Re: [R] How to install Defaults package offline
On Fri, 9 Apr 2010, dbonneau wrote: Hi, I just installed R software on my machine which is not supposed to have an internet access. I installed several package that I need, which are quantmod, xts, TTR etc. When I typed require(quantmod), I get Error: package 'Defaults' could not be loaded. How do you install Defaults package if you don't have an internet access ? Does anyone know where I can find the file so I can install it manually ? The same place you found the packages quantmod, xts and TTR? Defaults is a CRAN package, see http://cran.r-project.org/web/packages/Defaults/index.html Now, you did not tell us your OS, R version or whether you were looking for source or binary packages, so you made it maximally difficult for us to give more precise details. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [stats-rosuda-devel] How to update JGR
On Apr 9, 2010, at 6:10 PM, mau...@alice.it mau...@alice.it wrote: I recently updated R on Linus/SuSE 11.1 I complained because no on-line help was available from JGR after R update. I was told to update JGR as well. How can I do that ? I installed JGR on SuSE three times in the past with different R versions.Every time it's been a nightmare. I am afraid to have to spend a whole day, maybe longer, to update JGR ... I would greatly appreciate some clear guidelines for JGR installation/update on SuSE. Thank you in advance. The upgrade should be trivial as long as your system is properly setup - simply run update.packages(ask=FALSE, checkBuilt=TRUE) that works for all packages. If that fails then either R or Java on your system are not setup properly. Instructions for installing JGR from scratch on SuSE are at http://jgr.markushelbig.org/JGR_on_Linux.html If all that doesn't help all I can say if you want easier setup get a more user-firendy distro or system ;). Cheers, Simon __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ranking correlation with R
On 04/10/2010 01:22 AM, David Nemer wrote: Hey Everyone, Im fresh new in R, and Im supposed to write a code to give me a correlation between two rankings. So I have two ranking lists, which contain file names, e.g.: Ranking list 1: file1.java file3.java file2.java Ranking list 2: fiile2.java file4.java file1.java I need to see how much are these two ranking lists are alike, get a correlation between them. I dont even know where to start. Can anyone bring me some light or tips? Thank you in advance. Hi David, Are you sure you don't want the concordance between the rankings? If so, look at the irr package for some concordance functions. The example shows pretty much no concordance. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] interpolating between lat/long position data with time
cbarcelo wrote: Hello, I am currently working with satellite tracking data for an organism with irregularly spaced location data in space and time (point data is occasionally spaced by 1-10 days). I have 4 columns of data, Lat, Long, Date, Time. I would like to linearly interpolate my data set so that I have one position per day with attached time stamps. I am fairly new to R, any pointers on code for this would be most helpful! Thanks! Hi, Take a look at the Spatial Task view, this provides an introduction to all kinds spatial data processing in R. In addition, the R-sig-geo mailing list is a more suitable list to ask this question, you will probably get more response there. cheers, Paul -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ranking correlation with R
Try this: A - c(file1.java, file3.java, file2.java) B - c(file2.java, file4.java, file1.java) cor(A, B, method = spearman) [1] 0.5 On Fri, Apr 9, 2010 at 11:22 AM, David Nemer davidne...@gmail.com wrote: Hey Everyone, Im fresh new in R, and Im supposed to write a code to give me a correlation between two rankings. So I have two ranking lists, which contain file names, e.g.: Ranking list 1: file1.java file3.java file2.java Ranking list 2: fiile2.java file4.java file1.java I need to see how much are these two ranking lists are alike, get a correlation between them. I dont even know where to start. Can anyone bring me some light or tips? Thank you in advance. Cheers, -- David Nemer [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Brier's score for bootstrap sample (coxph)
paaventhan jeyaganth wrote: Dear all, How can i get brier's score for the bootsrap sample for survival analysis. this are the code i am using for the validation. f1 - cph(Surv(time,dead ) ~ strata(x1)+strata(x2)+strata(x3), x=TRUE, y=TRUE, surv=TRUE, time.inc=12, data=new) validate(f1,B=200,u=12,dxy=T) Thanks Paaveen You did not following the posting guide. You mixed two package; the functions you used did not match the subject line of your e-mail. You are attempting to validate a model containing no covariates, which is not impossible but will be noisy. You did not point to a function or package that claims to be able to compute a Brier score with censored data. Frank -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] minimization function
Hi all,
I am trying to minimize the quardratic form w'Aw, with certain
constraints.
