06/05/07 3:17 --- Rina Miehs [EMAIL PROTECTED] wrote: hello what do i write for R to recognize both columns? In the R-script downunder you can see that i use tapply to get my information out of my data, and then i need to use it as a dataframe with both columns! It is like R is using the first column as an observationnumber or something, how can i change that?? It is using the names of the variables as rownames. try n.ant - names(antall) antal1 - data.frame(n.antal1, antal1) antal1 -tapply(l1$omlob1,l1$farid,length) antal1 1437987 1100 10007995 10008295 10008792 10010203 10018703 10033401 2 3 3 2 3 1 1 2 10048900 10050492 10055897 10076495 10081892 10094801 10100692 10101395 3 1 3 3 6 2 5 20 10101495 10101595 10104692 10113592 10113697 10114297 10120797 10120897 1 5 4 2 6 11 1 4 10121697 10121897 10121997 10133592 10142892 10142995 10146495 10150497 16 3 6 1 1 6 4 4 10150692 10157092 10157292 10164792 10170892 10171795 10171895 10172300 5 2 4 4 4 4 4 1 10175195 10187802 10192499 10192897 10198295 10200493 10201693 10211593 1 2 2 3 5 1 3 5 antal1 - data.frame(antal1) antal1 antal1 14379872 1100 3 10007995 3 10008295 2 10008792 3 10010203 NA 10018703 NA 10033401 2 10048900 3 10050492 1 10055897 3 10076495 3 10081892 6 10094801 2 10100692 5 Thanks Rina [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R ( http://www.r/ )-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Get news delivered with the All new Yahoo! Mail. Enjoy RSS feeds right on your Mail page. Start today at http://mrd.mail.yahoo.com/try_beta?.intl=ca [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] naiveBayes other than e1071
Dear Max,
thanks for your work on this!
I totally agree in all points and have added some check for zero
variances to my working copy of NaiveBayes.default() which will be
published in the next klaR release.
if(!usekernel){
temp - apply(sapply(tables, function(x) x[,2]), 2,
function(x) any(!x))
if(any(temp))
stop(Zero variances for at least one class in variables: ,
paste(names(tables)[temp], collapse=, ))
}
Thanks again,
Uwe
Kuhn, Max wrote:
Saeed and Uwe,
The underlying problem is the distribution of the data. For example:
table(x.x[,91], y.y)
y.y
01
0.000675027 24120
0.0021848920 481
When the function tries to estimate the distribution of this feature for
each class, it gets:
nb$tables[[91]]
[,1] [,2]
0 0.0006750270
1 0.0021848920
(Saeed - column 1 contains the means for each class and column 2
contains the variances)
For class 0, if a new data point for this variable has a value of
0.000675027, then dnorm(0.000675027, 0.000675027, 0) = Inf (all other
points have density values of zero). When the data are normalized by
p(x), this produces a NaN. A few of the predictors have this problem.
There should probably be some sort of check for this, but that might be
hard to do when usekernel = TRUE. Uwe - do you agree and/or have ideas?
Good news Saeed! Just use variable 91 and you don't need a model.
Seriously, you might want to think about these data a bit. Many of them
are highly skewed and have a large point mass at zero. Modeling the
conditional probabilities using a normal distribution may not be the
best idea.
Max
-Original Message-
From: Uwe Ligges [mailto:[EMAIL PROTECTED]
Sent: Tuesday, June 05, 2007 3:56 PM
To: Saeed Abu Nimeh
Cc: Kuhn, Max; r-help@stat.math.ethz.ch
Subject: Re: [R] naiveBayes other than e1071
Saeed Abu Nimeh wrote:
Max,
Thanks. I have tried it but i keep getting an error:
Error in as.vector(x, mode) : invalid argument 'mode'
Do I have to do something specific when using the class column. I
tried
both y.y-as.vector and y.y-as.factor.
dread-read.table('dataset.csv',sep=,)
x.x-as.matrix(dread[,2:256])
y.y-as.vector(dread[,1])
nb- NaiveBayes(x=x.x,grouping=y.y)
pred.nb-predict(nb)
Error in as.vector(x, mode) : invalid argument 'mode'
Please tell us (according to the posting guide): Which version of R?
Which version of klaR? Example data that reproduce the error?
Uwe Ligges
Thanks,
Saeed
Kuhn, Max wrote:
Saeed,
There is a version in the klaR package. I recently submitted a change
to
the predict function that may be related to your problem.
If:
1. the posterior probabilities (apart from the prior) are being
approximated by the product of the p(x_i|y_j) and
2. a lot of predictors are being used
then posterior probabilities may have values of absolute zero.
When the approximation is used, the approximate posterior
probabilities
are normalized by their sum (which is zero in such cases).
The patch in klaR uses the product of the conditional divided by the
marginal of x_i (per the true formula). I haven't seen the problem
occur
with this patch.
HTH,
Max
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Saeed Abu
Nimeh
Sent: Monday, June 04, 2007 2:45 PM
To: r-help@stat.math.ethz.ch
Subject: [R] naiveBayes other than e1071
Hi List,
Is there a naiveBayes interface other than the one in e1071 package.
For
some reason on certain datasets all predicted values are NaN, but it
predicts well on others.
Thanks,
Saeed
---
model - naiveBayes(x.train, y.train, laplace = 3)
pred - predict(model,x.test,type=raw)
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[R] list
hello, I wanna know how to create a list of list if it's possible and if it isn't possible how to do without. thanks. _ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] opening vignetten
?vignette Original Message Subject: [R] opening vignetten From: Schmitt, Corinna [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Date: 06.06.2007 10:41 Dear R-Users, I have a quite stupid question. I load the GO-package with the command require(GO). Now I want to read the corresponding vignetten but I forgot the command for opening it. Please help me, Corinna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] list
There's no special method, just create a list in the usual way. For example: l1-list(a=letters[1:5],b=letters[6:10]) l1 $a [1] a b c d e $b [1] f g h i j l2-list(c=LETTERS[1:5],d=LETTERS[6:10]) l2 $c [1] A B C D E $d [1] F G H I J l3-list(l1,l2) l3 [[1]] [[1]]$a [1] a b c d e [[1]]$b [1] f g h i j [[2]] [[2]]$c [1] A B C D E [[2]]$d [1] F G H I J On 06/06/07, elyakhlifi mustapha [EMAIL PROTECTED] wrote: hello, I wanna know how to create a list of list if it's possible and if it isn't possible how to do without. thanks. _ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] spgrass6 and aggregation (bis)
Dear all, I have some additionale question concerning the spgrass6 package. * When you set a region in GRASS, does the readGRASS6 function in R only load data contained in the zoomed region or the whole map ? * When you have a MASK map in grass, does the readGRASS6 function in R only load data contained inside the MASK area ? Could this be the problem ? Thanks, Jessica 3 Dear all, I am exporting grass map into R thanks to the very useful spgrass6 package. library(spgrass6) # I have 3 map I am working with a MASK map of a specific area. # 1) a landuse map landuse-readRAST6(landuse_mapname_in_grass) # 2) a catchment map which divide the area in several catchements catchment-readRAST6(catchement_mapname_in_grass) # 3) a precipitation map precipitation-readRAST6(precipitation_mapname_in_grass) # then I would like to sum the precipitation spatialy over each catchment and landuse. So, first I cbind all maps with cbind MAP-cbind(landuse,catchment,precipitation) # then I use the aggregate function SUM-aggregate(MAP[3],by=list(MAP[1],MAP[2]),sum,na.rm=TRUE) # here is the problem !!! Error in as.vector(x, mode) : invalid argument 'mode' I don't find any idea to solve this... Does anyone has a suggestion ?? Thanks in advance Jess __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] list
Sure you can. list(list(), list(), list()) library(fortunes) fortune(Yoda) Evelyn Hall: I would like to know how (if) I can extract some of the information from the summary of my nlme. Simon Blomberg: This is R. There is no if. Only how. -- Evelyn Hall and Simon 'Yoda' Blomberg R-help (April 2005) Cheers, 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 Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens elyakhlifi mustapha Verzonden: woensdag 6 juni 2007 10:59 Aan: R-help@stat.math.ethz.ch Onderwerp: [R] list hello, I wanna know how to create a list of list if it's possible and if it isn't possible how to do without. thanks. __ ___ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Svar: Re: help with simple R-question
--- Rina Miehs [EMAIL PROTECTED] wrote: thanks, that works great!! just have another thing...i the same area What if the class is list instead of array, how can you name the first unrecognized column? I am not sure that I understand the question. You don't really have an unrecognised column in the dataframe but an array of rownames ( I don't know how they are stored). I think you can do the same thing as you did for the data.frame but as I say, I am not sure I understand the question. Would you post a little example? Rina John Kane [EMAIL PROTECTED] 06/05/07 3:17 --- Rina Miehs [EMAIL PROTECTED] wrote: hello what do i write for R to recognize both columns? In the R-script downunder you can see that i use tapply to get my information out of my data, and then i need to use it as a dataframe with both columns! It is like R is using the first column as an observationnumber or something, how can i change that?? It is using the names of the variables as rownames. try n.ant - names(antall) antal1 - data.frame(n.antal1, antal1) antal1 -tapply(l1$omlob1,l1$farid,length) antal1 1437987 1100 10007995 10008295 10008792 10010203 10018703 10033401 2 3 3 2 3 1 1 2 10048900 10050492 10055897 10076495 10081892 10094801 10100692 10101395 3 1 3 3 6 2 5 20 10101495 10101595 10104692 10113592 10113697 10114297 10120797 10120897 1 5 4 2 6 11 1 4 10121697 10121897 10121997 10133592 10142892 10142995 10146495 10150497 16 3 6 1 1 6 4 4 10150692 10157092 10157292 10164792 10170892 10171795 10171895 10172300 5 2 4 4 4 4 4 1 10175195 10187802 10192499 10192897 10198295 10200493 10201693 10211593 1 2 2 3 5 1 3 5 antal1 - data.frame(antal1) antal1 antal1 14379872 1100 3 10007995 3 10008295 2 10008792 3 10010203 NA 10018703 NA 10033401 2 10048900 3 10050492 1 10055897 3 10076495 3 10081892 6 10094801 2 10100692 5 Thanks Rina [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R ( http://www.r/ )-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Get news delivered with the All new Yahoo! Mail. Enjoy RSS feeds right on your Mail page. Start today at http://mrd.mail.yahoo.com/try_beta?.intl=ca __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] list
--- elyakhlifi mustapha [EMAIL PROTECTED] wrote: hello, I wanna know how to create a list of list if it's possible and if it isn't possible how to do without. thanks. Why? The question is not clear and could mean several things. Can you explain a bit? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Svar: Re: help with simple R-question
