Re: [R] Fast nested List-data.frame
Dieter,
I'd approach this by first making a matrix, then converting to a data
frame with appropriate types. I'm sure there is a way to do it with
structure in one step. Operations on matrices are usually faster than on
dataframes.
len - 10
d - replicate(len, list(pH = 3, marker = TRUE, position = A), FALSE)
toDF - function(alist){
d.matrix - matrix(unlist(alist), ncol = 3, byrow = TRUE)
d.df - as.data.frame(d.matrix)
names(d.df) - c('pH', 'marker', 'position')
d.df$pH - as.numeric(d.df$pH)
d.df$marker - as.logical(d.df$marker)
return(d.df)
}
on my system,
system.time(b-toDF(d))
user system elapsed
0.560 0.033 0.592
and
head(b)
pH marker position
1 1 TRUEA
2 1 TRUEA
3 1 TRUEA
4 1 TRUEA
5 1 TRUEA
6 1 TRUEA
and
sapply(b, class)
pHmarker position
numeric logical factor
I hope this helps,
Greg
sessionInfo() ##old, I know.
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] cimis_0.1-3 RLastFM_0.1-4 RCurl_0.98-1bitops_1.0-4.1
XML_2.5-3
[6] lattice_0.17-22
loaded via a namespace (and not attached):
[1] grid_2.9.0
On 1/4/10 11:43 PM, Dieter Menne wrote:
I have very large data sets given in a format similar to d below. Converting
these to a data frame is a bottleneck in my application. My fastest version
is given below, but it look clumsy to me.
Any ideas?
Dieter
# ---
len = 10
d = replicate(len, list(pH = 3,marker = TRUE,position = A),FALSE)
# Data are given as d
# preallocate vectors
pH =rep(0,len)
marker =rep(0,len)
position =rep(0,len)
system.time(
{
for (i in 1:len)
{
d1 = d[[i]]
#Assign to vectors
pH[i] = d1[[1]]
marker[i] = d1[[2]]
position[i] = d1[[3]]
}
# combine vectors
pHAll = data.frame(pH,marker,position)
}
)
--
Greg Hirson
ghir...@ucdavis.edu
Graduate Student
Agricultural and Environmental Chemistry
1106 Robert Mondavi Institute North
One Shields Avenue
Davis, CA 95616
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Fast nested List-data.frame
The as.numeric(d.df$pH) should have been an
as.numeric(as.character(d.df$pH)).
Sorry for the confusion.
Greg
On 1/5/10 12:33 AM, Greg Hirson wrote:
Dieter,
I'd approach this by first making a matrix, then converting to a data
frame with appropriate types. I'm sure there is a way to do it with
structure in one step, but here it is:
a - function() {
len - 10
d - replicate(len, list(pH = 3, marker = TRUE, position = A), FALSE)
d.matrix - matrix(unlist(d), ncol = 3, byrow = TRUE)
d.df - as.data.frame(d)
names(d.df) - c('pH', 'marker', 'position')
#d.df$pH - as.numeric(d.df$pH) #incorrect
d.df$pH - as.numeric(as.character(d.df$pH)) #correct
d.df$marker - as.logical(d.df$marker)
return(d.df)
}
system.time(a)
On 1/4/10 11:43 PM, Dieter Menne wrote:
I have very large data sets given in a format similar to d below. Converting
these to a data frame is a bottleneck in my application. My fastest version
is given below, but it look clumsy to me.
Any ideas?
Dieter
# ---
len = 10
d = replicate(len, list(pH = 3,marker = TRUE,position = A),FALSE)
# Data are given as d
# preallocate vectors
pH =rep(0,len)
marker =rep(0,len)
position =rep(0,len)
system.time(
{
for (i in 1:len)
{
d1 = d[[i]]
#Assign to vectors
pH[i] = d1[[1]]
marker[i] = d1[[2]]
position[i] = d1[[3]]
}
# combine vectors
pHAll = data.frame(pH,marker,position)
}
)
--
Greg Hirson
ghir...@ucdavis.edu
Graduate Student
Agricultural and Environmental Chemistry
1106 Robert Mondavi Institute North
One Shields Avenue
Davis, CA 95616
--
Greg Hirson
ghir...@ucdavis.edu
Graduate Student
Agricultural and Environmental Chemistry
1106 Robert Mondavi Institute North
One Shields Avenue
Davis, CA 95616
[[alternative HTML version deleted]]
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[R] R-package related to the topic of INARMA models
Dear R, I am looking for R-package related to INARMA (Integer-valued ARMA). Can anyone give me some information? I did not get information from task view. Many thanks. Feng -- Feng Li Department of Statistics Stockholm University 106 91 Stockholm, Sweden http://feng.li/ [[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] Fast nested List-data.frame
Greg Hirson wrote: I'd approach this by first making a matrix, then converting to a data frame with appropriate types. Well, I knew that matrixes are faster for numerics, but I also knew that the required conversion to character would be a show-stopper. My second wisdom was bogus. Your version is 30% faster on my computer. Dieter -- View this message in context: http://n4.nabble.com/Fast-nested-List-data-frame-tp998871p998897.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] Fast nested List-data.frame
This is better by a factor of 4:
len = 10
d = replicate(len, list(pH = 3,marker = TRUE,position = A),FALSE)
system.time(
{
pHAll = data.frame(
pH = unlist(lapply(d,[[,1)),
pH = unlist(lapply(d,[[,2)),
pH = unlist(lapply(d,[[,3)))
}
)
Dieter
--
View this message in context:
http://n4.nabble.com/Fast-nested-List-data-frame-tp998871p998902.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-package related to the topic of INARMA models
