Re: [R] radial.plot(plotrix) - plotting multiple polygons?
Stefan Uhmann wrote: Dear List, Dear Jim, is it possible to draw multiple polygons with different line types? lty=c or line.lty=c do not work with radial.plot (in the matrix case) as well as add=TRUE. Hi Stefan, As this is the second request for multiple line characteristics this week, I suppose I should get to work on it. I'll see if I can solve it without breaking any code that is already written using radial.plot. 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.
[R] Value Lookup from File without Slurping
Dear all, I have a repository file (let's call it repo.txt) that contain two columns like this: # tag value AAA0.2 AAT0.3 AAC 0.02 AAG 0.02 ATA0.3 ATT 0.7 Given another query vector qr - c(AAC, ATT) I would like to find the corresponding value for each query above, yielding: 0.02 0.7 However, I want to avoid slurping whole repo.txt into an object (e.g. hash). Is there any ways to do that? The reason I want to do that because repo.txt is very2 large size (milions of lines, with tag length 30 bp), and my PC memory is too small to keep it. - Gundala Viswanath Jakarta - Indonesia __ 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] Value Lookup from File without Slurping
On Fri, 2009-01-16 at 18:02 +0900, Gundala Viswanath wrote: Dear all, I have a repository file (let's call it repo.txt) that contain two columns like this: # tag value AAA0.2 AAT0.3 AAC 0.02 AAG 0.02 ATA0.3 ATT 0.7 Given another query vector qr - c(AAC, ATT) I would like to find the corresponding value for each query above, yielding: 0.02 0.7 However, I want to avoid slurping whole repo.txt into an object (e.g. hash). Is there any ways to do that? The reason I want to do that because repo.txt is very2 large size (milions of lines, with tag length 30 bp), and my PC memory is too small to keep it. - Gundala Viswanath Jakarta - Indonesia Hello, You can always store your repo.txt into a database, say, SQLite, and select only the values you want via an SQL query. Thus, you will prevent loading the full file into memory. Best regards, Carlos J. Gil Bellosta http://www.datanalytics.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] Value Lookup from File without Slurping
you might try to iteratively read a limited number of line of lines in a
batch using readLines:
# filename, the name of your file
# n, the maximal count of lines to read in a batch
connection = file(filename, open=rt)
while (length(lines - readLines(con=connection, n=n))) {
# do your stuff here
}
close(connection)
?file
?readLines
vQ
Gundala Viswanath wrote:
Dear all,
I have a repository file (let's call it repo.txt)
that contain two columns like this:
# tag value
AAA0.2
AAT0.3
AAC 0.02
AAG 0.02
ATA0.3
ATT 0.7
Given another query vector
qr - c(AAC, ATT)
I would like to find the corresponding value for each query above,
yielding:
0.02
0.7
However, I want to avoid slurping whole repo.txt into an object (e.g. hash).
Is there any ways to do that?
The reason I want to do that because repo.txt is very2 large size
(milions of lines,
with tag length 30 bp), and my PC memory is too small to keep it.
__
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] reading data from Excel Spread sheet
Hi all, I tried to read data from Excel spread sheet with using read.csv(file.choose()) and read.delim(file.choose()) but its showing *ÐÏ.à.*. and also i tried with read.table(file.choose()) then its showing* V1 1 ÐÏ\021ࡱ* can any one suggest how to read data from Excel Spread sheet thanks regards; kiran [[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] Value Lookup from File without Slurping
The sqldf package can read a large file to a database without going through R followed by extracting it. The package makes it easier to use RSQLite by setting up the database for you and after extracting the portion you want removing the database automatically. You can specify all this in two lines: one to name the file and one to specify the extraction using SQL. See the examples in example 6 on the home page: http://sqldf.googecode.com#Example_6._File_Input On Fri, Jan 16, 2009 at 4:12 AM, Carlos J. Gil Bellosta c...@datanalytics.com wrote: On Fri, 2009-01-16 at 18:02 +0900, Gundala Viswanath wrote: Dear all, I have a repository file (let's call it repo.txt) that contain two columns like this: # tag value AAA0.2 AAT0.3 AAC 0.02 AAG 0.02 ATA0.3 ATT 0.7 Given another query vector qr - c(AAC, ATT) I would like to find the corresponding value for each query above, yielding: 0.02 0.7 However, I want to avoid slurping whole repo.txt into an object (e.g. hash). Is there any ways to do that? The reason I want to do that because repo.txt is very2 large size (milions of lines, with tag length 30 bp), and my PC memory is too small to keep it. - Gundala Viswanath Jakarta - Indonesia Hello, You can always store your repo.txt into a database, say, SQLite, and select only the values you want via an SQL query. Thus, you will prevent loading the full file into memory. Best regards, Carlos J. Gil Bellosta http://www.datanalytics.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] reading data from Excel Spread sheet
Hi, http://tolstoy.newcastle.edu.au/R/e2/help/06/12/6702.html Cheers, Thomas venkata kirankumar schrieb: Hi all, I tried to read data from Excel spread sheet with using read.csv(file.choose()) and read.delim(file.choose()) but its showing *ÐÏ.à.*. and also i tried with read.table(file.choose()) then its showing* V1 1 ÐÏ\021ࡱ* can any one suggest how to read data from Excel Spread sheet thanks regards; kiran [[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] reading data from Excel Spread sheet
See the 'R Data Import/Export' manual (and please study the posting guide, which asked you to check the manuals before posting). On Fri, 16 Jan 2009, venkata kirankumar wrote: Hi all, I tried to read data from Excel spread sheet with using read.csv(file.choose()) and read.delim(file.choose()) but its showing *??.??*. and also i tried with read.table(file.choose()) then its showing* V1 1 ??\021ࡱ* can any one suggest how to read data from Excel Spread sheet thanks regards; kiran [[alternative HTML version deleted]] -- 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.
[R] faster version of split()?
Hi all,
I want to calculate the number of unique observations of y in each level
of x from my data frame df.
this does the job but it is very slow for this big data frame (159503 rows,
11 columns).
group.list - split(df$y,df$x)
count - function(x) length(unique(na.omit(x)))
sapply(group.list, count, USE.NAMES=TRUE)
I couldnt find the answer searching for slow split and split time on
help forum.
I am running R version 2.2.1, on a machine with 4gb of memory and I'm using
windows 2000.
thanks in advance,
Simon.
- Original Message -
From: Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no
To: Gundala Viswanath gunda...@gmail.com
Cc: R help r-h...@stat.math.ethz.ch
Sent: Friday, January 16, 2009 9:30 AM
Subject: Re: [R] Value Lookup from File without Slurping
you might try to iteratively read a limited number of line of lines in a
batch using readLines:
# filename, the name of your file
# n, the maximal count of lines to read in a batch
connection = file(filename, open=rt)
while (length(lines - readLines(con=connection, n=n))) {
# do your stuff here
}
close(connection)
?file
?readLines
vQ
Gundala Viswanath wrote:
Dear all,
I have a repository file (let's call it repo.txt)
that contain two columns like this:
# tag value
AAA0.2
AAT0.3
AAC 0.02
AAG 0.02
ATA0.3
ATT 0.7
Given another query vector
qr - c(AAC, ATT)
I would like to find the corresponding value for each query above,
yielding:
0.02
0.7
However, I want to avoid slurping whole repo.txt into an object (e.g.
hash).
Is there any ways to do that?
The reason I want to do that because repo.txt is very2 large size
(milions of lines,
with tag length 30 bp), and my PC memory is too small to keep it.
__
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] Value Lookup from File without Slurping
Something like this should work
library(R.utils)
out = numeric()
qr = c(AAC, ATT)
n =countLines(test.txt)
file = file(test.txt, r)
for (i in 1:n){
line = readLines(file, n = 1)
A = strsplit (line, split = )[[1]][1]
if(is.element(A, qr)) {
value = as.numeric(strsplit (line, split = )[[1]][2])
out = c(out, value)
}
}
You may want to improve execution speed by reading data in chunks
instead of line by line. Code requires a little modification
Carlos J. Gil Bellosta wrote:
On Fri, 2009-01-16 at 18:02 +0900, Gundala Viswanath wrote:
Dear all,
I have a repository file (let's call it repo.txt)
that contain two columns like this:
# tag value
AAA0.2
AAT0.3
AAC 0.02
AAG 0.02
ATA0.3
ATT 0.7
Given another query vector
qr - c(AAC, ATT)
I would like to find the corresponding value for each query above,
yielding:
0.02
0.7
However, I want to avoid slurping whole repo.txt into an object (e.g. hash).
Is there any ways to do that?
The reason I want to do that because repo.txt is very2 large size
(milions of lines,
with tag length 30 bp), and my PC memory is too small to keep it.
- Gundala Viswanath
Jakarta - Indonesia
Hello,
You can always store your repo.txt into a database, say, SQLite, and
select only the values you want via an SQL query.
Thus, you will prevent loading the full file into memory.
Best regards,
Carlos J. Gil Bellosta
http://www.datanalytics.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] function return output
Hi, I wrote the function which outputs a matrix 'c' and a single value 'd',
as follows (simplified example):
procedure - function(a,b){
...
list(c,d)
}
now I want to use 'c' and 'd' in code as follows:
d - matrix(0,1,1)
value - procedure(a,b)
and d[1,1] - value[2] breaks telling that:
Error in d[1, 1] : incorrect number of dimensions
What I did wrong??, best, robert
--
View this message in context:
http://www.nabble.com/function-return-output-tp21496413p21496413.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] faster version of split()?
Maybe:
with(df, tapply(y, x, count))
On Fri, Jan 16, 2009 at 8:10 AM, Simon Pickett simon.pick...@bto.orgwrote:
Hi all,
I want to calculate the number of unique observations of y in each level
of x from my data frame df.
this does the job but it is very slow for this big data frame (159503 rows,
11 columns).
group.list - split(df$y,df$x)
count - function(x) length(unique(na.omit(x)))
sapply(group.list, count, USE.NAMES=TRUE)
I couldnt find the answer searching for slow split and split time on
help forum.
I am running R version 2.2.1, on a machine with 4gb of memory and I'm using
windows 2000.
thanks in advance,
Simon.
- Original Message - From: Wacek Kusnierczyk
waclaw.marcin.kusnierc...@idi.ntnu.no
To: Gundala Viswanath gunda...@gmail.com
Cc: R help r-h...@stat.math.ethz.ch
Sent: Friday, January 16, 2009 9:30 AM
Subject: Re: [R] Value Lookup from File without Slurping
you might try to iteratively read a limited number of line of lines in a
batch using readLines:
# filename, the name of your file
# n, the maximal count of lines to read in a batch
connection = file(filename, open=rt)
while (length(lines - readLines(con=connection, n=n))) {
# do your stuff here
}
close(connection)
?file
?readLines
vQ
Gundala Viswanath wrote:
Dear all,
I have a repository file (let's call it repo.txt)
that contain two columns like this:
# tag value
AAA0.2
AAT0.3
AAC 0.02
AAG 0.02
ATA0.3
ATT 0.7
Given another query vector
qr - c(AAC, ATT)
I would like to find the corresponding value for each query above,
yielding:
0.02
0.7
However, I want to avoid slurping whole repo.txt into an object (e.g.
hash).
Is there any ways to do that?
The reason I want to do that because repo.txt is very2 large size
(milions of lines,
with tag length 30 bp), and my PC memory is too small to keep it.
__
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.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Smooth periodic splines
Hello group! Is there a package that allows to fit smooth *periodic* splines to data? I'm interested in a function which combines the functionality of smooth.spline and splines::periodicSpline. Thanks, Andrey __ 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] faster version of split()?
df = data.frame(x = sample(7:9, 100, rep = T), y = sample(1:5, 100, rep
= T))
fun = function(x){length(unique(x))}
by(df$x, df$y, fun)
Simon Pickett wrote:
Hi all,
I want to calculate the number of unique observations of y in each
level of x from my data frame df.
this does the job but it is very slow for this big data frame (159503
rows, 11 columns).
group.list - split(df$y,df$x)
count - function(x) length(unique(na.omit(x)))
sapply(group.list, count, USE.NAMES=TRUE)
I couldnt find the answer searching for slow split and split time
on help forum.
I am running R version 2.2.1, on a machine with 4gb of memory and I'm
using windows 2000.
thanks in advance,
Simon.
- Original Message - From: Wacek Kusnierczyk
waclaw.marcin.kusnierc...@idi.ntnu.no
To: Gundala Viswanath gunda...@gmail.com
Cc: R help r-h...@stat.math.ethz.ch
Sent: Friday, January 16, 2009 9:30 AM
Subject: Re: [R] Value Lookup from File without Slurping
you might try to iteratively read a limited number of line of lines in a
batch using readLines:
# filename, the name of your file
# n, the maximal count of lines to read in a batch
connection = file(filename, open=rt)
while (length(lines - readLines(con=connection, n=n))) {
# do your stuff here
}
close(connection)
?file
?readLines
vQ
Gundala Viswanath wrote:
Dear all,
I have a repository file (let's call it repo.txt)
that contain two columns like this:
# tag value
AAA 0.2
AAT 0.3
AAC 0.02
AAG 0.02
ATA 0.3
ATT 0.7
Given another query vector
qr - c(AAC, ATT)
I would like to find the corresponding value for each query above,
yielding:
0.02
0.7
However, I want to avoid slurping whole repo.txt into an object
(e.g. hash).
Is there any ways to do that?
The reason I want to do that because repo.txt is very2 large size
(milions of lines,
with tag length 30 bp), and my PC memory is too small to keep it.