The left column is boar id number, and the right is the random effect estimate. I need the numbers in the left column when i merge far1 together with other data.frames based on the id numbers. When i use ranef the output is the class list and R only sees the intercepts, but i need a data.frame with 'boar id' and 'niveau', two columns not just one... fx far1 - ranef(resultat1)[1] far1 $farid (Intercept) 1437987 -3.775851e-03 1100 -3.220044e-03 10007995 1.848914e-02 10008295 -4.583903e-03 10008792 -9.518371e-03 10033401 -7.538132e-03 10048900 1.540309e-02 far1 - as.data.frame(far1) far1 X.Intercept. 1437987 -3.775851e-03 1100 -3.220044e-03 10007995 1.848914e-02 10008295 -4.583903e-03 10008792 -9.518371e-03 10033401 -7.538132e-03 10048900 1.540309e-02 Thanks again Rina John Kane [EMAIL PROTECTED] 06/06/07 11:38 --- Rina Miehs [EMAIL PROTECTED] wrote: thanks, that works great!! just have another thing...i the same area What if the class is list instead of array, how can you name the first unrecognized column? I am not sure that I understand the question. You don't really have an unrecognised column in the dataframe but an array of rownames ( I don't know how they are stored). I think you can do the same thing as you did for the data.frame but as I say, I am not sure I understand the question. Would you post a little example? Rina John Kane [EMAIL PROTECTED] 06/05/07 3:17 --- Rina Miehs [EMAIL PROTECTED] wrote: hello what do i write for R to recognize both columns? In the R-script downunder you can see that i use tapply to get my information out of my data, and then i need to use it as a dataframe with both columns! It is like R is using the first column as an observationnumber or something, how can i change that?? It is using the names of the variables as rownames. try n.ant - names(antall) antal1 - data.frame(n.antal1, antal1) antal1 -tapply(l1$omlob1,l1$farid,length) antal1 1437987 1100 10007995 10008295 10008792 10010203 10018703 10033401 2 3 3 2 3 1 1 2 10048900 10050492 10055897 10076495 10081892 10094801 10100692 10101395 3 1 3 3 6 2 5 20 10101495 10101595 10104692 10113592 10113697 10114297 10120797 10120897 1 5 4 2 6 11 1 4 10121697 10121897 10121997 10133592 10142892 10142995 10146495 10150497 16 3 6 1 1 6 4 4 10150692 10157092 10157292 10164792 10170892 10171795 10171895 10172300 5 2 4 4 4 4 4 1 10175195 10187802 10192499 10192897 10198295 10200493 10201693 10211593 1 2 2 3 5 1 3 5 antal1 - data.frame(antal1) antal1 antal1 14379872 1100 3 10007995 3 10008295 2 10008792 3 10010203 NA 10018703 NA 10033401 2 10048900 3 10050492 1 10055897 3 10076495 3 10081892 6 10094801 2 10100692 5 Thanks Rina [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R ( http://www.r/ ) ( http://www.r/ )-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Get news delivered with the All new Yahoo! Mail. Enjoy RSS feeds right on your Mail page. Start today at http://mrd.mail.yahoo.com/try_beta?.intl=ca Be smarter than spam. See how smart SpamGuard is at giving junk email the boot with the All-new Yahoo! Mail at http://mrd.mail.yahoo.com/try_beta?.intl=ca [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Svar: Re: help with simple R-question
[EMAIL PROTECTED] napsal dne 06.06.2007 10:56:18: thanks, that works great!! just have another thing...i the same area What if the class is list instead of array, how can you name the first unrecognized column? Hi look in some intro manual and learn about R data structures. Matrix, array, vector, data.frame, list and some others have some distinct features and they sometimes can be interchanged and sometimes not. To learn how objects are organised see str(), class(), typeof(), mode(). Regards Petr Rina John Kane [EMAIL PROTECTED] 06/05/07 3:17 --- Rina Miehs [EMAIL PROTECTED] wrote: hello what do i write for R to recognize both columns? In the R-script downunder you can see that i use tapply to get my information out of my data, and then i need to use it as a dataframe with both columns! It is like R is using the first column as an observationnumber or something, how can i change that?? It is using the names of the variables as rownames. try n.ant - names(antall) antal1 - data.frame(n.antal1, antal1) antal1 -tapply(l1$omlob1,l1$farid,length) antal1 1437987 1100 10007995 10008295 10008792 10010203 10018703 10033401 2 3 3 2 3 1 1 2 10048900 10050492 10055897 10076495 10081892 10094801 10100692 10101395 3 1 3 3 6 2 5 20 10101495 10101595 10104692 10113592 10113697 10114297 10120797 10120897 1 5 4 2 6 11 1 4 10121697 10121897 10121997 10133592 10142892 10142995 10146495 10150497 16 3 6 1 1 6 4 4 10150692 10157092 10157292 10164792 10170892 10171795 10171895 10172300 5 2 4 4 4 4 4 1 10175195 10187802 10192499 10192897 10198295 10200493 10201693 10211593 1 2 2 3 5 1 3 5 antal1 - data.frame(antal1) antal1 antal1 14379872 1100 3 10007995 3 10008295 2 10008792 3 10010203 NA 10018703 NA 10033401 2 10048900 3 10050492 1 10055897 3 10076495 3 10081892 6 10094801 2 10100692 5 Thanks Rina [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R ( http://www.r/ )-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Get news delivered with the All new Yahoo! Mail. Enjoy RSS feeds right on your Mail page. Start today at http://mrd.mail.yahoo.com/try_beta?.intl=ca [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] spgrass6 and aggregation (bis)
On Wed, 6 Jun 2007 [EMAIL PROTECTED] wrote: Dear all, I have some additionale question concerning the spgrass6 package. * When you set a region in GRASS, does the readGRASS6 function in R only load data contained in the zoomed region or the whole map ? readRAST6() uses the current region, readVECT6() should not clip to the current region. * When you have a MASK map in grass, does the readGRASS6 function in R only load data contained inside the MASK area ? MASK is respected (in spearfish): r.mask input=rushmore d.rast elevation.dem R library(spgrass6) el - readRAST6(elevation.dem) summary(el) image(el) Could this be the problem ? No, the problem was that you did not pay attention to the class of the data objects you were reading. You could have done: my_SGDF - readRAST6(c(landuse_mapname_in_grass, catchement_mapname_in_grass, precipitation_mapname_in_grass), cat=c(TRUE, TRUE, FALSE)) treating the whole as a single SpatialGridDataFrame, and the first two maps as factors (categorical). Please remember that class(), summary(), image(), and other methods let you look at the data you have read - here I would certainly do: summary(my_SGDF) image(my_SGDF, precipitation_mapname_in_grass) You can then try: my_DF - as(my_SGDF, data.frame) aggregate(my_DF, by=list(my_DF$catchement_mapname_in_grass, my_DF$landuse_mapname_in_grass), sum, na.rm=TRUE) although I'm not sure whether this is what you need. There are two mailing lists that are better suited to this question, R-sig-geo on the R side, and STATGRASS on the GRASS side, both with a fair number of experienced helpers. Thanks, Jessica 3 Dear all, I am exporting grass map into R thanks to the very useful spgrass6 package. library(spgrass6) # I have 3 map I am working with a MASK map of a specific area. # 1) a landuse map landuse-readRAST6(landuse_mapname_in_grass) # 2) a catchment map which divide the area in several catchements catchment-readRAST6(catchement_mapname_in_grass) # 3) a precipitation map precipitation-readRAST6(precipitation_mapname_in_grass) # then I would like to sum the precipitation spatialy over each catchment and landuse. So, first I cbind all maps with cbind MAP-cbind(landuse,catchment,precipitation) # then I use the aggregate function SUM-aggregate(MAP[3],by=list(MAP[1],MAP[2]),sum,na.rm=TRUE) # here is the problem !!! Error in as.vector(x, mode) : invalid argument 'mode' I don't find any idea to solve this... Does anyone has a suggestion ?? Thanks in advance Jess __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Refactor all factors in a data frame
Hilmar Berger hilmar.berger at imise.uni-leipzig.de writes:
...
So, is there any way in drop the unused factor levels from *all* factors
of a data frame without import/export ?
There is a generic drop.levels in gdata. Here is part of its help page:
\code{drop.levels} is a generic function, where default method does
nothing, while method for factor \code{s} drops all unused levels.
There are also convenient methods for \code{list} and \code{data.frame},
where all unused levels are dropped in all factors (one by one) in a
\code{list} or a \code{data.frame}.
Gregor
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Re: [R] correspondence analysis
Artem Mariupol artem.mariupol at gmail.com writes: Hello, I am new to R and I have a question about the difference between correspondence analysis in R and SPSS. This is the input table I am working with (4 products and 18 attributes): mytable 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 1 15 11 20 4 14 7 1 2 1 4 12 12 17 19 11 20 9 10 2 19 18 14 14 16 4 14 11 11 15 22 19 22 16 21 19 15 16 3 16 13 10 9 15 4 10 7 11 13 18 17 14 14 16 16 13 11 4 21 18 16 14 20 6 12 14 14 17 23 20 19 18 21 18 19 18 I found the function corresp() in the package MASS, but the results are different from the output in SPSS. Also, I don't understand the coordinates; in the biplot I cannot find a -2 limit for example from the first product on any of the x axes. At a quick look, there is nothing strange in the result. Have you contacted SPSS and asked them to explain their deviant results? It seems that biplot.correspondence is undocumented. However, it has argument 'type' which defaults to symmetric, other alternative being rows and columns. Intelligent guess is that this selects the scaling of row and column scores, and type=symmetric scales both. By selecting type=columns, only columns are scaled and the -2 value for a row will be displayed (which proves that the guess was correct). I don't have a clue how SPSS scales results, but I guess that the differences in the results may be due to different scalings. Function corresp gives you weighted orthonormal row and column scores, but scales these in the plot like specified. It may be that SPSS does the scaling already in the printout (and does not give you the choice of type?). Another possible source of difference is that corresp gives you canonical correlations whereas some other program or function may give you their squares, a.k.a. eigenvalues. Moreover, the sign is arbitrary so that negative and positive scores may be switched between programs. I hope this helps, Jari Oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mandriva Spring 2007 and R
Jonathan, If you are not willing to use the very last version of R, there is always a RPM package for R under Mandriva, called R-base. So that basically, connected as root, just type: urpmi R-base to install it. HTH, Yvonnick Noel U. of Rennes 2 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Svar: Re: help with simple R-question
I think that you have the same situation as before though I have never used ranef(). The boar ids are acting as the row names and are not really part of the data.frame. It just looks like that when R prints the data.frame. Try boars - rownames(far1) far1 - cbind( boars, far1) The results may look a bit funny with two printed columns looking the same but one will be a column in the data.frame and the other will be the row names column. I hope :) --- Rina Miehs [EMAIL PROTECTED] wrote: The left column is boar id number, and the right is the random effect estimate. I need the numbers in the left column when i merge far1 together with other data.frames based on the id numbers. When i use ranef the output is the class list and R only sees the intercepts, but i need a data.frame with 'boar id' and 'niveau', two columns not just one... fx far1 - ranef(resultat1)[1] far1 $farid (Intercept) 1437987 -3.775851e-03 1100 -3.220044e-03 10007995 1.848914e-02 10008295 -4.583903e-03 10008792 -9.518371e-03 10033401 -7.538132e-03 10048900 1.540309e-02 far1 - as.data.frame(far1) far1 X.Intercept. 1437987 -3.775851e-03 1100 -3.220044e-03 10007995 1.848914e-02 10008295 -4.583903e-03 10008792 -9.518371e-03 10033401 -7.538132e-03 10048900 1.540309e-02 Thanks again Rina John Kane [EMAIL PROTECTED] 06/06/07 11:38 --- Rina Miehs [EMAIL PROTECTED] wrote: thanks, that works great!! just have another thing...i the same area What if the class is list instead of array, how can you name the first unrecognized column? I am not sure that I understand the question. You don't really have an unrecognised column in the dataframe but an array of rownames ( I don't know how they are stored). I think you can do the same thing as you did for the data.frame but as I say, I am not sure I understand the question. Would you post a little example? Rina John Kane [EMAIL PROTECTED] 06/05/07 3:17 --- Rina Miehs [EMAIL PROTECTED] wrote: hello what do i write for R to recognize both columns? In the R-script downunder you can see that i use tapply to get my information out of my data, and then i need to use it as a dataframe with both columns! It is like R is using the first column as an observationnumber or something, how can i change that?? It is using the names of the variables as rownames. try n.ant - names(antall) antal1 - data.frame(n.antal1, antal1) antal1 -tapply(l1$omlob1,l1$farid,length) antal1 1437987 1100 10007995 10008295 10008792 10010203 10018703 10033401 2 3 3 2 3 1 1 2 10048900 10050492 10055897 10076495 10081892 10094801 10100692 10101395 3 1 3 3 6 2 5 20 10101495 10101595 10104692 10113592 10113697 10114297 10120797 10120897 1 5 4 2 6 11 1 4 10121697 10121897 10121997 10133592 10142892 10142995 10146495 10150497 16 3 6 1 1 6 4 4 10150692 10157092 10157292 10164792 10170892 10171795 10171895 10172300 5 2 4 4 4 4 4 1 10175195 10187802 10192499 10192897 10198295 10200493 10201693 10211593 1 2 2 3 5 1 3 5 antal1 - data.frame(antal1) antal1 antal1 14379872 1100 3 10007995 3 10008295 2 10008792 3 10010203 NA 10018703 NA 10033401 2 10048900 3 10050492 1 10055897 3 10076495 3 10081892 6 10094801 2 10100692 5 Thanks Rina [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R ( http://www.r/ ) ( http://www.r/ )-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Get news delivered with the All new Yahoo! Mail. Enjoy RSS feeds right on your Mail page. Start today at http://mrd.mail.yahoo.com/try_beta?.intl=ca Be smarter than spam. See how smart SpamGuard is at giving junk http://mrd.mail.yahoo.com/try_beta?.intl=ca === message truncated === __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE
[R] [R-pkgs] Package update: pmml version 1.1.1
Version 1.1.1 of the pmml package (PMML = Predictive Modelling Markup Language) has been uploaded to CRAN. This version adds pmml.lm to generate PMML for linear models (currently, without interactions). The PMML package is part of the Rattle toolkit for data mining. Further information from http://rattle.togaware.com. Regards, Graham ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] New Package on Lancet Surveys of Iraq Mortality
Hello, I have placed a package on CRAN about two surveys of mortality in Iraq that were published in the Lancet. http://cran.at.r-project.org/src/contrib/Descriptions/lancet.iraqmortality.html install.packages(lancet.iraqmortality) ... library(lancet.iraqmortality) Loading required package: foreign ?lancet.iraqmortality vignette(mortality) This is a rough version. Suggestions and feedback are welcome. Dave Kane ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Svar: Re: help with simple R-question
Thanks that helped in the right way:D Thanks alot! Rina John Kane [EMAIL PROTECTED] 06/06/07 1:46 I think that you have the same situation as before though I have never used ranef(). The boar ids are acting as the row names and are not really part of the data.frame. It just looks like that when R prints the data.frame. Try boars - rownames(far1) far1 - cbind( boars, far1) The results may look a bit funny with two printed columns looking the same but one will be a column in the data.frame and the other will be the row names column. I hope :) --- Rina Miehs [EMAIL PROTECTED] wrote: The left column is boar id number, and the right is the random effect estimate. I need the numbers in the left column when i merge far1 together with other data.frames based on the id numbers. When i use ranef the output is the class list and R only sees the intercepts, but i need a data.frame with 'boar id' and 'niveau', two columns not just one... fx far1 - ranef(resultat1)[1] far1 $farid (Intercept) 1437987 -3.775851e-03 1100 -3.220044e-03 10007995 1.848914e-02 10008295 -4.583903e-03 10008792 -9.518371e-03 10033401 -7.538132e-03 10048900 1.540309e-02 far1 - as.data.frame(far1) far1 X.Intercept. 1437987 -3.775851e-03 1100 -3.220044e-03 10007995 1.848914e-02 10008295 -4.583903e-03 10008792 -9.518371e-03 10033401 -7.538132e-03 10048900 1.540309e-02 Thanks again Rina John Kane [EMAIL PROTECTED] 06/06/07 11:38 --- Rina Miehs [EMAIL PROTECTED] wrote: thanks, that works great!! just have another thing...i the same area What if the class is list instead of array, how can you name the first unrecognized column? I am not sure that I understand the question. You don't really have an unrecognised column in the dataframe but an array of rownames ( I don't know how they are stored). I think you can do the same thing as you did for the data.frame but as I say, I am not sure I understand the question. Would you post a little example? Rina John Kane [EMAIL PROTECTED] 06/05/07 3:17 --- Rina Miehs [EMAIL PROTECTED] wrote: hello what do i write for R to recognize both columns? In the R-script downunder you can see that i use tapply to get my information out of my data, and then i need to use it as a dataframe with both columns! It is like R is using the first column as an observationnumber or something, how can i change that?? It is using the names of the variables as rownames. try n.ant - names(antall) antal1 - data.frame(n.antal1, antal1) antal1 -tapply(l1$omlob1,l1$farid,length) antal1 1437987 1100 10007995 10008295 10008792 10010203 10018703 10033401 2 3 3 2 3 1 1 2 10048900 10050492 10055897 10076495 10081892 10094801 10100692 10101395 3 1 3 3 6 2 5 20 10101495 10101595 10104692 10113592 10113697 10114297 10120797 10120897 1 5 4 2 6 11 1 4 10121697 10121897 10121997 10133592 10142892 10142995 10146495 10150497 16 3 6 1 1 6 4 4 10150692 10157092 10157292 10164792 10170892 10171795 10171895 10172300 5 2 4 4 4 4 4 1 10175195 10187802 10192499 10192897 10198295 10200493 10201693 10211593 1 2 2 3 5 1 3 5 antal1 - data.frame(antal1) antal1 antal1 14379872 1100 3 10007995 3 10008295 2 10008792 3 10010203 NA 10018703 NA 10033401 2 10048900 3 10050492 1 10055897 3 10076495 3 10081892 6 10094801 2 10100692 5 Thanks Rina [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R ( http://www.r/ ) ( http://www.r/ ) ( http://www.r/ )-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Get news delivered with the All new Yahoo! Mail. Enjoy RSS feeds right on your Mail page. Start today at http://mrd.mail.yahoo.com/try_beta?.intl=ca Be smarter than spam. See how smart SpamGuard is at giving junk email the boot with the All-new Yahoo! Mail at http://mrd.mail.yahoo.com/try_beta?.intl=ca
[R] generating many matrices
I'd like to generate many matrices (let's say 100 matrices of 4x4), of which diagonal elements are being drawn from each set of sample of known distribution. What would be the best way? I've been trying to find any previous threads for this topic, but haven't been able to find one. Thanks. Kevin [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R: x-y data
Hello I have an Excel file with x-y data. I saved this file as a cvs file. Then I used the read.table() function to read the data into R. If I have a formula like (x+y)/2, how would I access x and y in R? I have the table named as something. But how do I access the individual columns if I want to plug them into the formula? Thanks -- View this message in context: http://www.nabble.com/R%3A-x-y-data-tf3874502.html#a10978448 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R help
Hi, I wonder whether R can finish the following project: I want to make a chart to represent 10 genes. Each gene has orientation and length. Therefore, a gene can be represented by arrows. Can R be used to draw 10 arrows in one line ? scott - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Neural Net. in R
Hi everyone, I'm a graduate student of engineering, lately introduced with R. and using R for my project and thesis. I'm trying to use R for implementing a neural network regression model and apply it to my database. I found three R packages (AMORE , grnnR , neural) in R website, but their manuals are not really user-friendly in my idea. I was wondering if anyone has a written code in R using any of these packages for a feed-forward back-propagation neural network in R that I can use it. That'll be a remedy for my nightmare which already took quite time from me. I would really appreciate it. Sincerely, Jason. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] name of the variable that will contain the result of a function
Hi everyone, say I have a function called 'foo', which takes the argument arg1. Is there any mechanism that I can use to learn about the variable where foo(arg1) is going to be stored? For example: x - foo(arg1) so, inside foo() I'd like to be able to get the string x. if, foo(arg1) was used insted, I'd like to get NA. thank you very much, b -- Benilton Carvalho PhD Candidate Department of Biostatistics Bloomberg School of Public Health Johns Hopkins University [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] sampling problem - new to R
I have a data set of individual trees and the plots that they are in: Tree Plot 567491 634941 873751 374942 927533 348473 387474 etc... So each plot is represented once for every individual that occurrs in it. Plots get different numbers of rows because there can be a different number of individuals in each plot. I want to make a data frame that consists of one individual from each plot. I would like to randomly choose one individual from each plot that is present in the data set. I will have to do this to multiple data sets which may contain different plots, and may contain up to 1200 plots, so I can't choose the plots by hand. Please help me with this. I'm an ecologist and I'm in Panama, with no one around who is educated in R. Whoever solves this problem for me will be acknowledged in any resulting publications. Thanks! -Claire -- View this message in context: http://www.nabble.com/sampling-problem---new-to-R-tf3872130.html#a10970708 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] p-value from GEE
Hi to all, I found in the R-help archive how to calculate the p-value for a gee result: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/74150.html but there are two questions (I am afraid they are basic questions ...) 1. why is the result multiplicated with 2 2. how could I decide between lower.tail =TRUE and FALSE: example: 2*pnorm(c(1.8691945,0.5882351,2.4903091,1.9287802,2.3172983,2.2092593,2.2625959,1.6395695), lower.tail =TRUE) I did not find anything about lower tail in my books only about one tailed and two tailed. With regards Carmen Jetzt Handykosten senken mit klarmobil - 14 Ct./Min.! Hier klicken produkte.shopping.freenet.de/handy_voip_isdn/klarmobil/index.html?pid=73025 [[alternative(swapped) HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R help
On 6/5/07, scott flemming [EMAIL PROTECTED] wrote: Can R be used to draw 10 arrows in one line ? Um, sure. Assuming you actually also want to know how to do it, why don't you take a look at the help for arrows(). Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R help
Yes, but you need to be a bit more specific... When it comes to graphs and drawing lines, there isn't much R can't do... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of scott flemming Sent: 06 June 2007 04:49 To: r-help@stat.math.ethz.ch Subject: [R] R help Hi, I wonder whether R can finish the following project: I want to make a chart to represent 10 genes. Each gene has orientation and length. Therefore, a gene can be represented by arrows. Can R be used to draw 10 arrows in one line ? scott - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R: x-y data
Can you provide an example of your data. Assuming that you have a .cvs file and the column names are 'x' and 'y' and you have used 'read.csv', then you would have: (something$x + something$y) / 2 On 6/5/07, tronter [EMAIL PROTECTED] wrote: Hello I have an Excel file with x-y data. I saved this file as a cvs file. Then I used the read.table() function to read the data into R. If I have a formula like (x+y)/2, how would I access x and y in R? I have the table named as something. But how do I access the individual columns if I want to plug them into the formula? Thanks -- View this message in context: http://www.nabble.com/R%3A-x-y-data-tf3874502.html#a10978448 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Neural Net. in R
Jason,
Your best bet is the nnet package. It is part of the VR bundle, which
may be why you missed it.
The code is well documented and the package is closely tied to two books
(see the references in ?nnet).
Also, it has a predict function, which many of the others do not. This
isn't too big of a deal, but it certainly speaks to good design.
