Re: [R] Faster union of polygons?
Martin,
thanks a lot! This speeds things up so much
Do you mind if I bundle your punion function in a package I am
developing (but of course I will name you the author of the function)?
greetings,
Remko
On Fri, Jun 4, 2010 at 12:17 PM, Martin Morgan mtmor...@fhcrc.org wrote:
On 06/03/2010 04:54 PM, Remko Duursma wrote:
Thanks for the tip - this cleans up the code a lot!
Unfortunately, there is no gain in speed.
Playing a little bit dirty,
punion -
function(...)
{
n - nargs()
if (0L == n) new(gpc.poly)
else if (1L == n is(..1, gpc.poly)) ..1
else {
polygons - list(...)
if (!all(sapply(polygons, is, gpc.poly)))
stop('...' must all be 'gpc.poly')
## avoid method look-up
to_numeric - selectMethod(coerce, c(gpc.poly, numeric))
vec - to_numeric(polygons[[1]])
for (p in polygons[-1]) {
clip - to_numeric(p)
vec - .Call(Rgpc_polygon_clip, vec, clip, 3,
PACKAGE=gpclib)
}
if (identical(vec, 0))
new(gpc.poly)
else
as(vec, gpc.poly)
}
}
is about 4x faster on your example
replicate(5, system.time(Reduce(union, leaves)))
[,1] [,2] [,3] [,4] [,5]
user.self 1.272 1.272 1.272 1.268 1.268
sys.self 0.000 0.000 0.000 0.000 0.000
elapsed 1.271 1.272 1.272 1.273 1.281
user.child 0.000 0.000 0.000 0.000 0.000
sys.child 0.000 0.000 0.000 0.000 0.000
replicate(5, system.time(do.call(punion, leaves)))
[,1] [,2] [,3] [,4] [,5]
user.self 0.308 0.312 0.304 0.308 0.312
sys.self 0.004 0.000 0.004 0.004 0.000
elapsed 0.311 0.311 0.309 0.314 0.317
user.child 0.000 0.000 0.000 0.000 0.000
sys.child 0.000 0.000 0.000 0.000 0.000
Rprof suggests that most of the time is now in the C code
Rprof(/tmp/leaves.Rprof)
x - replicate(5, system.time(do.call(punion, leaves)))
Rprof(NULL)
summaryRprof(/tmp/leaves.Rprof)
$by.self
self.time self.pct total.time total.pct
.Call 1.24 69.7 1.24 69.7
gc 0.24 13.5 0.24 13.5
FUN 0.08 4.5 1.78 100.0
[...SNIP...]
Martin
remko
On Thu, Jun 3, 2010 at 10:46 PM, nikhil kaza nikhil.l...@gmail.com wrote:
Reduce might work. Not sure about the speed advantages though. It does
simplify code.
Unionall - function(x) Reduce('union', x)
leaveout - Unionall(leaves)
On Tue, Jun 1, 2010 at 9:53 PM, Remko Duursma remkoduur...@gmail.com
wrote:
Dear R-helpers,
thanks for yesterday's speeding-up tip. Here is my next query:
I have lots of polygons (not necessarily convex ones, and they never
have holes) given by x,y coordinates.
I want to get the polygon that is the union of these polygons. This is
my current method, but I am hoping there is a faster method (up to
thousands of polygons, each with ca. 40 xy points).
Example:
library(gpclib)
# A polygon
leaf - structure(c(0, 1, 12.9, 16.5, 18.8, 17, 16.8, 15.5, 12.1, 8.2,
6.3, 5, 2, 0, -1.5, -4.3, -6.6, -10.3, -14.8, -19.4, -22.2, -23.5,
-22.2, -17.6, -7.8, 0, 0, -2.4, 2.8, 8.9, 19.9, 33.9, 34.8, 40.4,
49.7, 69.2, 77.4, 83.4, 91.4, 99, 92.8, 87.3, 81.2, 71.1, 57.6,
45.4, 39.2, 26, 15.6, 5.3, 0.6, 0), .Dim = c(26L, 2L), .Dimnames = list(
NULL, c(X, Y)))
# Lots of polygons:
releaf -
function(leaf)cbind(leaf[,1]+rnorm(1,0,50),leaf[,2]+rnorm(1,0,50))
leaves - replicate(500, releaf(leaf), simplify=FALSE)
# Make into gpc.poly class:
leaves - lapply(leaves, as, gpc.poly)
# Make union .
system.time({
leavesoutline - union(leaves[[1]], leaves[[2]])
for(i in 3:length(leaves))leavesoutline - union(leavesoutline,
leaves[[i]])
})
# about 1sec here.
# Check it:
plot(leavesoutline)
thanks!
Remko
-
Remko Duursma
Research Lecturer
Centre for Plants and the Environment
University of Western Sydney
Hawkesbury Campus
Richmond NSW 2753
Dept of Biological Science
Macquarie University
North Ryde NSW 2109
Australia
Mobile: +61 (0)422 096908
www.remkoduursma.com
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Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
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Location: Arnold Building M1 B861
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Re: [R] parttioning a matrix corresponding to different levels of y
Suman take a look if this suffices your purpous x - data.frame(y=as.factor(sample(0:2,1000,replace=TRUE)),x=runif(1000)) x1 - x[x$y==0,] x2 - x[x$y==1,] x3 - x[x$y==2,] On Fri, Jun 4, 2010 at 10:29 AM, suman dhara suman.dhar...@gmail.comwrote: Sir, I have a problem regarding partitioning a matrix.I state my problem as follows: I have a y vector of length say 1000.Variable y has 4 levels say 0,1,2.Corresponding to each y(response), I have a x-vector(explanatory) as a row of X matrix.Now, I want to partition the X matrix into 3 submatrices say x1,x2,x3 corresponding to each level of y.Is there any function to do this in R or how can I do this in R? For your convinience I attach a sample version of data. Use dput() and paste it in your mail Thanks, Suman Dhara __ 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.
[R] Boxplot: what is shown by default?
hi, i'm using /boxplot()/ to show some data: x - c(0.99, 0.97, 0.91, 0.72, 1.00, 0.99, 1.02, 0.90, 0.91, 0.90, 1.02, 0.90, 1.35, 1.01, 0.92) boxplot(x) is it correct when i say: /Boxes represent interquartile ranges (IQRs); bold horizontal lines, medians; whiskers, lowest and highest values still within 1.5 x IQR; open circles, outliers.? /thanks in advance for any help! cheers, tom human genetics, bern/ / [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R implementation for Text analytics
Hi there, is there any R package which address the Text analytics topic? It would also be great if someone point me about some good text books on Text analytics and what statistical tools and techniques are generally used on that field. Thanks and regards, [[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] R Newbie, please help!
Hey Jeff,
I have a few ideas. Each has some different requirements, and to help
you choose, I bench marked them.
###START###
##Basic data
test - data.frame(totret=rnorm(10^7), id=rep(1:10^4, each=10^3),
time=rep(c(1, rep(0, 999)), 10^4))
##Option 1: probably the most general, but also the slowest by far.
##The idea is it does the calculation for each stock/ID, and then
concatenates [c()] an NA in front.
system.time(test[,dailyreturns] - unlist(by(test[,totret], test[,id],
function(x) {c(NA, x[-1]/x[-length(x)])})), gcFirst=TRUE)
user system elapsed
49.110.42 49.86
##Option 2: Assumes that you have the same number of measurements for
each stock/ID so you can just assign an NA every nth row.
##This is fairly fast
system.time(test[-1,dailyreturns] -
test[-1,totret]/test[-nrow(test),totret], gcFirst=TRUE)
user system elapsed
1.110.211.31
system.time(test[seq(1, 10^7, by=10^3),dailyreturns] - NA, gcFirst=TRUE)
user system elapsed
0.390.040.42
##Option 3: Assumes that you have some variable (time in my little
test data) that somehow indicates when each stock/ID has its first
measurement. In the example, the first measurement gets a 1 and
subsequent ones a 0. So we just assign NA in 'dailyreturns' everytime
the other time column has a 1. Again, a big assumption, but fairly
quick.
system.time(test[-1,dailyreturns] -
test[-1,totret]/test[-nrow(test),totret], gcFirst=TRUE)
user system elapsed
1.060.171.25
system.time(test[which(test[,time]==1),dailyreturns] - NA, gcFirst=TRUE)
user system elapsed
0.460.090.55
###END###
I really feel like there should be a faster way that is also more
general, but it is late and I am not coming up with any better ideas
at the moment. Perhaps somehow finding the first instance of a
stock/ID? Anyway, this was simulated on 10 million rows, so maybe
by() works plenty fast for you.
Josh
On Thu, Jun 3, 2010 at 10:20 PM, Jeff08 jefferyd...@gmail.com wrote:
Hey Josh,
Thanks for the quick response!
I guess I have to switch from the Java mindset to the matrix/vector mindset
of R.
Your code worked very well, but I just have one problem:
Essentially I have a time series of stock A, followed by a time series of
stock B, etc.
So there are break points in the data (the points where it switches stocks
have incorrect returns, and should be NA at t=0 for each stock)
Is there an easy way to account for this in R? What I was thinking of is if
there is a way to make a filter rule. Such as if the ID of the row matches
Stock A, then perform this.
Hello Jeff,
Try this:
test - data.frame(totret=rnorm(10^7)) #create some sample data
test[-1,dailyreturn] - test[-1,totret]/test[-nrow(test),totret]
The general idea is to take the column totret excluding the first 1,
dividided by totret exluding the last row. This gives in effect t+1
(since t is now shorter)/t
I assigned the result to a new column dailyreturn. For 10^7 rows,
it tooks 1.92 seconds on my system.
--
View this message in context:
http://r.789695.n4.nabble.com/R-Newbie-please-help-tp2242633p2242703.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.
--
Joshua Wiley
Senior in Psychology
University of California, Riverside
http://www.joshuawiley.com/
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[R] Help on ARFIMA modeling
Please I want to perform full data analysis using ARFIMA model but I dont know the right package that can perform all the necessary test on the time series data. ERIC AIDOO [[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] R Newbie, please help!
I am not exactly sure how your filtering code is working, but take a look at
?na.omit
You will probably need a few additional steps if you want to remove
all rows related to a particular id. Also look at ?subset which is a
good general way to subset your data.
Josh
On Thu, Jun 3, 2010 at 11:45 PM, Jeffery Ding jefferyd...@gmail.com wrote:
Thanks, you have been tremendously helpful!
I will be able to implement option 2, after I filter out stocks with
incomplete data sets.
So far, for my filtering code I have:
##Filtering
x-length(unique(Returns$date_))
y-unique(Returns$id)
Returns.filter-Returns
i-1
while(i=length(y)) {
a-sum(Returns$id==y[i])
if(ax) {
##need code that will remove all rows with id a
}
i-i+1
}
On Fri, Jun 4, 2010 at 2:40 PM, Joshua Wiley jwiley.ps...@gmail.com wrote:
Hey Jeff,
I have a few ideas. Each has some different requirements, and to help
you choose, I bench marked them.
###START###
##Basic data
test - data.frame(totret=rnorm(10^7), id=rep(1:10^4, each=10^3),
time=rep(c(1, rep(0, 999)), 10^4))
##Option 1: probably the most general, but also the slowest by far.
##The idea is it does the calculation for each stock/ID, and then
concatenates [c()] an NA in front.
system.time(test[,dailyreturns] - unlist(by(test[,totret],
test[,id], function(x) {c(NA, x[-1]/x[-length(x)])})), gcFirst=TRUE)
user system elapsed
49.11 0.42 49.86
##Option 2: Assumes that you have the same number of measurements for
each stock/ID so you can just assign an NA every nth row.
##This is fairly fast
system.time(test[-1,dailyreturns] -
test[-1,totret]/test[-nrow(test),totret], gcFirst=TRUE)
user system elapsed
1.11 0.21 1.31
system.time(test[seq(1, 10^7, by=10^3),dailyreturns] - NA,
gcFirst=TRUE)
user system elapsed
0.39 0.04 0.42
##Option 3: Assumes that you have some variable (time in my little
test data) that somehow indicates when each stock/ID has its first
measurement. In the example, the first measurement gets a 1 and
subsequent ones a 0. So we just assign NA in 'dailyreturns' everytime
the other time column has a 1. Again, a big assumption, but fairly
quick.
system.time(test[-1,dailyreturns] -
test[-1,totret]/test[-nrow(test),totret], gcFirst=TRUE)
user system elapsed
1.06 0.17 1.25
system.time(test[which(test[,time]==1),dailyreturns] - NA,
gcFirst=TRUE)
user system elapsed
0.46 0.09 0.55
###END###
I really feel like there should be a faster way that is also more
general, but it is late and I am not coming up with any better ideas
at the moment. Perhaps somehow finding the first instance of a
stock/ID? Anyway, this was simulated on 10 million rows, so maybe
by() works plenty fast for you.
Josh
On Thu, Jun 3, 2010 at 10:20 PM, Jeff08 jefferyd...@gmail.com wrote:
Hey Josh,
Thanks for the quick response!
I guess I have to switch from the Java mindset to the matrix/vector
mindset
of R.
Your code worked very well, but I just have one problem:
Essentially I have a time series of stock A, followed by a time series
of
stock B, etc.
So there are break points in the data (the points where it switches
stocks
have incorrect returns, and should be NA at t=0 for each stock)
Is there an easy way to account for this in R? What I was thinking of is
if
there is a way to make a filter rule. Such as if the ID of the row
matches
Stock A, then perform this.
Hello Jeff,
Try this:
test - data.frame(totret=rnorm(10^7)) #create some sample data
test[-1,dailyreturn] - test[-1,totret]/test[-nrow(test),totret]
The general idea is to take the column totret excluding the first 1,
dividided by totret exluding the last row. This gives in effect t+1
(since t is now shorter)/t
I assigned the result to a new column dailyreturn. For 10^7 rows,
it tooks 1.92 seconds on my system.
--
View this message in context:
http://r.789695.n4.nabble.com/R-Newbie-please-help-tp2242633p2242703.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.
--
Joshua Wiley
Senior in Psychology
University of California, Riverside
http://www.joshuawiley.com/
--
Jeffery Ding
Duke University, Class of 2012
(224) 622-3398 | jd...@duke.edu
--
Joshua Wiley
Senior in Psychology
University of California, Riverside
http://www.joshuawiley.com/
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Re: [R] import text file into R
On 2010-06-03 22:51, Dhanasekaran wrote: please look at the error.. LosA-read.table(E:\\Temporary Tasks\\rub\\Los_R\\ca_los.txt,header=T,sep=\t) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 11022 did not have 87 elements That error message seems pretty explicit to me: you have a problem with line 11022. Did you check it with a text editor? It's always a good idea to run count.fields() on the file, as recommended on the help page for read.table. If you're trying to import SAS data, you might want to check out the 'foreign' package. Note also that read.delim is convenient for tab-delimited files. -Peter Ehlers ca_los.txt is my tab delimited large text file which contains about 16lakhs observations. thank you On Fri, Jun 4, 2010 at 9:44 AM, Erik Iversoner...@ccbr.umn.edu wrote: Dhanasekaran wrote: Sorry guys It is a tab delimited text file which I just exported from SAS. I want to import this in R. Pl let me know what is the delimiter I should use and R syntax. You still don't say the error you're getting when you try your read.table command. __ 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] import text file into R
On Fri, Jun 4, 2010 at 2:51 PM, Dhanasekaran dhana...@gmail.com wrote: ca_los.txt is my tab delimited large text file which contains about 16lakhs observations. Most readers of this list probably won't know that a 'lakh' is a hundred thousand. 16lakhs means 1.6 million. Glen __ 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] Shapes in barplots
Hi,
I am making barplots . I am using the default shape of barplots with a pipe
but I wants to build bars in various 3d shapes. I have install rgl using
install.packages('rgl') for this purpose, but when I am doing library(rgl),
it shows
Error in library(rgl) : there is no package called 'rgl'
What are the other ways to build such plots of variuos shapes.
Is that *TeachingDemos *replace it..I am not sure how to use it for such
task.