On Tue, 5 Jan 2010, Feng Li wrote: Dear R, I am looking for R-package related to INARMA (Integer-valued ARMA). Can anyone give me some information? I did not get information from task view. That's a very specialized topic, and you have not said what you want to do with such processes. I suggest you approach the handful of authors of papers on the subject (often called discrete-valued ARMA) -- quite possibly none of them work with R. Many thanks. Feng -- Feng Li Department of Statistics Stockholm University 106 91 Stockholm, Sweden http://feng.li/ [[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] xyplot - help with multiple Y's vs. X of a member data in multiple panels
Thanks for your email.. Yes, I am looking for lattice version of matplot... Attached are some codes for simplicity for rapid testing..Any suggestions would be highly appreciated... library(lattice) dat - data.frame(x = rep(1:10,2), y1 = rnorm(20), y2=rnorm(20,sd=1.3), y3=rnorm(20,sd=0.3), gp1 = rep(letters[1:8],each=10), gp2=rep(LETTERS[1:4],each=20), gp3=rep(c(P,Q),each=40)) pset - simpleTheme(lty = c(0,1,2), col=c(blue,red,green)) xyplot(y1+y2+y3~x|factor(gp3)+factor(gp2), data=dat, groups=gp1, allow.multiple=T, panel=panel.superpose, distribute.type=T, type=c(b,l,l), par.settings=pset, strip=strip.custom(strip.names=F,strip.levels=T)) Thanks.. Santosh On Mon, Jan 4, 2010 at 11:16 PM, Dennis Murphy djmu...@gmail.com wrote: Hi: I think Santosh wants a Lattice version of matplot. I didn't find anything with help.search(), though... Dennis On Mon, Jan 4, 2010 at 8:14 PM, Santosh santosh2...@gmail.com wrote: Hi, Thanks for your email.. Each panel (in a multiple panel) is identified by DS1, DS2 DS3 in the dataset sent earlier. I would like an overlay of Y1, Y2 Y3 (each by different lines) for each ID in the group. Each ID in the group is represented by a color. Regards Thanks, Santosh On Mon, Jan 4, 2010 at 5:07 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Can you clarify how many curves you want in each panel? You have 3 Ys and your original email indicated at least 7 ID values. Do you really want 21 curves in each panel? Or do you want separate panels for the Ys? Re your code: note that, regarding a formula of the type y1 + y2 ~ x, ?xyplot says: This feature cannot be used in conjunction with the groups argument. -Peter Ehlers Santosh wrote: Hi Jim and others, I tried suggestions and somehow the graphs do not seem to be aligned on X-axis (i.e. they appear to be shifted on x-axis).. I guess panel.xyplot or panel.superpose is needed? I am not sure what the group variable be panel.xyplot, whether it is the ID or the newFactor. I tried panel.xyplot(x,y,) with group=ID and group=newFactor and it did not work. Your suggestions would be highly appreciated!! Regards, Santosh On Thu, Dec 31, 2009 at 6:59 PM, jim holtman jholt...@gmail.com wrote: I am not too sure if this is what you are after, but I just created a new factor for the panel: # create a new factor d1$newFactor - factor(paste(d1$DS1, +, d1$DS2, +, d1$DS3)) xyplot(Y1+Y2+Y3~X1|newFactor,data=d1,group=ID) On Thu, Dec 31, 2009 at 6:25 AM, Santosh santosh2...@gmail.com wrote: Dear R experts, Wish you all a HAPPY NEW YEAR! How do I go about plotting (using lattice) overlays of an ID (group=ID) observed, fitted data in each panel of a multiple panel plot (each panel identified by DS1 + DS2 + DS3)? x variable is X1 in the accompanying section of a dataset. each individual is identified by color and Y's are identified by pch or lty. I guess the code goes something like the one below, but could not get the proper use of panel functions xyplot(Y1+Y2+Y3~X1|DS1+DS2+DS3,data=d1,group=ID,...)... [[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 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. -- Peter Ehlers University of Calgary 403.202.3921 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Checking for normality and homogeneity of variance
Haiyang AI wrote: Dear all, I'm a beginner of R and I need to carry out some three-way mixed ANOVAs. Following examples at http://personality-project.org/r/r.anova.html, I managed to get the ANOVA part, but I don't know how can I check data normality and homogeneity of variance in R (since they're the required assumptions of ANOVA analysis). No..normality and homogeneity of the data it is not an assumption! It is normality and homogeneity of the residuals! See also: http://www3.interscience.wiley.com/cgi-bin/fulltext/122683826/PDFSTART Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. URL: www.springer.com/0-387-45967-7 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. http://www.springer.com/life+sci/ecology/book/978-0-387-87457-9 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer http://www.springer.com/statistics/computational/book/978-0-387-93836-3 Other books: http://www.highstat.com/books.htm Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Tel: 0044 1358 788177 Email: highs...@highstat.com URL: www.highstat.com URL: www.brodgar.com -- View this message in context: http://n4.nabble.com/Checking-for-normality-and-homogeneity-of-variance-tp998821p998923.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] Tranpose and Aggregate Data - now Reshape - cast