Max
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Ehsan Rasa
Sent: Tuesday, June 05, 2007 11:45 PM
To: r-help@stat.math.ethz.ch
Subject: [R] Neural Net. in R
Hi everyone,
I'm a graduate student of engineering, lately introduced with R. and
using R
for my project and thesis. I'm trying to use R for implementing a neural
network regression model and apply it to my database. I found three R
packages (AMORE , grnnR , neural) in R website, but their manuals
are
not really user-friendly in my idea. I was wondering if anyone has a
written
code in R using any of these packages for a feed-forward
back-propagation
neural network in R that I can use it. That'll be a remedy for my
nightmare
which already took quite time from me.
I would really appreciate it.
Sincerely,
Jason.
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] generating many matrices
Is this what you want?
x - diag(4) # 4x4 matrix
result - list() # list to store the 100 matrices
for (i in 1:100){
diag(x) - runif(4) # fill with random values
result[[i]] - x # save the result
}
On 6/5/07, Keun-Hyung Choi [EMAIL PROTECTED] wrote:
I'd like to generate many matrices (let's say 100 matrices of 4x4), of
which
diagonal elements are being drawn from each set of sample of known
distribution.
What would be the best way? I've been trying to find any previous threads
for this topic, but haven't been able to find one.
Thanks. Kevin
[[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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[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.
Re: [R] sampling problem - new to R
This should create your samples:
x - Tree Plot
567491
634941
873751
374942
927533
348473
387474
x - read.table(textConnection(x), header=TRUE)
for(i in 1:10){ # take 10 sample
# partition data by plot
z - by(x, x$Plot, function(.plot){
.plot[sample(nrow(.plot),1),] # choose a random sample from the
plot
})
z - do.call('rbind', z) # create dataframe
print(z)
}
On 6/5/07, baldeck [EMAIL PROTECTED] wrote:
I have a data set of individual trees and the plots that they are in:
Tree Plot
567491
634941
873751
374942
927533
348473
387474 etc...
So each plot is represented once for every individual that occurrs in it.
Plots get different numbers of rows because there can be a different
number
of individuals in each plot.
I want to make a data frame that consists of one individual from each
plot.
I would like to randomly choose one individual from each plot that is
present in the data set. I will have to do this to multiple data sets
which
may contain different plots, and may contain up to 1200 plots, so I can't
choose the plots by hand.
Please help me with this. I'm an ecologist and I'm in Panama, with no one
around who is educated in R. Whoever solves this problem for me will be
acknowledged in any resulting publications.
Thanks!
-Claire
--
View this message in context:
http://www.nabble.com/sampling-problem---new-to-R-tf3872130.html#a10970708
Sent from the R help mailing list archive at Nabble.com.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] sampling problem - new to R
Claire, Here's one way to do it: # first, generate some sample data to try treedata - cbind.data.frame(Tree=1:25, Plot=sample(1:5, 25, replace=TRUE)) treedata - treedata[order(treedata$Plot),] treedata Tree Plot 1 11 2 21 6 61 9 91 11 111 17 171 18 181 23 231 13 132 16 162 25 252 5 53 10 103 4 44 7 74 8 84 24 244 3 35 12 125 14 145 15 155 19 195 20 205 21 215 22 225 # then randomly choose one tree from each plot # getting a different random set each time sapply(split(treedata$Tree, treedata$Plot), sample, 1) 1 2 3 4 5 2 25 10 4 21 sapply(split(treedata$Tree, treedata$Plot), sample, 1) 1 2 3 4 5 23 13 5 4 14 Hope that solves it for you, Sarah On 6/5/07, baldeck [EMAIL PROTECTED] wrote: I have a data set of individual trees and the plots that they are in: Tree Plot 567491 634941 873751 374942 927533 348473 387474 etc... So each plot is represented once for every individual that occurrs in it. Plots get different numbers of rows because there can be a different number of individuals in each plot. I want to make a data frame that consists of one individual from each plot. I would like to randomly choose one individual from each plot that is present in the data set. I will have to do this to multiple data sets which may contain different plots, and may contain up to 1200 plots, so I can't choose the plots by hand. Please help me with this. I'm an ecologist and I'm in Panama, with no one around who is educated in R. Whoever solves this problem for me will be acknowledged in any resulting publications. Thanks! -Claire -- -- Sarah Goslee http://www.functionaldiversity.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A question about riskmeasures() vs. qgpd() in library(evir)
Dear List, This inquiry probably does not directly pertain to R. I am using library(evir) to learn EVT. Based on my reading of things, it is my understanding that if one wants to calculate quantiles of GPD, one could use either riskmeasures() or qgpd(). However, using data(danish) as an example, the quantile estimates produced by riskmeasures() are considerably different from those produced by qgpd() as follows: library(evir) data(danish) out - gpd(danish, 10) riskmeasures(out, c(0.999, 0.)) p quantile sfall [1,] 0.9990 94.28956 191.3697 [2,] 0. 304.62448 609.3696 qgpd(c(0.999, 0.), out$par.ests[xi], out$par.ests[beta]) [1] 67.22493 200.41271 Any insights would be greatly appreciated. Regards, Jacques platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 5.0 year 2007 month 04 day23 svn rev41293 language R version.string R version 2.5.0 (2007-04-23) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sampling problem - new to R
On Tue, 5 Jun 2007, baldeck wrote:
I have a data set of individual trees and the plots that they are in:
Tree Plot
567491
634941
873751
374942
927533
348473
387474 etc...
You haven't told us what form the 'data set' is, but I will presume a data
frame called DF.
The obvious first step is to split by Plot. Using 'resample' from ?sample
sapply(with(DF, split(Tree, Plot)), resample, size=1)
give a vector of trees ('individuals'?) with names the plots sampled from.
That seems to be what you want, but if not please come back to us with a
more extensive example including the desired output.
So each plot is represented once for every individual that occurrs in it.
Plots get different numbers of rows because there can be a different number
of individuals in each plot.
I want to make a data frame that consists of one individual from each plot.
I would like to randomly choose one individual from each plot that is
present in the data set. I will have to do this to multiple data sets which
may contain different plots, and may contain up to 1200 plots, so I can't
choose the plots by hand.
Please help me with this. I'm an ecologist and I'm in Panama, with no one
around who is educated in R. Whoever solves this problem for me will be
acknowledged in any resulting publications.
Thanks!
-Claire
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@stat.math.ethz.ch mailing list
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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] Odp: sampling problem - new to R
Hi If I understand correctly, use split and sample with lapply. If DF is your dataframe lapply(split(DF$Tree, DF$Plot), function(x) sample(x,1)) shall select random tree from each plot. Or you can get it in tabular form with sapply. Regards Petr [EMAIL PROTECTED] napsal dne 05.06.2007 16:29:49: I have a data set of individual trees and the plots that they are in: Tree Plot 567491 634941 873751 374942 927533 348473 387474 etc... So each plot is represented once for every individual that occurrs in it. Plots get different numbers of rows because there can be a different number of individuals in each plot. I want to make a data frame that consists of one individual from each plot. I would like to randomly choose one individual from each plot that is present in the data set. I will have to do this to multiple data sets which may contain different plots, and may contain up to 1200 plots, so I can't choose the plots by hand. Please help me with this. I'm an ecologist and I'm in Panama, with no one around who is educated in R. Whoever solves this problem for me will be acknowledged in any resulting publications. Thanks! -Claire -- View this message in context: http://www.nabble.com/sampling-problem---new-to- R-tf3872130.html#a10970708 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] generating many matrices
On 6/6/07, Keun-Hyung Choi [EMAIL PROTECTED] wrote: I'd like to generate many matrices (let's say 100 matrices of 4x4), of which diagonal elements are being drawn from each set of sample of known distribution. What would be the best way? I've been trying to find any previous threads for this topic, but haven't been able to find one. One approach would be: replicate(100, diag(runif(4)), simplify=FALSE) Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sampling problem - new to R
I dealt with something like this recently.
x - data.frame(plot = gl(2,5), tree = rnorm(10))
y - split(x, x$plot)
ss - numeric(2)
for(i in 1:2){
ss[i] - sample(row.names(y[[i]][1]), 1)
}
z - x[ss,]
People help out of the goodness of the hearts and not for publication
recognition.
Harold
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of baldeck
Sent: Tuesday, June 05, 2007 10:30 AM
To: r-help@stat.math.ethz.ch
Subject: [R] sampling problem - new to R
I have a data set of individual trees and the plots that they are in:
Tree Plot
567491
634941
873751
374942
927533
348473
387474 etc...
So each plot is represented once for every individual that
occurrs in it.
Plots get different numbers of rows because there can be a
different number of individuals in each plot.
I want to make a data frame that consists of one individual
from each plot.
I would like to randomly choose one individual from each plot
that is present in the data set. I will have to do this to
multiple data sets which may contain different plots, and may
contain up to 1200 plots, so I can't choose the plots by hand.
Please help me with this. I'm an ecologist and I'm in
Panama, with no one around who is educated in R. Whoever
solves this problem for me will be acknowledged in any
resulting publications.
Thanks!
-Claire
--
View this message in context:
http://www.nabble.com/sampling-problem---new-to-R-tf3872130.ht
ml#a10970708
Sent from the R help mailing list archive at Nabble.com.
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[R] Sargan Test and Hansen J Statistc for Simultaneous Equation Model
Dear R Users, I am estimation a Simultaneous Equation Model with systemfit. Does anyone of you know how to do a Sargan Test for overidentifiaction and a Hansen J statistic for instrument adequacy. Is there a possibility in R to do a Hausman-Wu test for the exogeneity of specific variables? Do you know any other possibilities in R to perform similar tests (overidentification, instrument adequacy and exogeneity)? Thank you very much for your help. Yours David -- ## David Stadelmann Lehrstuhl für Makroökonomie, Internationale Industrie- und Wachstumspolitik Université de Fribourg Bureau F410 Bd de Pérolles 90 CH-1700 Fribourg SCHWEIZ Tel: +41 (026) 300 93 82 Fax: +41 (026) 300 96 78 Mob (priv): +41 (076) 542 33 48 Email: [EMAIL PROTECTED] Internet: http://www.unifr.ch/natoek Internet (priv): http://david.stadelmann-online.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Odp: sampling problem - new to R
Hi If I understand correctly, use split and sample with lapply. If DF is your dataframe lapply(split(DF$Tree, DF$Plot), function(x) sample(x,1)) shall select random tree from each plot. Or you can get it in tabular form with sapply. Regards Petr Sorry, you shall use resample from sample help page as Prof.Ripley pointed if you can have length=1 plot. Regards Petr [EMAIL PROTECTED] napsal dne 05.06.2007 16:29:49: I have a data set of individual trees and the plots that they are in: Tree Plot 567491 634941 873751 374942 927533 348473 387474 etc... So each plot is represented once for every individual that occurrs in it. Plots get different numbers of rows because there can be a different number of individuals in each plot. I want to make a data frame that consists of one individual from each plot. I would like to randomly choose one individual from each plot that is present in the data set. I will have to do this to multiple data sets which may contain different plots, and may contain up to 1200 plots, so I can't choose the plots by hand. Please help me with this. I'm an ecologist and I'm in Panama, with no one around who is educated in R. Whoever solves this problem for me will be acknowledged in any resulting publications. Thanks! -Claire -- View this message in context: http://www.nabble.com/sampling-problem---new-to- R-tf3872130.html#a10970708 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] the biggest integer R can display in complete form but not scientific form
You could try the gmp multi precision arithmetic package. library(gmp) urand.bigz(10,64) [1] 11691875040763095143 15618480061048441861 13311871202921807091 419603425985430936 [5] 1009212057431928522 7087885826104674385 12844267011818015745 12455584250595618327 [9] 13509505397081611804 17712034795004058021 Rob Francisco J. Zagmutt wrote: Also, look at options(digits) to set the number digits to be printed in the console, i.e. pi [1] 3.141593 options(digits=22) pi [1] 3.141592653589793 Regards Francisco Roland Rau wrote: 李俊杰 wrote: Dear R-lister, One of my friends wanted to produce random number which is 64 bits. He did it with Fortune. I think R can do it also. But I don't know how to display a very big integer in the complete form but not scientific form. And what's the biggest integer R can display in complete form ? Thanks in advance, Li Junjie I guess the biggest integer R can represent (if this is what you mean) is machine dependent and you can find it out via: .Machine help(.Machine) I hope this helps, Roland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] anova(lme)
I'd like to do 2 ANOVA with repeated measurement. First:response = AS 1.within-factor = modal 2.within-factor = ref (all stairs of the factors are repeated measured) so that random = vp I did it like this: (anova(lme(AS~modal*ref,random=~1|vp))) Is it correct? Second: response = AS between-factor = sehsinn within-factor = ref (all stairs of the within factor are repeated measured) so that random = vpT I did it like this: (anova(lme(AS~sehsinn*ref,random=~1|vpT))) Is it correct? In the help for R is written that p-values are calculated by Wald tests. How does R for this calculate the denominator degrees of freedom? (they are looking very strange) Thanks [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sampling problem - new to R
A variation of Brian's idea of using resample in ?sample would be:
set.seed(1) # makes sample reproducible
aggregate(DF[1], DF[2], resample, size = 1)
Using resample ensures that the solution works even if some
of the Plots only have one Tree. Some of the solutions
that were presented in this thread do not work properly in that case
as sample acts differently according to whether its first argument's
length is 1 or 1.