Thanks in advance
Jeet
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[R] Handling of par() with variables
Hello! In order to plot multiple graphs with the same set-up I use the following code-structure: ### # storing old parameter set oldpar - par(no.readonly=T) #copying old parameter set newpar - par(no.readonly=T) #adjusting parameters newpar - par(mar=c(3.1,3.1,0.1,0.1), # margin for figure area oma=c(0,0,0,0), # margin for outer figure area cex.axis=0.9, # axeneinteilung mgp=c(2,0.6,0), # abstand der achsenbeschriftung tck=0.02# major ticks innen ) ... ... postscript(...) par(newpar) ... dev.off() ### Calling the variable newpar delivers the old paramter set only (from code-line newpar - par(no.readonly=T)). If the code-segment newpar - par(mar=... runs a second time, the correct paramter set is stored, however, just the 5 parameters adjusted and not the full list. My question is, why must the code segment newpar-par(mar...) run twice? Is there a better way to handle the graphics output? I would be grateful for a pointer on a FAQ-section or to an older discussion thread in this group! Thank you very much in advance! Regards, /steffen __ 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] strange behaviour of CairoPNG
Hi, could it be that the text() fuction gives different output for normal png() and CarioPNG()? See the following example and the attached images: the font=2 and font=3 seem to be exchanged! Thanks for help, Thomas CairoPNG(Test-cairo.png,width=750,height=690) #png(Test-normal.png,width=750,height=690) plot(1,1,type=n,main=normal) text(1,1,normal,adj=c(1,1)) text(1,1,bold,font=2,adj=c(-1,-1)) text(1,1,italic,font=3,adj=c(1,-1)) text(1,1,italicbold,font=4,adj=c(-1,1)) dev.off() attachment: Test-cairo.pngattachment: Test-normal.png__ 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] plot polar coordinates
On 06/04/2010 05:05 AM, Thomas Steiner wrote: Thank you Greg, I'll add 180 then. Thanks for the hint with longer radial.lim arguments it works woderfull. The lines function is plotting in Cartesian coordinates, not the polar coordinates. Is there any (lines) function that plots polar coordinates to an existing plot? Hi Thomas, Greg has already given you most of the solutions. I was a bit surprised to find that if you include the negative values in the radial.lim argument, the polygon appears _and_ in the right place! I'll have to add this to the help page. Note that your labels may not be where you think they should be, as 0 degrees is east in your example. Maybe you want start=90? I have thought about reprogramming the radial plot functions with an add argument, but haven't gotten around to it. I'll have a look and if I can do this without too much work, I'll let you know. As far as 100 being prettier than 90, my experience is that I ain't gettin' any prettier as I get older. 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] StatET plot problem
Dear all, after trying several suggestions from the list for a nice R-Editor / IDE for MacOS X and really trying some of those that needed to be configured a little more (such as emacs, aquamacs and StatET / Eclipse), I prefer StatET at the moment. I found more experienced like John suggesting this combination (http://www.mail-archive.com/r-help@r-project.org/msg38883.html) on Mac OS X. So far I am really happy with it except for the plotting. I just can´t get plots to go. everytime I plot(x) nothing happens. What´s striking is that the edit() works and opens up in X11. Is there some configuration option I just missed ? best regards matt __ 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] import text file into R
On 06/03/2010 09:32 PM, dhanush wrote: can anyone tell me how to import a text file in R? the text file I want to import is a large file, about 800MB in size. Thanks in advance. I tried using the following data-read.table(file,header=T,sep=\t) Hi dhanush, If the problem is with read.table, maybe: # whatlist is a list of data types defining what # is in each line of data - see the help page data-scan(file,skip=1,sep=\t,what=whatlist) will get it in for you. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Boxplot: what is shown by default?
On 2010-06-04 0:14, Thomas von Känel wrote: hi, i'm using /boxplot()/ to show some data: x- c(0.99, 0.97, 0.91, 0.72, 1.00, 0.99, 1.02, 0.90, 0.91, 0.90, 1.02, 0.90, 1.35, 1.01, 0.92) boxplot(x) is it correct when i say: /Boxes represent interquartile ranges (IQRs); bold horizontal lines, medians; whiskers, lowest and highest values still within 1.5 x IQR; open circles, outliers.? That's essentially correct, except that quartiles can be defined in more than one way; see ?quantile and the discussion leading to comments in https://stat.ethz.ch/pipermail/r-help/2010-May/239074.html. Note that the box limits are the 'hinges' given by fivenum(x) and their difference need not equal IQR(x) which uses quantile(..., type=7). [For your data above, they do happen to coincide.] -Peter Ehlers /thanks in advance for any help! cheers, tom human genetics, bern/ / __ 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] StatET plot problem
On 04/06/10 10:37, Bunny, lautloscrew.com wrote: Dear all, after trying several suggestions from the list for a nice R-Editor / IDE for MacOS X and really trying some of those that needed to be configured a little more (such as emacs, aquamacs and StatET / Eclipse), I prefer StatET at the moment. I found more experienced like John suggesting this combination (http://www.mail-archive.com/r-help@r-project.org/msg38883.html) on Mac OS X. So far I am really happy with it except for the plotting. I just can´t get plots to go. everytime I plot(x) nothing happens. What´s striking is that the edit() works and opens up in X11. Is there some configuration option I just missed ? best regards You haven't try SciViews-K/Komodo, don't you? (http://www.sciviews.org/SciViews-K). Best, Philippe matt __ 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] Comparing a 4-point and 5-point Likert scale
On 06/03/2010 11:11 PM, Simon Kiss wrote: Help with survey data: Hello R colleagues, I hope this is an appropriate place to direct this question. It relates specifically to the comparability of a 5-point likert to a 4-point likert scale. One question in my dataset asks How much should be done to reduce the gap between rich and poor Much more, somewhat more, about the same, somewhat less and much less. The second questions ask: People who can afford to, should be able to pay for their own health care strongly agree, agree, disagree, strongly agree. Now, assuming that I rescale them so that 1 equals the most egalitarian position and the highest number (4 or 5) equals the least egalitarian position, how can I make these two results comparable. Two ways come to mind: one is to collapse both into a dichotomous variable and do a logistic regression on both. The danger here is that I have to decide what to do with the middle position in the first question, assign it to the egalitarian or non-egalitarian category. A second way would be to multiply the scores in the first question by 4 (to get results that are either 4, 8, 12, 16 or 20) and then multiply the second question by five to get responses that are either 5, 10, 15 or 20. My idea is then to add the two, average them and use that value as an index of economic egalitarianism? Yes / no? Suggestions? I am an R user and I hope that a purely statistical question is not especially misplaced. Hi Simon, Strictly speaking, only the second question is a Likert scale, as that assumes a measure of agreement, not some other quantitative dimension. Assuming that the fourth option on Q2 is Strongly disagree, and you wish to argue that this and the first option on Q1 (Much more) both represent the maximally egalitarian responses, you could reverse Q2 and scale it to the same range (i.e. 1,2,3,4,to 5,3.67,2.33,1) so that it would have the same weight in an additive composite score. If I was reviewing a paper that suggested this, I would expect a pretty sound defense of the notion that income redistribution and public health care were strongly linked attitudes. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] deduplication
Please try this
## Import data
id1-c(4,17,9,1,1,1,3,3,6,15,1,1,1,1,3,3,3,3,4,4,4,5,5,12,9,9,10,10)
id2-c(8,18,10,3,6,7,6,7,7,16,4,5,12,18,4,5,12,18,5,12,18,12,18,18,15,16,15,16)
id-data.frame(id1 = id1, id2 = id2)
## Create same structure table
id - id0 - unique(id)
leng - nrow(id)
n - 0
repeat {
if (n == leng) {break}
n - 0
id - id[order(-id$id1, -id$id2),]
for (i in 1:leng) {
if (id$id1[i] == id$id2[i]) {
n - n+1
next }
smal - min(id[i,])
larg - max(id[i,])
id$id2[which(id$id2 == larg)] - smal
id$id1[which(id$id1 == larg)] - smal
}}
## Create results
tab - table(as.matrix(id0),
as.matrix(id[order(as.numeric(rownames(id))),]))
res - list()
for (i in 1:ncol(tab)) {
res[[i]] - rownames(tab[(tab[,i] != 0),])}
res
-
A R learner.
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Re: [R] For Loop help needed
Hi r-help-boun...@r-project.org napsal dne 03.06.2010 18:18:33: One option: t - data.frame(x1=c(1,1,0,0,0,1), x2=c(0,0,0,1,0,1), Count=c(523,23,2,45,3,433)) t.sum - function(df, x1, x2) sum(df[df$x1==x1 df$x2==x2,]$Count) t.sum(t, 1, 0) # [1] 546 t.sum(t, 0, 0) # [1] 5 If this is what Khan wants so aggregate(t$Count, list(interaction(t$x1, t$x2)), sum) Group.1 x 1 0.0 5 2 1.0 546 3 0.1 45 4 1.1 433 could be better option Regards Petr Hope this helps a little. Allan On 03/06/10 16:18, Geeti Khan wrote: Hi, I have a dataset with three column like this x1 x2 Count 1 0 523 1 0 23 0 0 2 0 1 45 0 0 3 1 1 433 I need to create a loop so that when c(x1,x2)=c(1,1), I can add the corresponding Counts.When c(x1,x2)=c(1,0), can add the corresponding counts and so on. Can anyone help me [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-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] moving average on irregular time series
Dear William and Gabor, Both solutions worked, and my problem is now solved. Many thanks to both of you! regards, Gustaf On Thu, Jun 3, 2010 at 10:23 AM, Gustaf Rydevik gustaf.ryde...@gmail.com wrote: Hi all, I wonder if there is any way to calculate a moving average on an irregular time series, or use the rollapply function in zoo? I have a set of dates where I want to check if there has been an event 14 days prior to each time point in order to mark these timepoints for removal, and can't figure out a good way to do it. Many thanks in advance! Gustaf Example data: exData-structure(list(Datebegin = structure(c(14476, 14569, 14576, 14621, 14627, 14632, 14661, 14671, 14705, 14715, 14751, 14756, 14495, 14518, 14523, 14526, 14528, 14529, 14545, 14548), class = Date), Event = c(TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE)), .Names = c(Datebegin, Event ), row.names = c(NA, 20L), class = data.frame) ###In this example, row 18 is a date less than 14 days after an event and should be marked for removal. -- 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. -- 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.
[R] Handling of par() with variables
Hello! In order to plot multiple graphs with the same setup I use the following code-structure: ### # storing old parameter set oldpar - par(no.readonly=T) #copying old parameter set newpar - par(no.readonly=T) #adjusting parameters newpar - par(mar=c(3.1,3.1,0.1,0.1), # margin for figure area oma=c(0,0,0,0), # margin for outer figure area cex.axis=0.9, # font size axis mgp=c(2,0.6,0), # distance of axis tck=0.02# major ticks inside ) ... ... postscript(...) par(newpar) ... dev.off() ### Calling the variable newpar delivers the old paramter set only (from code-line newpar - par(no.readonly=T)). If the code-segment newpar - par(mar=... runs a second time, the correct paramter set is stored, however, just the 5 parameters adjusted and not the full list. My question is, why must the code segment newpar-par(mar...) run twice? Is there a better way to handle the graphics output? I would be grateful for a pointer on a FAQ-section or to an older discussion thread in this group! Thank you very much in advance! Regards, /steffen -- Steffen Uhlig, PhD Mechatronik und Sensortechnik HTW des Saarlandes Goebenstraße 40 66117 Saarbrücken Tel.: +49 (0) 681 58 67 274 __ 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] plot polar coordinates
Thank you Jim, I had a liitle off-list conversation with Greg and finally I got the solution. All the code is now on http://commons.wikimedia.org/wiki/File:Sonnenstand.png I got the workaround with my own (sun)lines function which does the shift from cartesian coordiantes to polar coordinates. An example result is attached. The negative vales where just a stupid try from my side, it does of course make no sense. Best, Thomas 2010/6/4 Jim Lemon j...@bitwrit.com.au: On 06/04/2010 05:05 AM, Thomas Steiner wrote: Thank you Greg, I'll add 180 then. Thanks for the hint with longer radial.lim arguments it works woderfull. The lines function is plotting in Cartesian coordinates, not the polar coordinates. Is there any (lines) function that plots polar coordinates to an existing plot? Hi Thomas, Greg has already given you most of the solutions. I was a bit surprised to find that if you include the negative values in the radial.lim argument, the polygon appears _and_ in the right place! I'll have to add this to the help page. Note that your labels may not be where you think they should be, as 0 degrees is east in your example. Maybe you want start=90? I have thought about reprogramming the radial plot functions with an add argument, but haven't gotten around to it. I'll have a look and if I can do this without too much work, I'll let you know. As far as 100 being prettier than 90, my experience is that I ain't gettin' any prettier as I get older. Jim attachment: sonnenstad-narvik.png__ 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] ps-output and LaTeX/DVIPS/PS2PDF - Greek letters disappear
Hello! My graphs are produced using the postscript-option in R (R version 2.10.1 (2009-12-14)). When Greek letters are used on the axis, everything looks fine in the *.ps-file. If included in a LaTeX-file and (on Ubuntu 10.04, fresh install), the Greek letters appear in the DVI- and PS-output, however, if converted with ps2pdf they suddenly disappear. Could anyone suggest a solution? Best regards, /steffen -- Steffen Uhlig, PhD Mechatronik und Sensortechnik HTW des Saarlandes Goebenstraße 40 66117 Saarbrücken Tel.: +49 (0) 681 58 67 274 __ 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] For Loop help needed
On 04/06/10 10:32, Petr PIKAL wrote: One option: t- data.frame(x1=c(1,1,0,0,0,1), x2=c(0,0,0,1,0,1), Count=c(523,23,2,45,3,433)) t.sum- function(df, x1, x2) sum(df[df$x1==x1 df$x2==x2,]$Count) [...] If this is what Khan wants so aggregate(t$Count, list(interaction(t$x1, t$x2)), sum) Group.1 x 1 0.0 5 2 1.0 546 3 0.1 45 4 1.1 433 could be better option Indeed it is better! Or even shorter with the formula interface: aggregate(Count ~ x1+x2, data=t, sum) # x1 x2 Count # 1 0 0 5 # 2 1 0 546 # 3 0 145 # 4 1 1 433 Allan __ 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] ordinal variables
Hi, If you look around a bit, there is some great material on the web about the powers and quirks of R. I've taught myself most of what I know from R through reading a lot and trying it out on the console. The help list is also a darn fine source of efficient code for a set of general problems. It won't help any more this year, but I'm working on a guide for R to bundle valuable information I got from the help list and the internet. It should be ready in a couple of months, and it will be available for all to use. In any case, Owen's guide is of great value for an introduction to the command line and basic statistics: http://cran.r-project.org/doc/contrib/Owen-TheRGuide.pdf Also the introduction to R is a must-read for all our students : http://cran.r-project.org/doc/manuals/R-intro.pdf Next to that, a couple of websites are great additional sources of code : Quick-R, a guide for those who come over from SAS/SPSS/Stata. It contains tons of examples for statistical analyses in about every field. If you didn't know it yet, you'll love it for sure : http://www.statmethods.net/ The R graph gallery, to show what exactly can be done with the graphical power of R : http://addictedtor.free.fr/graphiques/ The R Graphics gallery, doing the same : http://research.stowers-institute.org/efg/R/ There's many more to be found, a whole community of users is contributing to the information in various ways. We give the sources mentioned here to our students, with the message that they should never underestimate the power of Google. Last but not least, there is a specific mailing list regarding teaching statistics using R: https://stat.ethz.ch/mailman/listinfo/r-sig-teaching You might want to take a look at their archives as well. Cheers Joris On Fri, Jun 4, 2010 at 6:39 AM, Iasonas Lamprianou lampria...@yahoo.com wrote: Thanks, I'll have a go and will let you know. I guess that the success has to do with how efficiently I help them to demonstrate the efficiency of code over menues. So part of the issue is how I teach them as well... Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary Research Fellow Department of Education The University of Manchester Oxford Road, Manchester M13 9PL, UK Tel. 0044 161 275 3485 iasonas.lampria...@manchester.ac.uk --- On Thu, 3/6/10, S Ellison s.elli...@lgc.co.uk wrote: From: S Ellison s.elli...@lgc.co.uk Subject: Re: [R] ordinal variables To: Joris Meys jorism...@gmail.com, Iasonas Lamprianou lampria...@yahoo.com Cc: r-help@r-project.org Date: Thursday, 3 June, 2010, 15:44 If you set them a problem that has them doing the same sort of thing five times and compare the time it takes with code pasted from an editor (eg Tinn-R) and the time it takes via menius, you may have more luck convincing them. A command line sequence is harder than menus the first two times but easier for any n iterations thereafter. Steve ellison Iasonas Lamprianou lampria...@yahoo.com 03/06/2010 14:51 Thank you Joris, I'll have a look into the commands you sent me. They look convincing. I hope my students will also see them in a positive way (although I can force them to pretend that they have a positive attitude)! Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary Research Fellow Department of Education The University of Manchester Oxford Road, Manchester M13 9PL, UK Tel. 0044 161 275 3485 iasonas.lampria...@manchester.ac.uk --- On Thu, 3/6/10, Joris Meys jorism...@gmail.com wrote: From: Joris Meys jorism...@gmail.com Subject: Re: [R] ordinal variables To: Iasonas Lamprianou lampria...@yahoo.com Cc: r-help@r-project.org Date: Thursday, 3 June, 2010, 14:35 see ?factor and ?as.factor. On ordered factors you can technically do a spearman without problem, apart from the fact that a spearman test by definition cannot give exact p-values with ties present. x - sample(c(a,b,c,d,e),100,replace=T) y - sample(c(a,b,c,d,e),100,replace=T) x.ordered - factor(x,levels=c(e,b,a,d,c),ordered=T) x.ordered y.ordered - factor(y,levels=c(e,b,a,d,c),ordered=T) y.ordered cor.test(x.ordered,y.ordered,method=spearman) require(pspearman) spearman.test(x.ordered,y.ordered) R commander has some menu options to deal with factors. R commander also provides a scripting window. Please do your students a favor, and show them how to use those commands. Cheers Joris On Thu, Jun 3, 2010 at 2:25 PM, Iasonas Lamprianou lampria...@yahoo.com wrote: Dear colleagues, I teach statistics using SPSS. I want to use R instead. I hit on one problem and I