__
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-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] Fitting of lognormal distribution to lower tail experimental data
Hi, I am beginner with R and need firm guidance with my problem. I have seen some other threads discussing the subject of right censored data, but I am not sure whether or not this problem can be regarded as such. Data: I have a vector with laboratory test data (strength of wood specimens, example attached as txt-file). This data is the full sample. It is a common view that this kind of data follows a lognormal distribution. Background: When fitting a distribution to the lower tail, it will usually be very different compared to fitting the whole data. The lower tail COV is the decisive measure in my analysis (due to resistance estimations of buildings). Problem: I would like to fit a lognormal distribution to the 10%-lower tail of the attached data. Question: Which function would you recommend me to use, and how to formulate it in R using the attached data? Best regards, Mattias Brännström PhD student Luleå Technical University14.8104060497551 16.0803849713769 17.4968110450967 20.1117010953086 21.6845345194074 22.1964808750696 22.6873957765245 22.7739430649247 23.9264878434242 24.0222175448625 24.2589089305143 25.0916485959638 25.6616713982665 26.42372554061 27.1110230291713 27.5506997537485 27.7723436488626 28.5526342456366 28.5937291162256 28.9858602338711 29.0613508454069 29.0909808586811 29.2550164645902 29.2592989298793 29.6618509042981 29.9425395348144 30.2713842375835 30.3578677416218 30.3691588410138 30.3828682984843 30.4226905469563 30.5067979753883 30.5374335721223 30.5377759972106 30.5388417498134 30.6197685055474 30.7562765495333 30.859344040433 31.0055304357074 31.1385745478821 31.2613609610913 31.3581765472267 31.3786215131359 31.3862882622892 31.5134036026533 31.5518777553211 31.6665459342876 31.6966977981316 31.7570612273693 31.7921492877195 31.8916639064893 32.0060685276589 32.0175653961169 32.0957893864849 32.2300707106859 32.2332967187291 32.2933752614657 32.3576534230736 32.4077953094961 32.440737957141 32.4555840754853 32.5778411557745 32.8123917532014 32.8938018752775 32.9005162471121 33.07109861048 33.2169544508162 33.2528421050785 33.2538040913417 33.2629253254612 33.5137399745455 33.646430499 33.6635730620378 33.8081149852229 33.9678615607469 34.0229870935982 34.1334960727572 34.2686698621255 34.281848082171 34.2835695816904 34.285140119695 34.3103279775051 34.3231318200957 34.3298117057378 34.3580807993554 34.375123159033 34.4358460611865 34.6628865380987 34.6882398181505 34.7138670512661 34.8319635103069 34.8543564286965 34.8740064707112 34.8831091812053 35.0783682108864 35.1589202345914 35.1940609286179 35.1963400807163 35.2225030547279 35.2948450801441 35.469980224983 35.4834158010586 35.5066986045073 35.50715377932 35.5581064872091 35.5929578196659 35.6202992874957 35.8503591228778 35.8864712453884 35.9236676029501 36.0272009858509 36.0582893169656 36.0697828249579 36.0733810205568 36.0796120864424 36.1046602505238 36.2146409925046 36.2439056981677 36.2519350403298 36.322995147923 36.3325951679294 36.3998442944923 36.4825302220394 36.5356445443208 36.542777089046 36.5472978834097 36.6042330833268 36.6859461526364 36.7276360969522 36.7559303592816 36.7634229191255 36.763717634632 36.7941371199203 36.7963035045816 37.0158687639306 37.0348436474432 37.0682601112198 37.0753839210413 37.1072512130614 37.218572715278 37.2365135026929 37.308997089496 37.4740533868667 37.5061839013662 37.5920632597573 37.5985612515559 37.6442491468094 37.7885711256696 37.8031769603556 37.8044638170924 37.8758257907878 37.9492755772546 37.9684449085749 38.1925855742105 38.3276830837628 38.36856145824 38.425438354474 38.4871152468451 38.5850141197061 38.7021862984193 38.7281733035293 38.7906053310133 38.8167873845123 38.879602998118 38.9257736530842 39.1219500124099 39.126766061353 39.1572739123381 39.1854685896754 39.2465242986911 39.2681394600736 39.3020749787304 39.3491652552564 39.3519847700339 39.4481343103317 39.4641601623938 39.495558462879 39.5276929723755 39.5743412754252 39.641904265762 39.6805873230154 39.7328651773131 39.7425791919387 39.7862127456679 39.7862858916594 39.8029935150385 39.8184701961103 39.83254032456 39.860678129295 39.9503278266256 39.9590265687971 39.9757707281345 40.0615365250434 40.1029961842667 40.1057284653796 40.2691606972348 40.2757445303632 40.3168035819963 40.3293541033457 40.5323828990285 40.5968897591303 40.6751634982263 40.6988406405023 40.7068328640941 40.7675314086004 40.7776623368738 40.7908603255974 40.7955349906672 40.8035933414247 40.9383315440048 40.9558208833268 40.9606594573753 40.9784894747295 41.0046771495095 41.0177042749474 41.1282624024752 41.1359777151937 41.1980177115138 41.2528202892208 41.4075724424903 41.4116661876018 41.4467994208966 41.4552126570036 41.4568329047393 41.6507621039357 41.7203545510097 41.7436507425138 41.7725271219265 41.8136233981782 41.8338507732199 41.9178452756984 41.9378524875993 41.9424929587518 42.0160174497851 42.0327031030869 42.0695865194719 42.1050583647999 42.154742564893 42.2913255282883
Re: [R] snow and different R versions
Just for the records. The problem was that the R version Rscript starts is determined at compile time, and I had to move my R installation to another place for some technical reasons. At the compile-time place there was another R version and Rscript started that one. The solution was to create a dummy rscript file that sets up the RHOME environment variable for the real Rscript: - #! /bin/sh export RHOME=/home/gabor/software/lib64/R /home/gabor/software/lib64/R/bin/Rscript $@ - and then use this file with snow, via the setDefaultClusterOptions function or some other way. Gabor On Tue, Jan 13, 2009 at 1:40 AM, l...@stat.uiowa.edu wrote: As far as I can tell looking at the code and running on my stytem this should use the one in rscript if you are starting via makeCluster or makeMPIcluster. You might double check by doing debug(makeMPIcluster) and stepping through and looking at what is uses in the call to mpi.comm.spawn for mpitask and args. luke On Fri, 9 Jan 2009, Gábor Csárdi wrote: Dear Luke and others, I have many R versions on my machine and want to start a particular one when snow builds its cluster. (The same version I start snow from.) It seems that everything is set up correctly in defaultClusterOptions: mget(ls(defaultClusterOptions), defaultClusterOptions) $homogeneous [1] TRUE $manual [1] FALSE $master nodename maya.unil.ch $outfile [1] /dev/null $port [1] 10187 $rhome R_HOME sessionInfo() R version 2.8.0 (2008-10-20) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] snow_0.3-3 /home/gabor/software/lib64/R $rlibs R_LIBS /usr/lib64/R/library:/usr/share/R/library $rprog [1] /home/gabor/software/lib64/R/bin/R $rscript [1] /home/gabor/software/lib64/R/bin/Rscript $rshcmd [1] ssh $scriptdir [1] /home/gabor/.R/library/snow $snowlib [1] /home/gabor/.R/library $timeout [1] 31536000 $type [1] MPI $user user gabor $useRscript [1] TRUE but snow still starts a different version, the one in /usr/bin/R. Is this a bug? If not, how can I tell snow to start the same version, the one that is listed in defaultClusterOptions? Thanks, Gabor sessionInfo() R version 2.8.0 (2008-10-20) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] snow_0.3-3 -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: l...@stat.uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu -- Gabor Csardi gabor.csa...@unil.ch UNIL DGM __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Value Lookup from File without Slurping
if the file is really large, reading it twice may add considerable penalty:
r...@quantide.com wrote:
Something like this should work
library(R.utils)
out = numeric()
qr = c(AAC, ATT)
n =countLines(test.txt)
# 1st pass
file = file(test.txt, r)
for (i in 1:n){
# 2nd pass
line = readLines(file, n = 1)
A = strsplit (line, split = )[[1]][1]
if(is.element(A, qr)) {
value = as.numeric(strsplit (line, split = )[[1]][2])
out = c(out, value)
}
}
if this is a one-go task, counting the lines does not pay, and why
bother. if this is a repetitive task, a database-based solution will
probably be a better idea.
vQ
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Re: [R] Value Lookup from File without Slurping
I agree on the database solution.
Database are the rigth tool to solve this kind of problem.
Only consider the start up cost of setting up the database. This could
be a very time consuming task if someone is not familiar with database
technology.
Using file() is not a real reading of all the file. This function will
simply open a connection to the file without reading it.
countLines should do something lile wc -l from a bash shell
I would say that if this is a one time job this solution should work
even thought is not the fastest. In case this job is a repetitive one,
then a database solution is surely better
A.
Wacek Kusnierczyk wrote:
if the file is really large, reading it twice may add considerable penalty:
r...@quantide.com wrote:
Something like this should work
library(R.utils)
out = numeric()
qr = c(AAC, ATT)
n =countLines(test.txt)
# 1st pass
file = file(test.txt, r)
for (i in 1:n){
# 2nd pass
line = readLines(file, n = 1)
A = strsplit (line, split = )[[1]][1]
if(is.element(A, qr)) {
value = as.numeric(strsplit (line, split = )[[1]][2])
out = c(out, value)
}
}
if this is a one-go task, counting the lines does not pay, and why
bother. if this is a repetitive task, a database-based solution will
probably be a better idea.
vQ
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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] faster version of split()?
Hi,
R version 2.2.1 is slightly old. You may want to upgrade to the current
version, R.2.8.1!!!
You can for example do
library(doBy)
dd - data.frame(x=c(1,1,1,2,2,2), y=c(1,1,2, 1,1,1))
summaryBy(y~x, data=dd, FUN=function(x)length(unique(x)))
Regards
Søren
-Oprindelig meddelelse-
Fra: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] På
vegne af Simon Pickett
Sendt: 16. januar 2009 11:10
Til: R help
Emne: [R] faster version of split()?
Hi all,
I want to calculate the number of unique observations of y in each level of
x from my data frame df.
this does the job but it is very slow for this big data frame (159503 rows,
11 columns).
group.list - split(df$y,df$x)
count - function(x) length(unique(na.omit(x))) sapply(group.list, count,
USE.NAMES=TRUE)
I couldnt find the answer searching for slow split and split time on help
forum.
I am running R version 2.2.1, on a machine with 4gb of memory and I'm using
windows 2000.
thanks in advance,
Simon.
- Original Message -
From: Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no
To: Gundala Viswanath gunda...@gmail.com
Cc: R help r-h...@stat.math.ethz.ch
Sent: Friday, January 16, 2009 9:30 AM
Subject: Re: [R] Value Lookup from File without Slurping
you might try to iteratively read a limited number of line of lines in a
batch using readLines:
# filename, the name of your file
# n, the maximal count of lines to read in a batch
connection = file(filename, open=rt)
while (length(lines - readLines(con=connection, n=n))) {
# do your stuff here
}
close(connection)
?file
?readLines
vQ
Gundala Viswanath wrote:
Dear all,
I have a repository file (let's call it repo.txt)
that contain two columns like this:
# tag value
AAA0.2
AAT0.3
AAC 0.02
AAG 0.02
ATA0.3
ATT 0.7
Given another query vector
qr - c(AAC, ATT)
I would like to find the corresponding value for each query above,
yielding:
0.02
0.7
However, I want to avoid slurping whole repo.txt into an object (e.g.
hash).
Is there any ways to do that?
The reason I want to do that because repo.txt is very2 large size
(milions of lines,
with tag length 30 bp), and my PC memory is too small to keep it.
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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] problems with extractPrediction in package caret
Häring, Tim (LWF) wrote: Hi list, I´m working on a predictive modeling task using the caret package. I found the best model parameters using the train() and trainControl() command. Now I want to evaluate my model and make predictions on a test dataset. I tried to follow the instructions in the manual and the vignettes but unfortunately I´m getting an error message I can`t figure out. Here is my code: rfControl - trainControl(method = oob, returnResamp = all, returnData=TRUE, verboseIter = TRUE) rftrain - train(x=train_x, y=trainclass, method=rf, tuneGrid=tuneGrid, tr.control=rfControl) pred - predict(rftrain) pred # this works fine expred - extractPrediction(rftrain) Error in models[[1]]$trainingData : $ operator is invalid for atomic vectors I cannot reproduce it (not having your data) and I doubt you are using the most recent version which is 3.51. Anyway, *if* it is a bug, then please report to the package maintainer. Best, Uwe Ligges My predictors are 28 numeric attributes and one factor. I`m working with the latest version of caret and R 2.7.2 on WinXP. Any advice is very welcome. Thanks. TIM --- Dipl.-Geogr. Tim Häring Sachgebiet Standort und Bodenschutz (SG 2.1) Bayerische Landesanstalt für Wald und Forstwirtschaft Am Hochanger 11 D-85354 Freising Tel.: +49-(0)8161/71-4769 E-Mail: tim.haer...@lwf.bayern.de http://www.lwf.bayern.de [[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] [r] How to Solve the Error( error:cannot allocate vector of size 1.1 Gb)
Kum-Hoe Hwang wrote: Hi, Gurus Thanks to your good helps, I have managed starting the use of a text mining package so called tm in R under the OS of Win XP. However, during running the tm package, I got another mine like memory problem. What is a the best way to solve this memory problem among increasing a physical RAM, or doing other recipes, etc? How can we know? We do not know anything about your problem. Maybe not even 64Gb are sufficient or maybe it is simplest to just use a huge machine with 16Gb Uwe Ligges ### ## my R Script's Outputs ## ### memory.limit(size = 2000) NULL corpus.ko - Corpus(DirSource(test_konews/), + readerControl = list(reader = readPlain, + language = UTF-8, load = FALSE)) corpus.ko.nowhite - tmMap(corpus.ko, stripWhitespace) corpus - tmMap(corpus.ko.nowhite, tmTolower) tdm - TermDocMatrix(corpus) findAssocs(tdm, city, 0.97) error:cannot allocate vector of size 1.1 Gb - Thanks for your precious time, -- Kum-Hoe Hwang, Ph.D. Phone : 82-31-250-3516 Email : phdhw...@gmail.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] function return output
threshold wrote:
Hi, I wrote the function which outputs a matrix 'c' and a single value 'd',
as follows (simplified example):
procedure - function(a,b){
...
list(c,d)
}
now I want to use 'c' and 'd' in code as follows:
d - matrix(0,1,1)
value - procedure(a,b)
and d[1,1] - value[2] breaks telling that:
Error in d[1, 1] : incorrect number of dimensions
What I did wrong??, best, robert
Probably value is a list, hence value[2] is also a list and you cannot
assign a list to an element of a *numeric* matrix. I guess you want
value[[2]].
Anyway, it is all a guess since we do not know what your procedure()
returns
Uwe Ligges
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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] Adressing list-elements
Thomas Schwander wrote:
Dear all,
I'm using R 2.8.1 under Vista.
I programmed a Simulation with the code enclosed at the end of the eMail.
After the simulation I want to analyse the columns of the single
simulation-runs, i.e. e.g. Simulation[[1]][,1] sth. like that but I
cannot address these columns...
I guess at least line
Simulation-list(input1)
can be omitted or at least replaced by some sensible list initialization?
I also guess that you intend to assign
Simulation[[i]] - FP
rather than
Simulation[[i]] - list(FP)
but untested without your data.
Uwe Ligges
Can anybody please help?