On 6/6/07, Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Tue, 5 Jun 2007, baldeck wrote:
I have a data set of individual trees and the plots that they are in:
Tree Plot
567491
634941
873751
374942
927533
348473
387474 etc...
You haven't told us what form the 'data set' is, but I will presume a data
frame called DF.
The obvious first step is to split by Plot. Using 'resample' from ?sample
sapply(with(DF, split(Tree, Plot)), resample, size=1)
give a vector of trees ('individuals'?) with names the plots sampled from.
That seems to be what you want, but if not please come back to us with a
more extensive example including the desired output.
So each plot is represented once for every individual that occurrs in it.
Plots get different numbers of rows because there can be a different number
of individuals in each plot.
I want to make a data frame that consists of one individual from each plot.
I would like to randomly choose one individual from each plot that is
present in the data set. I will have to do this to multiple data sets which
may contain different plots, and may contain up to 1200 plots, so I can't
choose the plots by hand.
Please help me with this. I'm an ecologist and I'm in Panama, with no one
around who is educated in R. Whoever solves this problem for me will be
acknowledged in any resulting publications.
Thanks!
-Claire
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] name of the variable that will contain the result of a function
On Wed, 6 Jun 2007, Benilton Carvalho wrote: Hi everyone, say I have a function called 'foo', which takes the argument arg1. Is there any mechanism that I can use to learn about the variable where foo(arg1) is going to be stored? No. This information isn't available explicitly even at the C level. For example: x - foo(arg1) so, inside foo() I'd like to be able to get the string x. if, foo(arg1) was used insted, I'd like to get NA. It could be much worse that this, for example, x[[7]][y][[4]] - foo(arg1) w - foo(arg2)+1 names(x)[foo(arg3)] - foo(arg4) -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] random numbers selection - simple example
Dear R-help, Which random number generator function would you recommend for simply picking 15 random numbers from the sequence 0-42? I want to use replacement (so that the same number could potentially be picked more than once). I have read the R-help archives and the statistics and computing book on modern Applied statistics with S but the advice seems to be for much form complicated examples, there must be a simpler way for what I am trying to do? If anybody can help me I would greatly appreciate your advice and time, Best Wishes, Jenny ~~ Jennifer Barnes PhD student: long range drought prediction Climate Extremes Group Department of Space and Climate Physics University College London Holmbury St Mary Dorking, Surrey, RH5 6NT Web: http://climate.mssl.ucl.ac.uk __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R: x-y data
tt-read.table(C:/temp/test.csv, header=T, sep=,) # Try: tt$x tt$y # OR tt[x] tt[y] # OR tt[[x]] tt[[y]] # OR tt[1] tt[2] tt[[1]] tt[[2]] # Is this what you want? I have an Excel file with x-y data. I saved this file as a cvs file. Then I used the read.table() function to read the data into R. If I have a formula like (x+y)/2, how would I access x and y in R? I have the table named as something. But how do I access the individual columns if I want to plug them into the formula? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Chow Test
Hello R-users! I tried to find a package to run a CHOW TEST. As a reference package I found the STRUCCHANGE package. Do you know if it works well otherwise can you recommend a different one? Thanks, Bernd -- View this message in context: http://www.nabble.com/Chow-Test-tf3878416.html#a10990270 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] the biggest integer R can display in complete form but not scientific form
Yeah, this is absolutely what I want! Thanks all above for your helpful suggestion. 2007/6/6, Rob Creecy [EMAIL PROTECTED]: You could try the gmp multi precision arithmetic package. library(gmp) urand.bigz(10,64) [1] 11691875040763095143 15618480061048441861 13311871202921807091 419603425985430936 [5] 1009212057431928522 7087885826104674385 12844267011818015745 12455584250595618327 [9] 13509505397081611804 17712034795004058021 Rob Francisco J. Zagmutt wrote: Also, look at options(digits) to set the number digits to be printed in the console, i.e. pi [1] 3.141593 options(digits=22) pi [1] 3.141592653589793 Regards Francisco Roland Rau wrote: Àî¿¡½Ü wrote: Dear R-lister, One of my friends wanted to produce random number which is 64 bits. He did it with Fortune. I think R can do it also. But I don't know how to display a very big integer in the complete form but not scientific form. And what's the biggest integer R can display in complete form ? Thanks in advance, Li Junjie I guess the biggest integer R can represent (if this is what you mean) is machine dependent and you can find it out via: .Machine help(.Machine) I hope this helps, Roland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Junjie Li, [EMAIL PROTECTED] Undergranduate in DEP of Tsinghua University, [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Linear Discriminant Analysis
Hello, I want to make a linear discriminant analysis for the dataset olive, and I get always this error:# Warning message: variables are collinear in: lda.default(x, grouping, ...) ## Loading Data library(MASS) olive - url( http://www.statistik.tuwien.ac.at/public/filz/students/multi/ss07/olive.R;) print(load(olive)) y - 1:572 x - sample(y) y1 - x[1:286] train - olive[y1,-11] test - olive[-y1,-11] summary(train) summary(test) table(train$Region) table(test$Region) # Linear Discriminant Analysis z - lda(Region ~ . , train) predict(z, train) z - lda(Region ~ . , test) predict(z, test) Thanks in advance! -- Mit freundlichen Grüssen / Best Regards Soare Marcian-Alin [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Neural Net. in R
Hi, there, I am surprised you didn't mention nnet package. You can find very good information in Dr Ripley's MASS book about the usage of nnet package. On 6/5/07, Ehsan Rasa [EMAIL PROTECTED] wrote: Hi everyone, I'm a graduate student of engineering, lately introduced with R. and using R for my project and thesis. I'm trying to use R for implementing a neural network regression model and apply it to my database. I found three R packages (AMORE , grnnR , neural) in R website, but their manuals are not really user-friendly in my idea. I was wondering if anyone has a written code in R using any of these packages for a feed-forward back-propagation neural network in R that I can use it. That'll be a remedy for my nightmare which already took quite time from me. I would really appreciate it. Sincerely, Jason. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- WenSui Liu A lousy statistician who happens to know a little programming (http://spaces.msn.com/statcompute/blog) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random numbers selection - simple example
You're all stars - thanks for the replies - I will go ahead and use sample... I need to do this about 10,000 times - any suggestions for this or simply put it in a loop 10,000 times outputting each time to an array? Best Wishes, Jenny use sample(c(0:42), 15, replace=T) hope it helps, kevin - Original Message - From: Jenny Barnes [EMAIL PROTECTED] Date: Wednesday, June 6, 2007 10:30 am Subject: [R] random numbers selection - simple example Dear R-help, Which random number generator function would you recommend for simply picking 15 random numbers from the sequence 0-42? I want to use replacement (so that the same number could potentially be picked more than once). I have read the R-help archives and the statistics and computing book on modern Applied statistics with S but the advice seems to be for much form complicated examples, there must be a simpler way for what I am trying to do? If anybody can help me I would greatly appreciate your advice and time, Best Wishes, Jenny ~~ Jennifer Barnes PhD student: long range drought prediction Climate Extremes Group Department of Space and Climate Physics University College London Holmbury St Mary Dorking, Surrey, RH5 6NT Web: http://climate.mssl.ucl.ac.uk __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.htmland provide commented, minimal, self-contained, reproducible code. ~~ Jennifer Barnes PhD student: long range drought prediction Climate Extremes Group Department of Space and Climate Physics University College London Holmbury St Mary Dorking, Surrey, RH5 6NT Tel: 01483 204149 Mob: 07916 139187 Web: http://climate.mssl.ucl.ac.uk __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random numbers selection - simple example
Assuming you want only integers, see ?sample Sarah On 6/6/07, Jenny Barnes [EMAIL PROTECTED] wrote: Dear R-help, Which random number generator function would you recommend for simply picking 15 random numbers from the sequence 0-42? I want to use replacement (so that the same number could potentially be picked more than once). I have read the R-help archives and the statistics and computing book on modern Applied statistics with S but the advice seems to be for much form complicated examples, there must be a simpler way for what I am trying to do? If anybody can help me I would greatly appreciate your advice and time, Best Wishes, Jenny -- Sarah Goslee http://www.functionaldiversity.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R: x-y data
There are a couple of ways but I think you need to read about R . Have a look at Managing data http://cran.r-project.org/doc/contrib/Lemon-kickstart/index.html and / or read the Intro to R manual available on CRAN or probably from the R help icon. you have a data.frame DF you can assign names to the variables ?names names(DF) - c(x, y) and attach the data.frame ?attach or you can reference the columns as DF[,1] and DF[,2] --- tronter [EMAIL PROTECTED] wrote: Hello I have an Excel file with x-y data. I saved this file as a cvs file. Then I used the read.table() function to read the data into R. If I have a formula like (x+y)/2, how would I access x and y in R? I have the table named as something. But how do I access the individual columns if I want to plug them into the formula? Thanks -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Courses: Traditional and Modern Approaches to Statistical Modelling with R by Dr Bill Venables. in Raleigh and Washington DC
__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Chow Test
On Wed, 6 Jun 2007, Bernd Stampfl wrote: Hello R-users! I tried to find a package to run a CHOW TEST. As a reference package I found the STRUCCHANGE package. Do you know if it works well If you have concerns regarding the reliability, you can check the underlying source code and read the accompanying publications (which also comment on reliability and reproducibility). otherwise can you recommend a different one? If the breakpoint is known, you can easily compute the Chow test by hand: set up a factor that codes the two regimes and then fit the un-segmented and segmented regressions: fac - my_time my_break fm0 - lm(y ~ x1 + x2 ...) fm1 - lm(y ~ fac / (x1 + x2 ...)) anova(fm0, fm1) If you want other covariances in the test, you can also use waldtest() from the lmtest package. If the breakpoint is not known in advance, a supF test (aka supChow) over all conceivable breakpoints is more appropriate. This is also provided in strucchange along with a rich set of other testing (and dating) techniques. Best, Z Thanks, Bernd -- View this message in context: http://www.nabble.com/Chow-Test-tf3878416.html#a10990270 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R: x-y data
Or read ?attach attach(something) (x+y)/2 detach(something) jim holtman wrote: Can you provide an example of your data. Assuming that you have a .cvs file and the column names are 'x' and 'y' and you have used 'read.csv', then you would have: (something$x + something$y) / 2 On 6/5/07, tronter [EMAIL PROTECTED] wrote: Hello I have an Excel file with x-y data. I saved this file as a cvs file. Then I used the read.table() function to read the data into R. If I have a formula like (x+y)/2, how would I access x and y in R? I have the table named as something. But how do I access the individual columns if I want to plug them into the formula? -- --- Jeff NewmillerThe . . Go Live... DCN:[EMAIL PROTECTED]Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random numbers selection - simple example