Re: [R] General-purpose GPU computing in statistics (using R)
On Thu, 3 Jun 2010, Ravi Varadhan wrote: Hi All, I have been reading about general purpose GPU (graphical processing units) computing for computational statistics. I know very little about this, but I read that GPUs currently cannot handle double-precision floating points Not so for a while, and the latest ones are quite fast at it. and also that they are not necessarily IEEE compliant. However, I am not sure what the practical impact of this limitation is likely to be on computational statistics problems (e.g. optimization, multivariate analysis, MCMC, etc.). What are the main obstacles that are likely to prevent widespread use of this technology in computational statistics? Developing highly parallel algorithms that can exploit the architectures. That's not just in statistics, see e.g. http://www.microway.com/pdfs/TeslaC2050-Fermi-Performance.pdf (A Tesla C2050 is the latest generation GPU -- shipping within the last month.) Can algorithms be coded in R to take advantage of the GPU architecture to speed up computations? I would appreciate hearing from R sages about their views on the usefulness of general purpose GPU (graphical processing units) computing for computational statistics. I would also like to hear about views on the future of GPGPU - i.e. is it here to stay or is it just a gimmick that will quietly disappear into the oblivion. They need a lot of programming work to use, and the R packages currently attempting to use them (cudaBayesreg and gputools) are very specialized. It seems likely that they will remain a niche area, In much the same way that enhanced BLAS are -- there are problems for which the latter can make a big difference, but they are far from universally useful. We've been here several times before: when I was on UK national supercomputing committees in the 1980s and 90s there were several similar contenders (SIMD arrays, Inmos Transputers ...) and all faded away. That is not to say that general purpose parallelism is not going to be central, as we each get (several) machines with many CPU cores. But that sort of parallelism is likely to be exploited in different ways from that of GPUs. Thanks very much. Best regards, Ravi. -- Ravi Varadhan, Ph.D. Assistant Professor, Center on Aging and Health, Johns Hopkins University School of Medicine (410)502-2619 rvarad...@jhmi.edu http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h tml [[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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Handling of par() with variables
I think you misunderstand the working of par(). If you set new parameters, R allows you to store the old parameters simultaneously. Take a look at : par(no.readonly=T) oldpar - par(mar=c(1,1,1,1),tck=0.02) par(no.readonly=T) par(oldpar) par(no.readonly=T) So your line : newpar - par(mar=c(3.1,3.1,0.1,0.1), # margin for figure area oma=c(0,0,0,0), # margin for outer figure area cex.axis=0.9, # font size axis mgp=c(2,0.6,0), # distance of axis tck=0.02# major ticks inside ) actually stores the OLD parameters in newpar, and not the new ones. If you want to set them using a variable, you'll need something like : newmar - c(3.1,3.1,1.0,1.0) # store the mar values in a variable oldpar - par(mar=newmar) # set the mar and store the old values ... par(oldpar) # back to the old parameters Cheers Joris On Fri, Jun 4, 2010 at 11:40 AM, Steffen Uhlig steffen.uh...@htw-saarland.de wrote: Hello! In order to plot multiple graphs with the same setup I use the following code-structure: ### # storing old parameter set oldpar - par(no.readonly=T)t #copying old parameter set newpar - par(no.readonly=T) #adjusting parameters newpar - par(mar=c(3.1,3.1,0.1,0.1), # margin for figure area oma=c(0,0,0,0), # margin for outer figure area cex.axis=0.9, # font size axis mgp=c(2,0.6,0), # distance of axis tck=0.02 # major ticks inside ) ... ... postscript(...) par(newpar) ... dev.off() ### Calling the variable newpar delivers the old paramter set only (from code-line newpar - par(no.readonly=T)). If the code-segment newpar - par(mar=... runs a second time, the correct paramter set is stored, however, just the 5 parameters adjusted and not the full list. My question is, why must the code segment newpar-par(mar...) run twice? Is there a better way to handle the graphics output? I would be grateful for a pointer on a FAQ-section or to an older discussion thread in this group! Thank you very much in advance! Regards, /steffen -- Steffen Uhlig, PhD Mechatronik und Sensortechnik HTW des Saarlandes Goebenstraße 40 66117 Saarbrücken Tel.: +49 (0) 681 58 67 274 __ 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. -- Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php __ 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] save in for loop
On a side note: On Thu, May 20, 2010 at 9:43 AM, Ivan Calandra ivan.calan...@uni-hamburg.de wrote: Thanks to all of you for your answers! ... Tao, I don't understand why you have backslashes before file and after .rda. I guess it's something about regular expression, but I'm still very new to it. eval(parse(text=paste(save(file, i, , file=\file, i, .rda\), sep=))) Very simple: You need to give a command as a string. In the save command, you have to put quotation marks around the filename. Now within the paste function, a simple quotation mark would make R believe the string to paste ends there, and you don't want that. So you escape the by typing \, then R knows you want to add the symbol to the string instead of end it. : paste(save(file, i, , file=\file, i, .rda\),sep=) [1] save(file2, file=\file2.rda\) parse(text=paste(save(file, i, , file=\file, i, .rda\),sep=)) expression(save(file2, file=file2.rda)) attr(,srcfile) text paste(save(file, i, , file=file, i, .rda),sep=) Error: unexpected symbol in paste(save(file, i, , file=file Hope it's a bit more clear now. Cheers Joris -- Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php __ 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] ps-output and LaTeX/DVIPS/PS2PDF - Greek letters disappear
That's a problem of LateX and Ubuntu, not R : https://bugs.launchpad.net/ubuntu/+source/poppler/+bug/319495 You'll have more luck on an Ubuntu list or forum. Cheers Joris On Fri, Jun 4, 2010 at 11:47 AM, Steffen Uhlig steffen.uh...@htw-saarland.de wrote: Hello! My graphs are produced using the postscript-option in R (R version 2.10.1 (2009-12-14)). When Greek letters are used on the axis, everything looks fine in the *.ps-file. If included in a LaTeX-file and (on Ubuntu 10.04, fresh install), the Greek letters appear in the DVI- and PS-output, however, if converted with ps2pdf they suddenly disappear. Could anyone suggest a solution? Best regards, /steffen -- Steffen Uhlig, PhD Mechatronik und Sensortechnik HTW des Saarlandes Goebenstraße 40 66117 Saarbrücken Tel.: +49 (0) 681 58 67 274 __ 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. -- Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php __ 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] moving average on irregular time series
On Thu, Jun 3, 2010 at 8:04 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Replace the non-events with NA and then use na.locf from the zoo package to move the last event date up to give lastEvent. Then simply select those rows whose lastEvent date is at least 14 days ago or if the row itself is an Event: library(zoo) # na.locf lastEvent - with(exData, na.locf(ifelse(Event, Datebegin, NA), na.rm = FALSE)) exData[beg = lastEvent + 14 | exData$Event, ] The last line should have been: exData[exData$Datebegin = lastEvent + 14 | exData$Event, ] Datebegin Event 1 2009-08-20 TRUE 2 2009-11-21 FALSE 3 2009-11-28 FALSE 4 2010-01-12 FALSE 5 2010-01-18 FALSE 6 2010-01-23 FALSE 7 2010-02-21 FALSE 8 2010-03-03 FALSE 9 2010-04-06 FALSE 10 2010-04-16 FALSE 11 2010-05-22 TRUE 12 2010-05-27 TRUE 13 2009-09-08 TRUE 14 2009-10-01 FALSE 15 2009-10-06 FALSE 16 2009-10-09 FALSE 17 2009-10-11 TRUE 19 2009-10-28 FALSE 20 2009-10-31 FALSE On Thu, Jun 3, 2010 at 10:23 AM, Gustaf Rydevik gustaf.ryde...@gmail.com wrote: Hi all, I wonder if there is any way to calculate a moving average on an irregular time series, or use the rollapply function in zoo? I have a set of dates where I want to check if there has been an event 14 days prior to each time point in order to mark these timepoints for removal, and can't figure out a good way to do it. Many thanks in advance! Gustaf Example data: exData-structure(list(Datebegin = structure(c(14476, 14569, 14576, 14621, 14627, 14632, 14661, 14671, 14705, 14715, 14751, 14756, 14495, 14518, 14523, 14526, 14528, 14529, 14545, 14548), class = Date), Event = c(TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE)), .Names = c(Datebegin, Event ), row.names = c(NA, 20L), class = data.frame) ###In this example, row 18 is a date less than 14 days after an event and should be marked for removal. -- 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. __ 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] Tinn-R keyboard problem
I have the same problem. I also installed the older stable version (1.17.2.4, compatible version with MDI), but with no success. The keyboard worked fine before. I use Windows XP. Is there any solution? Many thanks, Carsten -- View this message in context: http://r.789695.n4.nabble.com/Tinn-R-keyboard-problem-tp839036p2242964.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] R with Emacs
I want to know how Emacs works with R. can anyone provide me a link or manual to read? Thank you -- View this message in context: http://r.789695.n4.nabble.com/R-with-Emacs-tp2243022p2243022.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] R with Emacs
Emacs ESS : http://ess.r-project.org/ Cheers Joris On Fri, Jun 4, 2010 at 12:55 PM, dhanush dhana...@gmail.com wrote: I want to know how Emacs works with R. can anyone provide me a link or manual to read? Thank you -- View this message in context: http://r.789695.n4.nabble.com/R-with-Emacs-tp2243022p2243022.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. -- Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php __ 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 with Emacs
Le 04/06/10 12:55, dhanush a écrit : I want to know how Emacs works with R. can anyone provide me a link or manual to read? Thank you http://lmgtfy.com/?q=R+emacs The first link is what you want. Romain -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://bit.ly/c6YnCi : graph gallery collage |- http://bit.ly/bZ7ltC : inline 0.3.5 `- http://bit.ly/8YUsiC : highlight 0.2-0 __ 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] Tinn-R keyboard problem
Tinn-R works with SDI. Make sure you have both the settings in R and the Rprofile.site correct. If the bug persists with the latest version of Tinn-R, look for help on : http://sourceforge.net/projects/tinn-r/support Cheers Joris On Fri, Jun 4, 2010 at 11:56 AM, dhidh23061972 carsten.giess...@gmx.net wrote: I have the same problem. I also installed the older stable version (1.17.2.4, compatible version with MDI), but with no success. The keyboard worked fine before. I use Windows XP. Is there any solution? Many thanks, Carsten -- View this message in context: http://r.789695.n4.nabble.com/Tinn-R-keyboard-problem-tp839036p2242964.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. -- Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php __ 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] ordinal variables
This is valuable material, thanks for all the help. I'll need many days to go through this information jason Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary Research Fellow Department of Education The University of Manchester Oxford Road, Manchester M13 9PL, UK Tel. 0044 161 275 3485 iasonas.lampria...@manchester.ac.uk --- On Fri, 4/6/10, Joris Meys jorism...@gmail.com wrote: From: Joris Meys jorism...@gmail.com Subject: Re: [R] ordinal variables To: Iasonas Lamprianou lampria...@yahoo.com Cc: r-help@r-project.org Date: Friday, 4 June, 2010, 11:24 Hi, If you look around a bit, there is some great material on the web about the powers and quirks of R. I've taught myself most of what I know from R through reading a lot and trying it out on the console. The help list is also a darn fine source of efficient code for a set of general problems. It won't help any more this year, but I'm working on a guide for R to bundle valuable information I got from the help list and the internet. It should be ready in a couple of months, and it will be available for all to use. In any case, Owen's guide is of great value for an introduction to the command line and basic statistics: http://cran.r-project.org/doc/contrib/Owen-TheRGuide.pdf Also the introduction to R is a must-read for all our students : http://cran.r-project.org/doc/manuals/R-intro.pdf Next to that, a couple of websites are great additional sources of code : Quick-R, a guide for those who come over from SAS/SPSS/Stata. It contains tons of examples for statistical analyses in about every field. If you didn't know it yet, you'll love it for sure : http://www.statmethods.net/ The R graph gallery, to show what exactly can be done with the graphical power of R : http://addictedtor.free.fr/graphiques/ The R Graphics gallery, doing the same : http://research.stowers-institute.org/efg/R/ There's many more to be found, a whole community of users is contributing to the information in various ways. We give the sources mentioned here to our students, with the message that they should never underestimate the power of Google. Last but not least, there is a specific mailing list regarding teaching statistics using R: https://stat.ethz.ch/mailman/listinfo/r-sig-teaching You might want to take a look at their archives as well. Cheers Joris On Fri, Jun 4, 2010 at 6:39 AM, Iasonas Lamprianou lampria...@yahoo.com wrote: Thanks, I'll have a go and will let you know. I guess that the success has to do with how efficiently I help them to demonstrate the efficiency of code over menues. So part of the issue is how I teach them as well... Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary Research Fellow Department of Education The University of Manchester Oxford Road, Manchester M13 9PL, UK Tel. 0044 161 275 3485 iasonas.lampria...@manchester.ac.uk --- On Thu, 3/6/10, S Ellison s.elli...@lgc.co.uk wrote: From: S Ellison s.elli...@lgc.co.uk Subject: Re: [R] ordinal variables To: Joris Meys jorism...@gmail.com, Iasonas Lamprianou lampria...@yahoo.com Cc: r-help@r-project.org Date: Thursday, 3 June, 2010, 15:44 If you set them a problem that has them doing the same sort of thing five times and compare the time it takes with code pasted from an editor (eg Tinn-R) and the time it takes via menius, you may have more luck convincing them. A command line sequence is harder than menus the first two times but easier for any n iterations thereafter. Steve ellison Iasonas Lamprianou lampria...@yahoo.com 03/06/2010 14:51 Thank you Joris, I'll have a look into the commands you sent me. They look convincing. I hope my students will also see them in a positive way (although I can force them to pretend that they have a positive attitude)! Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary Research Fellow Department of Education The University of Manchester Oxford Road, Manchester M13 9PL, UK Tel. 0044 161 275 3485 iasonas.lampria...@manchester.ac.uk --- On Thu, 3/6/10, Joris Meys jorism...@gmail.com wrote: From: Joris Meys jorism...@gmail.com Subject: Re: [R] ordinal variables To: Iasonas Lamprianou lampria...@yahoo.com Cc: r-help@r-project.org Date: Thursday, 3 June, 2010,
Re: [R] string handling
On Thu, Jun 3, 2010 at 4:06 PM, Wu Gong w...@mtmail.mtsu.edu wrote: Hope it helps. text - var1 var2 9G/G09 abd89C/T90 10A/T9 32C/C 90G/G A/A x - read.table(textConnection(text), header = T) Or with the stringr package: library(stringr) str_match(x$var1, (.)/(.)) Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] string handling
This solution using strapply in gsubfn is along the same lines as the stringr solution. First we read in the data using as.is = TRUE so that we get character rather than factor columns. On the other hand, if your data is already in columns with class factor then just replace strappy(x, ...) with strapply(as.character(x), ...) below. Then lapply over the columns of DF using strapply on each one.See home page at http://gsubfn.googlecode.com for more. Lines - var1var2 + 9G/G09abd89C/T90 + 10A/T932C/C + 90G/G A/A library(gsubfn) DF - read.table(textConnection(Lines), header = TRUE, as.is = TRUE) lapply(DF, function(x) strapply(x, (.)/(.), c, simplify = rbind)) $var1 [,1] [,2] [1,] G G [2,] A T [3,] G G $var2 [,1] [,2] [1,] C T [2,] C C [3,] A A Also a slight simplification is possible using gsubfn's capability of representing a one line function as a formula. We just preface lapply with fn$ and then formulas appearing in the arguments (subject to certain rules) are interpreted as functions. Here, the formula in the second argument to lapply is interpreted as the anonymous function we used above: fn$lapply(DF, x ~ strapply(x, (.)/(.), c, simplify = rbind)) $var1 [,1] [,2] [1,] G G [2,] A T [3,] G G $var2 [,1] [,2] [1,] C T [2,] C C [3,] A A On Thu, Jun 3, 2010 at 2:18 PM, karena dr.jz...@gmail.com wrote: I have a data.frame as the following: var1 var2 9G/G09 abd89C/T90 10A/T9 32C/C 90G/G A/A . . . . . . 10T/C 00G/G90 What I want is to get the letters which are on the left and right of '/'. for example, for 9G/G09, I only want G, G, and for abd89C/T90, I only want C and T, how to get these? thank you, karena -- View this message in context: http://r.789695.n4.nabble.com/string-handling-tp2242119p2242119.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] multinomial
Hi I carried out multinomial logistic reg. in R by package 'nnet'. response variable has 7 level and predictors (4 variable) are classifier and continuous. I want to present results as figur but I can't. also, I read R example but I have cell grid and I can't define data.frame. please help me thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] setMethod does not work in Window 7??