library(reshape) names(harvest.dat) = c(CROP_ID, CROPTYPE, PERIOD,CUT_AGE) harvest -cast(harvest.dat, CROP_ID + CROPTYPE ~ PERIOD) It seems that I am getting the frequencies instead of the individual values. Output ~ CROP_ID CROPTYPE 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 1 1 OTO 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 SORI 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 OTO 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 SORI 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 2 SORM 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 3 OTO 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 3 OTRM 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 3 SORI 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 3 SORM 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ~ Desired table CROP_ID CROPTYPE P1P2P3P4 P5P6 P7 P8P9P10 83 SORI31 84 SORI32 85 SORI33 86 SORI34 82 SORI28 83 SORI29 84 SORI30 93 SORM35 62 OTRM30 82 SORI27 3 SORM35 82 SORI26 4 SORM34 5 OTRI25 5 OTRM29 5 SORM32 5 SORM33 5 SORM35 6 OTRI22 6 OTRI23 6 OTRI24 6 OTRM26 6 OTRM27 6 OTRM28 7 OTRM26 8 OTRM26 How do I do this properly. Thanks in advance. Noli __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] xyplot - help with multiple Y's vs. X of a member data in multiple panels
You should reshape the data into a long format, and an easy way to do that is to use the 'reshape' package: library(reshape) mdat - melt(dat, measure.vars = c(y1, y2, y3)) I'm still not sure what you want in the plot. Confusingly, your last example dropped the ID you referred to earlier, and appears to use grp1 in the same role. Maybe something like this: xyplot(value ~ x | paste(gp2, gp3), mdat, groups = paste(variable, gp1), type = l, auto.key = list(lines = TRUE, columns = 3), par.settings = simpleTheme(col = 1:8, lty = rep(1:3, each = 8))) 2010/1/5 Santosh santosh2...@gmail.com: Thanks for your email.. Yes, I am looking for lattice version of matplot... Attached are some codes for simplicity for rapid testing..Any suggestions would be highly appreciated... library(lattice) dat - data.frame(x = rep(1:10,2), y1 = rnorm(20), y2=rnorm(20,sd=1.3), y3=rnorm(20,sd=0.3), gp1 = rep(letters[1:8],each=10), gp2=rep(LETTERS[1:4],each=20), gp3=rep(c(P,Q),each=40)) pset - simpleTheme(lty = c(0,1,2), col=c(blue,red,green)) xyplot(y1+y2+y3~x|factor(gp3)+factor(gp2), data=dat, groups=gp1, allow.multiple=T, panel=panel.superpose, distribute.type=T, type=c(b,l,l), par.settings=pset, strip=strip.custom(strip.names=F,strip.levels=T)) Thanks.. Santosh On Mon, Jan 4, 2010 at 11:16 PM, Dennis Murphy djmu...@gmail.com wrote: Hi: I think Santosh wants a Lattice version of matplot. I didn't find anything with help.search(), though... Dennis On Mon, Jan 4, 2010 at 8:14 PM, Santosh santosh2...@gmail.com wrote: Hi, Thanks for your email.. Each panel (in a multiple panel) is identified by DS1, DS2 DS3 in the dataset sent earlier. I would like an overlay of Y1, Y2 Y3 (each by different lines) for each ID in the group. Each ID in the group is represented by a color. Regards Thanks, Santosh On Mon, Jan 4, 2010 at 5:07 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Can you clarify how many curves you want in each panel? You have 3 Ys and your original email indicated at least 7 ID values. Do you really want 21 curves in each panel? Or do you want separate panels for the Ys? Re your code: note that, regarding a formula of the type y1 + y2 ~ x, ?xyplot says: This feature cannot be used in conjunction with the groups argument. -Peter Ehlers Santosh wrote: Hi Jim and others, I tried suggestions and somehow the graphs do not seem to be aligned on X-axis (i.e. they appear to be shifted on x-axis).. I guess panel.xyplot or panel.superpose is needed? I am not sure what the group variable be panel.xyplot, whether it is the ID or the newFactor. I tried panel.xyplot(x,y,) with group=ID and group=newFactor and it did not work. Your suggestions would be highly appreciated!! Regards, Santosh On Thu, Dec 31, 2009 at 6:59 PM, jim holtman jholt...@gmail.com wrote: I am not too sure if this is what you are after, but I just created a new factor for the panel: # create a new factor d1$newFactor - factor(paste(d1$DS1, +, d1$DS2, +, d1$DS3)) xyplot(Y1+Y2+Y3~X1|newFactor,data=d1,group=ID) On Thu, Dec 31, 2009 at 6:25 AM, Santosh santosh2...@gmail.com wrote: Dear R experts, Wish you all a HAPPY NEW YEAR! How do I go about plotting (using lattice) overlays of an ID (group=ID) observed, fitted data in each panel of a multiple panel plot (each panel identified by DS1 + DS2 + DS3)? x variable is X1 in the accompanying section of a dataset. each individual is identified by color and Y's are identified by pch or lty. I guess the code goes something like the one below, but could not get the proper use of panel functions xyplot(Y1+Y2+Y3~X1|DS1+DS2+DS3,data=d1,group=ID,...)... [[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 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. -- Peter Ehlers University of Calgary 403.202.3921 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list
Re: [R] importing data from BUGS format to R?