On 06-Jun-07 14:30:44, Jenny Barnes wrote: Dear R-help, Which random number generator function would you recommend for simply picking 15 random numbers from the sequence 0-42? I want to use replacement (so that the same number could potentially be picked more than once). R has the function sample() which samples a given number of items from a given set, without replacement by default, but with replacement if you specify this. Enter ?sample for more information. In the above case sample((0:42), 15, replace=TRUE) will do what you seem to describe above. Example: sample((0:42), 15, replace=TRUE) [1] 26 38 1 41 11 30 22 37 28 0 0 25 10 39 27 if you want them in random order (i.e. as they come off the line), or sort(sample((0:42), 15, replace=TRUE)) [1] 1 3 5 8 8 10 16 17 21 25 30 30 33 34 40 if you want them sorted. Best wishes, Ted. I have read the R-help archives and the statistics and computing book on modern Applied statistics with S but the advice seems to be for much form complicated examples, there must be a simpler way for what I am trying to do? If anybody can help me I would greatly appreciate your advice and time, Best Wishes, Jenny E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 06-Jun-07 Time: 16:24:15 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random numbers selection - simple example
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jenny Barnes Sent: Wednesday, June 06, 2007 7:55 AM To: r-help@stat.math.ethz.ch Subject: Re: [R] random numbers selection - simple example You're all stars - thanks for the replies - I will go ahead and use sample... I need to do this about 10,000 times - any suggestions for this or simply put it in a loop 10,000 times outputting each time to an array? Best Wishes, Jenny use sample(c(0:42), 15, replace=T) hope it helps, kevin You could try something like the following s-matrix(sample(c(0:42), 1*15, replace=TRUE), 1, 15) which will give you a 1 row matrix with 1 sample of size 15 per row. Hope this is helpful, Dan Daniel Nordlund Bothell, WA USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linear Discriminant Analysis
Thanks for explaining... Im just sitting at the homework for 6 hours after taking for one week antibiotica, because i had an amygdalitis... I just wanted some tipps for solving this homework, but thanks, I will try to get help on another way :) I think i solved it, but I still get this Error :( ## Loading Data library(MASS) olive - url( http://www.statistik.tuwien.ac.at/public/filz/students/multi/ss07/olive.R;) print(load(olive)) dim(olive) summary(olive) index - sample(nrow(olive), 286) train - olive[index,-11] test - olive[-index,-11] summary(train) summary(test) table(train$Region) table(test$Region) # Linear Discriminant Analysis z - lda(Region ~ . , train) zn - predict(z, newdata=test)$class mean(zn != test$Region) 2007/6/6, Uwe Ligges [EMAIL PROTECTED]: So what about asking your teacher (who seems to be Peter Filzmoser) and try to find out your homework yourself? You might want to think about some assumptions that must hold for LDA and look at the class of your explaining variables ... Uwe Ligges Soare Marcian-Alin wrote: Hello, I want to make a linear discriminant analysis for the dataset olive, and I get always this error:# Warning message: variables are collinear in: lda.default(x, grouping, ...) ## Loading Data library(MASS) olive - url( http://www.statistik.tuwien.ac.at/public/filz/students/multi/ss07/olive.R ) print(load(olive)) y - 1:572 x - sample(y) y1 - x[1:286] train - olive[y1,-11] test - olive[-y1,-11] summary(train) summary(test) table(train$Region) table(test$Region) # Linear Discriminant Analysis z - lda(Region ~ . , train) predict(z, train) z - lda(Region ~ . , test) predict(z, test) Thanks in advance! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mit freundlichen Grüssen / Best Regards Soare Marcian-Alin [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linear Discriminant Analysis
So what about asking your teacher (who seems to be Peter Filzmoser) and try to find out your homework yourself? You might want to think about some assumptions that must hold for LDA and look at the class of your explaining variables ... Uwe Ligges Soare Marcian-Alin wrote: Hello, I want to make a linear discriminant analysis for the dataset olive, and I get always this error:# Warning message: variables are collinear in: lda.default(x, grouping, ...) ## Loading Data library(MASS) olive - url( http://www.statistik.tuwien.ac.at/public/filz/students/multi/ss07/olive.R;) print(load(olive)) y - 1:572 x - sample(y) y1 - x[1:286] train - olive[y1,-11] test - olive[-y1,-11] summary(train) summary(test) table(train$Region) table(test$Region) # Linear Discriminant Analysis z - lda(Region ~ . , train) predict(z, train) z - lda(Region ~ . , test) predict(z, test) Thanks in advance! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Using odesolve to produce non-negative solutions
Hello,
I am using odesolve to simulate a group of people moving through time and
transmitting infections to one another.
In Matlab, there is a NonNegative option which tells the Matlab solver to keep
the vector elements of the ODE solution non-negative at all times. What is the
right way to do this in R?
Thanks,
Jeremy
P.S., Below is a simplified version of the code I use to try to do this, but I
am not sure that it is theoretically right
dynmodel - function(t,y,p)
{
## Initialize parameter values
birth - p$mybirth(t)
death - p$mydeath(t)
recover - p$myrecover
beta - p$mybeta
vaxeff - p$myvaxeff
vaccinated - p$myvax(t)
vax - vaxeff*vaccinated/100
## If the state currently has negative quantities (shouldn't have), then reset
to reasonable values for computing meaningful derivatives
for (i in 1:length(y)) {
if (y[i]0) {
y[i] - 0
}
}
S - y[1]
I - y[2]
R - y[3]
N - y[4]
shat - (birth*(1-vax)) - (death*S) - (beta*S*I/N)
ihat - (beta*S*I/N) - (death*I) - (recover*I)
rhat - (birth*(vax)) + (recover*I) - (death*R)
## Do we overshoot into negative space, if so shrink derivative to bring state
to 0
## then rescale the components that take the derivative negative
if (shat+S0) {
shat_old - shat
shat - -1*S
scaled_transmission - (shat/shat_old)*(beta*S*I/N)
ihat - scaled_transmission - (death*I) - (recover*I)
}
if (ihat+I0) {
ihat_old - ihat
ihat - -1*I
scaled_recovery - (ihat/ihat_old)*(recover*I)
rhat - scaled_recovery +(birth*(vax)) - (death*R)
}
if (rhat+R0) {
rhat - -1*R
}
nhat - shat + ihat + rhat
if (nhat+N0) {
nhat - -1*N
}
## return derivatives
list(c(shat,ihat,rhat,nhat),c(0))
}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Neural Net. in R
I have written some bindings from the SNNS (Stuttgart Neural Network Simulator) to R. However, this work is not finished since the lack of interest to it and lack of time. At the moment, I use the mixture of scripts for R, cmd.exe, bash, and SNNS' batchman (latter two under cygwin) in my work. SNNS by itself is rather feature rich and well documented. Unfortunately its development has stopped many years ago, and it contains bugs, which I still failed to find and eliminate. Ehsan Rasa wrote: Hi everyone, I'm a graduate student of engineering, lately introduced with R. and using R for my project and thesis. I'm trying to use R for implementing a neural network regression model and apply it to my database. I found three R packages (AMORE , grnnR , neural) in R website, but their manuals are not really user-friendly in my idea. I was wondering if anyone has a written code in R using any of these packages for a feed-forward back-propagation neural network in R that I can use it. That'll be a remedy for my nightmare which already took quite time from me. I would really appreciate it. Sincerely, Jason. -- View this message in context: http://www.nabble.com/Neural-Net.-in-R-tf3877741.html#a10991934 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to update R version
Hello, I am new in using Linux R. Would someone tell me what the best way to update my current R 2.3.0 to R 2.5.0? I want to keep my current library packages. Do I have to erase the older version and install the newer version? In that case, I need to re-download all the packages I need. Any short way to do the update? Thanks for your help! yanqin - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Meaning of locfit warnings procv: parameters out of bounds?
I'm getting the following warning from locfit: Warning: procv: parameters out of bounds Does anyone know what this means? (I haven't found anything about it in the locfit documentation or the list's archives). thanks, Barnet Wagman __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: Using odesolve to produce non-negative solutions
Hello,
I am using odesolve to simulate a group of people moving through time and
transmitting infections to one another.
In Matlab, there is a NonNegative option which tells the Matlab solver to keep
the vector elements of the ODE solution non-negative at all times. What is the
right way to do this in R?
Thanks,
Jeremy
P.S., Below is a simplified version of the code I use to try to do this, but I
am not sure that it is theoretically right
dynmodel - function(t,y,p)
{
## Initialize parameter values
birth - p$mybirth(t)
death - p$mydeath(t)
recover - p$myrecover
beta - p$mybeta
vaxeff - p$myvaxeff
vaccinated - p$myvax(t)
vax - vaxeff*vaccinated/100
## If the state currently has negative quantities (shouldn't have), then reset
to reasonable values for computing meaningful derivatives
for (i in 1:length(y)) {
if (y[i]0) {
y[i] - 0
}
}
S - y[1]
I - y[2]
R - y[3]
N - y[4]
shat - (birth*(1-vax)) - (death*S) - (beta*S*I/N)
ihat - (beta*S*I/N) - (death*I) - (recover*I)
rhat - (birth*(vax)) + (recover*I) - (death*R)
## Do we overshoot into negative space, if so shrink derivative to bring state
to 0
## then rescale the components that take the derivative negative
if (shat+S0) {
shat_old - shat
shat - -1*S
scaled_transmission - (shat/shat_old)*(beta*S*I/N)
ihat - scaled_transmission - (death*I) - (recover*I)
}
if (ihat+I0) {
ihat_old - ihat
ihat - -1*I
scaled_recovery - (ihat/ihat_old)*(recover*I)
rhat - scaled_recovery +(birth*(vax)) - (death*R)
}
if (rhat+R0) {
rhat - -1*R
}
nhat - shat + ihat + rhat
if (nhat+N0) {
nhat - -1*N
}
## return derivatives
list(c(shat,ihat,rhat,nhat),c(0))
}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Question on RandomForest in unsupervised mode
Hi, I attempted to run the randomForest() function on a dataset without predefined classes. According to the manual, running randomForest without a response variable/class labels should result in the function assuming you are running in unsupervised mode. In this case, I understand that my data is all assigned to one class whereas a second synthetic class is made up, which is assigned to a second class. The online manual suggests that an oob misclassification error in this two-class problem of ~40% or more would indicate that the x- variables look like independent variables to random forests (and I assume that in this case the proximities obtained by the randomForest would not be informative for clustering). When I run randomForest() in the unsupervised mode my first problem is that I get NULL entries for the confusion matrix and the err.rate, but I suppose this is normal behaviour. My only information (apart from the proximities of course), seems to be the votes, from which I can deduce whether the variables are meaningful or not. The second problem is that, in my case, all my observations seem to have about 20-40% of the votes from class 1 and the rest from class 2 (i.e. class 2 wins always). Assuming that class 1 was assigned to my original data, I'd say this is rather surprising. Initially I thought this was simply a problem of my data not being meaningful, but I repeated simply the forest with the iris example data and I get more or less the same result. I did simply: iris.urf - randomForest(iris[,-5]) iris.urf$votes and I got again most of the votes coming from class 2, although here vote percentages are slightly more balanced than with my data (approximately 40 to 60% most of the time). Has anyone got experience with unsupervised randomForest() in R and can explain to me why I'm observing this behaviour? In general, any hints about pitfalls regarding random forests in unsupervised mode would be very much appreciated. Many thanks in advance, Irilenia - Irilenia (Irene) Nobeli Randall Division of Cell and Molecular Biophysics New Hunt's House (room 3.14) King's College London, Guy's Campus London, SE1 1UL U.K. [EMAIL PROTECTED] +44(0)207-8486329 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Question: RMySQL bulk load/update one column, dbWriteTable()?