Best,
Thomas
CODE
analyse-read.csv2(C:\\Users\\Thomas\\Desktop\\PCA_Kohle_2007.csv,sep=;)
rownames(analyse)-analyse[,1]
analyse-analyse[,-1]
require(tseries)
require(fSeries)
st_rendite-apply(apply(analyse,2,log),2,diff)*100
pca-princomp(st_rendite)
summary(pca)
summary(pca)$loadings
screeplot(pca,type=l,main=Screeplot der Prinzipalkomponenten)
loadings_pca1--summary(pca)$loadings[1:6]
loadings_pca2--summary(pca)$loadings[7:12]
loadings_pca3--summary(pca)$loadings[13:18]
loadings_pca4--summary(pca)$loadings[19:24]
loadings_pca5--summary(pca)$loadings[25:30]
loadings_pca6--summary(pca)$loadings[31:36]
loadmatrix-as.matrix(cbind(loadings_pca1,loadings_pca2,loadings_pca3,loadings_pca4,loadings_pca5,loadings_pca6),princomp,dim(analyse)[2])
eigen-summary(pca)$sdev
#Monte-Carlo-Simulation
trials-1
Step-1/365
princomp-3
input1-matrix(0,365,dim(analyse)[2])
Simulation-list(input1)
shocklist-list(input1)
Initialwerte-analyse[dim(analyse)[1],]
days-365
shockmatrix-matrix(0,365,princomp)
for(i in 1:trials){
if(i==1) now-Sys.time()
FP-matrix(0,365,dim(analyse)[2])
for(k in 1:days){
shocks-rnorm(princomp,0,1)
shockmatrix[k,]-shocks
#shocks-shocks_fak
# for(j in 1:1){
for(j in 1:dim(analyse)[2]){
if(k==1) {
FP[k,j]-as.numeric(Initialwerte[j])*
exp(-0.5*Step*sum((loadmatrix[j,1:princomp]*eigen[1:princomp])^2)
+(sqrt(Step)*sum(loadmatrix[j,1:princomp]*eigen[1:princomp]*shocks)))
} else {
FP[k,j]-FP[k-1,j]*
exp(-0.5*Step*sum((loadmatrix[j,1:princomp]*eigen[1:princomp])^2)
+(sqrt(Step)*sum(loadmatrix[j,1:princomp]*eigen[1:princomp]*shocks)))
}
}
}
Simulation[[i]]-list(FP)
shocklist[[i]]-list(shockmatrix)
}
endzeit-Sys.time()
Berechnungsdauer-endzeit-now
Berechnungsdauer
Simulation[[1]]
shocklist[[1]]
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PLEASE do read the posting guide
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__
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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] Value Lookup from File without Slurping
r...@quantide.com wrote:
Using file() is not a real reading of all the file. This function will
simply open a connection to the file without reading it.
countLines should do something lile wc -l from a bash shell
just for a test:
cat(rep('', 10^7), file='test.txt', fill=1)
library(R.utils)
system.time(countLines('test.txt'))
... and the file is just about 30MB (and it makes no real difference if
it is stuffed with newlines or not).
vQ
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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] Value Lookup from File without Slurping
r...@quantide.com wrote: I agree on the database solution. Database are the rigth tool to solve this kind of problem. Only consider the start up cost of setting up the database. This could be a very time consuming task if someone is not familiar with database technology. and won't pay if you want to do the lookup just once. Using file() is not a real reading of all the file. This function will simply open a connection to the file without reading it. countLines should do something lile wc -l from a bash shell ... and wc knows the count of lines in a file without reading it vQ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to create a chromosome location map by locus ID
Sake wrote: Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here: http://www.nabble.com/file/p21474206/genlocus.csv genlocus.csv I've tried some things, but nothing worked like I would like it to see. Maybe there is some kind of package that does this for you, but I did not find it yet. Thanx Sake Whats wrong with things like the HapMap Genome Browser that allows you to zoom in and out and to produce customised annotations of chromosomal regions at varying resolutions (see http://www.hapmap.org/)? Of course I'm assuming that you are looking at human chromosomes ;-) If not then perhaps the UCSC Genome Browser may be of use as it has a large number genomes you can browse (see http://genome.ucsc.edu/cgi-bin/hgGateway ). If you really want to do this in R You might get some mileage out of the lodplot package which can draw ideograms (which is what a schematic of a choromsome with bandings from different stainings is called), although the dataset available for it is again for human chromosomes (see http://cran.r-project.org/web/packages/lodplot/index.html ). Perhaps worth checking out the Genetics Task View too thats linked from CRAN. Neil -- View this message in context: http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21497479.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] How to create a chromosome location map by locus ID
Neil Shephard wrote: Whats wrong with things like the HapMap Genome Browser that allows you to zoom in and out and to produce customised annotations of chromosomal regions at varying resolutions (see http://www.hapmap.org/)? Of course I'm assuming that you are looking at human chromosomes ;-) If not then perhaps the UCSC Genome Browser may be of use as it has a large number genomes you can browse (see http://genome.ucsc.edu/cgi-bin/hgGateway ). If you really want to do this in R You might get some mileage out of the lodplot package which can draw ideograms (which is what a schematic of a choromsome with bandings from different stainings is called), although the dataset available for it is again for human chromosomes (see http://cran.r-project.org/web/packages/lodplot/index.html ). Perhaps worth checking out the Genetics Task View too thats linked from CRAN. Neil I'm well known with all the tools on the internet which allow you to find the position of genes on a chromosome. The only thing is, none of them has the function to upload a list of e.g. 300 genes. I have a list of over expressed genes, and I want to know on which chromosome they are so I can see if there is some kind of link between the genes and the position on a chromosome. I already have made a list of the locus of each gene, but now I want to make some sort of plot that allows me to visualise where the genes are located. So the reason I don't use those webtools is because I have 300 genes and I'm not planning to search for each gene individual. The lodplot package looks promising (already found it;-), but thanx anyway!), but I did not yet figured out how to use it properly. I've not found any tutorial or example data to test it. -- View this message in context: http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21497719.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] PDF slided (beamer or prosper) to an editable PPT
zubin-2 wrote: Hello, I am getting requests to place our PDF slides (output from beamer) into Microsoft Powerpoint formats (.ppt). What's the best practice or any recommended software packages (any success with open or commercial) that we can use to convert PDF slides into an EDITABLE powerpoint deck? Plenty of suggestions out there... http://www.google.co.uk/search?q=pdf+to+powerpoint+converter Never used any of them though, so I can't comment on which is the best or recommend one over the other. Personally though I don't see the need for them to be editable beyond someone wanting to plagirise the work. Neil -- View this message in context: http://www.nabble.com/PDF-slided-%28beamer-or-prosper%29-to-an-editable-PPT-tp21491357p21497540.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] Predictions with GAM
Dear, I am trying to get a prediction of my GAM on a response type. So that I eventually get plots with the correct values on my ylab. I have been able to get some of my GAM's working with the example shown below: * model1-gam(nsdall ~ s(jdaylitr2), data=datansd) newd1 - data.frame(jdaylitr2=(244:304)) pred1 - predict.gam(model1,newd1,type=response)* The problem I am encountering now is that I cannot seem to get it done for the following type of model: *model3-gam(y_no~s(day,by=mapID),family=binomial, data=mergeday)* My mapID consists of 8 levels of which I get individual plots with * plot(model3)*. When I do predict with a newdata in it just like my first model I need all columns to have the same amount of rows or else R will not except it ofcourse, the col.names need to at least include day and mapID. This way I can not get a prediction working for this GAM, I am confused because of this part in the model: *s(day,by=mapID). *I have been reading through the GAM, an introduction with R book from Wood, S. but could not find anything about predictions with BY in the model. I hope someone can help me out with this, Sincerely yours, Robbert Langenberg [[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] Smooth periodic splines
cmr.p...@gmail.com wrote: Hello group! Is there a package that allows to fit smooth *periodic* splines to data? I'm interested in a function which combines the functionality of smooth.spline and splines::periodicSpline. I don't know one, but you could use the same technique that periodicSpline uses: repeat a copy of the data to the left and right of the main copy (similarly replicating the knots if you want regression splines rather than smoothing splines), then fit to the augmented dataset. I don't think it is guaranteed to be exactly periodic, but it will be very close. There is also the periodic option to splinefun and you might be able to use it to construct a true periodic basis, but you'll have to work out some tricky details to get that right. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Value Lookup from File without Slurping
On Fri, Jan 16, 2009 at 5:52 AM, r...@quantide.com r...@quantide.com wrote: I agree on the database solution. Database are the rigth tool to solve this kind of problem. Only consider the start up cost of setting up the database. This could be a very time consuming task if someone is not familiar with database technology. Using sqldf as mentioned previously on this thread allows one to use the SQLite database with no setup at all. sqldf automatically creates the database, generates the record layout, loads the file (not going through R but outside of R so R does not slow it down) and extracts the portion you want into R issuing the appropriate calls to RSQLite/DBI and destroying the database afterwards all automatically. When you install sqldf it automatically installs RSQLite and the SQLite database itself so the entire installation is just one line: install.packages(sqldf) __ 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] re name vector
I´m a really R beginer,
so I have a simply question.
I would like to rename a vector in a loop.
I´d like to have as output:
vector1-whatever
vector2-whatever
vector3-whatever
etc..
so I thought it´s easily
for (s in c(1:3)){
vectorn- whatever
}
but I´m getting an error.
cheers
--
View this message in context:
http://www.nabble.com/rename-vector-tp21497882p21497882.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] re name vector
Its a FAQ:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-turn-a-string-into-a-variable_003f
On Fri, Jan 16, 2009 at 6:58 AM, canadiangirl19 canadiangir...@sms.at wrote:
I´m a really R beginer,
so I have a simply question.
I would like to rename a vector in a loop.
I´d like to have as output:
vector1-whatever
vector2-whatever
vector3-whatever
etc..
so I thought it´s easily
for (s in c(1:3)){
vectorn- whatever
}
but I´m getting an error.
cheers
--
View this message in context:
http://www.nabble.com/rename-vector-tp21497882p21497882.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] reading data from Excel Spread sheet
Kiran,
One, not very elegant way, to solve your problem is to first save the
Excel spreadsheet as a CSV file (open the Excel file in Excel and the
use file-save as CSV, i.e. xxx.CSV) and then use read.csv()
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
venkata kirankumar kiran4u2...@gmail.com 1/16/2009 4:32 AM
Hi all,
I tried to read data from Excel spread sheet with using
read.csv(file.choose())
and
read.delim(file.choose())
but its showing *ÐÏ.à.*.
and also i tried with
read.table(file.choose())
then its showing* V1
1 ÐÏ\021ࡱ*
can any one suggest how to read data from Excel Spread sheet
thanks regards;
kiran
[[alternative HTML version deleted]]
Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Predictions with GAM
On Fri, 2009-01-16 at 12:36 +0100, Robbert Langenberg wrote: Dear, I am trying to get a prediction of my GAM on a response type. So that I eventually get plots with the correct values on my ylab. I have been able to get some of my GAM's working with the example shown below: * model1-gam(nsdall ~ s(jdaylitr2), data=datansd) newd1 - data.frame(jdaylitr2=(244:304)) pred1 - predict.gam(model1,newd1,type=response)* Hi Robert, You want predictions for the covariate over range 244:304 for each of your 8 mapID's, yes? This is not tested, but why not something like: newd2 - data.frame(jdaylitr2 = rep(seq(244, 304, length = 100), 8), mapID = rep(levels(datansd$mapID), each = 100)) Then use newd2 in your call to predict. I am assuming that datansd$mapID is a factor in the above. If it is just some other indicator variable, then perhaps something like: newd2 - data.frame(jdaylitr2 = rep(seq(244, 304, length = 100), 8), mapID = rep(sort(unique(datansd$mapID)), each = 100)) Does that work for you? HTH G The problem I am encountering now is that I cannot seem to get it done for the following type of model: *model3-gam(y_no~s(day,by=mapID),family=binomial, data=mergeday)* My mapID consists of 8 levels of which I get individual plots with * plot(model3)*. When I do predict with a newdata in it just like my first model I need all columns to have the same amount of rows or else R will not except it ofcourse, the col.names need to at least include day and mapID. This way I can not get a prediction working for this GAM, I am confused because of this part in the model: *s(day,by=mapID). *I have been reading through the GAM, an introduction with R book from Wood, S. but could not find anything about predictions with BY in the model. I hope someone can help me out with this, Sincerely yours, Robbert Langenberg [[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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% signature.asc Description: This is a digitally signed message part __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Efficiency challenge: MANY subsets
Hello,
I have a list of character vectors like this:
sequences - list(
c(M,G,L,W,I,S,F,G,T,P,P,S,Y,T,Y,L,L,I,M,
N,H,K,L,L,L,I,N,N,N,N,L,T,E,V,H,T,Y,F,
N,I,N,I,N,I,D,K,M,Y,I,H,*)
)
and another list of subset ranges like this:
indexes - list(
list(
c(1,22),c(22,46),c(46, 51),c(1,46),c(22,51),c(1,51)
)
)
What I now want to do is to subset each entry in sequences
(sequences[[1]]) with all ranges in the corresponding low level list in
indexes (indexes[[1]]). Here is what I came up with.
fragments - list()
for(iN in seq(length(sequences))){
cat(paste(iN,\n))
tmpFragments - sapply(
indexes[[iN]],
function(x){
sequences[[iN]][seq.int(x[1],x[2])]
}
)
fragments[[iN]] - tmpFragments
}
This works fine, but sequences contains thousands of entries and the
corresponding indexes are sometimes hundreds of ranges long, so this whole
process is EXTREMELY inefficient.
Does somebody out there take the challenge and show me a way on how to speed
this up?
Thanks for any hints,
Joh
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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] function return output
On Jan 16, 2009, at 5:22 AM, threshold wrote:
Hi, I wrote the function which outputs a matrix 'c' and a single
value 'd',
as follows (simplified example):
procedure - function(a,b){
...
list(c,d)
}
now I want to use 'c' and 'd' in code as follows:
d - matrix(0,1,1)
value - procedure(a,b)
and d[1,1] - value[2] breaks telling that:
Error in d[1, 1] : incorrect number of dimensions
What I did wrong??, best, robert
Who knows? No reproducible code.
The usual way of accessing just the second element of a list would be
value[[2]]. value[2] will be a list that contains whatever was d,
rather than what was d in the procedure() call itself. It will not
have the name d. It is possible to use the same names inside and
outside a function but it may be more clear for beginners to keep them
separate.
--
David Winsemius
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[R] data frames with å, ä, and ö (=n on-ASCII-characters) from windows to mac os x
Hi, I ran into this issue previously and managed to solve it, but I've forgotten how and am getting frustrated... I have a data frame (see below) with scandinavian characters in R (2.7.1) running on a Win Xp-computer. I save the data frame in an RData-file on a usb stick, and load() it in R (2.8.0) running on OS X 10.5. Now the name of the data frame and all factor labels with scandinavian characters are scrambled. How do I make R in OS X read my data frame? From what I've managed to find in the list archives and the FAQ I either 1) run Sys.setlocale(LC_ALL,en_US.UTF-8) ### Doesn't change anything or 2) run defaults write org.R-project.R force.LANG en_US.UTF-8 in the terminal, which doesn't help either. I must admit that I couldn't quite follow what documentation i found on locales, so I might have messed up somewhere along the line. Many thanks in advance for your help! Regards, Gustaf Länkarta - structure(list(LANKOD = structure(c(11L, 19L, 10L, 13L, 21L, 7L, 9L, 18L, 8L, 3L, 16L, 6L, 5L, 4L, 15L, 2L, 20L, 17L, 1L, 14L, 12L), .Label = c(AB, AC, BD, C, D, E, F, G, H, I, K, M, N, O, S, T, U, W, X, Y, Z ), class = factor), Län = structure(c(1L, 4L, 3L, 5L, 6L, 7L, 8L, 2L, 9L, 10L, 20L, 21L, 13L, 14L, 15L, 16L, 17L, 18L, 12L, 19L, 11L), .Label = c(Blekinge län, Dalarnas län, Gotlands län, Gävleborgs län, Hallands län, Jämtlands län, Jönköpings län, Kalmar län, Kronobergs län, Norrbottens län, Skåne län, Stockholms län, Södermanlands län, Uppsala län, Värmlands län, Västerbottens län, Västernorrlands län, Västmanlands län, Västra Götalands län, Örebro län, Östergötlands län), class = factor)), .Names = c(LANKOD, Län), class = data.frame, row.names = c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)) -- Gustaf Rydevik, M.Sci. tel: +46(0)703 051 451 address:Essingetorget 40,112 66 Stockholm, SE skype:gustaf_rydevik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficiency challenge: MANY subsets
Dear Johannes,
Try this:
sequences - c(M,G,L,W,I,S,F,G,T,P,P,S,Y,T,
Y,L,L,I,M,N,H,K,L,L,L,I,N,N,N,N,L,T,E,V,
H,T,Y,F,N,I,N,I,N,I,D,K,M,Y,I,H,*)
indexes - matrix(c(1,22,22,46,46,51,1,46,22,51,1,51),ncol=2,byrow=TRUE)
apply(indexes,1,function(x){
ind- x[1]:x[2]
sequences[ind]
}
)
HTH,
Jorge
On Fri, Jan 16, 2009 at 8:06 AM, Johannes Graumann johannes_graum...@web.de
wrote:
Hello,
I have a list of character vectors like this:
sequences - list(
c(M,G,L,W,I,S,F,G,T,P,P,S,Y,T,Y,L,L,I,M,
N,H,K,L,L,L,I,N,N,N,N,L,T,E,V,H,T,Y,F,
N,I,N,I,N,I,D,K,M,Y,I,H,*)
)
and another list of subset ranges like this:
indexes - list(
list(
c(1,22),c(22,46),c(46, 51),c(1,46),c(22,51),c(1,51)
)
)
What I now want to do is to subset each entry in sequences
(sequences[[1]]) with all ranges in the corresponding low level list in
indexes (indexes[[1]]). Here is what I came up with.
fragments - list()
for(iN in seq(length(sequences))){
cat(paste(iN,\n))
tmpFragments - sapply(
indexes[[iN]],
function(x){
sequences[[iN]][seq.int(x[1],x[2])]
}
)
fragments[[iN]] - tmpFragments
}
This works fine, but sequences contains thousands of entries and the
corresponding indexes are sometimes hundreds of ranges long, so this
whole
process is EXTREMELY inefficient.