In particular,
(1) A=(a_{ij}) is n by n matrix and it is symmetric positive definite,
a_{ii}=1 for all i;
and 0a_{ij}1 for i not equal j.
(2) w'1=n;
(3) w_{i}=0
Analytically, for n=2, it is easy to come up with a result. For larger n, it
seems
difficult to obtain the result.
Does any one know whether it is possible to use R to numerically compute it?
Thank you so much in advance!
Hannah
[[alternative HTML version deleted]]
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Re: [R] str: how to use no list recursively?
Try this: cat(gsub(:List of .*, , capture.output(str(x, no.list = TRUE))), sep = '\n') On Fri, Apr 9, 2010 at 11:11 PM, Jeff Brown dopethatwantsc...@yahoo.com wrote: Hi, In the help file for str(), the following line appears: no.list logical; if true, no ‘list of ...’ nor the class are printed. However, that appears to be true only on the top level; setting no.list to TRUE still leaves the remaining levels with the `list of ...' statement intact: x - list( + a = list(list()), + b = list(list()) + ); str(x) List of 2 $ a:List of 1 ..$ : list() $ b:List of 1 ..$ : list() str(x, no.list = TRUE) $ a:List of 1 ..$ : list() $ b:List of 1 ..$ : list() For readability reasons, I'd like to keep the indented $ signs and the names of the sub-lists but suppress printing of `List of ...'. Is that possible? Thanks, Jeff -- View this message in context: http://n4.nabble.com/str-how-to-use-no-list-recursively-tp1820073p1820073.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] use read.table for a partial reading
- Original Message - From: Covelli Paolo pcove...@tele2.it To: r-help@r-project.org Sent: Thursday, April 08, 2010 9:05 AM Subject: [R] use read.table for a partial reading Hi everyone, I've got a matrix data with 20 variables (V1, V2, V3, ...) and 215 rows (observations). I'm interested to read only the first and second variables using read.table function. How can I do? You do not provide a reproducible example (see http://www.R-project.org/posting-guide.html), so my comments are somewhat of a guess. Typically, when you read in data from a file in R, you read it into a 'data frame' not a matrix. (To earn more http://cran.r-project.org/doc/manuals/R-intro.html#Lists-and-data-frames) This is how you would get your data (the dataframe) in the form you desire: dat - read.table(mydata.txt, header = TRUE) dat2 - dat[,1:2] # contains just the first two variables, V1 and V2 Thanks in advance. Paolo. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] minimization function
On Sat, Apr 10, 2010 at 4:58 PM, li li hannah@gmail.com wrote:
I am trying to minimize the quardratic form w'Aw, with certain
constraints.
In particular,
(1) A=(a_{ij}) is n by n matrix and it is symmetric positive definite,
a_{ii}=1 for all i;
and 0a_{ij}1 for i not equal j.
(2) w'1=n;
(3) w_{i}=0
Analytically, for n=2, it is easy to come up with a result. For larger n, it
seems
difficult to obtain the result.
Does any one know whether it is possible to use R to numerically compute it?
And your decision variables are? Both w[i] and a[i,j] ?
Paul
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] use read.table for a partial reading
Try this also:
your_data - read.table('your_file.txt', colClasses = c('character',
'character', rep(NULL, 18)))
On Thu, Apr 8, 2010 at 11:05 AM, Covelli Paolo pcove...@tele2.it wrote:
Hi everyone,
I've got a matrix data with 20 variables (V1, V2, V3, ...) and 215 rows
(observations). I'm interested to read only the first and second variables
using read.table function. How can I do?
Thanks in advance.
Paolo.
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--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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Re: [R] minimization function
On Sat, Apr 10, 2010 at 5:13 PM, Paul Smith phh...@gmail.com wrote:
I am trying to minimize the quardratic form w'Aw, with certain
constraints.
In particular,
(1) A=(a_{ij}) is n by n matrix and it is symmetric positive definite,
a_{ii}=1 for all i;
and 0a_{ij}1 for i not equal j.
(2) w'1=n;
(3) w_{i}=0
Analytically, for n=2, it is easy to come up with a result. For larger n, it
seems
difficult to obtain the result.
Does any one know whether it is possible to use R to numerically compute it?