Hi, I have a question reading using RMySQL trying to load one R vector into a table column. To be more specifically, the table is there populated. Now I add a new column and want to populate this. Can some colleagues on this list teach me how to do this? I know how to write one R object/table into MYSQL table using dbWriteTable. But in this situation, I just want to do one column. Thanks much in advance. -- Waverley [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R help
--- scott flemming [EMAIL PROTECTED] wrote: Hi, I wonder whether R can finish the following project: I want to make a chart to represent 10 genes. Each gene has orientation and length. Therefore, a gene can be represented by arrows. Can R be used to draw 10 arrows in one line ? scott Do you mean something like this? x - 1:10 y - 1:10 plot(x,y, type=n ) arrows(c(1,4,6),c(3,3,3), c(2,3, 7), c(4,4,2)) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to update R version
Yanqin Yang wrote: Hello, I am new in using Linux R. Would someone tell me what the best way to update my current R 2.3.0 to R 2.5.0? I want to keep my current library packages. Do I have to erase the older version and install the newer version? In that case, I need to re-download all the packages I need. Any short way to do the update? Thanks for your help! yanqin Since I compile from source, I simply compile the new version and install it to the same location as the old. Then I run update.packages() to update the additional packages I have installed. Of course, I may get bit by this approach one day. It is possible to have more than one directory for packages. One suggestion I've seen is to collect your user installed packages in a different directory than the base and recommended packages. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.864.5776 Fax: 416.864.6057 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Removing vertical line in Tinn R editor
Hi, I haven't been able to figure out how to remove a vertical line that appears when I open an r file. How can I do this? Thank you, Judith Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing vertical line in Tinn R editor
Go to Options/Main/Editor Click on EdgeColor and select white as the color (or to whatever color you have set your page's background). This will make the edge line disappear. -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Judith Flores Sent: Wednesday, June 06, 2007 1:50 PM To: RHelp Subject: [R] Removing vertical line in Tinn R editor Hi, I haven't been able to figure out how to remove a vertical line that appears when I open an r file. How can I do this? Thank you, Judith __ __ Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linear Discriminant Analysis
Region and Name are effectively the same variable cor(olive[,4:11]) will also show you that there are strong correlations between some of the variables - this is something you might want to avoid From: [EMAIL PROTECTED] on behalf of Soare Marcian-Alin Sent: Wed 06/06/2007 4:45 PM To: Uwe Ligges; R-help@stat.math.ethz.ch Subject: Re: [R] Linear Discriminant Analysis Thanks for explaining... Im just sitting at the homework for 6 hours after taking for one week antibiotica, because i had an amygdalitis... I just wanted some tipps for solving this homework, but thanks, I will try to get help on another way :) I think i solved it, but I still get this Error :( ## Loading Data library(MASS) olive - url( http://www.statistik.tuwien.ac.at/public/filz/students/multi/ss07/olive.R;) print(load(olive)) dim(olive) summary(olive) index - sample(nrow(olive), 286) train - olive[index,-11] test - olive[-index,-11] summary(train) summary(test) table(train$Region) table(test$Region) # Linear Discriminant Analysis z - lda(Region ~ . , train) zn - predict(z, newdata=test)$class mean(zn != test$Region) 2007/6/6, Uwe Ligges [EMAIL PROTECTED]: So what about asking your teacher (who seems to be Peter Filzmoser) and try to find out your homework yourself? You might want to think about some assumptions that must hold for LDA and look at the class of your explaining variables ... Uwe Ligges Soare Marcian-Alin wrote: Hello, I want to make a linear discriminant analysis for the dataset olive, and I get always this error:# Warning message: variables are collinear in: lda.default(x, grouping, ...) ## Loading Data library(MASS) olive - url( http://www.statistik.tuwien.ac.at/public/filz/students/multi/ss07/olive.R ) print(load(olive)) y - 1:572 x - sample(y) y1 - x[1:286] train - olive[y1,-11] test - olive[-y1,-11] summary(train) summary(test) table(train$Region) table(test$Region) # Linear Discriminant Analysis z - lda(Region ~ . , train) predict(z, train) z - lda(Region ~ . , test) predict(z, test) Thanks in advance! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mit freundlichen Grüssen / Best Regards Soare Marcian-Alin [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem with Axis labels
Hi I am using the pamr.plotsurvival fucntion to plot the KM curves,how can I change the x axis and y axis labels according to my interest. Thanks Looking for people who are YOUR TYPE? Find them at in.groups.yahoo.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] handling a cancelled file.choose()
Hello, I have a file reading function that prompts the user with a file dialog if a filename is not provided in the argument list. It is desirable to return gracefully if the user selects Cancel, but file.choose() throws an error instead of returning something like a character. file.choose() [1] /Users/ben/ben_idl.pref file.choose() Error in file.choose() : file choice cancelled I naively planned to use nchar() to test the length, assuming cancellation would return a zero-length character. That appears to be out of the question. Are there other options available in the base package? Thanks! Ben __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] R package: Mchtest - Monte Carlo hypothesis testing allowing Sequential Stopping
Hi, This is an announcement for a package that has been up on CRAN since March 2006 but was never announced. The package is Mchtest - for Monte Carlo hypothesis tests allowing sequential stopping. The idea is to use the sequential probability ratio test boundaries to stop resampling for a Monte Carlo hypothesis test such as a bootstrap or permutation test. This means that you will take many samples when the p-value is close to the significance level (e.g., 0.05), but you may stop after a much fewer samples if it becomes clear that the p-value is either very likely to be less than or more than 0.05. The details are described in: Fay, MP, Kim, H-J, and Hachey, M. (2007). On using Truncated Sequential Probability Ratio Test Boundaries for Monte Carlo Implementation of Hypothesis Tests. (to appear in Journal of Graphical and Computational Statistics). http://www3.niaid.nih.gov/about/organization/dcr/BRB/staff/michael Please let me know of any problems or if you have any comments. Mike ** Michael P. Fay, PhD Mathematical Statistician National Institute of Allergy and Infectious Diseases Tel: 301-451-5124 Fax:301-480-0912 (U.S. postal mail address) 6700B Rockledge Drive MSC 7609 Bethesda, MD 20892-7609 (Overnight mail address) 6700-A Rockledge Drive, Room 5133 Bethesda, MD 20817 ** Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives [[alternative HTML version deleted]] ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] R Package: ssanv - Sample size adjustments for nonadherence and variability of input parameters
Hi, This is a late announcement for a package that has been up on CRAN since Feb 2006. The package is called ssanv and it calculates sample sizes for two group tests with adjustments for nonadherence and variability of the input parameters. As an example, suppose you want a sample size for a two group difference in normal means but you get your estimate of your variance from a previous study. Then with this package, you can account for the variability of that variance estimate in your sample size calculations. The details are described in: Fay, MP, Halloran, ME, Follmann, DA. Accounting for Variability in Sample Size Estimation with Applications to Nonadherence and Estimation of Variance and Effect Size. Biometrics 2007, 63: 465-474. http://www.blackwell-synergy.com/doi/abs/10./j.1541-0420.2006.00703.x Please let me know of any problems with the package or have any comments. Thanks, Mike ** Michael P. Fay, PhD Mathematical Statistician National Institute of Allergy and Infectious Diseases Tel: 301-451-5124 Fax:301-480-0912 (U.S. postal mail address) 6700B Rockledge Drive MSC 7609 Bethesda, MD 20892-7609 (Overnight mail address) 6700-A Rockledge Drive, Room 5133 Bethesda, MD 20817 ** Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives [[alternative HTML version deleted]] ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] New Package: rateratio.test
Hi, I just uploaded a new package rateratio.test. The package contains one function of the same name and it performs an exact rate ratio test for Poisson counts. Unlike binom.test and fisher.test the p-values and confidence intervals are internally consistent. In other words, if the p-value implies that the null hypothesis should be rejected, then the confidence interval also implies that the null should be rejected. There is a vignette discussing this issue. Mike ** Michael P. Fay, PhD Mathematical Statistician National Institute of Allergy and Infectious Diseases Tel: 301-451-5124 Fax:301-480-0912 (U.S. postal mail address) 6700B Rockledge Drive MSC 7609 Bethesda, MD 20892-7609 (Overnight mail address) 6700-A Rockledge Drive, Room 5133 Bethesda, MD 20817 ** Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives [[alternative HTML version deleted]] ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] handling a cancelled file.choose()
Try this: tryCatch(file.choose(), error = function(e) ) On 6/6/07, Ben Tupper [EMAIL PROTECTED] wrote: Hello, I have a file reading function that prompts the user with a file dialog if a filename is not provided in the argument list. It is desirable to return gracefully if the user selects Cancel, but file.choose() throws an error instead of returning something like a character. file.choose() [1] /Users/ben/ben_idl.pref file.choose() Error in file.choose() : file choice cancelled I naively planned to use nchar() to test the length, assuming cancellation would return a zero-length character. That appears to be out of the question. Are there other options available in the base package? Thanks! Ben __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] handling a cancelled file.choose()
See ?tryCatch.
Example: Function returning NULL if cancelled:
fileChoose - function(...) {
pathname - NULL;
tryCatch({
pathname - file.choose();
}, error = function(ex) {
})
pathname;
}
/Henrik
On 6/6/07, Ben Tupper [EMAIL PROTECTED] wrote:
Hello,
I have a file reading function that prompts the user with a file dialog
if a filename is not provided in the argument list. It is desirable to
return gracefully if the user selects Cancel, but file.choose() throws
an error instead of returning something like a character.
file.choose()
[1] /Users/ben/ben_idl.pref
file.choose()
Error in file.choose() : file choice cancelled
I naively planned to use nchar() to test the length, assuming
cancellation would return a zero-length character. That appears to be
out of the question. Are there other options available in the base package?
Thanks!