Does somebody out there take the challenge and show me a way on how to
speed
this up?
Thanks for any hints,
Joh
__
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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.
[[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] Efficiency challenge: MANY subsets
Try this:
lapply(indexes[[1]], function(g)sequences[[1]][do.call(seq, as.list(g))])
On Fri, Jan 16, 2009 at 11:06 AM, Johannes Graumann
johannes_graum...@web.de wrote:
Hello,
I have a list of character vectors like this:
sequences - list(
c(M,G,L,W,I,S,F,G,T,P,P,S,Y,T,Y,L,L,I,M,
N,H,K,L,L,L,I,N,N,N,N,L,T,E,V,H,T,Y,F,
N,I,N,I,N,I,D,K,M,Y,I,H,*)
)
and another list of subset ranges like this:
indexes - list(
list(
c(1,22),c(22,46),c(46, 51),c(1,46),c(22,51),c(1,51)
)
)
What I now want to do is to subset each entry in sequences
(sequences[[1]]) with all ranges in the corresponding low level list in
indexes (indexes[[1]]). Here is what I came up with.
fragments - list()
for(iN in seq(length(sequences))){
cat(paste(iN,\n))
tmpFragments - sapply(
indexes[[iN]],
function(x){
sequences[[iN]][seq.int(x[1],x[2])]
}
)
fragments[[iN]] - tmpFragments
}
This works fine, but sequences contains thousands of entries and the
corresponding indexes are sometimes hundreds of ranges long, so this
whole
process is EXTREMELY inefficient.
Does somebody out there take the challenge and show me a way on how to
speed
this up?
Thanks for any hints,
Joh
__
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-SIG-Mac] data frames with å, ä , and ö (=non-ASCII-characters) from win dows to mac os x
You need to use CP1252 not UTF-8 to read the data. It tells you how to do so on the help page ... under 'encoding'. So something like A - read.table(con - file(myfile, encoding=CP1252));close(con) Please don't cross-post ... I am being brief because you did. On Fri, 16 Jan 2009, Gustaf Rydevik wrote: Hi, I ran into this issue previously and managed to solve it, but I've forgotten how and am getting frustrated... I have a data frame (see below) with scandinavian characters in R (2.7.1) running on a Win Xp-computer. I save the data frame in an RData-file on a usb stick, and load() it in R (2.8.0) running on OS X 10.5. Now the name of the data frame and all factor labels with scandinavian characters are scrambled. How do I make R in OS X read my data frame? From what I've managed to find in the list archives and the FAQ I either 1) run Sys.setlocale(LC_ALL,en_US.UTF-8) ### Doesn't change anything or 2) run defaults write org.R-project.R force.LANG en_US.UTF-8 in the terminal, which doesn't help either. I must admit that I couldn't quite follow what documentation i found on locales, so I might have messed up somewhere along the line. Many thanks in advance for your help! Regards, Gustaf Länkarta - structure(list(LANKOD = structure(c(11L, 19L, 10L, 13L, 21L, 7L, 9L, 18L, 8L, 3L, 16L, 6L, 5L, 4L, 15L, 2L, 20L, 17L, 1L, 14L, 12L), .Label = c(AB, AC, BD, C, D, E, F, G, H, I, K, M, N, O, S, T, U, W, X, Y, Z ), class = factor), Län = structure(c(1L, 4L, 3L, 5L, 6L, 7L, 8L, 2L, 9L, 10L, 20L, 21L, 13L, 14L, 15L, 16L, 17L, 18L, 12L, 19L, 11L), .Label = c(Blekinge län, Dalarnas län, Gotlands län, Gävleborgs län, Hallands län, Jämtlands län, Jönköpings län, Kalmar län, Kronobergs län, Norrbottens län, Skåne län, Stockholms län, Södermanlands län, Uppsala län, Värmlands län, Västerbottens län, Västernorrlands län, Västmanlands län, Västra Götalands län, Örebro län, Östergötlands län), class = factor)), .Names = c(LANKOD, Län), class = data.frame, row.names = c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)) -- Gustaf Rydevik, M.Sci. tel: +46(0)703 051 451 address:Essingetorget 40,112 66 Stockholm, SE skype:gustaf_rydevik -- 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.
[R] basic boxplot questions
dear R experts: I am playing with boxplots for the first time. most of it is intuitive, although there was less info on the web than I had hoped. alas, for some odd reason, my R boxplots have some fat black dots, not just the hollow outlier plots. Is there a description of when R draws hollow vs. fat dots somewhere? [and what is the parameter to change just the size of these dots?] Also, let me show my fundamental ignorance: I am a little surprised that the average box boxplot would not show the mean and sdv, too, at least optionally. Is there a common way to accomplish this (e.g., in a different color), or do I just construct it myself with standard R graphics line() commands? advice appreciated. regards, /iaw __ 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] Predictions with GAM
Thanks for the swift reply, I might have been a bit sloppy with describing my datasets and problem. I showed the first model as an example of the type of GAM that I had been able to use the predict function on. What I am looking for is how to predict my m3: model3-gam(y_no~s(day,by=mapID),family=binomial, data=mergeday) When I plot this I get 8 different graphs. Each showing me a different habitat type with on the x-axis days and on the y-axis s(day,2,81):mapID. With predict I was hoping to get the scale of the y-axis right for a selection of days (for example 244,304). I have tried to reform the script you gave me to match my dataset in m3, but it all did not seem to work. newd2 - data.frame(day = rep(seq(244, 304, length = 100), 8), mapID = rep(levels(mergeday$mapID), each = 100)) newd2 - data.frame(day = rep(seq(244, 304, length = 100), 8), mapID = rep(sort(unique(mergeday$mapID)), each = 100)) I am guessing it must have something to do with the by in s(day,by=mapID). I haven't come across any examples that used a GAM with by and then used the predict function. (A sample of the dataset: mapID day y_no Urban Areas and Water25 1 Urban Areas and Water26 1 Early Succesional Forest 27 0 Agriculture 28 0 Early Succesional Forest 29 0 Mature Coniferous Forest 30 0) I am sorry that I have to bother you even more with this, and I hope that my additional explanation about my problem might help solve it. Sincerely yours, Robbert Langenberg 2009/1/16 Gavin Simpson gavin.simp...@ucl.ac.uk On Fri, 2009-01-16 at 12:36 +0100, Robbert Langenberg wrote: Dear, I am trying to get a prediction of my GAM on a response type. So that I eventually get plots with the correct values on my ylab. I have been able to get some of my GAM's working with the example shown below: * model1-gam(nsdall ~ s(jdaylitr2), data=datansd) newd1 - data.frame(jdaylitr2=(244:304)) pred1 - predict.gam(model1,newd1,type=response)* Hi Robert, You want predictions for the covariate over range 244:304 for each of your 8 mapID's, yes? This is not tested, but why not something like: newd2 - data.frame(jdaylitr2 = rep(seq(244, 304, length = 100), 8), mapID = rep(levels(datansd$mapID), each = 100)) Then use newd2 in your call to predict. I am assuming that datansd$mapID is a factor in the above. If it is just some other indicator variable, then perhaps something like: newd2 - data.frame(jdaylitr2 = rep(seq(244, 304, length = 100), 8), mapID = rep(sort(unique(datansd$mapID)), each = 100)) Does that work for you? HTH G The problem I am encountering now is that I cannot seem to get it done for the following type of model: *model3-gam(y_no~s(day,by=mapID),family=binomial, data=mergeday)* My mapID consists of 8 levels of which I get individual plots with * plot(model3)*. When I do predict with a newdata in it just like my first model I need all columns to have the same amount of rows or else R will not except it ofcourse, the col.names need to at least include day and mapID. This way I can not get a prediction working for this GAM, I am confused because of this part in the model: *s(day,by=mapID). *I have been reading through the GAM, an introduction with R book from Wood, S. but could not find anything about predictions with BY in the model. I hope someone can help me out with this, Sincerely yours, Robbert Langenberg [[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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/http://www.ucl.ac.uk/%7Eucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% -- www.lowlandpaddies.nl [[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] reading data from Excel Spread sheet
or maybe by using the xlsReadWrite package: mydata - read.xls(mydata.xls, sheet = 'Sheet1) On Fri, Jan 16, 2009 at 4:32 AM, venkata kirankumar kiran4u2...@gmail.com wrote: Hi all, I tried to read data from Excel spread sheet with using read.csv(file.choose()) and read.delim(file.choose()) but its showing *ÐÏ.à.*. and also i tried with read.table(file.choose()) then its showing* V1 1 ÐÏ\021ࡱ* can any one suggest how to read data from Excel Spread sheet thanks regards; kiran [[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] basic boxplot questions
ivo welch kirjoitti: dear R experts: I am playing with boxplots for the first time. most of it is intuitive, although there was less info on the web than I had hoped. alas, for some odd reason, my R boxplots have some fat black dots, not just the hollow outlier plots. Is there a description of when R draws hollow vs. fat dots somewhere? [and what is the parameter to change just the size of these dots?] Also, let me show my fundamental ignorance: I am a little surprised that the average box boxplot would not show the mean and sdv, too, at least optionally. Is there a common way to accomplish this (e.g., in a different color), or do I just construct it myself with standard R graphics line() commands? advice appreciated. regards, /iaw __ 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] basic boxplot questions
Hi Ivo, ivo welch wrote: alas, for some odd reason, my R boxplots have some fat black dots, not just the hollow outlier plots. Is there a description of when R draws hollow vs. fat dots somewhere? [and what is the parameter to change just the size of these dots?] Have you tried the command '?boxplot' already? It should help you to understand the syntax. Also, let me show my fundamental ignorance: I am a little surprised that the average box boxplot would not show the mean and sdv, too, at least optionally. Is there a common way to accomplish this (e.g., in a different color), or do I just construct it myself with standard R graphics line() commands? Could you post the command(s) you have entered? Without a reproducible example we are tapping in the dark. Kind regards, Kimmo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to create a chromosome location map by locus ID
Sake tlep.nav.e...@hccnet.nl writes:
Neil Shephard wrote:
Whats wrong with things like the HapMap Genome Browser that allows you to
zoom in and out and to produce customised annotations of chromosomal
regions at varying resolutions (see http://www.hapmap.org/)? Of course
I'm assuming that you are looking at human chromosomes ;-) If not
then perhaps the UCSC Genome Browser may be of use as it has a large
number genomes you can browse (see
http://genome.ucsc.edu/cgi-bin/hgGateway ).
If you really want to do this in R You might get some mileage out of the
lodplot package which can draw ideograms (which is what a schematic of a
choromsome with bandings from different stainings is called), although the
dataset available for it is again for human chromosomes (see
http://cran.r-project.org/web/packages/lodplot/index.html ).
Perhaps worth checking out the Genetics Task View too thats linked from
CRAN.
Neil
I'm well known with all the tools on the internet which allow you to find
the position of genes on a chromosome. The only thing is, none of them has
the function to upload a list of e.g. 300 genes. I have a list of over
expressed genes, and I want to know on which chromosome they are so I can
see if there is some kind of link between the genes and the position on a
chromosome. I already have made a list of the locus of each gene, but now I
want to make some sort of plot that allows me to visualise where the genes
are located. So the reason I don't use those webtools is because I have 300
genes and I'm not planning to search for each gene individual.
There are many tools in the R / Bioconductor project that address
these types of issues; a typical use case might use one of the 'org'
packages, e.g., org.Hs.eg.db though there are many others, to extract
information or to map between inforamtion types.
library(org.Hs.eg.db)
ls(2)
[snip]
toTable(org.Hs.egCHRLOC[c('1000', '1')])
gene_id start_location Chromosome
11000 -23784933 18
2 1 -241718157 1
3 1 -241733106 1
toTable(org.Hs.egSYMBOL[c('1000', '1')])
gene_id symbol
11000 CDH2
2 1 AKT3
There are a number of packages for displaying this information, but
usually in conjunction with additional covariates. GenomeGraphs
provides really pretty pictures (though is more for detailed
presentation of individual genes). rtracklayer is an interface that
lets you lay and navigate tracks on web-based genome browsers.
The place to start with Bioconductor is http://bioconductor.org, e.g.,
basic install: http://bioconductor.org/docs/install/
package list: http://bioconductor.org/packages/release/Software.html
source('http://bioconductor.org/biocLite.R')
biocLite() # default packages
biocLite('org.Hs.eg.db') # specific package
library(org.Hs.eg.db)
Look to the AnnotationDbi 'vignettes', either on-line (link to the
AnnotationDbi package page from the list above) or in the package
itself (via openVignettes()).
Any follow-up questions about Bioconductor should go to the
Bioconductor mailing list
http://bioconductor.org/docs/mailList.html
Martin
The lodplot package looks promising (already found it;-), but thanx
anyway!), but I did not yet figured out how to use it properly. I've not
found any tutorial or example data to test it.
--
View this message in context:
http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21497719.html
Sent from the R help mailing list archive at Nabble.com.
__
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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.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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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] Predictions with GAM
Hi, Robbert Langenberg mcrelay at gmail.com writes: I am trying to get a prediction of my GAM on a response type. So that I eventually get plots with the correct values on my ylab. The problem I am encountering now is that I cannot seem to get it done for the following type of model: *model3-gam(y_no~s(day,by=mapID),family=binomial, data=mergeday)* My mapID consists of 8 levels of which I get individual plots with * plot(model3)*. When I do predict with a newdata in it just like my first model I need all columns to have the same amount of rows or else R will not except it ofcourse, the col.names need to at least include day and mapID. This way I can not get a prediction working for this GAM, I am confused because of this part in the model: *s(day,by=mapID). I hope someone can help me out with this, Sincerely yours, Robbert Langenberg I'm not sure that this will work for you, but I had a similar situation and was able to get predict to work (after helpful advice from Simon Wood) with a by variable by generating a model matrix for a model with the interaction of the covariate and the by term, something like model.matrix(~ day:mapID - 1, data = mergeday) in your case. I added the appropriate columns into my data frame and also to the newdata for predict. You can see an example in the appendix of http://www.journalofvision.org/8/16/10/ HTH, Ken -- Ken Knoblauch Inserm U846 Institut Cellule Souche et Cerveau Département Neurosciences Intégratives 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 http://www.sbri.fr __ 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] Lattice: how to have multiple wireframe nice intersection?