And your decision variables are? Both w[i] and a[i,j] ?
In addition, what do you mean by larger n? n = 20 is already large
(in your sense)?
Paul
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Read data in sequences
On 2010-04-09 10:04, Dieter Menne wrote:
RockO wrote:
I tried to find a solution in the search list, but I cannot find it. I
would like to read a .txt file with, let say, three variables, with two of
which have repeated values in a number a columns.
The variables: Treat, x1, x2.
The values:
A 2.5 3.4 2.7 5.6 5.7 5.4 10.1 9.4 ...
B 5.3 5.4 6.5 7.5 1.3 4.5 10.5 4.1 ...
...
In the first column, the letters represent the variable Treat, and the
sequence of numbers on a same line represent pairs of values for x1 and
x2.
Looks like SAS is quite elegant here (don't kill me, I could not afford
using SAS, R has save my retirement fund).
I would first read it in as usual, and do the reformatting later.
library(reshape)
wide = read.table(wideseq.txt,sep= )
# renames columns
names(wide) = c(varname,rep(c(x1,x2),ncol(wide)%/%2))
str(wide)
melt(wide)
Now you have the long format, which is not exactly what you want, but
typically much more useful in R than the format you require. You might use
one of the function in package reshape to get your format.
Almost. But you're a bit too clever with the names() because
melt() will just re-read the first x1, x2 values.
wide - as above ...
dm - melt(wide)
# replace dm$variable with appropriate factor
dm$variable - gl(2, 2, nrow(dm), c('x1','x2'))
# choose names for columns
names(dm) - c('Treat', 'x', 'value')
I agree that this 'long' format is usually most useful for
further analysis.
-Peter
--
Peter Ehlers
University of Calgary
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Re: [R] Read data in sequences
Try this. The data portion DF[-1] is transposed forming length 2 columns composed of successive elements of DF rows. This is then transposed back and the id's added in: # read in Lines - A 2.5 3.4 2.7 5.6 5.7 5.4 10.1 9.4 B 5.3 5.4 6.5 7.5 1.3 4.5 10.5 4.1 DF - read.table(textConnection(Lines)) # form required data frame data.frame(id = DF[gl(2,4),1], t(matrix(t(DF[-1]), 2))) On Fri, Apr 9, 2010 at 11:25 AM, RockO rock.oui...@gmail.com wrote: Dear R users, I tried to find a solution in the search list, but I cannot find it. I would like to read a .txt file with, let say, three variables, with two of which have repeated values in a number a columns. An example: The variables: Treat, x1, x2. The values: A 2.5 3.4 2.7 5.6 5.7 5.4 10.1 9.4 ... B 5.3 5.4 6.5 7.5 1.3 4.5 10.5 4.1 ... ... In the first column, the letters represent the variable Treat, and the sequence of numbers on a same line represent pairs of values for x1 and x2. In SAS, this type of dataset is easy to read using @@ as in: data a; input Treat @ x1 x2 @@; But I would like to know how to read it with R, to get rid of my addiction to SAS. Thank You, Rock Ouimet DRF-MRNF, Quebec -- View this message in context: http://n4.nabble.com/Read-data-in-sequences-tp1819487p1819487.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] I can´t run the example shown in the inline pa ckage
On 09.04.2010 17:43, satu wrote:
Dear Romain, you are right. Apologies, here is the complete result from your
script:
code- '#includeRdefines.h\nSEXP f(){\n return R_NilValue ; }'
writeLines( code, test.c )
system( R CMD SHLIB test.c )
gcc -IC:/R/R-210~1.1/include-O3 -Wall -std=gnu99 -c test.c -o
test.o
gcc -shared -s -o test.dll tmp.def test.o -LC:/R/R-210~1.1/bin -lR
dyn.load( test.so )
On Windows it is names test.dll.
Uwe Ligges
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared library 'C:/Documents and Settings/L01359.BCRA/Mis
documentos/R/test.so':
LoadLibrary failure: No se puede encontrar el módulo especificado.