Wrong R version? Maybe loaded some other plot definition before your experiment? Works for me in R-2.11.1. Uwe Ligges Am 03.06.2010 23:05, schrieb Fang, Jianwen: I am developing a S4 class but have had trouble to make setMethod work in Window 7. I tested an example found in the setMethod manual: require(graphics) setMethod(plot, signature(x=track, y=missing), + function(x, y, ...) plot(slot(x, x), slot(x, y), ...) + ) It gave me: Error in setMethod(plot, signature(x = track, y = missing), function(x, : unused argument(s) (function(x, y, ...) plot(slot(x, x), slot(x, y), ...)) It works perfectly fine in Linux. Does anybody know why? Thanks in advance! JF [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Reading newlines with read.table?
I have a text file that is UTF-16LE encoded with CRLF line endings and '@' as field separators that I want to read in R on a Linux system. Which would be fine as read.table(foo.txt, file.encoding = UTF-16LE, sep = @, ...) *except* that the data may contain the LF character which R treats as end-of-line and then barfs that there are too few elements on that line. Any suggestions for how to process this one efficiently in R? There is probably a solution using read.table(..., nrows = 1, ...) to get the header, split it on '@', build a list with that many character(0) elements, and then using scan(..., multi.line=TRUE, ...) . but that all sounds very complicated. Allan. __ 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] package mgcv inconsistency in help files? cyclic P-spline cs not cyclic?
Dear all, I'm a bit stunned by the behaviour of a gam model using cyclic P-spline smoothers. I cannot provide the data, as I have about 61.000 observations from a time series. I use the following model : testgam - gam(NO~s(x)+s(y,bs=cs)+s(DD,bs=cs)+s(TT),data=Final) The problem lies with the cyclic smoother I use for seasonal trends. The variable Final$y is a numerical variable, going from 1 to 366, representing the day of the year. I have hourly data from 2003 until 2009, so each day is represented 168 times in the dataset (apart from 366, that one only 48). DD is the wind direction, going from 1 to 3600, and is also modeled with the same cyclic smoother. Yet, if I check the predictions, the smoother for y is far from cyclic. I checked the help files ?smooth.terms, and found about 10 lines apart : bs=cs specifies a shrinkage version of cr. bs=cs gives a cyclic version of a P-spline. When I use the (bs=cc) option, I get the results as I want them, so I keep with the cyclic cubic splines for now. Yet, I find the behaviour of bs=cs puzzling, and I'm wondering whether I missed something, or if this really is an inconsistency in the package. I currently run mgcv 1.6-1 on R 2.10.1 A small example showing what I experience. Mind you that here x is in fact NOT cyclic, whereas in my data I'm sure it has to be : y - rep(1:20,200) x - 1:4000 DD - sample(1:360,4000,replace=T) TT - sample(-10:10,4000,replace=T) NO - TT^2 + (10-y+2)^2 + 10*sin(DD*2*pi/360) - 0.002*sqrt(x) +rnorm(4000,0,100) model - gam(NO~s(x)+s(y,bs=cs)+s(DD,bs=cs)+s(TT)) plot(model) model - gam(NO~s(x)+s(y,bs=cc)+s(DD,bs=cc)+s(TT)) plot(model) Cheers Joris -- Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] i need help about reverse axes
scatterplot3d() currently does not supoort it, but you can hack an ugly
workaround:
If you want to do it only once ot twice:
mirror your z data at mean(range of z axis) and add z.ticklabs manually
(the reverse numbers)
Example:
x - 1:10
y - 1:10
z - 1:10
s3d - scatterplot3d(x, y, z)
env - environment(s3d[[1]])
zmin - get(z.min, env=env) * get(z.scal, env=env)
zmax - get(z.max, env=env) * get(z.scal, env=env)
zmean - mean(c(zmin, zmax))
znew - 2*zmean - z
scatterplot3d(x, y, znew, z.ticklabs=rev(get(z.prty, env=env)))
Best,
Uwe Ligges
Am 04.06.2010 02:48, schrieb Ali Alsamawi:
Hello
im trying to plot 3d with scatterplot packages , everything is work on my program
below but my problenm i want to set my pressure level or axis(z-axis) to reverse like
from bottom to top, i used function rev but not work just for 2d plots the
figure in attachment and the program shows below, can anyone help me to do this
Thanks
Ali
##load rgl package
library()
library(scatterplot3d)
## open binary file to read
dat- file(/srv/scratch/z3303149/back_Traj/parcel1_1,open=rb)
skip1st1 = seek(dat,where=4)
alldata = readBin(dat,numeric(),n=5040,size=4)
dim(alldata)- c(10,504)
totlen= 504
## replace zeros in lon,lat,pres,wv_cont with missing
for (i in 1:totlen) {
if (alldata[2,i]==0) alldata[2,i] = NA
if (alldata[3,i]==0) alldata[3,i] = NA
if (alldata[4,i]==0) alldata[4,i] = NA
if (alldata[10,i]==0) alldata[10,i] = NA
}
## total number of non-missing values
len = totlen - sum(is.na(alldata[2,]))
## set the dataset to use for colouring
coldat = alldata[10,1:len]
## creat colour from wv_cont - in hsv
hcol = cumsum(coldat)
hcol = hcol/max(hcol,na.rm=TRUE)
print(hcol)
col- hsv(h=hcol,s=1,v=1)
X- scatterplot3d(alldata[2,1:len],alldata[3,1:len],alldata[4,1:len],
xlab=lon,ylab=lat,zlab=pres,main=The Trajectory of the parcel1_1
(%),zlim=rev(range(alldata[4,1:len])))
#to show the first point of the trajectory
X$points3d(alldata[2,1],alldata[3,1],alldata[4,1],col =col, type = p, pch =
15)
X$points3d(alldata[2,1:len],alldata[3,1:len],alldata[4,1:len],col =col, type =
p, pch = 1)
## create labelbar - need to create an image in order to do so
lbcol = hsv(h=seq(0,1,0.01),s=1,v=1)
tmp1=c(1:len)
tmp3=matrix(coldat,len,1)
par(oma=c( 0,0,0,0),font.axis=1,mar=(c(14.1,4.1,4.1,1.1)),cex=0.8)
image.plot(tmp1,1,tmp3,add=TRUE,legend.only=TRUE,col=lbcol,nlevel=10
,legend.shrink=0.8,legend.width=1)
#png()
Rplot001.png
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__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] package mgcv inconsistency in help files? cyclic P-spline cs not cyclic?
On Fri, 2010-06-04 at 15:56 +0200, Joris Meys wrote: Dear all, I'm a bit stunned by the behaviour of a gam model using cyclic P-spline smoothers. I cannot provide the data, as I have about 61.000 observations from a time series. snip / I checked the help files ?smooth.terms, and found about 10 lines apart : bs=cs specifies a shrinkage version of cr. bs=cs gives a cyclic version of a P-spline. This is a typo in the help file ?smooth.terms. ?p.spline indicates that bs = cp is what is needed for a cyclic P spline. In ?smooth.terms ‘bs=cs’ gives a cyclic version of a P-spline. should read ‘bs=cp’ gives a cyclic version of a P-spline. in in the P Spline section. By specifying bs = cs, you weren't getting a cyclic spline at all, it is a cubic regression spline with shrinkage (so a smooth can potentially be penalized out of the model entirely during the fitting). If cc'd the author maintainer of mgcv (Simon Wood) so that this doesn't get overlooked amongst the other R-Help traffic. HTH G When I use the (bs=cc) option, I get the results as I want them, so I keep with the cyclic cubic splines for now. Yet, I find the behaviour of bs=cs puzzling, and I'm wondering whether I missed something, or if this really is an inconsistency in the package. I currently run mgcv 1.6-1 on R 2.10.1 A small example showing what I experience. Mind you that here x is in fact NOT cyclic, whereas in my data I'm sure it has to be : y - rep(1:20,200) x - 1:4000 DD - sample(1:360,4000,replace=T) TT - sample(-10:10,4000,replace=T) NO - TT^2 + (10-y+2)^2 + 10*sin(DD*2*pi/360) - 0.002*sqrt(x) +rnorm(4000,0,100) model - gam(NO~s(x)+s(y,bs=cs)+s(DD,bs=cs)+s(TT)) plot(model) model - gam(NO~s(x)+s(y,bs=cc)+s(DD,bs=cc)+s(TT)) plot(model) Cheers Joris -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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 %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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 the design matrix to correctly configure contrasts
Rich, Walmes, Thank you for enriching my understanding of the concept of interaction: succinctly and clearly explained. I feel i can better phrase my question, the context being much clearer now. In my case, i want to see the simple effects of changing levels of time, whilst holding Photperiod and Tissue constant. And i wnat to do this for each of the (total) 6 levels of Photoperiod and Tissue. My poor working knowledge of R leaves me stuck, for now, with the default treatment constrasts i get when using the function model.matrix. In fact thats been fine, once i decoded the interpretation of the colnames of the model.matrix using available examples, at least for analyses no more complex than 2-way interactions. Now im faced with 3 factors, and a model.matrix where i am unble to see the constrasts im interested in explictly stated. Does this mean they are not possible, ie., i lack enough observations for the contrasts i want? If so then i'm still missing some basic concepts of ANOVA. #I have three photoperiod treatments: Pperiod - factor(targets$Pperiod, levels = c(E, L, S)) #Two different tissues were sampled from each* subject: Tissue - factor(targets$Tissue, levels = c(R, C)) #*Such samples are said to be 'paired', no? Not sure how to deal with #this, how necessary dealing with it is, or how possible... #And where 16 unique subjects were sampled (for tissues R asnd C # at 16 different times giving the #third factor: Time - factor(targets$Time, levels = c(1, 2, 3, 4, 5, 6, 7, 8, 9,10,11,12,13,14,15, 16)) My primary question is- what changes occur across all times for each p.period and tissue combination., ie., ER, LR, SR, EC, LC SC? Contrast wise, this appears straight forward to me for ER, LR, SR EC which are explicit in the model.matrix i get from R (shown again below). That is, *assuming* my interpretation of the contrast is correct which is what my original post focused on. But, its just not obvious to me how LC and SC (for all times) contrasts can be specified. This is my practical problem i'm yet to overcome. And using the package contrast hasn't helped me overcome this so far (thank you no less Walmes). Further thoughts and advice gratefully received, Karl colnames(design) [1] (Intercept) Time2 [3] Time3Time4 [5] Time5Time6 [7] Time7Time8 [9] Time9Time10 [11] Time11 Time12 [13] Time13 Time14 [15] Time15 Time16 [17] TissueC PperiodL [19] PperiodS Time2:TissueC [21] Time3:TissueCTime4:TissueC [23] Time5:TissueCTime6:TissueC [25] Time7:TissueCTime8:TissueC [27] Time9:TissueCTime10:TissueC [29] Time11:TissueC Time12:TissueC [31] Time13:TissueC Time14:TissueC [33] Time15:TissueC Time16:TissueC [35] Time2:PperiodL Time3:PperiodL [37] Time4:PperiodL Time5:PperiodL [39] Time6:PperiodL Time7:PperiodL [41] Time8:PperiodL Time9:PperiodL [43] Time10:PperiodL Time11:PperiodL [45] Time12:PperiodL Time13:PperiodL [47] Time14:PperiodL Time15:PperiodL [49] Time16:PperiodL Time2:PperiodS [51] Time3:PperiodS Time4:PperiodS [53] Time5:PperiodS Time6:PperiodS [55] Time7:PperiodS Time8:PperiodS [57] Time9:PperiodS Time10:PperiodS [59] Time11:PperiodS Time12:PperiodS [61] Time13:PperiodS Time14:PperiodS [63] Time15:PperiodS Time16:PperiodS [65] TissueC:PperiodL TissueC:PperiodS On 6/2/2010 8:26 PM, RICHARD M. HEIBERGER wrote: Karl, The definition and interpretation of contrasts is part of any intermediate design of experiments text. Contrasts for interactions say that the effect of moving from level 1 of A to level 2 of A depends on the level of B. I will use notation YAB to indicate the levels of A and B. For example, if (Y11 - Y21) differs from (Y12 - Y22) we say that A and B have an interaction. When A and B interact, then the interpretation of main effects is ambiguous at best. Instead, we use the concept of simple effects, which, for example, are the effects of changing levels of A while holding the levels of B constant. Interpreting the interactions themselves depends on knowing something about the structure of the design, for example whether the effects (A and B, here) are treatments, blocks, nested effects, or repeated measures. Simple effects are usually interpretable. Interactions are tougher. Rich https://mail.google.com/a/temple.edu/?AuthEventSource=SSO#inbox -- Karl Brand k.br...@erasmusmc.nl Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam P +31 (0)10 704 3409 | F +31 (0)10 704 4743 | M +31 (0)642 777 268 __ 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] Build Design Matrix with avoiding loops
Dear R users,
I'd like to build a simple design matrix in a efficient way. I naively
wrote the code below.
n = 15
k = 3
nbPerGrp = c(5,5,5)
xT - list()
for (i in 1:k){
xT[[i]] - rep(0, k)
xT[[i]][i] - 1
}
X - matrix(nrow = n, ncol = k) #design matrix
for (i in 1:nbPerGrp[1]){
X[i,] - xT[[1]]
}
for (i in 1:k-1){
for (j in nbPerGrp[i]+1:nbPerGrp[i+1]){
X[j,] - xT[[i]]
}}
for (i in 1:nbPerGrp[k]){
X[n - nbPerGrp[k] + i, ] - xT[[k]]
}
X # That's I wanna get.