Martyn Plummer-2 wrote: I wrote a function called bugs2jags, which you will find in the coda package, for converting WinBUGS data files into the data format used by JAGS which is, by no coincidence, the format used by the R function dump(). First of all excuse me for reviving this very old thread - if it is the preferred way in this forum/ mailinglist, I will start a new one instead. I'm a computational biologist programming in C++ and I'm actually not familiar with R. But I wrote a small program to analyse Win-/OpenBugs output (CODA) according to this paper: http://dx.doi.org/10.1016/j.anbehav.2004.08.011 . As I'm working with Mac and Linux (Kubuntu 9.10 „Karmic Koala“ at the moment) and WINbugs only runs on Windows natively (as it's name says), I want to switch to JAGS instead. Now I have the problem to change the WinBugs formatted model and data into JAGS/R formatted ones, which is quite difficult without knowing the actual differences between R and S(-PLUS) programming languages. (The latter one seems to be the basis of WinBugs' format.) I'm not completely sure whether bugs2jags can be applied to this case, but when I tried to execute it with the main example from the above mentioned paper (see attachment), it showed this error message: library(coda) Lade nötiges Paket: lattice bugs2jags(WinBugs.txt,Jags.txt) Fehler in parse(file = file) : WinBugs.txt:19:9: Unerwartetes Symbol 18: list(individuals = 5, dyads = 9) 19: ind1[ ] ind2 ^ Thank you in anticipation Sascha Siemann http://n4.nabble.com/file/n998943/WinBugs.txt WinBugs.txt -- View this message in context: http://n4.nabble.com/importing-data-from-BUGS-format-to-R-tp794525p998943.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] by function ??
I wrote : (some may return vectors, others may return vectors) Its been pointed out there was a typo, and wasn't very clear anyway. It should read '(some may return vectors, others may return scalars)'. I've been asked for further explanation so here goes ... The point I was trying to make is that the following expression is very natural to write. It takes a bit of getting used to though. A reminder of the 2 column Dataset (containing a group of 4 rows and a group of 3 rows) then the R expression and then the output : LEAID ratio 6307 0.720 6307 0.7623810 6307 0.860 6307 0.920 8300 0.5678462 8300 0.770 8300 0.830 the syntax : Dataset = data.table(Dataset) Dataset[,DT(ratio,scaled=abs(ratio-median(ratio)),sum=sum(ratio)),by=LEAID] and the 4 column output : LEAID ratio scaled sum 6307 0.720 0.0911905 3.262381 6307 0.7623810 0.0488095 3.262381 6307 0.860 0.0488095 3.262381 6307 0.920 0.1088095 3.262381 8300 0.5678462 0.2021538 2.167846 8300 0.770 0.000 2.167846 8300 0.830 0.060 2.167846 The 2nd argument (the call to DT()) contains 3 expressions, which are executed for each subset of the Dataset grouped by LEAID. The row order is maintained for each subset, and these expressions operate on ordered vectors as usual in R. We can use column names as variable names directly (like an implicit ?with). Note that Dataset doesn't have to be ordered by LEAID, but it just happens to be in this example. A comment on each of the 3 expressions (the 3 arguments passed to DT() above) is perhaps useful : ratio : just repeats the ratio vector as is. You don't have to include this but I wanted to keep the input data in the output to demonstrate. abs(ratio-median(ratio)) : median() returns a scalar, subtracted from each element from ratio, and returns a vector. abs() takes a vector, and returns a vector. Standard R and basic stuff. Any R expresssion can be used, so its more powerful than SQL in thats sense because SQL is restricted to a small set of functions (avg, min, max, etc), which has been said before and been true about R for a long time. Its the overall syntax of the single 'query' that I'm trying to demonstrate. sum(ratio) : returns a scalar aggregate on the vector input. Thats what I meant by others may return scalars. Notice the the value of sum(ratio) is repeated in the final column of the output. The reason is because at least one of the other expressions return vectors, and standard R silent repetition rules are coming into play inside DT(). Then the 2 data.table's (one for each of the 2 groups) are combined and a single data.table is returned. Very similar to SQL really and some other ways to aggregate in R, but more compact, more natural, easier and more convenient (and therefore quicker) to write, debug and maintain. Matthew Dowle mdo...