.Call( f )
Error in .Call(f) : C symbol name f not in load table
The system(,,,) bit seems to work, but then errors show up
Sergio
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[R] writing function help
Hi, I have written a function, ( or 2 functions) becasue there are only tiny difference, One of them has lines == #c2 (price.mat) call option price c2=c( max(S.mat[1,3]-K,0), max(S.mat[2,3]-K,0), max(S.mat[3,3]-K,0) ) (some lines) list( Stock Value=round(S.mat,dp), Call Price=round(price.mat,dp), Phi=round(phi.mat,dp), Psi=round(psi.mat,dp) ) === and the other one is == #c2 (price.mat) put option price c2=c( max(K-S.mat[1,3],0), -difference max(K-S.mat[2,3],0), -difference max(K-S.mat[3,3],0) -difference ) (some lines) list( Stock Value=round(S.mat,dp), Put Price=round(price.mat,dp), -label difference Phi=round(phi.mat,dp), Psi=round(psi.mat,dp) ) === Can I combine them into one function? just by adding a 'dummy variable' say 'type' which takes call/put or values 1,2 The full codes are in attachment. Thanks! http://n4.nabble.com/file/n1835638/mycall.r mycall.r http://n4.nabble.com/file/n1835638/myput.r myput.r casper -- View this message in context: http://n4.nabble.com/writing-function-help-tp1835638p1835638.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] fill in values between rollapply
Dennis: I had never used the rep() function and that works out great, thank you. Brad -- View this message in context: http://n4.nabble.com/fill-in-values-between-rollapply-tp1816885p1835513.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] simple data import of .csv
Hello, I am a complete beginner to R. I use a mac and want to import and read a .csv dataset stored as .csv file. I understand I eventually enter - read.csv(size.csv, header=T) , but I can't get R to find my file, which is called size.csv and located /Users/davidoconnor/Desktop/Eart-125/size.csv Thank you very much! David -- View this message in context: http://n4.nabble.com/simple-data-import-of-csv-tp1835620p1835620.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple data import of .csv
Hello, I am a complete beginner to R. I use a mac and want to import and read a .csv dataset stored as .csv file. I understand I eventually enter - read.csv(size.csv, header=T) , but I can't get R to find my file, which is called size.csv and located /Users/davidoconnor/Desktop/Eart-125/size.csv Thank you very much! David -- View this message in context: http://n4.nabble.com/simple-data-import-of-csv-tp1835620p1835620.html Sent from the R help mailing list archive at Nabble.com. Two solutions: To find the file, use file.choose() e.g., my.file.name - file.choose()#and then use the normal mac tools to find the file my.data - read.csv(my.file.name,header=TRUE) or, if you want to just read it from the clipboard: library(psych) my.data - read.clipboard.csv()#after copying the data to the clipboard Bill __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for psychology http://personality-project.org/r It is 6 minutes to midnight http://www.thebulletin.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] minimization function
Hi, thanks for the reply.
A will be a given matrix satisfying condition 1. I want to find the
vector w that minimizes the
quadratic form. w satisfies condition 2.
2010/4/10 Paul Smith phh...@gmail.com
On Sat, Apr 10, 2010 at 5:13 PM, Paul Smith phh...@gmail.com wrote:
I am trying to minimize the quardratic form w'Aw, with certain
constraints.
In particular,
(1) A=(a_{ij}) is n by n matrix and it is symmetric positive
definite,
a_{ii}=1 for all i;
and 0a_{ij}1 for i not equal j.
(2) w'1=n;
(3) w_{i}=0
Analytically, for n=2, it is easy to come up with a result. For larger
n, it
seems
difficult to obtain the result.
Does any one know whether it is possible to use R to numerically compute
it?
And your decision variables are? Both w[i] and a[i,j] ?
In addition, what do you mean by larger n? n = 20 is already large
(in your sense)?
Paul
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http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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Re: [R] minimization function
Check out the quadprog package.
On Sat, Apr 10, 2010 at 5:36 PM, li li hannah@gmail.com wrote:
Hi, thanks for the reply.
A will be a given matrix satisfying condition 1. I want to find the
vector w that minimizes the
quadratic form. w satisfies condition 2.
2010/4/10 Paul Smith phh...@gmail.com
On Sat, Apr 10, 2010 at 5:13 PM, Paul Smith phh...@gmail.com wrote:
I am trying to minimize the quardratic form w'Aw, with certain
constraints.
In particular,
(1) A=(a_{ij}) is n by n matrix and it is symmetric positive
definite,
a_{ii}=1 for all i;
and 0a_{ij}1 for i not equal j.