But as soon as n, k increase it takes too much time because of the loops.
Then my question is how can I get such a design matrix X without too
much loops ? Which function I should look at ?
Thanks in advance for responding me,
Gildas
__
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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] Build Design Matrix with avoiding loops
Hi,
Something like
x = as.factor(rep(1:k,rep(n/k,k))
X = model.matrix(~x-1)
Might be what you are looking for
Martyn
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Gildas Mazo
Sent: 04 June 2010 16:19
To: r-help@r-project.org
Subject: [R] Build Design Matrix with avoiding loops
Dear R users,
I'd like to build a simple design matrix in a efficient way. I naively
wrote the code below.
n = 15
k = 3
nbPerGrp = c(5,5,5)
xT - list()
for (i in 1:k){
xT[[i]] - rep(0, k)
xT[[i]][i] - 1
}
X - matrix(nrow = n, ncol = k) #design matrix
for (i in 1:nbPerGrp[1]){
X[i,] - xT[[1]]
}
for (i in 1:k-1){
for (j in nbPerGrp[i]+1:nbPerGrp[i+1]){
X[j,] - xT[[i]]
}}
for (i in 1:nbPerGrp[k]){
X[n - nbPerGrp[k] + i, ] - xT[[k]]
}
X # That's I wanna get.
But as soon as n, k increase it takes too much time because of the
loops.
Then my question is how can I get such a design matrix X without too
much loops ? Which function I should look at ?
Thanks in advance for responding me,
Gildas
__
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.
This e-mail has been scanned for all viruses by Star.\ _...{{dropped:12}}
__
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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] R plotting on linux, regardless of architecture of local machine
Hello, I just installed R 2.11.0 on a 64 bit Linux machine: Red Hat Enterprise Linux Server release 5.5 (Tikanga) I am still in the learning process in terms of handling Unix and have used R on both windows and Unix before. I am wondering when running R in this linux machine is there a way to be able to see plots pop up right on the screen after using the plot() function instead of saving it directly to a picture to view it later. I am connecting to the linux machine remotely through my Windows machine through Putty, I also have Cygwin installed as well. I realize this question may have been examined before in this forum and others and it seems a very common solution proposed depends on what machine you're accessing linux from remotely and if it's Windows you can install a X windows system to manage this which I know can be done through Cygwin. However I anticipate R on this linux machine to be used by several different users and it seems like it would be too difficult to anticipate what the architecture of all their local machines are as well as expect them to each install their own X windows manager as this is never present by default. So what I am wondering is there an easy way to install a package or configure something on the Linux machine so that when any user logs in and starts up R they can execute the plot() function and a plot window will pop up without having to execute any additional commands preferably? Also if there is a way I would be curious to know how to save the plots through that method as well unless it is still thru the usual functions (png, jpeg...) Appreciate the help! -- View this message in context: http://r.789695.n4.nabble.com/R-plotting-on-linux-regardless-of-architecture-of-local-machine-tp2243391p2243391.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] Build Design Matrix with avoiding loops
help.search(design matrix) will lead you to ?model.matrix ...
Gildas Mazo wrote:
Dear R users,
I'd like to build a simple design matrix in a efficient way. I naively
wrote the code below.
n = 15
k = 3
nbPerGrp = c(5,5,5)
xT - list()
for (i in 1:k){
xT[[i]] - rep(0, k)
xT[[i]][i] - 1
}
X - matrix(nrow = n, ncol = k) #design matrix
for (i in 1:nbPerGrp[1]){
X[i,] - xT[[1]]
}
for (i in 1:k-1){
for (j in nbPerGrp[i]+1:nbPerGrp[i+1]){
X[j,] - xT[[i]]
}}
for (i in 1:nbPerGrp[k]){
X[n - nbPerGrp[k] + i, ] - xT[[k]]
}
X # That's I wanna get.
But as soon as n, k increase it takes too much time because of the loops.
Then my question is how can I get such a design matrix X without too
much loops ? Which function I should look at ?
Thanks in advance for responding me,
Gildas
__
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.
Re: [R] reformat time from hhmm
Thanks much for the advice. These solutions have worked great! -Pete On Thu, Jun 3, 2010 at 8:10 PM, William Dunlap wdun...@tibco.com wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Peter Moore Sent: Thursday, June 03, 2010 2:22 PM To: r-help@r-project.org Subject: [R] reformat time from hhmm Hi, I'm newish to R, a recent convert from Matlab... So far I'm impressed, and determined to solve the following problem, which seems like it should be easy: I have a long (millions of points) data series recorded with a datalogger that produced a timestamp in 4 columns: Year, Day of Year, Time in (H)HMM and Seconds. I would like to have R interpret these columns as a time object and have made some progress (e.g., using paste() to create a single column and then strptime() to interpret -- is that too roundabout??), but one thing is throwing me off and I can't seem to conquer it. The hour-minute column in the raw data has no colon, so noon looks like 1200. Morning times have only 3 characters and afternoon times have 4. I've been playing around with a fake set of times: times - c(110, 230, 459, 1001, 1238, 1922) When I use strptime(data, %k%M You must have done this with 'times', not 'data'. strptime's first argument should be character data, not numeric and the default conversion of numeric to character changes 110-110, not 0110. I like to use sprintf() (with its C syntax) to control the conversion: strptime(sprintf(%04d, times), %k%M) [1] 2010-06-03 01:10:00 2010-06-03 02:30:00 2010-06-03 04:59:00 2010-06-03 10:01:00 2010-06-03 12:38:00 [6] 2010-06-03 19:22:00 You could put the year-month-day part into the sprintf's format argument as well if you don't want it to use today's date for that. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com the last three are interpreted fine but the first three are messed up because, for some reason, (even though I use %k for hour format?) the first two characters are assumed to be hour and the remaining one is minutes. For times[3] I get NA because R doesn't know what to do with 45 hours... [1] 2010-06-03 11:00:00 2010-06-03 23:00:00 NA [4] 2010-06-03 10:01:00 2010-06-03 12:38:00 2010-06-03 19:22:00 Fair enough, so I tried a different angle, using an if...else statement: hours - if(nchar(times)3) strtrim(times,2) else strtrim(times,1) This worked great when times was only a vector of length=1, but when I try to apply it to something larger, I get the following warning: Warning message: In if(nchar(times)3) strtrim(times,2) else strtrim(times,1) : the condition has length 1 and only the first element will be used and the output hours are only the first character. Not entirely sure if I understand this. Any advice on how to do this? Are there packages or commands that I'm not aware of that know how to deal with (h)hmm times? Thanks much, -Pete - platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 10.1 year 2009 month 12 day14 svn rev50720 language R version.string R version 2.10.1 (2009-12-14) -- Pete Moore Postdoctoral Research Associate Dept. Geological Atmospheric Sciences Iowa State University [[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. -- Peter L. Moore Postdoctoral Research Associate Dept. Geological Atmospheric Sciences Iowa State University Ames, IA 515-294-7201 [[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] using string as variable name in model
I think you're looking for the update() function. -thomas On Thu, 3 Jun 2010, Roni Kobrosly wrote: Hi, I made a small table of strings that will serve as variable names for lm models I will run. The table looks like this: varnames numname 11 zCANTAB_log_IED_totaltrials 22 zCANTAB_log_IED_preED 33zCANTAB_logPALerrors 44 zCANTAB_PALstages 55 zCANTAB_logRTI 66 zCANTAB_RVP_Totalmisses 77 zCANTAB_log_RVP_falsealarm 88 zCANTAB_DMS_12000 99 zCANTAB_PRM_Percent 10 10 zCANTAB_SRM_Percent 11 11 zCANTAB_sqrt_SWM_within 12 12 zCANTAB_sqrt_SWM_Total 13 13 zSS_WJ_PC 14 14 zSS_WJ_CALC 15 15 zSS_WJ_LW 16 16 zSS_WJ_AP 17 17 zSS_WJ_MF What I'm trying to do is varnames[1,2] - outcome lm(outcome ~ income + covariate1 + coviarate2, data=my.data) - model I get the following error message: Error in model.frame.default(formula = outcome ~ Hollings_Enroll + Child_sex + : variable lengths differ (found for 'Hollings_Enroll') But when I run the model: lm(zCANTAB_log_IED_totaltrials ~ income + covariate1 + coviarate2, data=my.data) - model it works fine. Eventually, once I resolve this, I'd like to make a custom R function to automatically generate 17 regression models with these 17 outcome variable strings. Do you have any ideas how to resolve this error? Thanks! -Roni __ 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. Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ 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 Newbie, please help!
Hi:
The key phrase in your mail was 'data.table'. Given the size of the object,
it is very likely to be a data.table, which (oddly enough) comes from
package
data.table. It is designed to quickly process information in very large
datasets. 3M rows is an 'average' sized data.table :)
Your request isn't very sophisticated - it appears this function should
work groupwise (group = ID):
dret - function(x) c(100.00, 100 * x[-1]/x[-length(x)])
This function can be processed in data.table or ddply (package plyr)
groupwise without much difficulty. I'm going to assume that the data are
ordered in time for simplicity. I'm also using 100 for the first entry in
the
function - if you want, you can change the initial 100.00 to NA.
Let's generate a little fake data:
id - as.character(rep(c(427225, 290157, 394025, 382940), each = 1000))
times - rep(seq(as.Date('2001-11-13'), by = 'days', length = 1000), 4)
totret - c(rnorm(1000, 20, 0.1), rnorm(1000, 25, 0.1), rnorm(1000, 30,
0.1),
rnorm(1000, 35, 0.1))
# data frame:
DF - data.frame(id = id, times = times, totret = totret)
# data table:
library(data.table)
DR - data.table(DF)
# data.table sets up id as the table's primary key - note that the storage
mode
# of the key has to be integer.
tables() # see what we've got
# set id as the table key, do the calculation by group and tack the result
onto DR
system.time({ setkey(DR, id); DR2 - DR[, dret(totret), by = id];
DR$return - DR2$V1 })
user system elapsed
0 0 0
library(plyr)
system.time(df2 - ddply(DF, .(id), transform, return = dret(totret)))
user system elapsed
0.030.000.05
The difference between the two is this. The data.table calculation returns a
data.table DR2 with the key and the returns, after which we add the column
of returns to the original data table DR. In contrast, the ddply calculation
tacks
on the column of returns to the original data frame as a result of
transform.
Notice that in the data.table code, we set the table key (which is often the
most time consuming task, since it orders the data by the values in its
key),
did the calculation and tacked the result onto the original table almost
instantaneously.
According to the data.table package author, the time savings in using
data.table scales upward as the size of the table increases - in other
words,
the bigger the table, the faster data.table will be relative to other
processing
methods currently available in R. You can see that there is a noticeable
time
difference at n = 4000, so the difference at n = 3M will be more dramatic.
Development work in plyr is showing that the gap between it and data.table
is narrowing, but both packages are in active development, so R users can
look forward to two very powerful packages for summarizing, transforming
and condensing data.
I would suggest that you read the vignette and FAQ from data.table
(available
from the on-line data.table help page) and the documentation of plyr
at its author's web site:
http://had.co.nz/plyr/
There is a tutorial with slides and a full-scale document.
HTH,
Dennis
On Thu, Jun 3, 2010 at 8:04 PM, Jeff08 jefferyd...@gmail.com wrote:
Hello Everyone,
I just started a new job it requires heavy use of R to analyze datasets.
I have a data.table that looks like this. It is sorted by ID Date, there
are about 150 different IDs the dataset spans 3 million rows. The main
columns of concern are ID, date, and totret. What I need to do is to derive
daily returns for each ID from totret, which is simply totret at time t+1
divided by totret at time t.
X id ticker date_ adjClosetotret RankStk
427225 427225 00174410AHS 2001-11-1321.66 100.01235
441910 441910 00174410AHS 2001-11-1421.60 99.723001235
458458 458458 00174410AHS 2001-11-1521.65 99.953801235
284003 284003 00174410AHS 2001-11-1621.59 99.676801235
Two problems for me:
1)I can't just apply it to the entire column since there will be problems
at
the boundary points where the ID changes from 1 to another. I need to find
out how to specify a restriction on the name of the ID
2) From Java, instinctively I would use a loop to calculate daily returns,
but I found out that R is very slow with loops, so I need to find an
efficient way to calculate daily returns with such a huge dataset.
Thanks a lot!
--
View this message in context:
http://r.789695.n4.nabble.com/R-Newbie-please-help-tp2242633p2242633.html
Sent from the R help mailing list archive at Nabble.com.
__
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[[alternative HTML version deleted]]
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Re: [R] R plotting on linux, regardless of architecture of local machine
Hi, If one wants to see an X GUI from a remote application, there's no other way than to run an X server locally (the easiest way to do that on Windows is with Xming IMHO). So if you don't want an X server locally, you should not use an X GUI. R can of course also be installed on Windows, including Windows servers, which may be accessible through Remote Desktop on your network (even from Linux machines). You could also try using Rweb (http://www.math.montana.edu/Rweb/) though that will require running R on a web server of course. And I guess you'd get some sort of bitmap images, maybe svg. In my opinion a local X server is the easiest solution, but there are other options. Good luck, Marius. On 06/04/2010 05:31 PM, vaneet wrote: Hello, I just installed R 2.11.0 on a 64 bit Linux machine: Red Hat Enterprise Linux Server release 5.5 (Tikanga) I am still in the learning process in terms of handling Unix and have used R on both windows and Unix before. I am wondering when running R in this linux machine is there a way to be able to see plots pop up right on the screen after using the plot() function instead of saving it directly to a picture to view it later. I am connecting to the linux machine remotely through my Windows machine through Putty, I also have Cygwin installed as well. I realize this question may have been examined before in this forum and others and it seems a very common solution proposed depends on what machine you're accessing linux from remotely and if it's Windows you can install a X windows system to manage this which I know can be done through Cygwin. However I anticipate R on this linux machine to be used by several different users and it seems like it would be too difficult to anticipate what the architecture of all their local machines are as well as expect them to each install their own X windows manager as this is never present by default. So what I am wondering is there an easy way to install a package or configure something on the Linux machine so that when any user logs in and starts up R they can execute the plot() function and a plot window will pop up without having to execute any additional commands preferably? Also if there is a way I would be curious to know how to save the plots through that method as well unless it is still thru the usual functions (png, jpeg...) Appreciate the help! __ 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 newlines with read.table?
I ended up pre-processing the files outside of R using a script along
the lines of
#!/bin/bash
for f in *_table_extract_*.txt; do
echo -n Processing $f...
o=${f}.xz
iconv -f UTF-16LE -t UTF-8 $f | \
tail -c +4 | \
perl -l012 -015 -pe 's/\n//g' | \
perl -ne 'print if (!m{\A \( \d+ \s row\(s\) \s affected \) \s*
\z}ixms !m{\A \s* \z}xms)' | \
xz -7 $o
echo done.
done
Ugly, but it worked for me. You can change the first perl regular
expression to do different things with line terminating \n versus
in-field \n characters but I just dropped them all. The tail command
drops the byte-order-mark (which we do not need for utf-8) and the
second perl command drops blanks and a stupid SQL tool output.
Thanks to Prof. Brian Ripley who, essentially, pointed out that with
embedded linefeed characters my file was a binary file and not really a
text file. Her Majesty's government respectfully begs to disagree [1]
but that's the R definition so we'll use it on this list.
Allan
[1] Original data sets described at
http://www.hm-treasury.gov.uk/psr_coins_data.htm and downloaded from
http://data.gov.uk/dataset/coins (hint: you'll need p7zip to unpack them
on a Linux box).
On 04/06/10 14:49, Allan Engelhardt wrote:
I have a text file that is UTF-16LE encoded with CRLF line endings and
'@' as field separators that I want to read in R on a Linux system.
Which would be fine as
read.table(foo.txt, file.encoding = UTF-16LE, sep = @, ...)
*except* that the data may contain the LF character which R treats as
end-of-line and then barfs that there are too few elements on that line.
Any suggestions for how to process this one efficiently in R? [...]