Hello, This code builds a simple example of 2 wireframes : require(lattice) x - c(1:10) y - c(1:10) g - expand.grid(x = 1:10, y = 1:10, gr = 1:2) g$z - c(as.vector(outer(x,y,*)), rep(50,100)) wireframe(z ~ x * y, data = g, groups = gr, scales = list(arrows = FALSE)) However, the intersection between the wireframes is not properly drawn. Is there a way to fix this with lattice, or should I use another package more suitable for this? Thanks! Guillaume __ 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] Odp: basic boxplot questions
Hi r-help-boun...@r-project.org napsal dne 16.01.2009 15:24:26: dear R experts: I am playing with boxplots for the first time. most of it is intuitive, although there was less info on the web than I had hoped. alas, for some odd reason, my R boxplots have some fat black dots, not just the hollow outlier plots. Is there a description of when R draws hollow vs. fat dots somewhere? Standard use of boxplot does not draw filled dots, just hollow points. Didnt you by chance use pch=19. [and what is the parameter to change just the size of these dots?] Details on bxp help page outlty, outlwd, outpch, outcex, outcol, outbg: outlier line type, line width, point character, point size expansion, color, and background color. The default outlty= blank suppresses the lines and outpch=NA suppresses points. Also, let me show my fundamental ignorance: I am a little surprised that the average box boxplot would not show the mean and sdv, too, at least optionally. Is there a common way to accomplish this (e.g., in a different color), or do I just construct it myself with standard R graphics line() commands? I always expect boxplot to show median and IQR, however I have seen such twisted boxplots elsewhere. Eg if you looked in CRAN search facility you would easily find R-help archive January 2004: Re: [R] adding mean to boxplot Regards Petr advice appreciated. regards, /iaw __ 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] data frames with å, ä, and ö (=n on-ASCII-characters) from windows to mac os x
Hi, On my system (see below), it works fine (inputing the code below at the R prompt). Make sure that the encoding of the input file is encoded UTF-8. Rgds, Ivan sessionInfo() R version 2.8.1 Patched (2009-01-14 r47602) i386-apple-darwin9.6.0 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base structure(list(LANKOD = structure(c(11L, 19L, 10L, 13L, 21L,7L, 9L, 18L, 8L, 3L, 16L, 6L, 5L, 4L, 15L, 2L, 20L, 17L, 1L,14L, 12L), .Label = c(AB, AC, BD, C, D, E, F, G,H, I, K, M, N, O, S, T, U, W, X, Y, Z), class = factor), Län = structure(c(1L, 4L, 3L, 5L, 6L, 7L,8L, 2L, 9L, 10L, 20L, 21L, 13L, 14L, 15L, 16L, 17L, 18L, 12L,19L, 11L), .Label = c(Blekinge län, Dalarnas län, Gotlands län,Gävleborgs län,Hallands län, Jämtlands län, Jönköpings län,Kalmar län, Kronobergs län, Norrbottens län, Skåne län,Stockholms län, Södermanlands län, Uppsala län, Värmlands län,Västerbottens län, Västernorrlands län, Västmanlands län,Västra Götalands län, Örebro län, Östergötlands län), class =factor)), .Names = c(LANKOD,Län), class = data.frame, row.names = c(0, 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20)) LANKOD Län 0 K Blekinge län 1 X Gävleborgs län 2 I Gotlands län 3 N Hallands län 4 ZJämtlands län 5 F Jönköpings län 6 H Kalmar län 7 W Dalarnas län 8 G Kronobergs län 9 BD Norrbottens län 10 T Örebro län 11 EÖstergötlands län 12 DSödermanlands län 13 C Uppsala län 14 SVärmlands län 15 ACVästerbottens län 16 Y Västernorrlands län 17 U Västmanlands län 18 AB Stockholms län 19 O Västra Götalands län 20 MSkåne län Länkarta - structure(list(LANKOD = structure(c(11L, 19L, 10L, 13L, 21L,7L, 9L, 18L, 8L, 3L, 16L, 6L, 5L, 4L, 15L, 2L, 20L, 17L, 1L,14L, 12L), .Label = c(AB, AC, BD, C, D, E, F, G,H, I, K, M, N, O, S, T, U, W, X, Y, Z), class = factor), Län = structure(c(1L, 4L, 3L, 5L, 6L, 7L,8L, 2L, 9L, 10L, 20L, 21L, 13L, 14L, 15L, 16L, 17L, 18L, 12L,19L, 11L), .Label = c(Blekinge län, Dalarnas län, Gotlands län,Gävleborgs län,Hallands län, Jämtlands län, Jönköpings län,Kalmar län, Kronobergs län, Norrbottens län, Skåne län,Stockholms län, Södermanlands län, Uppsala län, Värmlands län,Västerbottens län, Västernorrlands län, Västmanlands län,Västra Götalands län, Örebro län, Östergötlands län), class =factor)), .Names = c(LANKOD,Län), class = data.frame, row.names = c(0, 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20)) ls() [1] Länkarta On 16 Jan 2009, at 14:13, Gustaf Rydevik wrote: Hi, I ran into this issue previously and managed to solve it, but I've forgotten how and am getting frustrated... I have a data frame (see below) with scandinavian characters in R (2.7.1) running on a Win Xp-computer. I save the data frame in an RData-file on a usb stick, and load() it in R (2.8.0) running on OS X 10.5. Now the name of the data frame and all factor labels with scandinavian characters are scrambled. How do I make R in OS X read my data frame? From what I've managed to find in the list archives and the FAQ I either 1) run Sys.setlocale(LC_ALL,en_US.UTF-8) ### Doesn't change anything or 2) run defaults write org.R-project.R force.LANG en_US.UTF-8 in the terminal, which doesn't help either. I must admit that I couldn't quite follow what documentation i found on locales, so I might have messed up somewhere along the line. Many thanks in advance for your help! Regards, Gustaf Länkarta - structure(list(LANKOD = structure(c(11L, 19L, 10L, 13L, 21L, 7L, 9L, 18L, 8L, 3L, 16L, 6L, 5L, 4L, 15L, 2L, 20L, 17L, 1L, 14L, 12L), .Label = c(AB, AC, BD, C, D, E, F, G, H, I, K, M, N, O, S, T, U, W, X, Y, Z ), class = factor), Län = structure(c(1L, 4L, 3L, 5L, 6L, 7L, 8L, 2L, 9L, 10L, 20L, 21L, 13L, 14L, 15L, 16L, 17L, 18L, 12L, 19L, 11L), .Label = c(Blekinge län, Dalarnas län, Gotlands län, Gävleborgs län, Hallands län, Jämtlands län, Jönköpings län, Kalmar län, Kronobergs län, Norrbottens län, Skåne län, Stockholms län, Södermanlands län, Uppsala län, Värmlands län, Västerbottens län, Västernorrlands län, Västmanlands län, Västra Götalands län, Örebro län, Östergötlands län), class = factor)), .Names = c(LANKOD, Län), class = data.frame, row.names = c(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)) -- Gustaf Rydevik, M.Sci. tel: +46(0)703 051 451 address:Essingetorget 40,112 66 Stockholm, SE skype:gustaf_rydevik __ 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
Re: [R] Fitting of lognormal distribution to lower tail experimental data
Thank you, David! I agree and apprechiate your analysis, which definitely will influence my analysis of this data, but still I would like you to disregard from it(!) The standard routine in the field is, beyond my control, to assume lognormal distribution to achieve comparable results also with other materials (comparison is made on COV). For that reason I have to use it, even if it is not statistically defendable for this particular data. So, if I rephrase the question to be (more general): How would you fit a lognormal distribution to the lower 10% tail of the data (assuming it was lognormal)? What functions to use? Best regards, Mattias 14.8104060497551 16.0803849713769 17.4968110450967 20.1117010953086 21.6845345194074 22.1964808750696 22.6873957765245 22.7739430649247 23.9264878434242 24.0222175448625 24.2589089305143 25.0916485959638 25.6616713982665 26.42372554061 27.1110230291713 27.5506997537485 27.7723436488626 28.5526342456366 28.5937291162256 28.9858602338711 29.0613508454069 29.0909808586811 29.2550164645902 29.2592989298793 29.6618509042981 29.9425395348144 30.2713842375835 30.3578677416218 30.3691588410138 30.3828682984843 30.4226905469563 30.5067979753883 30.5374335721223 30.5377759972106 30.5388417498134 30.6197685055474 30.7562765495333 30.859344040433 31.0055304357074 31.1385745478821 31.2613609610913 31.3581765472267 31.3786215131359 31.3862882622892 31.5134036026533 31.5518777553211 31.6665459342876 31.6966977981316 31.7570612273693 31.7921492877195 31.8916639064893 32.0060685276589 32.0175653961169 32.0957893864849 32.2300707106859 32.2332967187291 32.2933752614657 32.3576534230736 32.4077953094961 32.440737957141 32.4555840754853 32.5778411557745 32.8123917532014 32.8938018752775 32.9005162471121 33.07109861048 33.2169544508162 33.2528421050785 33.2538040913417 33.2629253254612 33.5137399745455 33.646430499 33.6635730620378 33.8081149852229 33.9678615607469 34.0229870935982 34.1334960727572 34.2686698621255 34.281848082171 34.2835695816904 34.285140119695 34.3103279775051 34.3231318200957 34.3298117057378 34.3580807993554 34.375123159033 34.4358460611865 34.6628865380987 34.6882398181505 34.7138670512661 34.8319635103069 34.8543564286965 34.8740064707112 34.8831091812053 35.0783682108864 35.1589202345914 35.1940609286179 35.1963400807163 35.2225030547279 35.2948450801441 35.469980224983 35.4834158010586 35.5066986045073 35.50715377932 35.5581064872091 35.5929578196659 35.6202992874957 35.8503591228778 35.8864712453884 35.9236676029501 36.0272009858509 36.0582893169656 36.0697828249579 36.0733810205568 36.0796120864424 36.1046602505238 36.2146409925046 36.2439056981677 36.2519350403298 36.322995147923 36.3325951679294 36.3998442944923 36.4825302220394 36.5356445443208 36.542777089046 36.5472978834097 36.6042330833268 36.6859461526364 36.7276360969522 36.7559303592816 36.7634229191255 36.763717634632 36.7941371199203 36.7963035045816 37.0158687639306 37.0348436474432 37.0682601112198 37.0753839210413 37.1072512130614 37.218572715278 37.2365135026929 37.308997089496 37.4740533868667 37.5061839013662 37.5920632597573 37.5985612515559 37.6442491468094 37.7885711256696 37.8031769603556 37.8044638170924 37.8758257907878 37.9492755772546 37.9684449085749 38.1925855742105 38.3276830837628 38.36856145824 38.425438354474 38.4871152468451 38.5850141197061 38.7021862984193 38.7281733035293 38.7906053310133 38.8167873845123 38.879602998118 38.9257736530842 39.1219500124099 39.126766061353 39.1572739123381 39.1854685896754 39.2465242986911 39.2681394600736 39.3020749787304 39.3491652552564 39.3519847700339 39.4481343103317 39.4641601623938 39.495558462879 39.5276929723755 39.5743412754252 39.641904265762 39.6805873230154 39.7328651773131 39.7425791919387 39.7862127456679 39.7862858916594 39.8029935150385 39.8184701961103 39.83254032456 39.860678129295 39.9503278266256 39.9590265687971 39.9757707281345 40.0615365250434 40.1029961842667 40.1057284653796 40.2691606972348 40.2757445303632 40.3168035819963 40.3293541033457 40.5323828990285 40.5968897591303 40.6751634982263 40.6988406405023 40.7068328640941 40.7675314086004 40.7776623368738 40.7908603255974 40.7955349906672 40.8035933414247 40.9383315440048 40.9558208833268 40.9606594573753 40.9784894747295 41.0046771495095 41.0177042749474 41.1282624024752 41.1359777151937 41.1980177115138 41.2528202892208 41.4075724424903 41.4116661876018 41.4467994208966 41.4552126570036 41.4568329047393 41.6507621039357 41.7203545510097 41.7436507425138 41.7725271219265 41.8136233981782 41.8338507732199 41.9178452756984 41.9378524875993 41.9424929587518 42.0160174497851 42.0327031030869 42.0695865194719 42.1050583647999 42.154742564893 42.2913255282883 42.2981875529339 42.3378903656232 42.40335129 42.437157423152 42.4731363693922 42.4809382643832 42.5203781472499 42.5249638381712 42.5444709444123 42.5741748422381 42.6845948827814 42.7094479620975 42.7756035736011 42.7789179566436 42.7914314897286 42.8199466233091 42.8302929470511 42.8867019728931
Re: [R] autocorrelation
Hi Is any multiple regression-like test with correction for autocorrelation ? If I understand your question, yes. Take a look at the spdep package for starters. Also you may find the following references helpful. Dormann et al. 2007. Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography 30:609-628 Also the book by Bivand et al. 2008. (Applied Spatial Data Analysis with R. from Springer) is very good. Hope this helps, Michael Denslow I.W. Carpenter Jr. Herbarium [BOON] Appalachian State University Boone, North Carolina U.S.A. -- AND -- Communications Manager Southeastern Regional Network of Expertise and Collections sernec.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] Value Lookup from File without Slurping
Hi Gabor, Do you mean storing data in sqldf', doesn't take memory? For example, I have 3GB data file. with standard R object using read.table() the object size will explode twice ~6GB. My current 4GB RAM cannot handle that. Do you mean with sqldf, this is not the issue? Why is that? Sorry for my naive question. - Gundala Viswanath Jakarta - Indonesia On Fri, Jan 16, 2009 at 9:09 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Fri, Jan 16, 2009 at 5:52 AM, r...@quantide.com r...@quantide.com wrote: I agree on the database solution. Database are the rigth tool to solve this kind of problem. Only consider the start up cost of setting up the database. This could be a very time consuming task if someone is not familiar with database technology. Using sqldf as mentioned previously on this thread allows one to use the SQLite database with no setup at all. sqldf automatically creates the database, generates the record layout, loads the file (not going through R but outside of R so R does not slow it down) and extracts the portion you want into R issuing the appropriate calls to RSQLite/DBI and destroying the database afterwards all automatically. When you install sqldf it automatically installs RSQLite and the SQLite database itself so the entire installation is just one line: install.packages(sqldf) __ 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] Value Lookup from File without Slurping
Only the portion your extract is ever in R -- the file itself is read into a database without ever going through R so your memory requirements correspond to what you extract, not the size of the file. On Fri, Jan 16, 2009 at 10:49 AM, Gundala Viswanath gunda...@gmail.com wrote: Hi Gabor, Do you mean storing data in sqldf', doesn't take memory? For example, I have 3GB data file. with standard R object using read.table() the object size will explode twice ~6GB. My current 4GB RAM cannot handle that. Do you mean with sqldf, this is not the issue? Why is that? Sorry for my naive question. - Gundala Viswanath Jakarta - Indonesia On Fri, Jan 16, 2009 at 9:09 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Fri, Jan 16, 2009 at 5:52 AM, r...@quantide.com r...@quantide.com wrote: I agree on the database solution. Database are the rigth tool to solve this kind of problem. Only consider the start up cost of setting up the database. This could be a very time consuming task if someone is not familiar with database technology. Using sqldf as mentioned previously on this thread allows one to use the SQLite database with no setup at all. sqldf automatically creates the database, generates the record layout, loads the file (not going through R but outside of R so R does not slow it down) and extracts the portion you want into R issuing the appropriate calls to RSQLite/DBI and destroying the database afterwards all automatically. When you install sqldf it automatically installs RSQLite and the SQLite database itself so the entire installation is just one line: install.packages(sqldf) __ 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] Missing file to run Rcmd batch on Windows
Hi, I'm trying to run an R script using Rcmd Batch from the command line on a Windows Vista machine. I am using R version 2.8.1. I installed the batch files 4-3 found at http://cran.r-project.org/contrib/extra/batchfiles/ and added them to my path. I also had to install the latest version of perl (it's Strawberry perl if that makes a difference) and have added this to my path. Now when I run the command: Rcmd batch TestBatch.R TestOutput.txt from the command line, I get the error: Can't open perl script C:\Progra~1\R\R-28~1.0\bin\batch: No such file or directory Just for reference, TestBatch.R contains only one line: print(hello world) Does anyone have any idea on what this file is that I might be missing? Or is there some other mistake I'm making in trying to run the a script from the command line. Thanks, -Brigid [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Missing file to run Rcmd batch on Windows
Try writing BATCH in upper case. On Fri, Jan 16, 2009 at 10:51 AM, Brigid Mooney bkmoo...@gmail.com wrote: Hi, I'm trying to run an R script using Rcmd Batch from the command line on a Windows Vista machine. I am using R version 2.8.1. I installed the batch files 4-3 found at http://cran.r-project.org/contrib/extra/batchfiles/ and added them to my path. I also had to install the latest version of perl (it's Strawberry perl if that makes a difference) and have added this to my path. Now when I run the command: Rcmd batch TestBatch.R TestOutput.txt from the command line, I get the error: Can't open perl script C:\Progra~1\R\R-28~1.0\bin\batch: No such file or directory Just for reference, TestBatch.R contains only one line: print(hello world) Does anyone have any idea on what this file is that I might be missing? Or is there some other mistake I'm making in trying to run the a script from the command line. Thanks, -Brigid [[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] Value Lookup from File without Slurping
Hi, Unless you specify an in-memory database the database is stored on disk. Thanks for your explanation. I just downloaded 'sqldf'. Where can I find the option for that? In sqldf I can't see the command. I looked at: envir = parent.frame() doesn't appear to be the one. - Gundala Viswanath Jakarta - Indonesia On Fri, Jan 16, 2009 at 10:59 AM, Gundala Viswanath gunda...@gmail.com wrote: Hi Gabor, the file itself is read into a database The above doesn't use RAM memory? Rgds, GV. without ever going through R so your memory requirements correspond to what you extract, not the size of the file. On Fri, Jan 16, 2009 at 10:49 AM, Gundala Viswanath gunda...@gmail.com wrote: Hi Gabor, Do you mean storing data in sqldf', doesn't take memory? For example, I have 3GB data file. with standard R object using read.table() the object size will explode twice ~6GB. My current 4GB RAM cannot handle that. Do you mean with sqldf, this is not the issue? Why is that? Sorry for my naive question. - Gundala Viswanath Jakarta - Indonesia On Fri, Jan 16, 2009 at 9:09 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Fri, Jan 16, 2009 at 5:52 AM, r...@quantide.com r...@quantide.com wrote: I agree on the database solution. Database are the rigth tool to solve this kind of problem. Only consider the start up cost of setting up the database. This could be a very time consuming task if someone is not familiar with database technology. Using sqldf as mentioned previously on this thread allows one to use the SQLite database with no setup at all. sqldf automatically creates the database, generates the record layout, loads the file (not going through R but outside of R so R does not slow it down) and extracts the portion you want into R issuing the appropriate calls to RSQLite/DBI and destroying the database afterwards all automatically. When you install sqldf it automatically installs RSQLite and the SQLite database itself so the entire installation is just one line: install.packages(sqldf) __ 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] Use of [:alnum:] or . in gsub() etc..