@mdowle.plus.com wrote in message news:hgnjev$3h...@ger.gmane.org... or if Dataset is a data.table : Dataset = data.table(Dataset) Dataset[,abs(ratio-median(ratio)),by=LEAID] LEAIDV1 [1,] 6307 0.0911905 [2,] 6307 0.0488095 [3,] 6307 0.0488095 [4,] 6307 0.1088095 [5,] 8300 0.2021538 [6,] 8300 0.000 [7,] 8300 0.060 rather than : Dataset$abs - with(Dataset, ave(ratio, LEAID, FUN=function(x)abs(x-median(x This is less code and more natural (to me anyway) e.g. it doesn't require use of function() or ave(). data.table knows that if the j expression returns a vector it should silently repeat the groups to match the length of the j result (which it is doing here). If the j expression returns a scalar you would just get 2 rows in this example. Note that the 'by' expression must evaluation to integer, or a list of integer vectors, so in this case LEAID must either be integer already or coerced to integer using by=as.integer(LEAID). To give the aggregate expression a name, just wrap with the DT function. This is also how to return multiple aggregate functions from each subset (some may return vectors, others may return vectors) by listing them inside DT() : Dataset[,DT(ratio,scaled=abs(ratio-median(ratio)),sum=sum(ratio)),by=LEAID] LEAID ratioscaled sum [1,] 6307 0.720 0.0911905 3.262381 [2,] 6307 0.7623810 0.0488095 3.262381 [3,] 6307 0.860 0.0488095 3.262381 [4,] 6307 0.920 0.1088095 3.262381 [5,] 8300 0.5678462 0.2021538 2.167846 [6,] 8300 0.770 0.000 2.167846 [7,] 8300 0.830 0.060 2.167846 William Dunlap wdun...@tibco.com wrote in message news:77eb52c6dd32ba4d87471dcd70c8d7000243c...@na-pa-vbe03.na.tibco.com... -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of L.A. Sent:
[R] Data Frame Transpose
Hi,
forests - read.csv(C:\\Down2\\R_forestmgt\\forest_cut-Age.csv)
m - forests
fn - function(x) {
y - t(x[,2])
data.frame( Croptype=x[1,1], Period =x[1,2], name=colnames(x)[2],
x01=y[,1])x01=y[,1], x02=y[,2], x03=y[,3] } ---Problem
here
m - do.call( rbind, lapply(split(m,list(m$Period,m$Croptype)),fn) )
m - m[order(m$Period,m$Croptype),]
I think I having a problem in here: x01=y[,1])x01=y[,1], x02=y[,2],
x03=y[,3]. how to address with my data. I have variable Period.
based on this http://www.mail-archive.com/r-h...@stat.math.ethz.ch/msg09264.html
P_ID Croptype Period Ini_Age Area_Cut
83 SORI1 31 528.2465512
84 SORI1 32 74.55179899
85 SORI1 33 72.45778618
86 SORI1 34 139.5272947
82 SORI2 28 1.711642933
83 SORI2 29 2.50071
84 SORI2 30 432.5139327
93 ORM2 35 316.8422545
62 OTRM3 30 64.60526438
82 SORI3 27 26.93674606
3 SORM3 35 223.3658345
82 SORI4 26 2.50071
4 SORM4 34 1008.643
5 OTRI5 25 32.42603214
5 OTRM5 29 65.9031344
5 SORM5 32 223.1489321
5 SORM5 33 72.59203041
5 SORM5 35 222.8402746
6 OTRI6 22 2.49851
6 OTRI6 23 3.374626509
6 OTRI6 24 96.13462257
6 OTRM6 26 830.7463641
6 OTRM6 27 731.6228643
6 OTRM6 28 16.3519762
7 OTRM7 26 1636.5693
8 OTRM8 26 553.0050146
9 OTRM9 26 894.414033
10 OTRM10 24 38.72597099
10 OTRM10 25 308.6452707
10 OTRM10 26 786.1761969
10 SORM10 31 235.8360136
To this.
P_ID Croptype P1P2P3P4 P5P6P7
P8P9P10
83 SORI31
84 SORI32
85 SORI33
86 SORI34
82 SORI28
83 SORI29
84 SORI30
93 SORM35
62 OTRM30
82 SORI27
3 SORM35
82 SORI26
4 SORM34
5 OTRI25
5 OTRM29
5 SORM32
5 SORM33
5 SORM35
6 OTRI22
6 OTRI23
6 OTRI24
6 OTRM26
6 OTRM27
6 OTRM28
7 OTRM26
8 OTRM26
9 OTRM
Thanks in advance. Noli
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[R] Is the Intercept Term always in First Position?