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Re: [R] horizontal and vertical line with arrow in a plot
# A very quick example of how to draw an arrow on a graph. plot(1:10) text(2,5, Point 5 , cex=.8) arrows(3,5, 4.5, 5) --- On Thu, 6/3/10, Roslina Zakaria zrosl...@yahoo.com wrote: From: Roslina Zakaria zrosl...@yahoo.com Subject: [R] horizontal and vertical line with arrow in a plot To: r-help@r-project.org Received: Thursday, June 3, 2010, 11:34 PM Hi r-users, I would like to add a plot of vertical line segment with arrow from (77,.6) to (77,0) and also a horizontal line segment with arrow from (0,0.6) to (77,.6) . So far this is what I have: plot(sq, cdf, type=l, lwd=4,col=blue,xaxs=i,yaxs=i, xlab= Rainfall (mm), ylab= Random no., main=Random number and rainfall totals (mm)) abline(v=77,h=0.6,col=2,lwd=2,lty=3) text(120,0.63, r = 0.6) text(120,0.05, x = 70) I also tried to use the 'diagram' and 'shape' package but not really sure how to use them. Thank you for all the help given. [[alternative HTML version deleted]] -Inline Attachment Follows- __ 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] Wrong symbol rendering in plots (Ubuntu)
Hi I am having problems with the rendering of scientific symbols (mu and degree) in my plots. Whenever I use these symbols they are rendered changed (mu is changed to the proportionality symbol and degree is changed to something resembling a gamma) in the X-device. If I make a pdf of the plot and open the file in Evince or Okular symbols are also rendered wrong, however if I open the file with Xpdf or Acroread they are rendered correctly. I did not have this problem before, it arose after I upgraded both R and my system (Ubuntu karmic koala to lucid lynx), so I can not tell for sure if the problem is R-related or Ubuntu related (I have posted in a Ubuntu forum also http://ubuntuforums.org/showthread.php?t=1325289). Please let me know if you have any idea of how to fix this, or if you can confirm this is not an R-related issue. Thank you very much in advance, Eduardo J. Chica Graduate student UF/IFAS-CREC __ 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 with iteration using while loop
Hello everyone,
I am trying to use while loop to iterate a function until convergence. But I
am having problem when I try to use a fixed number of iterations.
Say I want to use maximum iteration of 150. If the value don't converge
within maximum iteration, show warning of no convergence.
Currently I don't have non- convergence problem so I think my code works
fine. But in future I may encounter such problem that are likely to not
converge easily.
Below is my function that is working when I don't provide maximum iteration.
iter- function (Fpi, Time, tolerance){
S = 22.4
Ts = 0.499
Ti = 0.25
K = 0.044
r- 1.5
M = Ts- Ti
Ks = 0.044
Fpt = K*Time + M*S*log(1+ Fpi/(M*S))
while((Fpt-Fpi) tolerance) {
Fpi = Fpt
Fpt = K*Time + M*S*log(1+ Fpi/(M*S))
Fp0 = Fpt
}
return(Fpt)
}
x- iter(Fpi = 0.224, Time = 0.2, tolerance = 0.01)
But I want do something like this ( conceptually)
for( i in 2:itermax) {
Fpt[i] = K*Time + M*S*log(1+ Fpi/(M*S))
if((Fpt[i]- Fpt[i-1])= tolerance) break
print(Fpt[i]
}
something like this.
any kind of help is highly appreciated.
thank you
--
Acharya, Subodh
[[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] Shapes in barplots
The TeachingDemos package does not in any way replace the rgl package. They
serve very different purposes (the TeachingDemos package does use rgl for a
couple of functions).
I would be very surprised if there was anything in the TeachingDemos package
that would be of help in creating barplots with 3d effects. 3d effects distort
the information in graphs without adding anything to their interpretation.
If you want to display information, then use the appropriate graph without the
extra chartjunk. If you want something to catch the reader's attention, use a
picture of a kitten.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of khush
Sent: Friday, June 04, 2010 1:45 AM
To: r-help@r-project.org
Subject: [R] Shapes in barplots
Hi,
I am making barplots . I am using the default shape of barplots with a
pipe
but I wants to build bars in various 3d shapes. I have install rgl
using
install.packages('rgl') for this purpose, but when I am doing
library(rgl),
it shows
Error in library(rgl) : there is no package called 'rgl'
What are the other ways to build such plots of variuos shapes.
Is that *TeachingDemos *replace it..I am not sure how to use it for
such
task.
Thanks in advance
Jeet
[[alternative HTML version deleted]]
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guide.html
and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
[R] How do I 'merge' a altered subset of a data.frame back into the same data.frame
Hi Step 1: I create a data.frame called iolm. Step 2: I create a conditional subset i_wtr. Step 3: In this subset I add 0.3 to all values in the IOLM_AST column. Step 4: Now I am looking for the best way to merge¹ the altered subset back into the original iolm data.frame ## STEP 1 iolm ID IOLM_AST IOLM_AXIS 1 1 1.15165.33 2 2 1.20 79.00 3 3 0.40 51.66 4 4 0.50 57.00 5 5 1.77 7.70 6 6 0.28 99.70 7 7 0.48160.00 8 8 0.74 84.00 9 9 1.63 87.00 10 10 0.43150.70 ## STEP 2 i_wtr-subset(iolm,IOLM_AXIS 60 IOLM_AXIS 120) i_wtr ID IOLM_AST IOLM_AXIS 2 2 1.20 79.0 6 6 0.28 99.7 8 8 0.74 84.0 9 9 1.63 87.0 16 16 0.93 94.0 20 20 1.37 91.0 21 21 1.19 63.0 ... ## STEP 3 i_wtr$IOLM_AST - i_wtr$IOLM_AST + 0.3 i_wtr ID IOLM_AST IOLM_AXIS 2 2 1.50 79.0 6 6 0.58 99.7 8 8 1.04 84.0 9 9 1.93 87.0 16 16 1.23 94.0 20 20 1.67 91.0 21 21 1.49 63.0 ... ## STEP 4 result (not what I wish to get) newiolm-merge(i_wtr, iolm, by.x=ID, by.y=ID, all = T) newiolm ID IOLM_AST.x IOLM_AXIS.x IOLM_AST.y IOLM_AXIS.y 1 1 NA NA 1.15 165.33 2 2 1.5079.0 1.20 79.00 3 3 NA NA 0.40 51.66 4 4 NA NA 0.50 57.00 5 5 NA NA 1.777.70 6 6 0.5899.7 0.28 99.70 7 7 NA NA 0.48 160.00 8 8 1.0484.0 0.74 84.00 9 9 1.9387.0 1.63 87.00 10 10 NA NA 0.43 150.70 ... ## The result I am looking to get: ID IOLM_AST IOLM_AXIS 1 1 1.15 165.33 2 2 1.50 79.00 3 3 0.40 51.66 4 4 0.50 57.00 5 5 1.77 7.70 6 6 0.58 99.70 7 7 0.48 160.00 8 8 1.04 84.00 9 9 1.93 87.00 10 10 0.43 150.70 ... What is the correct way to do this? Thanks a lot for your help. Dominik [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R-Package FDTH
We whish to announce the new package FDTH - Frequency Distribution Table and Associated Histogram The package contains a high level main function which easily allows the user to make a frequency distribution table and its associated histogram. The results of the table can be formatted in many ways which may be suited to publication in many different ways as for example papers or books. The plot of the method is the histogram and poligons which can be dealt with the easiness and flexibility of a high level function. José Claudio Faria Enio Jelihovschi Professor titular Professor Adjunto DCET - Estatística DCET - Estatística UESC UESC [[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] Help with iteration using while loop
Code inline:
On Fri, Jun 4, 2010 at 1:30 PM, Subodh Acharya shoeb...@gmail.com wrote:
Hello everyone,
I am trying to use while loop to iterate a function until convergence. But I
am having problem when I try to use a fixed number of iterations.
Say I want to use maximum iteration of 150. If the value don't converge
within maximum iteration, show warning of no convergence.
Currently I don't have non- convergence problem so I think my code works
fine. But in future I may encounter such problem that are likely to not
converge easily.
Below is my function that is working when I don't provide maximum iteration.
iter- function (Fpi, Time, tolerance){
S = 22.4
Ts = 0.499
Ti = 0.25
K = 0.044
r- 1.5
M = Ts- Ti
Ks = 0.044
Fpt = K*Time + M*S*log(1+ Fpi/(M*S))
while((Fpt-Fpi) tolerance) {
Fpi = Fpt
Fpt = K*Time + M*S*log(1+ Fpi/(M*S))
Fp0 = Fpt
}
return(Fpt)
}
x- iter(Fpi = 0.224, Time = 0.2, tolerance = 0.01)
Add a counter variable and a second check in your `while` criteria:
...
...
iter - 0
while (((Fpt - Fpi) tolerance) (iter itermax)) {
Fpi = Fpt
Fpt = K*Time + M*S*log(1+ Fpi/(M*S))
Fp0 = Fpt
iter - iter + 1
}
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I 'merge' a altered subset of a data.frame back into the same data.frame
On Jun 4, 2010, at 1:09 PM, dominik beck wrote: Hi Step 1: I create a data.frame called iolm. Step 2: I create a conditional subset i_wtr. Step 3: In this subset I add 0.3 to all values in the IOLM_AST column. Step 4: Now I am looking for the best way to ‘merge’ the altered subset back into the original iolm data.frame ## STEP 1 iolm ID IOLM_AST IOLM_AXIS 1 1 1.15165.33 2 2 1.20 79.00 3 3 0.40 51.66 4 4 0.50 57.00 5 5 1.77 7.70 6 6 0.28 99.70 7 7 0.48160.00 8 8 0.74 84.00 9 9 1.63 87.00 10 10 0.43150.70 ## STEP 2 i_wtr-subset(iolm,IOLM_AXIS 60 IOLM_AXIS 120) i_wtr ID IOLM_AST IOLM_AXIS 2 2 1.20 79.0 6 6 0.28 99.7 8 8 0.74 84.0 9 9 1.63 87.0 16 16 0.93 94.0 20 20 1.37 91.0 21 21 1.19 63.0 ... ## STEP 3 i_wtr$IOLM_AST - i_wtr$IOLM_AST + 0.3 i_wtr ID IOLM_AST IOLM_AXIS 2 2 1.50 79.0 6 6 0.58 99.7 8 8 1.04 84.0 9 9 1.93 87.0 16 16 1.23 94.0 20 20 1.67 91.0 21 21 1.49 63.0 ... ## STEP 4 – result (not what I wish to get) newiolm-merge(i_wtr, iolm, by.x=ID, by.y=ID, all = T) newiolm ID IOLM_AST.x IOLM_AXIS.x IOLM_AST.y IOLM_AXIS.y 1 1 NA NA 1.15 165.33 2 2 1.5079.0 1.20 79.00 3 3 NA NA 0.40 51.66 4 4 NA NA 0.50 57.00 5 5 NA NA 1.777.70 6 6 0.5899.7 0.28 99.70 7 7 NA NA 0.48 160.00 8 8 1.0484.0 0.74 84.00 9 9 1.9387.0 1.63 87.00 10 10 NA NA 0.43 150.70 ... ## The result I am looking to get: ID IOLM_AST IOLM_AXIS 1 1 1.15 165.33 2 2 1.50 79.00 3 3 0.40 51.66 4 4 0.50 57.00 5 5 1.77 7.70 6 6 0.58 99.70 7 7 0.48 160.00 8 8 1.04 84.00 9 9 1.93 87.00 10 10 0.43 150.70 ... What is the correct way to do this? Thanks a lot for your help. Dominik Just replace the values that meet the condition with the new values, leaving the others alone: iolm ID IOLM_AST IOLM_AXIS 1 1 1.15165.33 2 2 1.20 79.00 3 3 0.40 51.66 4 4 0.50 57.00 5 5 1.77 7.70 6 6 0.28 99.70 7 7 0.48160.00 8 8 0.74 84.00 9 9 1.63 87.00 10 10 0.43150.70 # See ?ifelse and ?with with(iolm, ifelse(IOLM_AXIS 60 IOLM_AXIS 120, IOLM_AST + 0.3, IOLM_AST)) [1] 1.15 1.50 0.40 0.50 1.77 0.58 0.48 1.04 1.93 0.43 # Replace the original column with the above result iolm$IOLM_AST - with(iolm, ifelse(IOLM_AXIS 60 IOLM_AXIS 120, IOLM_AST + 0.3, IOLM_AST)) iolm ID IOLM_AST IOLM_AXIS 1 1 1.15165.33 2 2 1.50 79.00 3 3 0.40 51.66 4 4 0.50 57.00 5 5 1.77 7.70 6 6 0.58 99.70 7 7 0.48160.00 8 8 1.04 84.00 9 9 1.93 87.00 10 10 0.43150.70 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] split a row into multiple columns
Thanks, that worked great, but I am having trouble generalizing it to my entire data set for some reason. I have 318 rows like this: Main Group\t1000\tMP Test\tMP Test, 1\tAudio (1, f1-qaddara.aiff)\tl (target is right word)\tl\tPressed\tl (target is right word)\tC\t3111\t\t\t\t\t and the command: mydata - matrix(strsplit(x, '\t')[[1]], nrow=1) gives me a matrix with only the 1st row of the data. I have tried playing around with it, but so far the best I can do is get 318 copies of row 1. How can I get a matrix with all 318 rows and 15 columns split by the '\t'? Thanks again. kevin On Thu, Jun 3, 2010 at 2:39 PM, jim holtman jholt...@gmail.com wrote: If you want a matrix, then just create one from the data you have: mydata - matrix(strsplit(x, '\t')[[1]], nrow=1) On Thu, Jun 3, 2010 at 1:30 PM, Kevin Burnham kburn...@gmail.com wrote: Would somebody please help me break this row: Main Group\t1000\tMP Test\tMP Test, 1\tAudio (1, f1-qaddara.aiff)\tl (target is right word)\tl\tPressed\tl (target is right word)\tC\t3111\t\t\t\t\t into multiple columns along the \t separator? When I try the strsplit (x,\t) command I get: [[1]] [1] Main Group 1000 MP TestMP Test, 1 Audio (1, f1-qaddara.aiff) [6] l (target is right word) l Pressedl (target is right word) C [11] 3111 Which which is closer to what I need, but still not in columns. Thanks, Kevin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R with Emacs
ess.r-project.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] string handling
Thank you guys very much, these help!! -- View this message in context: http://r.789695.n4.nabble.com/string-handling-tp2242119p2243388.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] R plotting on linux, regardless of architecture of local machine
I can try having an X server locally, but what are the other options? Isn't there anything that can be installed on Linux to be able to display graph windows in R without too much trouble? As I said I was looking for a solution to benefit many users not just me as I can't assume or expect everyone logging in to the linux machine to have a local X server running. Thanks -- View this message in context: http://r.789695.n4.nabble.com/R-plotting-on-linux-regardless-of-architecture-of-local-machine-tp2243391p2243650.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] using string as variable name in model
update() works! Thank you thomas On Jun 4, 2010, at 11:47 AM, Thomas Lumley wrote: I think you're looking for the update() function. -thomas On Thu, 3 Jun 2010, Roni Kobrosly wrote: Hi, I made a small table of strings that will serve as variable names for lm models I will run. The table looks like this: varnames numname 11 zCANTAB_log_IED_totaltrials 22 zCANTAB_log_IED_preED 33zCANTAB_logPALerrors 44 zCANTAB_PALstages 55 zCANTAB_logRTI 66 zCANTAB_RVP_Totalmisses 77 zCANTAB_log_RVP_falsealarm 88 zCANTAB_DMS_12000 99 zCANTAB_PRM_Percent 10 10 zCANTAB_SRM_Percent 11 11 zCANTAB_sqrt_SWM_within 12 12 zCANTAB_sqrt_SWM_Total 13 13 zSS_WJ_PC 14 14 zSS_WJ_CALC 15 15 zSS_WJ_LW 16 16 zSS_WJ_AP 17 17 zSS_WJ_MF What I'm trying to do is varnames[1,2] - outcome lm(outcome ~ income + covariate1 + coviarate2, data=my.data) - model I get the following error message: Error in model.frame.default(formula = outcome ~ Hollings_Enroll + Child_sex + : variable lengths differ (found for 'Hollings_Enroll') But when I run the model: lm(zCANTAB_log_IED_totaltrials ~ income + covariate1 + coviarate2, data=my.data) - model it works fine. Eventually, once I resolve this, I'd like to make a custom R function to automatically generate 17 regression models with these 17 outcome variable strings. Do you have any ideas how to resolve this error? Thanks! -Roni __ 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. Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.edu University of Washington, Seattle __ 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] Convolution vector to be derived
I want to generate the following outcome using convolution of two sequences. x - c(1,2,3,4,5) y - c(6,7,8,9) The resulting convolution vector is 6 19 40 70 100 94 76 45 When using convolve(), it is hard to produce the result above. Would you help me out to get that? Best regards Moohwan Kim __ 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] Convolution vector to be derived
Dear R-help, I want to generate the following outcome using the convolution of two sequences. x - c(1,2,3,4,5) y - c(6,7,8,9) The resulting convolution vector is 6 19 40 70 100 94 76 45 When using convolve(), it is hard to produce the result above. Would you help me out to get that? Best regards Moohwan Kim __ 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] string handling
Here is a slightly simpler variant of the strapply solution: lapply(DF, strapply, (.)/(.), c, simplify = rbind) $var1 [,1] [,2] [1,] G G [2,] A T [3,] G G $var2 [,1] [,2] [1,] C T [2,] C C [3,] A A On Fri, Jun 4, 2010 at 8:08 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: This solution using strapply in gsubfn is along the same lines as the stringr solution. First we read in the data using as.is = TRUE so that we get character rather than factor columns. On the other hand, if your data is already in columns with class factor then just replace strappy(x, ...) with strapply(as.character(x), ...) below. Then lapply over the columns of DF using strapply on each one. See home page at http://gsubfn.googlecode.com for more. Lines - var1 var2 + 9G/G09 abd89C/T90 + 10A/T9 32C/C + 90G/G A/A library(gsubfn) DF - read.table(textConnection(Lines), header = TRUE, as.is = TRUE) lapply(DF, function(x) strapply(x, (.)/(.), c, simplify = rbind)) $var1 [,1] [,2] [1,] G G [2,] A T [3,] G G $var2 [,1] [,2] [1,] C T [2,] C C [3,] A A Also a slight simplification is possible using gsubfn's capability of representing a one line function as a formula. We just preface lapply with fn$ and then formulas appearing in the arguments (subject to certain rules) are interpreted as functions. Here, the formula in the second argument to lapply is interpreted as the anonymous function we used above: fn$lapply(DF, x ~ strapply(x, (.)/(.), c, simplify = rbind)) $var1 [,1] [,2] [1,] G G [2,] A T [3,] G G $var2 [,1] [,2] [1,] C T [2,] C C [3,] A A On Thu, Jun 3, 2010 at 2:18 PM, karena dr.jz...@gmail.com wrote: I have a data.frame as the following: var1 var2 9G/G09 abd89C/T90 10A/T9 32C/C 90G/G A/A . . . . . . 10T/C 00G/G90 What I want is to get the letters which are on the left and right of '/'. for example, for 9G/G09, I only want G, G, and for abd89C/T90, I only want C and T, how to get these? thank you, karena -- View this message in context: http://r.789695.n4.nabble.com/string-handling-tp2242119p2242119.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Creating a maxtrix from conditional prints
Hi guys :)
I'm dealing with this problem, perhaps conceptually not that complex, but
still - I'm stuck.