(2) w'1=n;
(3) w_{i}=0
Analytically, for n=2, it is easy to come up with a result. For larger
n, it
seems
difficult to obtain the result.
Does any one know whether it is possible to use R to numerically compute
it?
And your decision variables are? Both w[i] and a[i,j] ?
In addition, what do you mean by larger n? n = 20 is already large
(in your sense)?
Paul
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http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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Re: [R] Rsge: recursive parallelization
On 04/09/2010 08:52 AM, Peter Danenberg wrote:
In principle, I'd like to be able to do something like this:
sge.parLapply(seq(10), function(x) parLapply(seq(x), function(x) x^2))
I'm not sure that's such a good principle! It seems like it would be
hard to think about the tasks that are being executed, how many
processes there are, how load balancing works, etc. What about starting
with some complicated data structure that requires processing
work - lapply(seq(10), function(x) as.list(seq(x)))
Then making a flat list of tasks that need to be done
idx0 - rep(seq_along(work), sapply(work, length))
idx1 - unlist(lapply(work, seq_along))
tasks - mapply(c, idx0, idx1, SIMPLIFY=oFALSE)
and actually do the work in an easily parallelizable lapply
answers - lapply(tasks, function(t, w) w[[ t ]]^2, work)
(the idea here is that work[[ c(3, 2) ]] selects the third element of
the outer list, and then the second element of that element). You could
transform the result back into the original form with
result - work
for (t in seq_along(tasks))
result[[ tasks[[t]] ]] - answers[[t]]
Martin
In practice, however, I have to resort to acrobatics like this:
sge.options(sge.remove.files=FALSE)
sge.options(sge.qsub.options='-cwd -V')
sge.parLapply(seq(10),
function(x) {
sge.options(sge.save.global=TRUE)
sge.options(sge.remove.files=FALSE)
sge.parLapply(seq(x),
function(x) x^2,
cluster=TRUE,
debug=FALSE,
trace=FALSE,
file.prefix='Rsge_data',
global.savelist=NULL,
packages=NULL)
},
function.savelist=c('sge.parLapply', 'sge.parParApply',
'sge.options', 'sge.taskPrep'),
global.savelist=c('sge.parParApply', 'sge.globalPrep',
'global.savelist', 'sge.taskPrep', 'sge.checkNotNow',
'sge.get.jobid', 'sge.get.result', 'docall',
'enquote'),
packages=NULL)
and I still get bizarre behavior: half of the results will be NULL,
for instance; the other half, incomplete.
Would non-trivial changes to Rsge be required to make something like
this possible?
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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Re: [R] fill in values between rollapply
Here are two solutions. Assuming x is a zoo object both return zoo objects: 1. rollapply with na.pad and na.locf: r - rollapply(x, 5, mean, by = 5, align = left, na.pad = TRUE) na.locf(r) 2. or try this which does not use rollapply at all but assumes x is 1 dimensional: n - length(x) a - ave(x, gl(n, 5, n), FUN = mean) On Fri, Apr 9, 2010 at 3:32 AM, Brad Patrick Schneid bpsch...@gmail.com wrote: Hi, Sorry ahead of time for not including data with this question. Using rollapply to calculate mean values for 5 day blocks, I'd use this: Roll5mean - rollapply(data, 5, mean, by=5, align = c(left)) My question is, can someone tell me how to fill in the days between each of these means with the previously calculated mean? If this doesn't make sense, I will clarify and provide data for an example. Thanks. Brad -- View this message in context: http://n4.nabble.com/fill-in-values-between-rollapply-tp1816885p1816885.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] .Call function crashes initializing matrix
Hello, I have a C function that I call from R using .Call. I recently discovered a bug in my code, and I am not sure if it is a problem with what I am doing in C or if it has something to do with my use of .Call. I have narrowed my problem down to these two C statements: int size = 5000; double matrix[size][size]; When I run this in R it crashes, with this message: *** caught segfault *** address 0xb4141d70, cause 'memory not mapped' It has no problem when size is smaller, like 50. Any idea what is going on? Thanks!, Erik sessionInfo() R version 2.10.1 (2009-12-14) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] selecting certain columns or rows from a .csv
Hello, I'm using read.csv(filename,header=TRUE) but need to extract just certain columns or rows from the file. Much thanks. -- View this message in context: http://n4.nabble.com/selecting-certain-columns-or-rows-from-a-csv-tp1835692p1835692.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple data import of .csv