test = c ( AAABBB, CCC ) This works : gsub ( [A-Z], 2, test ) None of these do : gsub ( [A-Z], [:alnum:], test ) gsub ( [A-Z], [[:alnum:]], test ) gsub ( [A-Z], [:alnum:], test ) gsub ( [A-Z], [[:alnum:]], test ) gsub ( [A-Z], ^[:alnum:]$, test ) What am I doing wrong, please ? -- View this message in context: http://www.nabble.com/Use-of--%3Aalnum%3A--or-.-in-gsub%28%29-etc..-tp21502786p21502786.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] Value Lookup from File without Slurping
If that refers to using a database on disk to temporarily hold the file then example 6 on the home page shows it, as mentioned, and you may wish to look at the other examples there too and there is further documentation in the ?sqldf help file. On Fri, Jan 16, 2009 at 11:11 AM, Gundala Viswanath gunda...@gmail.com wrote: Hi, Unless you specify an in-memory database the database is stored on disk. Thanks for your explanation. I just downloaded 'sqldf'. Where can I find the option for that? In sqldf I can't see the command. I looked at: envir = parent.frame() doesn't appear to be the one. - Gundala Viswanath Jakarta - Indonesia On Fri, Jan 16, 2009 at 10:59 AM, Gundala Viswanath gunda...@gmail.com wrote: Hi Gabor, the file itself is read into a database The above doesn't use RAM memory? Rgds, GV. without ever going through R so your memory requirements correspond to what you extract, not the size of the file. On Fri, Jan 16, 2009 at 10:49 AM, Gundala Viswanath gunda...@gmail.com wrote: Hi Gabor, Do you mean storing data in sqldf', doesn't take memory? For example, I have 3GB data file. with standard R object using read.table() the object size will explode twice ~6GB. My current 4GB RAM cannot handle that. Do you mean with sqldf, this is not the issue? Why is that? Sorry for my naive question. - Gundala Viswanath Jakarta - Indonesia On Fri, Jan 16, 2009 at 9:09 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Fri, Jan 16, 2009 at 5:52 AM, r...@quantide.com r...@quantide.com wrote: I agree on the database solution. Database are the rigth tool to solve this kind of problem. Only consider the start up cost of setting up the database. This could be a very time consuming task if someone is not familiar with database technology. Using sqldf as mentioned previously on this thread allows one to use the SQLite database with no setup at all. sqldf automatically creates the database, generates the record layout, loads the file (not going through R but outside of R so R does not slow it down) and extracts the portion you want into R issuing the appropriate calls to RSQLite/DBI and destroying the database afterwards all automatically. When you install sqldf it automatically installs RSQLite and the SQLite database itself so the entire installation is just one line: install.packages(sqldf) __ 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] Use of [:alnum:] or . in gsub() etc..
on 01/16/2009 10:13 AM ppaarrkk wrote: test = c ( AAABBB, CCC ) This works : gsub ( [A-Z], 2, test ) None of these do : gsub ( [A-Z], [:alnum:], test ) gsub ( [A-Z], [[:alnum:]], test ) gsub ( [A-Z], [:alnum:], test ) gsub ( [A-Z], [[:alnum:]], test ) gsub ( [A-Z], ^[:alnum:]$, test ) What am I doing wrong, please ? The syntax ordering is off. You are in effect trying to replace the characters A-Z with the character vector [[:alnum:]]. Thus: gsub ([A-Z], [[:alnum:]], test ) [1] [[:alnum:]][[:alnum:]][[:alnum:]][[:alnum:]][[:alnum:]][[:alnum:]] [2] [[:alnum:]][[:alnum:]][[:alnum:]] Recall the basic syntax for gsub() is: gsub(SearchPattern, ReplacementVector, Source) What you want is: gsub ([[:alnum:]], 2 , test ) [1] 22 222 HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Missing file to run Rcmd batch on Windows
On 1/16/2009 10:51 AM, Brigid Mooney wrote: Hi, I'm trying to run an R script using Rcmd Batch from the command line on a Windows Vista machine. I am using R version 2.8.1. I installed the batch files 4-3 found at http://cran.r-project.org/contrib/extra/batchfiles/ and added them to my path. I also had to install the latest version of perl (it's Strawberry perl if that makes a difference) and have added this to my path. Now when I run the command: Rcmd batch TestBatch.R TestOutput.txt from the command line, I get the error: Can't open perl script C:\Progra~1\R\R-28~1.0\bin\batch: No such file or directory Just for reference, TestBatch.R contains only one line: print(hello world) Does anyone have any idea on what this file is that I might be missing? Or is there some other mistake I'm making in trying to run the a script from the command line. Rcmd runs some commands based on internal matches to the name, and if not found there, it looks in the file system. So there is no internal command batch, and no external command of that name either. The actual name (as Rcmd --help will tell you) is BATCH, and it is implemented as an internal command, so case matters. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sweave documents have corrupted double quotes
I'm attaching a file foo.Rnw and I'm hoping some of you might run it through your R latex systems to find out if the double-quotes in typewriter font turn out as black boxes (as they do for me). If you don't use Sweave, but you have a system with a working version of R and LaTeX, the file gives the instructions you need to use to process the file. The The file itself explains the problem. You can see the flawed output on my web site http://pj.freefaculty.org/latex/foo.pdf I'm running Ubuntu Linux 8.10 with R 2.8.1 and TexLive 2007 (which is provided with the distribution). This is not a new problem, I noticed it two years ago while using TeTeX on Fedora Linux, and so I doubt that this is specific to TeXLive. Back then, I took the path of resistance and stopped using the typewriter font. That is becoming inconvenient, however. I would sincerely appreciate any pointers you have. -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ 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] Sweave documents have corrupted double quotes
Paul Johnson pauljohn32 at gmail.com writes: I'm attaching a file foo.Rnw and I'm hoping some of you might run it through your R latex systems to find out if the double-quotes in typewriter font turn out as black boxes (as they do for me). If you don't use Sweave, but you have a system with a working version of R and LaTeX, the file gives the instructions you need to use to process the file. The I can't help except to say that I replicated the problem (but I'm running exactly the same OS/R combination so maybe that's not too surprising. Oddly enough upquote.sty says explicitly It does not affect \tt, \texttt, etc. But that seems to be false. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave documents have corrupted double quotes
Paul,
The file did not make it to the list.
Did you try loading Sweave with the 'noae' option, that is:
\usepackage[noae]{Sweave}
This *may* solve your issue.
HTH Vincent
Le ven. 16 janv. à 11:31, Paul Johnson a écrit :
I'm attaching a file foo.Rnw and I'm hoping some of you might run it
through your R latex systems to find out if the double-quotes in
typewriter font turn out as black boxes (as they do for me). If you
don't use Sweave, but you have a system with a working version of R
and LaTeX, the file gives the instructions you need to use to process
the file. The
The file itself explains the problem. You can see the flawed output on
my web site
http://pj.freefaculty.org/latex/foo.pdf
I'm running Ubuntu Linux 8.10 with R 2.8.1 and TexLive 2007 (which is
provided with the distribution).
This is not a new problem, I noticed it two years ago while using
TeTeX on Fedora Linux, and so I doubt that this is specific to
TeXLive. Back then, I took the path of resistance and stopped using
the typewriter font. That is becoming inconvenient, however.
I would sincerely appreciate any pointers you have.
--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas
__
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.
---
Vincent Goulet
Acting Chair, Associate Professor
École d'actuariat
Université Laval, Québec
vincent.gou...@act.ulaval.ca http://vgoulet.act.ulaval.ca
__
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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] (no subject)
Dear users, i just installed the lastest version of R, 2.8.1 on my computer (OS Windows XP). Then i tried to update the packages copied from my old R version by update.packages(ask=F) However i get the following warning: Warning: unable to access index for repository http://cran.ch.r-project.org/bin/windows/contrib/2.8 Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.8; and the updating fails. Is it a server problem of CRAN? Thanks for your help, Henning -- Sensationsangebot verlängert: GMX FreeDSL - Telefonanschluss + DSL für nur 16,37 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K1308T4569a [[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] Sweave documents have corrupted double quotes
On Fri, Jan 16, 2009 at 10:43 AM, David Winsemius dwinsem...@comcast.net wrote: Dear Dr Johnson; I'm not sure if you get copies of your posts. If you do can you check to see if the list-server kept the attachment? My copy did not have one. -- Best David winsemius Hm. Well, I do get the attachment, and don't understand why you don't. But if you are willing, you can get the file here, same directory as the dvi and pdf output: http://pj.freefaculty.org/latex/foo.Rnw -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ 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] installing mclust and flexmix on linux
I've been trying to install some R packages such as mclust and flexmix on linux
but have had the following error messages.
I've been trying to install mclust on my notebook which has linpus linux lite
os and I have installed R as well as some packages all right. However, when
I tried to install mclust, it gave me the following messages. Any
suggestions?
Tim
install.packages('mclust','/usr/lib/R/library',destdir='/usr/tmp')
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/mclust_3.1-10.tar.gz'
Content type 'application/x-gzip' length 231992 bytes (226 Kb)
opened URL
==
downloaded 226 Kb
* Installing *source* package 'mclust' ...
** libs
WARNING: R include directory is empty -- perhaps need to install R-devel.rpm or
similar
/usr/lib/R/bin/SHLIB: line 162: make: command not found
ERROR: compilation failed for package 'mclust'
** Removing '/usr/lib/R/library/mclust'
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(mclust, /usr/lib/R/library, destdir = /usr/tmp) :
installation of package 'mclust' had non-zero exit status
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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] (no subject)
Dear all, Can anybody help me with an RExcel tutorial? Maybe some example on which functions can be used/how to use it... I have installed it on my computer, using the R(D)COM server. Thank you all in advance, Irina Ursachi. __ 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 optim with exponential power distribution
Hello,
I am trying to fit a exponential power distribution
y = b/(2*pi*a^2*gamma(2/b))*exp(-(x/a)^b)
to a bunch of data for x and y I have in a table.
data
x y
1 2527
2 7559
3125 219
...
25912925 1
26012975 0
I know optim should do a minimisation, therefor I used as the
optimisation function
opt.power - function(val, x, y) {
a - val[1];
b - val[2];
sum(y - b/(2*pi*a^2*gamma(2/b))*exp(-(x/a)^b));
}
I call: (with xm and ym the data from the table)
a1 - c(0.2, 100)
opt - optim(a1, opt.power, method=BFGS, x=xm, y=ym)
but no optimisation of the parameter in a1 takes place.
Any ideas?
--
Ciao
Ronald
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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] faster version of split()?
Henrique's solution seems sensible. Another might be:
df = data.frame(x = sample(7:9, 10, rep = T), y = sample(1:5, 10,
rep = T))
table(df)
y
x 1 2 3 4 5
7 1 0 1 0 2
8 0 1 0 0 1
9 0 1 1 2 0
rowSums(table(df) 0)
7 8 9
3 2 3
#-same as Henrique's
count - function(x) length(unique(na.omit(x)))
with(df, tapply(y, x, count))
7 8 9
3 2 3
--
David Winsemius
On Jan 16, 2009, at 5:10 AM, Simon Pickett wrote:
Hi all,
I want to calculate the number of unique observations of y in each
level of x from my data frame df.
this does the job but it is very slow for this big data frame
(159503 rows, 11 columns).
group.list - split(df$y,df$x)
count - function(x) length(unique(na.omit(x)))
sapply(group.list, count, USE.NAMES=TRUE)
I couldnt find the answer searching for slow split and split
time on help forum.