Two columns, values 1x10, only integers. I want to check when the first
column's index is identical to the second's (and vice versa). If that's
true, I want to add a further column with value 1 (if true) or NA (if
false).
Thus, I obtain 100 matrices (for each columns I will have 1-1, 1-2, 1-3
etc). Now, I want R to consider only those matrices whose new column has
value = 1 whose total number of rows is equal to 2. I can get R to print
this result inside the for cycle, yet I can't manage to build a single
matrix, to store all the results altoghether - which is what I really want.
Code example:
for (x in 1:10) {
for (y in 1:10) {
qui - ifelse((mac[,1] == x) (mac[,5] == y) | (mac[,1] == y) (mac[,5]
== x), 1, NA)
quo - cbind(mac,qui)
qua - subset(quo, qui ==1)
if(nrow(qua) == 2)
print(qua)
}}
result (wrong, now):
ricevente genere_r abo_r classieta_r donatore genere_d abo_d
classieta_deta_d mismatch pra comp mum qui
[1,] 80 1 391 1
4 56.174372 11 -6.645437 1
[2,] 91 1 280 1
3 48.775792 11 -5.905579 1
ricevente genere_r abo_r classieta_r donatore genere_d abo_d
classieta_deta_d mismatch pra comp mum qui
[1,] 80 1 3 100 0
3 48.775792 11 -5.905579 1
[2,]100 2 580 1
3 48.775791 11 -5.391579 1
ricevente genere_r abo_r classieta_r donatore genere_d abo_d
classieta_deta_d mismatch pra comp mum qui
[1,] 80 1 391 1
4 56.174372 11 -6.645437 1
[2,] 91 1 280 1
3 48.775792 11 -5.905579 1
ricevente genere_r abo_r classieta_r donatore genere_d abo_d
classieta_deta_d mismatch pra comp mum qui
[1,] 91 1 2 100 0
3 48.775790 11 -4.877579 1
[2,]100 2 591 1
4 56.174370 11 -5.617437 1
what I'd like to get:
ricevente genere_r abo_r classieta_r donatore genere_d abo_d
classieta_deta_d mismatch pra comp mum qui
[1,] 80 1 391 1
4 56.174372 11 -6.645437 1
[2,] 91 1 280 1
3 48.775792 11 -5.905579 1
[3,] 80 1 3 100 0
3 48.775792 11 -5.905579 1
[4,]100 2 580 1
3 48.775791 11 -5.391579 1
[5,] 80 1 391 1
4 56.174372 11 -6.645437 1
[6,] 91 1 280 1
3 48.775792 11 -5.905579 1
[7,] 91 1 2 100 0
3 48.775790 11 -4.877579 1
[8,]100 2 591 1
4 56.174370 11 -5.617437 1
(don't mind the values names, this is just a small part of a longer
algorithm)
Thanks for your help, in advance :)
[[alternative HTML version deleted]]
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Re: [R] split a row into multiple columns
Hi: Maybe something like this? txt - Main Group\t1000\tMP Test\tMP Test, 1\tAudio (1, f1-qaddara.aiff)\tl (target is right word)\tl\tPressed\tl (target is right word)\tC\t3111\t\t\t\t\t txtdf - as.data.frame(rbind(txt, txt, txt, txt, txt)) # create toy data frame res - t(as.matrix(apply(txtdf, 1, function(x) strsplit(x, '\t')[[1]]))) res [,1] [,2] [,3] [,4] [,5] txt Main Group 1000 MP Test MP Test, 1 Audio (1, f1-qaddara.aiff) txt Main Group 1000 MP Test MP Test, 1 Audio (1, f1-qaddara.aiff) txt Main Group 1000 MP Test MP Test, 1 Audio (1, f1-qaddara.aiff) txt Main Group 1000 MP Test MP Test, 1 Audio (1, f1-qaddara.aiff) txt Main Group 1000 MP Test MP Test, 1 Audio (1, f1-qaddara.aiff) [,6][,7] [,8] [,9] txt l\n(target is right word) l Pressed l (target is right\nword) txt l\n(target is right word) l Pressed l (target is right\nword) txt l\n(target is right word) l Pressed l (target is right\nword) txt l\n(target is right word) l Pressed l (target is right\nword) txt l\n(target is right word) l Pressed l (target is right\nword) [,10] [,11] [,12] [,13] [,14] [,15] txt C 3111 txt C 3111 txt C 3111 txt C 3111 txt C 3111 The rownames are an artifice of having copied txt five times to create the df. HTH, Dennis On Fri, Jun 4, 2010 at 11:42 AM, Kevin Burnham kburn...@gmail.com wrote: Thanks, that worked great, but I am having trouble generalizing it to my entire data set for some reason. I have 318 rows like this: Main Group\t1000\tMP Test\tMP Test, 1\tAudio (1, f1-qaddara.aiff)\tl (target is right word)\tl\tPressed\tl (target is right word)\tC\t3111\t\t\t\t\t and the command: mydata - matrix(strsplit(x, '\t')[[1]], nrow=1) gives me a matrix with only the 1st row of the data. I have tried playing around with it, but so far the best I can do is get 318 copies of row 1. How can I get a matrix with all 318 rows and 15 columns split by the '\t'? Thanks again. kevin On Thu, Jun 3, 2010 at 2:39 PM, jim holtman jholt...@gmail.com wrote: If you want a matrix, then just create one from the data you have: mydata - matrix(strsplit(x, '\t')[[1]], nrow=1) On Thu, Jun 3, 2010 at 1:30 PM, Kevin Burnham kburn...@gmail.com wrote: Would somebody please help me break this row: Main Group\t1000\tMP Test\tMP Test, 1\tAudio (1, f1-qaddara.aiff)\tl (target is right word)\tl\tPressed\tl (target is right word)\tC\t3111\t\t\t\t\t into multiple columns along the \t separator? When I try the strsplit (x,\t) command I get: [[1]] [1] Main Group 1000 MP TestMP Test, 1 Audio (1, f1-qaddara.aiff) [6] l (target is right word) l Pressedl (target is right word) C [11] 3111 Which which is closer to what I need, but still not in columns. Thanks, Kevin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] sem R: singular and Could not compute QR decomposition of Hessian
Can somebody help me with the following issue (SEM in R), please: When I run the model (includes second order models) in R, it gives me the following: 1) In sem.default(ram = ram, S = S, N = N, param.names = pars, var.names = vars, : Could not compute QR decomposition of Hessian. Optimization probably did not converge. 2) I have aliased parameters and NaNS or sometimes when I run it again I have the following message: 1) Error in solve.default(C) : The system is computationally singular: condition number = 4.28182e-19 (it says so in Spanish) Since the items are measured in likert scales I was using polychoric correlations, however, I saw that it can cause troubles, so I decided not to use it anymore. I also check the following: 1) Variables with variance 0 (I do not have) 2) Linear combinations of variables (I do not have high correlations) 3) I already used initial values for the aliased parameters 4) I do not have missing data 5) The eigenvalues of the S matrix are all positive (no zeros) 6) I calculate the determinant of the correlation matrix, adding one variable at a time, in order to look for multivariate dependencies, but the determinants are not cero, the lowest one is:0.0004054475 Since the model has constructs that are measured with only one item, I decided to connect directly the variable (item) to the other constructs. Thanks Ana [[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] R plotting on linux, regardless of architecture of local machine
On Jun 4, 2010, at 1:53 PM, vaneet wrote: I can try having an X server locally, but what are the other options? Isn't there anything that can be installed on Linux to be able to display graph windows in R without too much trouble? As I said I was looking for a solution to benefit many users not just me as I can't assume or expect everyone logging in to the linux machine to have a local X server running. Thanks I think that the goal is noble, but you are asking Windows to emulate functionality specific to Linux/Unix. Kind of like asking BP to stop an oil leak... Windows does not natively support X11, which is the default graphic device on Linux. Even on OSX (which is a BSD Unix derivative), X11 is not installed by default, though it is on the OSX installation DVD. You are going to have to install something on the client machines. At minimum on Windows, you would have to install an SSH client, like PuTTY or similar, to connect to the RHEL server to run R at the CLI. So while somebody is doing that, they can take one more step and add in Xming or perhaps Cygwin/X. It is either going to be a combination of an SSH client and an X server, or R for Windows itself, if you want local display graphics. I am not cognizant of other options, but will defer to others with more recent Windows experience. 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] Convolution vector to be derived
On the contrary: it is trivial to produce the result. x - c(1,2,3,4,5) y - c(6,7,8,9) convolve(x, rev(y), type=open) # [1] 6 19 40 70 100 94 76 45 Try help(convolve). Allan On 04/06/10 19:21, Moohwan Kim wrote: Dear R-help, I want to generate the following outcome using the convolution of two sequences. x- c(1,2,3,4,5) y- c(6,7,8,9) The resulting convolution vector is 6 19 40 70 100 94 76 45 When using convolve(), it is hard to produce the result above. Would you help me out to get that? __ 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 plotting on linux, regardless of architecture of local machine
So just so I understand properly, if there are multiple users connecting to this remote linux machine in which I installed R and lets just say they all have Windows machines. To view plots they would all need to have an SSH client and an X server installed on their local machine to do this? You said that X11 is the default graphic device on Linux, isn't there some way of using X11 in R to show the plot while logged in to the remote linux machine? Thanks -- View this message in context: http://r.789695.n4.nabble.com/R-plotting-on-linux-regardless-of-architecture-of-local-machine-tp2243391p2243732.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] R plotting on linux, regardless of architecture of local machine
vaneet wrote: So just so I understand properly, if there are multiple users connecting to this remote linux machine in which I installed R and lets just say they all have Windows machines. To view plots they would all need to have an SSH client and an X server installed on their local machine to do this? Yes, with X11-forwarding enabled when the SSH connection is established. Usually this would not be the default. You said that X11 is the default graphic device on Linux, isn't there some way of using X11 in R to show the plot while logged in to the remote linux machine? Yes, by running an X11 server on the Windows machine, as others have suggested. In some situations, I have just left open a GUI SFTP client to some directory where my R plots get generated. After my script is done, I then simply double-click the graphics file to open it. Perhaps there is some image or PDF viewer out there that can load a remote file, and then 'watch' it so that when it changes, it reloads automatically. I suppose that's another option. I know programs exist that can do this when the file is local. Perhaps Dropbox could be used as a solution. Running the X server is going to be the easiest in my opinion, though. __ 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] Wrong symbol rendering in plots (Ubuntu)
Eduardo J. Chica ejchica at gmail.com writes: Hi I am having problems with the rendering of scientific symbols (mu and degree) in my plots. Whenever I use these symbols they are rendered changed (mu is changed to the proportionality symbol and degree is changed to something resembling a gamma) in the X-device. If I make a pdf of the plot and open the file in Evince or Okular symbols are also rendered wrong, however if I open the file with Xpdf or Acroread they are rendered correctly. I did not have this problem before, it arose after I upgraded both R and my system (Ubuntu karmic koala to lucid lynx), so I can not tell for sure if the problem is R-related or Ubuntu related (I have posted in a Ubuntu forum also http://ubuntuforums.org/showthread.php?t=1325289). Could you please post a reproducible example? It would be good to see exactly what you are doing, and it will save time for anyone who wants to try your example on their machine to try to narrow down the problem. 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] R plotting on linux, regardless of architecture of local
On 04-Jun-10 20:26:50, vaneet wrote: So just so I understand properly, if there are multiple users connecting to this remote linux machine in which I installed R and lets just say they all have Windows machines. To view plots they would all need to have an SSH client and an X server installed on their local machine to do this? Yes. You said that X11 is the default graphic device on Linux, isn't there some way of using X11 in R to show the plot while logged in to the remote linux machine? Thanks It is important to understand one thing about the X11 system. Namely, that the notions of X-server and X-client are the oposite way round from what a user might naively expect. When you are sitting at one machine, remotely logged in to another machine which is running some program which you have requested, you are likely to think that your machine is the client, requesting service from the remote machine. So you request an action from the remote machine, and the remote machine serves you with the result. However, an X-capable program (say R), running on the remote machine, will need to enable you to see (e.g.) graphics results computed by thbe remote machine. This it will do by sending requests to your local machine to make marks on the local screen. So your local machine must be running a program which can accept these requests and make the marks on the screen. Thus the local machine is now the *server*, responding to requests from the remote machine (the *client*). Thus an X system must be installed on your local machine so that it can respond to the requests from the remote machine. I.e. your local machine must be capable of acting as an X-server. Therefore you must install X on your local machine. Hoping this helps! Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 04-Jun-10 Time: 21:45:46 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plotting on linux, regardless of architecture of local
Thanks for explaining it in detail, that really helps. -- View this message in context: http://r.789695.n4.nabble.com/R-plotting-on-linux-regardless-of-architecture-of-local-machine-tp2243391p2243757.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] subsetting a dataframe
Hi there, a-data.frame(c(1,2,2,5,9,9),c(A,B,C,D,E,F)) names(a)-c(x1,x2) max(table(a$x1)) [1] 2 The above shows the max count for x1 is 2, which is correct. But we can't tell there are 2 groups that meet this criteria: 2,2 and 9,9. I then want to extract the records that has the hightest count a[max(table(a$x1)),] x1 x2 2 2 B This is not working, since it is equvalent to a[2,] What I want is x1 x2 2 2 B 3 2 C 5 9 E 5 9 F I think this should be very easy, but I'm a beginner :-) Thanks YJM __ 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] tapply help
Dear R gurus,
I am trying perform what I believe will be a pretty simple task, but I'm
struggling to figure out how to do it. I have two vectors of the same length,
the first is numeric and the second is factor. I understand that tapply is
perfect for applying a function to the numeric vector by subsets of the factors
in the second vector. My issue is trying to make use of two other vectors
within the custom function I've written for tapply. The two other vectors are a
high and low value for each subset I am breaking my data into, and I want to
calculate the percentage of data points that fall into each respective range. I
will attempt to provide a coherent example:
# create range for each possible class
lows-c(1,2,3,4,5)
highs-c(5,6,7,8,9)
# data values
vals-sample(1:10,100,replace=T)
#classes
classes-sample(letters[1:5],100,replace=T)
# Try to calculate percentage of values that fall
# into the respective range for the given class.
percentages-tapply(vals,classes,
function(i){
length(i[i=lows[index] i=highs[index]])/length(i) # I
don't know how to actually keep an index count in tapply, but I'm guessing
there's a better way.