Perfect, thank you!! -- View this message in context: http://n4.nabble.com/simple-data-import-of-csv-tp1835620p1835678.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple data import of .csv
A related question: how do I make R return only one column or row of the .csv file. For example, I have about 1000 rows and three columns - can I import only certain rows or columns, like just column 1? Thank you!!! -- View this message in context: http://n4.nabble.com/simple-data-import-of-csv-tp1835620p1835683.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple data import of .csv
For that size file, it is the easiest to read in the entire file and then index just the portion that you want. On Sat, Apr 10, 2010 at 5:38 PM, doconnor oconnor.davi...@gmail.com wrote: A related question: how do I make R return only one column or row of the .csv file. For example, I have about 1000 rows and three columns - can I import only certain rows or columns, like just column 1? Thank you!!! -- View this message in context: http://n4.nabble.com/simple-data-import-of-csv-tp1835620p1835683.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] selecting certain columns or rows from a .csv
?read.csv colCLasses nrows On Sat, Apr 10, 2010 at 6:11 PM, doconnor oconnor.davi...@gmail.com wrote: Hello, I'm using read.csv(filename,header=TRUE) but need to extract just certain columns or rows from the file. Much thanks. -- View this message in context: http://n4.nabble.com/selecting-certain-columns-or-rows-from-a-csv-tp1835692p1835692.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] writing function (plot problem）
Hi, === x=rnorm(20) y=rnorm(20) t=lm(y~x) plot(t) === you will get click or hit enter to next page... how do I write a function to archieve this ? say plot(x,y) then pause, wait plot(y,x) Thanks! casper -- View this message in context: http://n4.nabble.com/writing-function-plot-problem-tp1835723p1835723.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] writing function (plot problem）
?devAskNewPage On Sat, Apr 10, 2010 at 7:49 PM, casperyc caspe...@hotmail.co.uk wrote: Hi, === x=rnorm(20) y=rnorm(20) t=lm(y~x) plot(t) === you will get click or hit enter to next page... how do I write a function to archieve this ? say plot(x,y) then pause, wait plot(y,x) Thanks! casper -- View this message in context: http://n4.nabble.com/writing-function-plot-problem-tp1835723p1835723.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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 that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] .Call function crashes initializing matrix
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Erik Wright Sent: Saturday, April 10, 2010 3:23 PM To: r help Subject: [R] .Call function crashes initializing matrix Hello, I have a C function that I call from R using .Call. I recently discovered a bug in my code, and I am not sure if it is a problem with what I am doing in C or if it has something to do with my use of .Call. I have narrowed my problem down to these two C statements: int size = 5000; double matrix[size][size]; When I run this in R it crashes, with this message: *** caught segfault *** address 0xb4141d70, cause 'memory not mapped' You may be overflowing the stack. Allocate the space for 'matrix' with the allocation functions described in section 5.9 of Writing R Extensions. They allocate space on the 'heap', which has much more space than the stack (where space for 'automatic' variables is allocated). Typical stack sizes are on the order of few megabytes and typical heap sizes are in the gigabytes. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com It has no problem when size is smaller, like 50. Any idea what is going on? Thanks!, Erik sessionInfo() R version 2.10.1 (2009-12-14) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plotting rpart objects, text.rpart, fancy option
I have created plots of rpart objects with the fancy option for text.rpart (fancy creates ellipses and rectangles and labels branches with splitting criteria). The ellipses and rectangles are supposed to interrupt the tree lines (as seen in Therneau and Atkinson 1997, page 48, Fig. 18, http://www.mayo.edu/hsr/techrpt/61.pdf), but they do not, even when I use Therneau and Atkinson's code. plot(tree, uniform = T, branch = 0.2, compress = T, margin = 0.1) text(tree, all = T, use.n=T, fancy = T) How do I interrupt the tree lines? Thank you, Claudia [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using BLAT in r