I am running R version 2.2.1, on a machine with 4gb of memory and
I'm using windows 2000.
thanks in advance,
Simon.
- Original Message - From: Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no
To: Gundala Viswanath gunda...@gmail.com
Cc: R help r-h...@stat.math.ethz.ch
Sent: Friday, January 16, 2009 9:30 AM
Subject: Re: [R] Value Lookup from File without Slurping
you might try to iteratively read a limited number of line of lines
in a
batch using readLines:
# filename, the name of your file
# n, the maximal count of lines to read in a batch
connection = file(filename, open=rt)
while (length(lines - readLines(con=connection, n=n))) {
# do your stuff here
}
close(connection)
?file
?readLines
vQ
Gundala Viswanath wrote:
Dear all,
I have a repository file (let's call it repo.txt)
that contain two columns like this:
# tag value
AAA0.2
AAT0.3
AAC 0.02
AAG 0.02
ATA0.3
ATT 0.7
Given another query vector
qr - c(AAC, ATT)
I would like to find the corresponding value for each query above,
yielding:
0.02
0.7
However, I want to avoid slurping whole repo.txt into an object
(e.g. hash).
Is there any ways to do that?
The reason I want to do that because repo.txt is very2 large size
(milions of lines,
with tag length 30 bp), and my PC memory is too small to keep it.
__
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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Updating packages under R 2.8.1
Dear users, i just installed the lastest version of R, 2.8.1 on my computer (OS Windows XP). Then i tried to update the packages copied from my old R version by update.packages(ask=F) However i get the following warning: Warning: unable to access index for repository http://cran.ch.r-project.org/bin/windows/contrib/2.8 Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.8; and the updating fails. Is it a server problem of CRAN? Thanks for your help, Henning -- Sensationsangebot verlängert: GMX FreeDSL - Telefonanschluss + DSL für nur 16,37 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K1308T4569a -- [[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] Sweave documents have corrupted double quotes
On Fri, Jan 16, 2009 at 11:06 AM, Vincent Goulet
vincent.gou...@act.ulaval.ca wrote:
Paul,
The file did not make it to the list.
Did you try loading Sweave with the 'noae' option, that is:
\usepackage[noae]{Sweave}
This *may* solve your issue.
HTH Vincent
Wow. That does fix it. I bow to you. I need to learn how this option
can be put into the Rnw file itself .
Are you the same Vincent Goulet who offers the customized Emacs for
windows? (http://vgoulet.act.ulaval.ca/ressources/emacs). If so,
thanks again for that. Keep up the good work. It has saved me and my
students tons of time setting up Windows systems.
--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas
__
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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] (no subject)
Dear Henning, Try other repositories. Best wishes, miltinho brazil On Fri, Jan 16, 2009 at 2:08 PM, Henning Wildhagen hwildha...@gmx.dewrote: Dear users, i just installed the lastest version of R, 2.8.1 on my computer (OS Windows XP). Then i tried to update the packages copied from my old R version by update.packages(ask=F) However i get the following warning: Warning: unable to access index for repository http://cran.ch.r-project.org/bin/windows/contrib/2.8 Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.8; and the updating fails. Is it a server problem of CRAN? Thanks for your help, Henning -- Sensationsangebot verlängert: GMX FreeDSL - Telefonanschluss + DSL für nur 16,37 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K1308T4569a [[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] Sweave documents have corrupted double quotes
Looking at the display I see this line:
\texttt{Typewriter Font has ``double quotes''}
... displayed with leading backquotes but trailing singlequotes.
Was that intended?
--
David Winsemius
On Jan 16, 2009, at 12:21 PM, Paul Johnson wrote:
On Fri, Jan 16, 2009 at 10:43 AM, David Winsemius
dwinsem...@comcast.net wrote:
Dear Dr Johnson;
I'm not sure if you get copies of your posts. If you do can you
check to see
if the list-server kept the attachment? My copy did not have one.
--
Best
David winsemius
Hm. Well, I do get the attachment, and don't understand why you don't.
But if you are willing, you can get the file here, same directory as
the dvi and pdf output:
http://pj.freefaculty.org/latex/foo.Rnw
--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas
__
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] Using optim with exponential power distribution
I know optim should do a minimisation, therefor I used as the
optimisation function
opt.power - function(val, x, y) {
a - val[1];
b - val[2];
sum(y - b/(2*pi*a^2*gamma(2/b))*exp(-(x/a)^b));
}
I call: (with xm and ym the data from the table)
a1 - c(0.2, 100)
opt - optim(a1, opt.power, method=BFGS, x=xm, y=ym)
but no optimisation of the parameter in a1 takes place.
Any ideas?
It looks to me like your optimising the _average_ of the differences
between y and the function, so as long as positive and negative
differences balance out you get a cost value of 0 (and you can make it
even smaller if the fitted function is much larger than the actual y
values, so all differences are negative).
You probably wanted to minimise the squared errors:
sum((y - b/(2*pi*a^2*gamma(2/b))*exp(-(x/a)^b)))^2)
Best regards,
Stefan Evert
[ stefan.ev...@uos.de | http://purl.org/stefan.evert ]
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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] Weighted Kaplan-Meier Statistics
Dear All, I could not locate an implementation of the Weighted Kaplan-Meier Statistics proposed by Pepe and Fleming, Biometrics. 1989 Jun;45(2):497-507 (http://www.ncbi.nlm.nih.gov/pubmed/2765634) in R. I am wondering if anyone is aware of a R implementation of the test statistics proposed in the paper. Thanks, Ritwik Sinha ritwik.si...@gmail.com | +12033042111 | http://ritwik.sinha.googlepages.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] problems with extractPrediction in package caret
The issue is the usage of extractPrediction. expred - extractPrediction(rftrain) should really be expred - extractPrediction(list(rftrain)) Since this function is intended to get predictions across multiple models, the man file has a description of the first argument to teh funtion being a list of objects of the class train. -- Max __ 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] faster version of split()?
Simon Pickett wrote:
Hi all,
I want to calculate the number of unique observations of y in each
level of x from my data frame df.
this does the job but it is very slow for this big data frame (159503
rows, 11 columns).
group.list - split(df$y,df$x)
count - function(x) length(unique(na.omit(x)))
sapply(group.list, count, USE.NAMES=TRUE)
wouldn't it do with something like
with(df,table(x, is.na(y)))[,1]
or
with(df, tapply(!is.na(y), x, sum))
?
I couldnt find the answer searching for slow split and split time on
help forum.
I am running R version 2.2.1, on a machine with 4gb of memory and I'm
using windows 2000.
thanks in advance,
Simon.
- Original Message - From: Wacek Kusnierczyk
waclaw.marcin.kusnierc...@idi.ntnu.no
To: Gundala Viswanath gunda...@gmail.com
Cc: R help r-h...@stat.math.ethz.ch
Sent: Friday, January 16, 2009 9:30 AM
Subject: Re: [R] Value Lookup from File without Slurping
you might try to iteratively read a limited number of line of lines in a
batch using readLines:
# filename, the name of your file
# n, the maximal count of lines to read in a batch
connection = file(filename, open=rt)
while (length(lines - readLines(con=connection, n=n))) {
# do your stuff here
}
close(connection)
?file
?readLines
vQ
Gundala Viswanath wrote:
Dear all,
I have a repository file (let's call it repo.txt)
that contain two columns like this:
# tag value
AAA0.2
AAT0.3
AAC 0.02
AAG 0.02
ATA0.3
ATT 0.7
Given another query vector
qr - c(AAC, ATT)
I would like to find the corresponding value for each query above,
yielding:
0.02
0.7
However, I want to avoid slurping whole repo.txt into an object (e.g.
hash).
Is there any ways to do that?
The reason I want to do that because repo.txt is very2 large size
(milions of lines,
with tag length 30 bp), and my PC memory is too small to keep it.
__
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.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907
__
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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] Updating packages under R 2.8.1
Henning Wildhagen wrote: Dear users, i just installed the lastest version of R, 2.8.1 on my computer (OS Windows XP). Then i tried to update the packages copied from my old R version by update.packages(ask=F) However i get the following warning: Warning: unable to access index for repository http://cran.ch.r-project.org/bin/windows/contrib/2.8 Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.8; and the updating fails. Check your internet connection and your proxy settings as well as the correpsonding entries in the R for Windows FAQs. Uwe Ligges Is it a server problem of CRAN? Thanks for your help, Henning __ 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] installing mclust and flexmix on linux
Tim F Liao wrote:
I've been trying to install some R packages such as mclust and flexmix on linux
but have had the following error messages.
I've been trying to install mclust on my notebook which has linpus linux lite
os and I have installed R as well as some packages all right. However, when I
tried to install mclust, it gave me the following messages. Any suggestions?
Tim
install.packages('mclust','/usr/lib/R/library',destdir='/usr/tmp')
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/mclust_3.1-10.tar.gz'
Content type 'application/x-gzip' length 231992 bytes (226 Kb)
opened URL
==
downloaded 226 Kb
* Installing *source* package 'mclust' ...
** libs
WARNING: R include directory is empty -- perhaps need to install R-devel.rpm or
similar
So, have you installed the header files / include directory?
Uwe Ligges
/usr/lib/R/bin/SHLIB: line 162: make: command not found
ERROR: compilation failed for package 'mclust'
** Removing '/usr/lib/R/library/mclust'
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(mclust, /usr/lib/R/library, destdir = /usr/tmp) :
installation of package 'mclust' had non-zero exit status
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[R] Memory allocation
Hello everyone,
I have the following issue: one function generates a very big array (can be
more than 1 Gb) and returns a few variables, including this big one. Memory
allocation is OK while the function is running, but the final steps make
some copies that can be problematic. I looked for a way to return the values
without copying (even tried Rmemprof), but without success. Any ideas?
The code looks like this:
myfunc - function() {
...
bigarray - ...
...
final - list(..., bigarray=bigarray, ...)
class(final) - myfunc
final
}
Thank you in advance,
Gabriel.
[[alternative HTML version deleted]]
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[R] glmer documentation
Hello, I am fitting a gmler using poisson, and I was looking for a documentation to interpret correctly the output. I'm quite a beginner with these kind of models. I couldn't find something in the lme4 package manual. and on the internet neither... Thank you, Raphaelle -- View this message in context: http://www.nabble.com/glmer-documentation-tp21506036p21506036.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] PHP and R
Hi, I know I've already asked this question, but I am really getting trouble getting a PHP document execute an R function on windows. I would appreciate if someone could give me a simple example code where a php calls an R function and passes to it arguments, specifying also how to set up the paths etc... (should the .r file be in the www directory, and what settings should be done?) Thanks! -- View this message in context: http://www.nabble.com/PHP-and-R-tp21507207p21507207.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] Missing file to run Rcmd batch on Windows
Regarding Perl, the batchfiles distribution batch files do not use Perl but R's own Rcmd.exe does. Based on comments recently I understand that Perl will be eliminated from the R batch scripts soon but in the meantime if you install Rtools (which is a set of tools that includes perl and is simple to install via its GUI installer similar to R's) from http://www.murdoch-sutherland.com/Rtools/ then Rcmd.bat will automatically detect it so you don't have to set a path to Perl. On Fri, Jan 16, 2009 at 11:00 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Try writing BATCH in upper case. On Fri, Jan 16, 2009 at 10:51 AM, Brigid Mooney bkmoo...@gmail.com wrote: Hi, I'm trying to run an R script using Rcmd Batch from the command line on a Windows Vista machine. I am using R version 2.8.1. I installed the batch files 4-3 found at http://cran.r-project.org/contrib/extra/batchfiles/ and added them to my path. I also had to install the latest version of perl (it's Strawberry perl if that makes a difference) and have added this to my path. Now when I run the command: Rcmd batch TestBatch.R TestOutput.txt from the command line, I get the error: Can't open perl script C:\Progra~1\R\R-28~1.0\bin\batch: No such file or directory Just for reference, TestBatch.R contains only one line: print(hello world) Does anyone have any idea on what this file is that I might be missing? Or is there some other mistake I'm making in trying to run the a script from the command line. Thanks, -Brigid [[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] Memory allocation
On 1/16/2009 12:46 PM, Gabriel Margarido wrote:
Hello everyone,
I have the following issue: one function generates a very big array (can be
more than 1 Gb) and returns a few variables, including this big one. Memory
allocation is OK while the function is running, but the final steps make
some copies that can be problematic. I looked for a way to return the values
without copying (even tried Rmemprof), but without success. Any ideas?
The code looks like this:
myfunc - function() {
...
bigarray - ...
...
final - list(..., bigarray=bigarray, ...)
class(final) - myfunc
final
}
Thank you in advance,
I believe this will do less copying, but I haven't profiled it to be
sure. Replace the last three lines with this one statement:
structure(list(..., bigarray=bigarray, ...),
class = myfunc)
If that doesn't help, then you really need to determine where the
copying is happening: you can use Rprofmem() to do that.
Duncan Murdoch
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[R] bootstrap validation of LR error message
when i try to validate my logistic regression model: fit-glm(y~x,binomial,data=dataname,x=TRUE,y=TRUE) validate(fit,method=boot,B=150,...) i get the following error message: Error in UseMethod(validate) : no applicable method for validate any insight would be appreciated. many thanks! -- View this message in context: http://www.nabble.com/bootstrap-validation-of-LR-error-message-tp21507695p21507695.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] Efficiency challenge: MANY subsets
Thanks. Very elegant, but doesn't solve the problem of the outer for loop,
since I now would rewrite the code like so:
fragments - list()
for(iN in seq(length(sequences))){
cat(paste(iN,\n))
fragments[[iN]] -
lapply(indexes[[1]], function(g)sequences[[1]][do.call(seq, as.list(g))])
}
still very slow for length(sequences) ~ 7000.
Joh
On Friday 16 January 2009 14:23:47 Henrique Dallazuanna wrote:
Try this:
lapply(indexes[[1]], function(g)sequences[[1]][do.call(seq, as.list(g))])
On Fri, Jan 16, 2009 at 11:06 AM, Johannes Graumann
johannes_graum...@web.de wrote:
Hello,
I have a list of character vectors like this:
sequences - list(
c(M,G,L,W,I,S,F,G,T,P,P,S,Y,T,Y,L,L,I
,M,
N,H,K,L,L,L,I,N,N,N,N,L,T,E,V,H,T,Y,
F, N,I,N,I,N,I,D,K,M,Y,I,H,*)
)
and another list of subset ranges like this:
indexes - list(
list(
c(1,22),c(22,46),c(46, 51),c(1,46),c(22,51),c(1,51)
)
)
What I now want to do is to subset each entry in sequences
(sequences[[1]]) with all ranges in the corresponding low level list in
indexes (indexes[[1]]). Here is what I came up with.
fragments - list()
for(iN in seq(length(sequences))){
cat(paste(iN,\n))
tmpFragments - sapply(
indexes[[iN]],
function(x){
sequences[[iN]][seq.int(x[1],x[2])]
}
)
fragments[[iN]] - tmpFragments
}
This works fine, but sequences contains thousands of entries and the
corresponding indexes are sometimes hundreds of ranges long, so this
whole
process is EXTREMELY inefficient.
Does somebody out there take the challenge and show me a way on how to
speed
this up?