})
I really appreciate any help.
ME
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[R] fixed intercept
Hi, is it possible to specify a constant intercept (based on prior knowledge) in linear regression using lm()? Thanks John __ 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] Your message to R-help awaits moderator approval
What filter rule is violated? So frustrated, why can't I post question! - Original Message From: r-help-boun...@r-project.org r-help-boun...@r-project.org To: yjmh...@yahoo.com Sent: Fri, June 4, 2010 12:28:37 PM Subject: Your message to R-help awaits moderator approval Your mail to 'R-help' with the subject subsetting a dataframe Is being held until the list moderator can review it for approval. The reason it is being held: The message headers matched a filter rule Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: https://stat.ethz.ch/mailman/confirm/r-help/151139c40b029d260fb9bde07e60a96a68dc572d __ 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] Help with iteration using while loop
Hi Subodh,
Minor note: please keep replies on list so everyone benefits from
answers/questions.
Now:
On Fri, Jun 4, 2010 at 2:49 PM, Subodh Acharya shoeb...@gmail.com wrote:
Thanks a lot Steve,
It worked. I appreciate. But I have another question, may be thats trivial.
Say, it doesn't converge at itermax. I need to display error message saying
values don't converge at at itermax. Is there another statement that
accompanies while for this?
Perhaps you can use warning(...). You can check whether (or not)
your Fpt - Fpi is tolerance after you loop. If it is, you know your
loop terminated because you hit itermax, and not because your algo
converged:
...
...
iter - 0
while (((Fpt - Fpi) tolerance) (iter itermax)) {
Fpi = Fpt
Fpt = K*Time + M*S*log(1+ Fpi/(M*S))
Fp0 = Fpt
iter - iter + 1
}
if (Fpt - Fpi tolerance) {
warning(Algorithm reached itermax and did not converge)
}
...
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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Re: [R] Wrong symbol rendering in plots (Ubuntu)
On Fri, Jun 4, 2010 at 1:44 PM, Ben Bolker bol...@ufl.edu wrote: Eduardo J. Chica ejchica at gmail.com writes: Hi I am having problems with the rendering of scientific symbols (mu and degree) in my plots. Whenever I use these symbols they are rendered changed (mu is changed to the proportionality symbol and degree is changed to something resembling a gamma) in the X-device. If I make a pdf of the plot and open the file in Evince or Okular symbols are also rendered wrong, however if I open the file with Xpdf or Acroread they are rendered correctly. I did not have this problem before, it arose after I upgraded both R and my system (Ubuntu karmic koala to lucid lynx), so I can not tell for sure if the problem is R-related or Ubuntu related (I have posted in a Ubuntu forum also http://ubuntuforums.org/showthread.php?t=1325289). Could you please post a reproducible example? It would be good to see exactly what you are doing, and it will save time for anyone who wants to try your example on their machine to try to narrow down the problem. Ben Bolker I have noticed something similar. Even a regular plot, say plot(c(1:10)) when put into a pdf file via pdf() device, will display incorrect symbols in linux pdf viewers (evince, okular). The circles (o) become q, literally the letter q, and lose colors. In Acroread I see the plots as they should be. This started happening around R-2.9 or so. Am also not sure whether it's the R pdf or pdfCairo, or whether it's a bug in the evince/okular backend. Peter __ 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] Wrong symbol rendering in plots (Ubuntu)
plot(c(1:10)) when put into a pdf file via pdf() device, will display incorrect symbols in linux pdf viewers (evince, okular). The circles (o) become q, literally the letter q, and lose colors. This issue is already in the Notes section of ?pdf. It remains to be seen if the OP's problem was this exact one, since they didn't specify an example. From ?pdf, On some systems the default plotting character ‘pch = 1’ is displayed in some PDF viewers incorrectly as a ‘q’ character. (These seem to be viewers based on the ‘poppler’ PDF rendering library). This may be due to incorrect or incomplete mapping of font names to those used by the system. Adding the following lines to ‘~/.fonts.conf’ or ‘/etc/fonts/local.conf’ may circumvent this problem. alias binding=same familyZapfDingbats/family acceptfamilyDingbats/family/accept /alias __ 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] Wrong symbol rendering in plots (Ubuntu)
This issue is already in the Notes section of ?pdf. It remains to be seen if the OP's problem was this exact one, since they didn't specify an example. aahhh, thank you for pointing this out. I never noticed this note. Peter __ 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] subsetting a dataframe
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of yjmha69 Sent: Friday, June 04, 2010 12:28 PM To: R-help@r-project.org Subject: [R] subsetting a dataframe Hi there, a-data.frame(c(1,2,2,5,9,9),c(A,B,C,D,E,F)) names(a)-c(x1,x2) max(table(a$x1)) [1] 2 The above shows the max count for x1 is 2, which is correct. But we can't tell there are 2 groups that meet this criteria: 2,2 and 9,9. I then want to extract the records that has the hightest count a[max(table(a$x1)),] x1 x2 2 2 B This is not working, since it is equvalent to a[2,] What I want is x1 x2 2 2 B 3 2 C 5 9 E 5 9 F I think this should be very easy, but I'm a beginner :-) One way is to use merge to combine your table with the original data.frame: tmp - merge(a, as.data.frame(table(a$x1)), by.x=x1, by.y=Var1) tmp[tmp$Freq==max(tmp$Freq), ,drop=FALSE] Another way is to use ave: tmp - with(a, ave(x1, x1, FUN=length)) a[tmp==max(tmp), , drop=FALSE] Another way is a[as.character(a$x1) %in% names(tmp[tmp==max(tmp)]), , drop=FALSE] (This last one might have problems when some values in a$x1 are different but so close that as.character() makes the same string out of them.) Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com Thanks YJM __ 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] Your message to R-help awaits moderator approval
This has happened to me too. The last time it occurred I was replying to another post and on my second attempt I deleted the replied-to portion and reposted just my portion and it worked. On Fri, Jun 4, 2010 at 4:35 PM, yjmha69 yjmh...@yahoo.com wrote: What filter rule is violated? So frustrated, why can't I post question! - Original Message From: r-help-boun...@r-project.org r-help-boun...@r-project.org To: yjmh...@yahoo.com Sent: Fri, June 4, 2010 12:28:37 PM Subject: Your message to R-help awaits moderator approval Your mail to 'R-help' with the subject subsetting a dataframe Is being held until the list moderator can review it for approval. The reason it is being held: The message headers matched a filter rule Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: https://stat.ethz.ch/mailman/confirm/r-help/151139c40b029d260fb9bde07e60a96a68dc572d __ 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 plotting on linux, regardless of architecture of local machine
On Jun 4, 2010, at 3:26 PM, vaneet wrote: So just so I understand properly, if there are multiple users connecting to this remote linux machine in which I installed R and lets just say they all have Windows machines. To view plots they would all need to have an SSH client and an X server installed on their local machine to do this? You said that X11 is the default graphic device on Linux, isn't there some way of using X11 in R to show the plot while logged in to the remote linux machine? Thanks There are two separate functions required: 1. SSH Client - This provides the ability to login securely to the RHEL server from a remote client system. That could be another Linux/Unix machine, a Windows machine or an OSX machine (could even be a smartphone). This, in isolation, strictly provides a text based, point-to-point encrypted communication mechanism for the two machines to interact, over some network connection (could be the internet). It provides the functional equivalent of you sitting at the server itself and logging in locally using text mode only. Since it is a remote connection, SSH encrypts the connection to provide for the security of the data going back and forth over the network connection. On a PC, think of the old DOS command line interface before Windows came along. With respect to R, you need the SSH client to connect to the RHEL server to be able to run R. R is not running (executing) on your Windows machine. R is actually running on the RHEL server and the SSH connection is providing the means to transmit your keystrokes to the server and to provide the text mode screen output back to you. So the SSH network connection is essentially providing really long cables between your keyboard, your display and the server. 2. X11 - Linux uses X11 to provide the basic substrate for creating the GUI or windowing functionality on the display. This provides the basic means of graphical interaction with the computer as we generally know it today. When R generates plots in response to your commands, the RHEL server needs to send the results (signal) back to you and your computer needs the ability to interpret those signals and display them on your machine. It is the X11 server (eg. Xming) running on your computer, that interprets those signals and enables the plot to be displayed on your machine. Without the X11 server running on your machine, all you have is a text based interaction with the RHEL server, because Windows would not know what to do with the signals coming from the RHEL server. If you are familiar with the difference between NTSC (aka Never The Same Color) and PAL, this would be something of a parallel. They are both TV display signal standards, but are not compatible. Now, in reality, there is another component here, called X11 port forwarding. Think call forwarding. We have to have some way for the RHEL server to know to send (forward) the signals for the plot, over the SSH connection, to your machine, rather than sending them to the display that is physically connected to the RHEL server. Otherwise, you won't see the plot on your end. In order to accomplish this, the RHEL server has to be configured to support this functionality (your SysAdmin will know how to do this) AND the SSH client needs to be configured to support the connection as well. In PuTTY for example, there is a setting in the application that enables this. But remember, this has to be supported on both ends, so you need to check with your SysAdmin. Sometimes, because of security concerns, X11 port forwarding will be disabled on the RHEL server side of things. I see that Ted has also provided an excellent reply, so hopefully this might supplement his in some fashion. 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] plotting a dataset with median 0
Dear R community, [[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] plotting a dataset with median 0
Dear R community, I am working on a dataset that has median 0 (due to many 0 entries) for my principal variable of interest (40 entries in total). I would like to plot a graph of this variable to show it visually, but have a hard time: boxplots are not informative (because median 0). Conventional scatterplots are neither. Is there a good way to do this (e.g. plotting the 0 values with a jitter or something else...)? Thanking you all and best regards, Georg. * Georg Ehret Johns Hopkins Baltimore [[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] What is the largest in memory data object you've worked with in R?
For me, I've found that I can easily work with 1 GB datasets. This includes linear models and aggregations. Working with 5 GB becomes cumbersome. Anything over that, and R croaks. I'm using a dual quad core Dell with 48 GB of RAM. I'm wondering if there is anyone out there running jobs in the 100 GB range. If so, what does your hardware look like? --Nathan [[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] Ignoring missing elements in data.frame()
Hello, I am trying to make a data frame from many elements after running a function which creates many elements, some of which may not end up being real elements due to errors or missing data. For example, I have the following three elements p1s, p2s, and p3s. p9s did not generate the same data as there was an error in the function for some reason. I currently have to delete p9s from the data.frame() command to get the data.frame to work. How can I make a data frame by somehow ignoring elements (e.g., p9s) that do not exist, without having to delete each missing element from data.frame()? The below is an example of the code. p1s statistic parameter p.value [1,] 3.606518 153 0.0004195377 p2s statistic parameter p.value [1,] -3.412436 8 0.009190015 p3s statistic parameter p.value [1,] 1.543685 599 0.1231928 t(data.frame(t(p1s),t(p2s),t(p3s),t(p9s))) Error in t(p9s) : object 'p9s' not found Thanks, Scott Chamberlain Rice University Houston, TX __ 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] 380x380 dataframe to list
Hi, This can't be hard, but I can't find the solution. I have a 380x380 data frame of numbers. I would like to turn it into a single column so I can do e.g. hist and mean on it without writing my own function. There must be a simple function for this, but I'm stumped -- reshape, dim, etc. don't seem to do it... Help appreciated! Thanks!! Nick -- Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200A Principles of Phylogenetics: Systematics http://ib.berkeley.edu/courses/ib200a/index.shtml Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: mat...@berkeley.edu Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 - [W]hen people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together. Isaac Asimov (1989). The Relativity of Wrong. The Skeptical Inquirer, 14(1), 35-44. Fall 1989. http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 380x380 dataframe to list
Hi Nick, Try unlist(yourdataframe). HTH, Jorge On Fri, Jun 4, 2010 at 8:47 PM, Nick Matzke wrote: Hi, This can't be hard, but I can't find the solution. I have a 380x380 data frame of numbers. I would like to turn it into a single column so I can do e.g. hist and mean on it without writing my own function. There must be a simple function for this, but I'm stumped -- reshape, dim, etc. don't seem to do it... Help appreciated! Thanks!! Nick -- Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200A Principles of Phylogenetics: Systematics http://ib.berkeley.edu/courses/ib200a/index.shtml Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: mat...@berkeley.edu Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 - [W]hen people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together. Isaac Asimov (1989). The Relativity of Wrong. The Skeptical Inquirer, 14(1), 35-44. Fall 1989. http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] Help with iteration using while loop
Hi Steve,
Actually I figured that out after I emailed you but I forgot to email
you before I left office.
Anyway thanks a lot.And thanks for the note. I'll do that from now on.
Subodh
On Fri, Jun 4, 2010 at 4:54 PM, Steve Lianoglou
mailinglist.honey...@gmail.com wrote:
Hi Subodh,
Minor note: please keep replies on list so everyone benefits from
answers/questions.
Now:
On Fri, Jun 4, 2010 at 2:49 PM, Subodh Acharya shoeb...@gmail.com wrote:
Thanks a lot Steve,
It worked. I appreciate. But I have another question, may be thats
trivial.
Say, it doesn't converge at itermax. I need to display error message
saying
values don't converge at at itermax. Is there another statement that
accompanies while for this?
Perhaps you can use warning(...). You can check whether (or not)
your Fpt - Fpi is tolerance after you loop. If it is, you know your
loop terminated because you hit itermax, and not because your algo
converged:
...
...
iter - 0
while (((Fpt - Fpi) tolerance) (iter itermax)) {
Fpi = Fpt
Fpt = K*Time + M*S*log(1+ Fpi/(M*S))
Fp0 = Fpt
iter - iter + 1
}
if (Fpt - Fpi tolerance) {
warning(Algorithm reached itermax and did not converge)
}
...
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
--
Acharya, Subodh
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] 380x380 dataframe to list
c(as.matrix(data)) will not do it? Peter On Fri, Jun 4, 2010 at 5:47 PM, Nick Matzke mat...@berkeley.edu wrote: Hi, This can't be hard, but I can't find the solution. I have a 380x380 data frame of numbers. I would like to turn it into a single column so I can do e.g. hist and mean on it without writing my own function. There must be a simple function for this, but I'm stumped -- reshape, dim, etc. don't seem to do it... Help appreciated! Thanks!! Nick -- Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200A Principles of Phylogenetics: Systematics http://ib.berkeley.edu/courses/ib200a/index.shtml Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html Lab phone: 510-643-6299 Dept. fax: 510-643-6264 Cell phone: 510-301-0179 Email: mat...@berkeley.edu Mailing address: Department of Integrative Biology 3060 VLSB #3140 Berkeley, CA 94720-3140 - [W]hen people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together. Isaac Asimov (1989). The Relativity of Wrong. The Skeptical Inquirer, 14(1), 35-44. Fall 1989. http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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.