Dear All, I have a question about formulas and model.matrix(). If one specifies a model via a formula, the corresponding design matrix can be obtained with the model.matrix() function. For example: x1 - c(1,4,2,3,5) x2 - c(1,1,2,2,2) myformula - ~ x1 + factor(x2) model.matrix(myformula) My question is: If an intercept term is in the model (like in the example above), is it always the first column in resulting design matrix? For example, if I add the intercept explicitly as the last term in the formula, it still ends up in the first column: myformula - ~ x1 + factor(x2) + 1 model.matrix(myformula) So, is this always true or is it in principle possible that the intercept column ends up somewhere else? Best, -- Wolfgang Viechtbauerhttp://www.wvbauer.com/ Department of Methodology and StatisticsTel: +31 (0)43 388-2277 School for Public Health and Primary Care Office Location: Maastricht University, P.O. Box 616 Room B2.01 (second floor) 6200 MD Maastricht, The Netherlands Debyeplein 1 (Randwyck) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Interception point between two lines
Dear All, Let mod2 and mod3 are two regression equations representing two distinct lines and i'm keen to find the intreception point between these two lines and the following are part of the codes. m1 - as.matrix(rbind(coef(mod2), coef(mod3))) a - cbind(c(1,1), -m1[, 2]) b - m1[,1] c - solve(a=a,b=b) Unfortunately, there is an error message given as stated below and i don't understand what it meants for. ' Error in drop(.Call(La_dgesv, a, as.matrix(b), tol, PACKAGE = base)) : system is computationally singular: reciprocal condition number = 1.14557e-16' Could anybody advice me on this matter? Thank you Fir __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Interception point between two lines
On 05.01.2010 14:37, FMH wrote: Dear All, Let mod2 and mod3 are two regression equations representing two distinct lines and i'm keen to find the intreception point between these two lines and the following are part of the codes. m1- as.matrix(rbind(coef(mod2), coef(mod3))) a- cbind(c(1,1), -m1[, 2]) b- m1[,1] c- solve(a=a,b=b) Unfortunately, there is an error message given as stated below and i don't understand what it meants for. ' Error in drop(.Call(La_dgesv, a, as.matrix(b), tol, PACKAGE = base)) : system is computationally singular: reciprocal condition number = 1.14557e-16' Could anybody advice me on this matter? Yes, you cannot compute the intersection if it is (numerically) non existant, i.e. coef(mod2), coef(mod3) are almost linear dependent and the regression lines are almost parallel. Uwe Ligges Thank you Fir __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Align two protein sequences using BLAST
Dear R users, I would like to align two protein sequences using BLAST (bl2seq). The question is whether this programm have been implemented in R. Thank you for your help, Alla. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 matching lat/lon pairs from two datasets?
Or if there is a requirement for speed or shorter more convenient syntax
then there is a data.table join.
Basically setkey(data1,V1,V2) and setkey(data2,V1,V2), then data1[data2]
does the merge very quickly. You probably then want to do something with the
merged data set, which you just add in like this data1[data2,something]
or like this data1[data2][,something]. The columns in the key need to
be either integers, or factors (which are internally integer), so it would
be a bit of extra work in this case to store the lat/lon as integer, if
multiplying by 100 is ok. Another option for you anyway.
jim holtman jholt...@gmail.com wrote in message
news:644e1f321001041828n2f2a160etd597ba7a8bf76...@mail.gmail.com...
couple of approaches:
merge(data1, data2, by.x=c(V1, V2), by.y=c(V2, V1))
V1 V2 V3
1 47.82 -123.75 11
2 47.82 -123.76 8
library(sqldf)
sqldf(select * from data2 x2, data1 x1 where x2.V1=x1.V2 and
x2.V2=x1.V1)
V1V2 V3 V1V2
1 -123.76 47.82 8 -123.76 47.82
2 -123.75 47.82 11 -123.75 47.82
On Mon, Jan 4, 2010 at 7:37 PM, Douglas M. Hultstrand
dmhul...@metstat.comwrote:
Hello,
I am trying to match lat/lon from one dataset with the lat/lon from a
second dataset and use that rows data for calculations. I am using
match,
but this is finding the first match and not comparing the pair, how can I
determine if the lat/lon are the same? See example below. Is there a
better way to determine to a matching pair of lat/lon values?