Thanks for any hints,
Joh
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[R] specifying model terms when using predict
I've recently encountered an issue when trying to use the predict.glm function. I've gotten into the habit of using the dataframe$variablename method of specifying terms in my model statements. I thought this unambiguous notation would be acceptable in all situations but it seems models written this way are not accepted by the predict function. Perhaps others have encountered this problem as well. The code below illustrates the issue. ## ## linear model example # this works x-1:100 y-2*x lm1-glm(y~x) pred1-predict(lm1,newdata=data.frame(x=101:150)) ## so does this x-1:100 y-2*x orig.df-data.frame(x1=x,y1=y) lm1-glm(y1~x1,data=orig.df) pred1-predict(lm1,newdata=data.frame(x1=101:150)) ## this does not run x-1:100 y-2*x orig.df-data.frame(x1=x,y1=y) lm1-glm(orig.df$y1~orig.df$x1,data=orig.df) pred1-predict(lm1,newdata=data.frame(x1=101:150)) The final statement generates the following warning: Warning message: 'newdata' had 50 rows but variable(s) found have 100 rows Hope this is of some help. Brian Van Hezewijk [[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] bootstrap validation of LR error message
on 01/16/2009 02:19 PM A Van Dyke wrote: when i try to validate my logistic regression model: fit-glm(y~x,binomial,data=dataname,x=TRUE,y=TRUE) validate(fit,method=boot,B=150,...) i get the following error message: Error in UseMethod(validate) : no applicable method for validate any insight would be appreciated. many thanks! You appear to be trying to use the validate() function from Frank Harrell's Design package. However, you are attempting to use it with a glm() created from R's stats package. The two don't mix. If you want to use Frank's validate() function, you will need to create your logistic regression model using Frank's lrm() function. See ?lrm and ?validate.lrm for more information. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error when running Kendall Package
I am new to R and am trying to run data through using the Kendall package. My first question is that I have NA values for certain criterias, will that be a problem or will they be ignored? ie:FallSpring Summer 1988 NA 1.321 1.564 1999 1.333 1.452NA When I try to run the test, I get this error: error: input must be ts object Thanks, Kou -- View this message in context: http://www.nabble.com/Error-when-running-Kendall-Package-tp21507235p21507235.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] User input in batch mode
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Re: [R] Lattice: how to have multiple wireframe nice intersection?
On Jan 16, 2009, at 9:43 AM, Guillaume Chapron wrote: Hello, This code builds a simple example of 2 wireframes : require(lattice) x - c(1:10) y - c(1:10) g - expand.grid(x = 1:10, y = 1:10, gr = 1:2) g$z - c(as.vector(outer(x,y,*)), rep(50,100)) wireframe(z ~ x * y, data = g, groups = gr, scales = list(arrows = FALSE)) However, the intersection between the wireframes is not properly drawn. Is there a way to fix this with lattice, or should I use another package more suitable for this? Exactly what not properly drawn means is not stated. If it is the jagged intersection, then expanding the grid would seem to be one way forward. Here's 100 x 100: require(lattice) x -seq(1,10, len=100); y - seq(1,10, len=100) g - expand.grid(x = seq(1,10, len=100), y = seq(1,10, len=100), gr = 1:2) g$z - c(as.vector(outer(x,y,*)), rep(50,1)) wireframe(z ~ x * y, data = g, groups = gr, scales = list(arrows = FALSE)) You do get some Moir`e effects, but the jagged intersection is no longer visible and the curvature is visible. With 50*50 points it has a less obvious curvature to the intersection (but four times as fast). require(lattice) x -seq(1,10, len=50); y - seq(1,10, len=50) g - expand.grid(x = x, y = y, gr = 1:2) g$z - c(as.vector(outer(x,y,*)), rep(50,length(x)*length(y))) wireframe(z ~ x * y, data = g, groups = gr, scales = list(arrows = FALSE)) Or you could emphasize the curvature by drawing it in. I'm not the guy to do that, but there is an example of adding contours to a wireframe plot in Sarkar's book. Figure 13.7: http://lmdvr.r-forge.r-project.org/figures/figures.html -- David Winsemius Thanks! Guillaume __ 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] Winsorizing Multiple Variables
Hi All,
I want to take a matrix (or data frame) and winsorize each variable.
So I can, for example, correlate the winsorized variables.
The code below will winsorize a single vector, but when applied to
several vectors, each ends up sorted independently in ascending order
so that a given observation is no longer on the same row for each
vector.
So I need to winsorize the variable but then return it to its original
order. Or another solution that will take a data frame, wisorize each
variable, and return a new data frame with all the variables in the
original order.
Thanks for any help!
-Karl
#The function I'm working from
win-function(x,tr=.2,na.rm=F){
if(na.rm)x-x[!is.na(x)]
y-sort(x)
n-length(x)
ibot-floor(tr*n)+1
itop-length(x)-ibot+1
xbot-y[ibot]
xtop-y[itop]
y-ifelse(y=xbot,xbot,y)
y-ifelse(y=xtop,xtop,y)
win-y
win
}
#Produces an example data frame, ss is the observation id, vars 1-5
are the variables I want to winzorise.
ss
=
c
(1
:
5
);var1
=
rnorm
(5
);var2
=
rnorm
(5
);var3
=rnorm(5);var4=rnorm(5);as.data.frame(cbind(ss,var1,var2,var3,var4))-
data
data
#Winsorizes each variable, but sorts them independently so the
observations no longer line up.
sapply(data,win)
___
M. Karl Healey
Ph.D. Student
Department of Psychology
University of Toronto
Sidney Smith Hall
100 St. George Street
Toronto, ON
M5S 3G3
k...@psych.utoronto.ca
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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] Smooth periodic splines
1. RSiteSearch('{periodic spline}') produced 12 hits. I looked
at the first five and found that four of them seemed relevant to your
question.
2. The third hit in this list notes that the DierckxSpline
package has periodic splines, while 'fda' recommends finite Fourier
series for periodic functions; this hit documents an as.fd function
that approximates a 'dierckx' periodic object with a periodic 'fd' object.
Hope this helps.
Spencer
Duncan Murdoch wrote:
cmr.p...@gmail.com wrote:
Hello group!
Is there a package that allows to fit smooth *periodic* splines to
data? I'm interested in a function which combines the functionality of
smooth.spline and splines::periodicSpline.
I don't know one, but you could use the same technique that
periodicSpline uses: repeat a copy of the data to the left and right
of the main copy (similarly replicating the knots if you want
regression splines rather than smoothing splines), then fit to the
augmented dataset. I don't think it is guaranteed to be exactly
periodic, but it will be very close.
There is also the periodic option to splinefun and you might be able
to use it to construct a true periodic basis, but you'll have to work
out some tricky details to get that right.
Duncan Murdoch
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[R] matching more than two vectors (?)
Dear listmembers, I am trying to obtain values for pointdistance from another dataframe by matching UTMX and UTMY coordinates, but I am not sure how to introduce the second coordinate. PointDF$pointdistance=DistanceDF$distance[match(PointDF$UTMX,DistanceDF$UTMX PointDF$UTMY,DistanceDF$UTMY )] is wrong but (hopefully) illustrates what I am trying to do. Could somebody help ? Thank you very much. Juliane __ 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] Winsorizing Multiple Variables
Might work better to determine top and bottom for each column with
quantile() using an appropriate quantile option, and then process
each variable in place with your ifelse logic.
I did find a somewhat different definition of winsorization with no
sorting in this code copied from a Patrick Burns posting from earlier
this year on R-SIG-Finance;
function(x, winsorize=5) {
s - mad(x) * winsorize
top - median(x) + s
bot - median(x) - s
x[x top] - top
x[x bot] - bot x }
--
David Winsemius
On Jan 16, 2009, at 3:50 PM, Karl Healey wrote:
Hi All,
I want to take a matrix (or data frame) and winsorize each variable.
So I can, for example, correlate the winsorized variables.
The code below will winsorize a single vector, but when applied to
several vectors, each ends up sorted independently in ascending
order so that a given observation is no longer on the same row for
each vector.
So I need to winsorize the variable but then return it to its
original order. Or another solution that will take a data frame,
wisorize each variable, and return a new data frame with all the
variables in the original order.
Thanks for any help!
-Karl
#The function I'm working from
win-function(x,tr=.2,na.rm=F){
if(na.rm)x-x[!is.na(x)]
y-sort(x)
n-length(x)
ibot-floor(tr*n)+1
itop-length(x)-ibot+1
xbot-y[ibot]
xtop-y[itop]
y-ifelse(y=xbot,xbot,y)
y-ifelse(y=xtop,xtop,y)
win-y
win
}
#Produces an example data frame, ss is the observation id, vars 1-5
are the variables I want to winzorise.
ss
=
c
(1
:
5
);var1
=
rnorm
(5
);var2
=
rnorm
(5
);var3
=rnorm(5);var4=rnorm(5);as.data.frame(cbind(ss,var1,var2,var3,var4))-
data
data
#Winsorizes each variable, but sorts them independently so the
observations no longer line up.
sapply(data,win)
___
M. Karl Healey
Ph.D. Student
Department of Psychology
University of Toronto
Sidney Smith Hall
100 St. George Street
Toronto, ON
M5S 3G3
k...@psych.utoronto.ca
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Barchart in lattice package: controlling order of bars in plot and color of a selected bar
Hi, I'm using the lattice function 'barchart' to make a series of 4 histograms. Currently, the y-axis values are graphed in order of the y-axis variable. I'd like to have the y-axis values sorted in ascending order of the x-axis values so that the longest bar horizontally is on top of the graph (in it's seciton) and the shortest bar is on the bottom. I can do this in 'barplot' with normal graphics; how can I do this in the lattice barchart function? In addition, i use the 'col' parameter in 'barplot' to make one particular value be a different color than the rest. Is this sort of control available in lattice's barchart? I didn't see it when reading the documentation. Thanks, Matt ### Regular barplot code that works # w02-08 ar pre-sorted in descending Sum oder, # barcolor column has names of colors to use. opar - par(mfrow=c(1,4)) barplot(w02[,Sum], horiz=T, col=w02[,barcolor], names.arg=w02[,sts.dist], main=2002) barplot(w04[,Sum], horiz=T, col=w04[,barcolor], names.arg=w04[,sts.dist], main=2004) barplot(w06[,Sum], horiz=T, col=w06[,barcolor], names.arg=w06[,sts.dist], main=2006) barplot(w08[,Sum], horiz=T, col=w08[,barcolor], names.arg=w08[,sts.dist], main=2008) ### Attempt with lattice # work contains w02-08 stacked on top of each other barchart(sts.dist[order(Sum),] ~ Sum | year, data=work, layout=c(4,1), main=Ranking of best turnout by SD) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficiency challenge: MANY subsets
Try this one; it is doing a list of 7000 in under 2 seconds:
sequences - list(
+
+
+ c(M,G,L,W,I,S,F,G,T,P,P,S,Y,T,Y,L,L,I
+ ,M,
+
+
+ N,H,K,L,L,L,I,N,N,N,N,L,T,E,V,H,T,Y,F,
N,I,N,I,N,I,D,K,M,Y,I,H,*)
+ )
indexes - list(
+ list(
+ c(1,22),c(22,46),c(46, 51),c(1,46),c(22,51),c(1,51)
+ )
+ )
indexes - rep(indexes,10)
sequences - rep(sequences,7000)
system.time({
+ fragments - lapply(indexes, function(.seq){
+ lapply(.seq, function(.range){
+ .range - seq(.range[1], .range[2]) # save since we use several times
+ lapply(sequences, '[', .range)
+ })
+ })
+ })
user system elapsed
1.240.001.26
On Fri, Jan 16, 2009 at 3:16 PM, Johannes Graumann
johannes_graum...@web.de wrote:
Thanks. Very elegant, but doesn't solve the problem of the outer for loop,
since I now would rewrite the code like so:
fragments - list()
for(iN in seq(length(sequences))){
cat(paste(iN,\n))
fragments[[iN]] -
lapply(indexes[[1]], function(g)sequences[[1]][do.call(seq, as.list(g))])
}
still very slow for length(sequences) ~ 7000.
Joh
On Friday 16 January 2009 14:23:47 Henrique Dallazuanna wrote:
Try this:
lapply(indexes[[1]], function(g)sequences[[1]][do.call(seq, as.list(g))])
On Fri, Jan 16, 2009 at 11:06 AM, Johannes Graumann
johannes_graum...@web.de wrote:
Hello,
I have a list of character vectors like this:
sequences - list(
c(M,G,L,W,I,S,F,G,T,P,P,S,Y,T,Y,L,L,I
,M,
N,H,K,L,L,L,I,N,N,N,N,L,T,E,V,H,T,Y,
F, N,I,N,I,N,I,D,K,M,Y,I,H,*)
)
and another list of subset ranges like this:
indexes - list(
list(
c(1,22),c(22,46),c(46, 51),c(1,46),c(22,51),c(1,51)
)
)
What I now want to do is to subset each entry in sequences
(sequences[[1]]) with all ranges in the corresponding low level list in
indexes (indexes[[1]]). Here is what I came up with.
fragments - list()
for(iN in seq(length(sequences))){
cat(paste(iN,\n))
tmpFragments - sapply(
indexes[[iN]],
function(x){
sequences[[iN]][seq.int(x[1],x[2])]
}
)
fragments[[iN]] - tmpFragments
}
This works fine, but sequences contains thousands of entries and the
corresponding indexes are sometimes hundreds of ranges long, so this
whole
process is EXTREMELY inefficient.
Does somebody out there take the challenge and show me a way on how to
speed
this up?
Thanks for any hints,
Joh
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] Winsorizing Multiple Variables
Don't sort y. Calculate xbot and xtop using
xtemp-quantile(y,c(tr,1-tr),na.rm=na.rm)
xbot-xtemp[1]
xtop-xtemp[2]
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Karl Healey
Sent: Friday, January 16, 2009 2:51 PM
To: r-help@r-project.org
Subject: [R] Winsorizing Multiple Variables
Hi All,
I want to take a matrix (or data frame) and winsorize each variable.
So I can, for example, correlate the winsorized variables.
The code below will winsorize a single vector, but when applied to
several vectors, each ends up sorted independently in ascending order
so that a given observation is no longer on the same row for each
vector.
So I need to winsorize the variable but then return it to its original
order. Or another solution that will take a data frame, wisorize each
variable, and return a new data frame with all the variables in the
original order.
Thanks for any help!
-Karl
#The function I'm working from
win-function(x,tr=.2,na.rm=F){
if(na.rm)x-x[!is.na(x)]
y-sort(x)
n-length(x)
ibot-floor(tr*n)+1
itop-length(x)-ibot+1
xbot-y[ibot]
xtop-y[itop]
y-ifelse(y=xbot,xbot,y)
y-ifelse(y=xtop,xtop,y)
win-y
win
}
#Produces an example data frame, ss is the observation id, vars 1-5
are the variables I want to winzorise.
ss
=
c
(1
:
5
);var1
=
rnorm
(5
);var2
=
rnorm
(5
);var3
=rnorm(5);var4=rnorm(5);as.data.frame(cbind(ss,var1,var2,var3,var4))-
data
data
#Winsorizes each variable, but sorts them independently so the
observations no longer line up.
sapply(data,win)
___
M. Karl Healey
Ph.D. Student
Department of Psychology
University of Toronto
Sidney Smith Hall
100 St. George Street
Toronto, ON
M5S 3G3
k...@psych.utoronto.ca
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and provide commented, minimal, self-contained, reproducible code.
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