Ben
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] handling a cancelled file.choose()
On 6/6/07, Ben Tupper [EMAIL PROTECTED] wrote: Hello, I have a file reading function that prompts the user with a file dialog if a filename is not provided in the argument list. It is desirable to return gracefully if the user selects Cancel, but file.choose() throws an error instead of returning something like a character. file.choose() [1] /Users/ben/ben_idl.pref file.choose() Error in file.choose() : file choice cancelled I naively planned to use nchar() to test the length, assuming cancellation would return a zero-length character. That appears to be out of the question. [...] Not really, errors can be caught and handled. This seems to give the behaviour you want: tryCatch(file.choose(), error = function(e) ) -Deepayan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Multiple color schemes for barchart (lattice)
Hello R-help. I am trying to make a stacked barplot where the color of the sections of each bar depend on another variable. myData[1:11,] score percentmarker cellType Malignant 1 0 100.0 ESR1 (ER) Bladder.M(5) TRUE 2 0 80.0 PAX8 Bladder.M(5) TRUE 3 1 20.0 PAX8 Bladder.M(5) TRUE 4 0 100.0 ESR1 (ER) Brain.N(3) FALSE 5 0 100.0 PAX8 Brain.N(3) FALSE 6 3 100.0 ESR1 (ER) Breast.M(11) TRUE 7 0 100.0 PAX8 Breast.M(11) TRUE 8 0 36.36364 ESR1 (ER) Cervix.M(11) TRUE 9 1 9.09091 ESR1 (ER) Cervix.M(11) TRUE 10 2 18.18182 ESR1 (ER) Cervix.M(11) TRUE 11 3 36.36364 ESR1 (ER) Cervix.M(11) TRUE palette - palette(gray(seq(0, 1,len=4))) trellis.par.set(list(par.xlab.text=list(cex=0.85) , superpose.polygon=list(col=palette()) , axis.text=list(cex=0.8))) barchart(percent~cellType|marker , groups=score , data=myData , stack=TRUE , xlab='N=Normal/Benign, M=Malignant' , ylab='Percentage of Cores Staining' , color=palette() , auto.key = list(points = FALSE, rectangles = TRUE, space = top) , scales=list(x=list(rot=70)) , layout=c(1,2)) I would like to make the color scheme of the bar differ according to the variable 'Malignant' and add a second color scheme to the key. Any help would be appreciated! --Sarah Sarah Hawley Data Coordinator/Analyst Canary Foundation [EMAIL PROTECTED] 415.412.2533 www.canaryfoundation.org Stopping cancer early... the best possible investment! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] handling a cancelled file.choose()
Deepayan Sarkar wrote: On 6/6/07, Ben Tupper [EMAIL PROTECTED] wrote: Hello, I have a file reading function that prompts the user with a file dialog if a filename is not provided in the argument list. It is desirable to return gracefully if the user selects Cancel, but file.choose() throws an error instead of returning something like a character. file.choose() [1] /Users/ben/ben_idl.pref file.choose() Error in file.choose() : file choice cancelled I naively planned to use nchar() to test the length, assuming cancellation would return a zero-length character. That appears to be out of the question. [...] Not really, errors can be caught and handled. This seems to give the behaviour you want: tryCatch(file.choose(), error = function(e) ) -Deepayan Thanks all, I am very pleased to know about conditions in the base package. Slick! Ben __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple color schemes for barchart (lattice)
On 6/6/07, Sarah Hawley [EMAIL PROTECTED] wrote: Hello R-help. I am trying to make a stacked barplot where the color of the sections of each bar depend on another variable. myData[1:11,] score percentmarker cellType Malignant 1 0 100.0 ESR1 (ER) Bladder.M(5) TRUE 2 0 80.0 PAX8 Bladder.M(5) TRUE 3 1 20.0 PAX8 Bladder.M(5) TRUE 4 0 100.0 ESR1 (ER) Brain.N(3) FALSE 5 0 100.0 PAX8 Brain.N(3) FALSE 6 3 100.0 ESR1 (ER) Breast.M(11) TRUE 7 0 100.0 PAX8 Breast.M(11) TRUE 8 0 36.36364 ESR1 (ER) Cervix.M(11) TRUE 9 1 9.09091 ESR1 (ER) Cervix.M(11) TRUE 10 2 18.18182 ESR1 (ER) Cervix.M(11) TRUE 11 3 36.36364 ESR1 (ER) Cervix.M(11) TRUE palette - palette(gray(seq(0, 1,len=4))) trellis.par.set(list(par.xlab.text=list(cex=0.85) , superpose.polygon=list(col=palette()) , axis.text=list(cex=0.8))) barchart(percent~cellType|marker , groups=score , data=myData , stack=TRUE , xlab='N=Normal/Benign, M=Malignant' , ylab='Percentage of Cores Staining' , color=palette() , auto.key = list(points = FALSE, rectangles = TRUE, space = top) , scales=list(x=list(rot=70)) , layout=c(1,2)) I would like to make the color scheme of the bar differ according to the variable 'Malignant' and add a second color scheme to the key. It's pretty easy to do this with ggplot2 - see http://had.co.nz/ggplot2/position_stack.html for some examples. Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] compiling from source on Vista
Dear R People: In the R Installation and Administration manual, there is a note that the process used to compile R from source will NOT work on Windows Vista. Does anyone know if that situation has changed, please? Thanks in advance! Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] electre decision analysis methods
Hello, Is there some library implementing the electre II and III multiple criteria decision analysis methods in R? Thanks in advance. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple color schemes for barchart (lattice)
On 6/6/07, Sarah Hawley [EMAIL PROTECTED] wrote: Hello R-help. I am trying to make a stacked barplot where the color of the sections of each bar depend on another variable. myData[1:11,] score percentmarker cellType Malignant 1 0 100.0 ESR1 (ER) Bladder.M(5) TRUE 2 0 80.0 PAX8 Bladder.M(5) TRUE 3 1 20.0 PAX8 Bladder.M(5) TRUE 4 0 100.0 ESR1 (ER) Brain.N(3) FALSE 5 0 100.0 PAX8 Brain.N(3) FALSE 6 3 100.0 ESR1 (ER) Breast.M(11) TRUE 7 0 100.0 PAX8 Breast.M(11) TRUE 8 0 36.36364 ESR1 (ER) Cervix.M(11) TRUE 9 1 9.09091 ESR1 (ER) Cervix.M(11) TRUE 10 2 18.18182 ESR1 (ER) Cervix.M(11) TRUE 11 3 36.36364 ESR1 (ER) Cervix.M(11) TRUE palette - palette(gray(seq(0, 1,len=4))) trellis.par.set(list(par.xlab.text=list(cex=0.85) , superpose.polygon=list(col=palette()) , axis.text=list(cex=0.8))) barchart(percent~cellType|marker , groups=score , data=myData , stack=TRUE , xlab='N=Normal/Benign, M=Malignant' , ylab='Percentage of Cores Staining' , color=palette() , auto.key = list(points = FALSE, rectangles = TRUE, space = top) , scales=list(x=list(rot=70)) , layout=c(1,2)) I would like to make the color scheme of the bar differ according to the variable 'Malignant' and add a second color scheme to the key. I may not have understood what you are looking for, but it seems like you just need groups = interaction(score, Malignant) For example, palette - palette(gray(seq(0, 1,len=8))) trellis.par.set(list(par.xlab.text=list(cex=0.85) , superpose.polygon=list(col=palette()) , axis.text=list(cex=0.8))) barchart(percent~cellType|marker , groups= interaction(score, Malignant) , data=myData , stack=TRUE , xlab='N=Normal/Benign, M=Malignant' , ylab='Percentage of Cores Staining' # , color=palette() # not doing anything , auto.key = list(points = FALSE, rectangles = TRUE, space = top, columns = 2) , scales=list(x=list(rot=70)) , layout=c(1,2)) -Deepayan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question: RMySQL bulk load/update one column, dbWriteTable()?
I have a question reading using RMySQL trying to load one R vector into a table column. To be more specifically, the table is there populated. Now I add a new column and want to populate this. Okay, this is more of an SQL question now, but you could just use dbWriteTable and then do an multi-table update. dbGetQuery(con, select * from tmp) id name 1 1A 2 2B 3 3C 4 4D 5 5E dbSendQuery(con, alter table tmp add column r2 float) ## calculate some statistic for all or some ids in table x-dataframe(id=1:5, r2=c(.1, .4, .9, .4,.7)) dbWriteTable(con, r2tmp, x ) dbSendQuery(con, update tmp t, r2tmp r set t.r2=r.r2 where t.id=r.id) dbGetQuery(con, select * from tmp) id name r2 1 1A 0.1 2 2B 0.4 3 3C 0.9 4 4D 0.4 5 5E 0.7 Chris __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Spectral analysis
Hi all, I am dealing with paleoceanographic data and I have a C14 time serie and one other variable. I would like to perform a spectral analysis (fft or wavelet) and plot it. Unfortunately I don't know the exact script to do this. Does anybody could send me an example to perform my spectral analysis ? I Thank you David Changez de tête et de tenue tous les jours si vous le voulez ! Volez la vedette sur Yahoo! Québec Avatars [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] correspondence analysis
Thanks very much Jari, I appreciate your guidance. I trust R very much, the only thing I can do is to dig up the methodology behind the SPSS result (and of course behind the correspondence analysis itself). Regards, am Jari Oksanen wrote: Artem Mariupol artem.mariupol at gmail.com writes: Hello, I am new to R and I have a question about the difference between correspondence analysis in R and SPSS. This is the input table I am working with (4 products and 18 attributes): mytable 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 1 15 11 20 4 14 7 1 2 1 4 12 12 17 19 11 20 9 10 2 19 18 14 14 16 4 14 11 11 15 22 19 22 16 21 19 15 16 3 16 13 10 9 15 4 10 7 11 13 18 17 14 14 16 16 13 11 4 21 18 16 14 20 6 12 14 14 17 23 20 19 18 21 18 19 18 I found the function corresp() in the package MASS, but the results are different from the output in SPSS. Also, I don't understand the coordinates; in the biplot I cannot find a -2 limit for example from the first product on any of the x axes. At a quick look, there is nothing strange in the result. Have you contacted SPSS and asked them to explain their deviant results? It seems that biplot.correspondence is undocumented. However, it has argument 'type' which defaults to symmetric, other alternative being rows and columns. Intelligent guess is that this selects the scaling of row and column scores, and type=symmetric scales both. By selecting type=columns, only columns are scaled and the -2 value for a row will be displayed (which proves that the guess was correct). I don't have a clue how SPSS scales results, but I guess that the differences in the results may be due to different scalings. Function corresp gives you weighted orthonormal row and column scores, but scales these in the plot like specified. It may be that SPSS does the scaling already in the printout (and does not give you the choice of type?). Another possible source of difference is that corresp gives you canonical correlations whereas some other program or function may give you their squares, a.k.a. eigenvalues. Moreover, the sign is arbitrary so that negative and positive scores may be switched between programs. I hope this helps, Jari Oksanen __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/correspondence-analysis-tf3876129.html#a10997356 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Metropolis-Hastings Markov Chain Monte Carlo in Spatstat
I'm testing some different formulations of pairwise interaction point processes in Spatstat (version 1.11-6) using R 2.5.0 on a Windows platform and I wish to simulate them using the Metropolis-Hastings algorithm implemented with Spatstat. Spatstat utilizes Fortran77 code with the preprocessor RatFor to do the Metropolis-Hastings MCMC, but the Makefile is more complicated than any I have worked with. Any suggestions on how I could get started working with the Fortran code in conjunction with RatFor is appreciated. Sincerely, Kevin Kevin Packard Department of Forestry, PhD student Department of Statistics, MS student Virginia Polytechnic Institute and State University Blacksburg, Virginia, USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Spectral analysis
On 06-Jun-07 20:55:09, David LEDU wrote: Hi all, I am dealing with paleoceanographic data and I have a C14 time serie and one other variable. I would like to perform a spectral analysis (fft or wavelet) and plot it. Unfortunately I don't know the exact script to do this. Does anybody could send me an example to perform my spectral analysis ? I Thank you David There are a lot of possible ramifications to your query, but for a basic spectral analysis of a series you can use the function spectrum() in the stats package. What is the role of the other variable? Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 06-Jun-07 Time: 22:34:07 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