Does anyone know how to use BLAT(Blast-Like alignment tool) in R? Thanks and regards. -- Fahim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Expectation of E(x^1/2)
Hi all, I am trying to find the expectation of x^1/2 where x~N(a,b) ( Normal with mean a and variance b). Any feedback would be highly appreciated. Have great day ! Haneef [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Expectation of E(x^1/2)
Dear Haneef, Pls see if this suits your requirement. sim.norm = rnorm(1,mean=a,sd=sqrt(b)) mean.est = mean(sqrt(sim.norm)) Thx S. On Sat, Apr 10, 2010 at 9:31 PM, Haneef Anver hane...@yahoo.com wrote: Hi all, I am trying to find the expectation of x^1/2 where x~N(a,b) ( Normal with mean a and variance b). Any feedback would be highly appreciated. Have great day ! Haneef [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] selecting certain columns or rows from a .csv
dataFile = read.csv(filename.csv,header= TRUE); #suppose u want col 1, col 9 and col 15 col1 = 1; col9 = 9; col15 = 15; modifiedDataFile1 = dataFile[,c(col1, col9, col15)]; #if u want rows from 1-100 and then 1000-5000 modifiedDataFile2 = dataFile[c(1:100, 1000:5000), ]; #If u want to select rows and col simultaneously as specified above then modifiedDataFile = dataFile[c(1:100, 1000:5000), c(col1, col9, col15)]; Hope this will work. Thanks Fahim Mohammad Grad student CECS, Univ of Louisville -- View this message in context: http://n4.nabble.com/selecting-certain-columns-or-rows-from-a-csv-tp1835692p1835760.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using BLAT in r
I am trying to use blat in R. I couldn't find any package in CRAN or bioconductor. I downloaded the windows executable from Jim Kent's (from ucsc) webpage. I was wondering how to use/call these executables or functions embedded in these executables. I am seeking for some direction or some material that addresses such problem. Help appreciated. Thanks -Fahim Mohammad cecs, univ of Louisville -- View this message in context: http://n4.nabble.com/using-BLAT-in-r-tp1835763p1835763.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Expectation of E(x^1/2)
On Sat, 10 Apr 2010, Haneef Anver wrote: Hi all, I am trying to find the expectation of x^1/2 where x~N(a,b) ( Normal with mean a and variance b). Any feedback would be highly appreciated. Start by constructing plots of x vs Re(sqrt(x)) and x vs Im(sqrt(x)) for -1 x 1. Do it by hand. With that plot as a hint you will see how to use integrate() to find the answer. See ?integrate BTW, you can get both the real and imaginary compoenents with one call to integrate(). HTH, Chuck Have great day ! Haneef [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Expectation of E(x^1/2)
Haneef Anver haneef9 at yahoo.com writes: I am trying to find the expectation of x^1/2 where x~N(a,b) ( Normal with mean a and variance b). Any feedback would be highly appreciated. I have no idea at the moment how to start doing this analytically, but is this at all helpful? mean(sqrt(complex(re=rnorm(100 [1] 0.4114712+0.4103866i __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Expectation of E(x^1/2)
Chuck showed how to do this: fn - function(x) sqrt(x) * dnorm(x) integrate(fn, 0, Inf) 0.4110895 with absolute error 4.7e-05 So the (almost) exact answer is 0.4110895 + 1i * 0.4110895 Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: Ben Bolker bol...@ufl.edu Date: Sunday, April 11, 2010 1:00 am Subject: Re: [R] Expectation of E(x^1/2) To: r-h...@stat.math.ethz.ch Haneef Anver haneef9 at yahoo.com writes: I am trying to find the expectation of x^1/2 where x~N(a,b) ( Normal with mean a and variance b). Any feedback would be highly appreciated. I have no idea at the moment how to start doing this analytically, but is this at all helpful? mean(sqrt(complex(re=rnorm(100 [1] 0.4114712+0.4103866i __ R-help@r-project.org mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Expectation of E(x^1/2)
And Mathematica says
In[2]:= 1/Sqrt[2 Pi] Integrate[Exp[-x^2/2] Sqrt[x],{x,0,Infinity}]
3
Gamma[-]
4
Out[2]= -
3/4
2Sqrt[Pi]
(I suppose there's probably a change-of-variables trick to do this ...)
in R:
gamma(3/4)/(2^(3/4)*sqrt(pi))
[1] 0.4110895
Ravi Varadhan wrote:
Chuck showed how to do this:
fn - function(x) sqrt(x) * dnorm(x)
integrate(fn, 0, Inf)
0.4110895 with absolute error 4.7e-05
So the (almost) exact answer is 0.4110895 + 1i * 0.4110895
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