Example Datasets:
data2
V1V2 V3
1 -123.76 47.82 8
2 -123.75 47.82 11
data[1:2]
V1 V2
1 47.82 -123.76
2 47.82 -123.75
3 47.82 -123.74
4 47.82 -123.73
#Subset of current R code :
lat - data$V1
lon - data$V2
yrs - c(1,2,5,10,25,50,100,200,500,1000)
lon2 - data2$V1
lat2 - data2$V2
ppt2 - data2$V3
for(i in 1:length(lat2)) {
loc - match(lat2[i],lat)
loc2 - match(lon2[i], lon)
print(loc); print(loc2)
#Need to test to make sure loc equals loc2
freq_ppt -
c(data[i,4],data[i,6],data[i,8],data[i,10],data[i,12],data[i,14],data[i,16],data[i,18],data[i,20],data[i,22])
print(freq_ppt)
return_value - approx(freq_ppt,yrs,xout=data2[i,3])
print(return_value)
}
Thanks for your help,
Doug
--
-
Douglas M. Hultstrand, MS
Senior Hydrometeorologist
Metstat, Inc. Windsor, Colorado
voice: 970.686.1253
email: dmhul...@metstat.com
web: http://www.metstat.com
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
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[R] Data replacement
Dear all, I have a question and need your help. I have a dataset that looks like this: data idcode1code2 1 114 2 123 3 244 4 315 5 324 6 411 7 434 8 643 9 622 10752 11114 12132 13344 14414 15432 16511 17543 18714 19723 20811 I want to change some numbers in the columns of “code1” and “code2” based on “indx” as below indx [[1]] code 1 1 2 3 3 4 4 6 5 8 [[2]] code 1 1 2 2 3 4 4 6 For example, for the first ten records (rows) of my dataset, I want to change 2 to 3, 3 to 4, 4 to 6, and 5 to 8 in both “code1” and “code2”, while for the last ten records, I want to change 3 to 4 and 4 to 6. Can anybody please help how to get this done? Thanks a lot in advance Lisa -- View this message in context: http://n4.nabble.com/Data-replacement-tp999060p999060.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] Is the Intercept Term always in First Position?
On Tue, 5 Jan 2010, Viechtbauer Wolfgang (STAT) wrote: Dear All, I have a question about formulas and model.matrix(). If one specifies a model via a formula, the corresponding design matrix can be obtained with the model.matrix() function. For example: x1 - c(1,4,2,3,5) x2 - c(1,1,2,2,2) myformula - ~ x1 + factor(x2) model.matrix(myformula) My question is: If an intercept term is in the model (like in the example above), is it always the first column in resulting design matrix? For example, if I add the intercept explicitly as the last term in the formula, it still ends up in the first column: myformula - ~ x1 + factor(x2) + 1 model.matrix(myformula) So, is this always true or is it in principle possible that the intercept column ends up somewhere else? Not in the current implementation, since terms(~ x1 + factor(x2) + 1) ~ x1 + factor(x2) + 1 attr(,variables) list(x1, factor(x2)) attr(,factors) x1 factor(x2) x1 1 0 factor(x2) 0 1 attr(,term.labels) [1] x1 factor(x2) attr(,order) [1] 1 1 attr(,intercept) [1] 1 attr(,response) [1] 0 it is the intercept attribute which controls the generation of the intercept (see ?terms.object). I can't imagine anyone wanting to change this implementation. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] solving cubic/quartic equations non-iteratively
To R-helpers, R offers the polyroot function for solving mentioned equations iteratively. However, Dr Math and Mathworld (and other places) show in detail how to solve mentioned equations non-iteratively. Do implementations for R that are non-iterative and that solve mentioned equations exists? Regards, Mads Jeppe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Align two protein sequences using BLAST
You should send this note to the biconductor mailing list rather than the R-help. As to your question, please look at the Biostrings bioconductor package. On Tue, Jan 5, 2010 at 6:09 AM, Alla Bulashevska alla.bullashev...@fdm.uni-freiburg.de wrote: Dear R users, I would like to align two protein sequences using BLAST (bl2seq). The question is whether this programm have been implemented in R. Thank you for your help, Alla. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Align two protein sequences using BLAST
On Jan 5, 2010, at 10:46 AM, Tony Chiang wrote: You should send this note to the biconductor mailing list rather than the R-help. As to your question, please look at the Biostrings bioconductor package. The BioC webpages give a link to the Gmane archive for searching. A search on blast protein sequences produced 15 hits and this one seemed to be potentially relevant: http://article.gmane.org/gmane.science.biology.informatics.conductor/26460/match=blast+protein+sequences There may be other postings in that group of fifteen with relevant material. I just wanted to get you going in the right location, which is not this list. -- David On Tue, Jan 5, 2010 at 6:09 AM, Alla Bulashevska alla.bullashev...@fdm.uni-freiburg.de wrote: Dear R users, I would like to align two protein sequences using BLAST (bl2seq). The question is whether this programm have been implemented in R. Thank you for your help, Alla. __ David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data Frame Transpose
Well, if nothing else, you have missing comma. :)
x01=y[,1]), x01=y[,1], x02=y[,2], x03=y[,3]
--
fn - function(x) {
y - t(x[,2])
data.frame( Croptype=x[1,1], Period =x[1,2],
name=colnames(x)[2],
x01=y[,1])x01=y[,1], x02=y[,2], x03=y[,3] }
---Problem
here
m - do.call( rbind,
lapply(split(m,list(m$Period,m$Croptype)),fn) )
m - m[order(m$Period,m$Croptype),]
I think I having a problem in here: x01=y[,1])x01=y[,1],
x02=y[,2],
x03=y[,3]. how to address with my data. I have variable
Period.
based on this
http://www.mail-archive.com/r-h...@stat.math.ethz.ch/msg09264.html
P_ID Croptype Period Ini_Age Area_Cut
83 SORI 1
31 528.2465512
84 SORI 1
32 74.55179899
85 SORI 1
33 72.45778618
86 SORI 1
34 139.5272947
82 SORI 2
28 1.711642933
83 SORI 2
29 2.50071
84 SORI 2
30 432.5139327
93 ORM 2
35 316.8422545
62 OTRM 3
30 64.60526438
82 SORI 3
27 26.93674606
3 SORM 3
35 223.3658345
82 SORI 4
26 2.50071
4 SORM 4
34 1008.643
5 OTRI 5
25 32.42603214
5 OTRM 5
29 65.9031344
5 SORM 5
32 223.1489321
5 SORM 5
33 72.59203041
5 SORM 5
35 222.8402746
6 OTRI 6
22 2.49851
6 OTRI 6
23 3.374626509
6 OTRI 6
24 96.13462257
6 OTRM 6
26 830.7463641
6 OTRM 6
27 731.6228643
6 OTRM 6
28 16.3519762
7 OTRM 7
26 1636.5693
8 OTRM 8
26 553.0050146
9 OTRM 9
26 894.414033
10 OTRM 10
24 38.72597099
10 OTRM 10
25 308.6452707
10 OTRM 10
26 786.1761969
10 SORM 10
31 235.8360136
To this.
P_ID Croptype P1 P2
P3 P4
P5 P6
P7
P8 P9
P10
83 SORI 31
84 SORI 32
85 SORI 33
86 SORI 34
82 SORI
28
83 SORI
29
84 SORI
30
93 SORM
35
62 OTRM
30
82 SORI
27
3 SORM
35
82 SORI
26
4 SORM
34
5 OTRI
25
5 OTRM
29
5 SORM
32
5 SORM
33
5 SORM
35
6 OTRI
22
6 OTRI
23
6 OTRI
24
6 OTRM
26
6 OTRM
27
6 OTRM
28
7 OTRM
26
8 OTRM
26
9 OTRM
Thanks in advance. Noli
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] solving cubic/quartic equations non-iteratively
There are certainly formulas for solving polynomials numerically up to 4th degree non-iteratively, but you will almost certainly get better results using iterative methods. Even the much more trivial formula for the 2nd degree (quadratic) is tricky to implement correctly and accurately, see: * George Forsythe, How do you solve a quadratic equation? * Yves Nievergelt, How (Not) to Solve Quadratic Equations Hope this helps. -s On Tue, Jan 5, 2010 at 10:11 AM, Mads Jeppe Tarp-Johansen s02m...@math.ku.dk wrote: To R-helpers, R offers the polyroot function for solving mentioned equations iteratively. However, Dr Math and Mathworld (and other places) show in detail how to solve mentioned equations non-iteratively. Do implementations for R that are non-iterative and that solve mentioned equations exists? Regards, Mads Jeppe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] solving cubic/quartic equations non-iteratively
Mads Jeppe Tarp-Johansen wrote: To R-helpers, R offers the polyroot function for solving mentioned equations iteratively. However, Dr Math and Mathworld (and other places) show in detail how to solve mentioned equations non-iteratively. Do implementations for R that are non-iterative and that solve mentioned equations exists? As far as I know, we don't even have the quadratic... They can't be hard to implement, though. However, you may need to take care that non-iterative solutions are not necessarily more precise or even faster than iterative ones. There may be cancellation issues and the closed-form expressions can be complicated and involve slow function calls. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bar plots with stacked and grouped (juxtaposed) bars together
I have the feeling that you can do this with ggplot2 but why? You are likely to be much better off using a dotchart. ?dotchart --- On Mon, 1/4/10, Elmer Wix elmer.cabekaziruronometu@gmail.com wrote: From: Elmer Wix elmer.cabekaziruronometu@gmail.com Subject: [R] Bar plots with stacked and grouped (juxtaposed) bars together To: r-help@r-project.org Received: Monday, January 4, 2010, 10:00 PM Using barplot, I can generate stacked bars if I pass beside=FALSE. I can generate grouped (juxtaposed) bars if I pass beside=TRUE. How can I generate stacked and grouped bars together? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] solving cubic/quartic equations non-iteratively
standard square root computation requires an iteration. Spencer Peter Dalgaard wrote: Mads Jeppe Tarp-Johansen wrote: To R-helpers, R offers the polyroot function for solving mentioned equations iteratively. However, Dr Math and Mathworld (and other places) show in detail how to solve mentioned equations non-iteratively. Do implementations for R that are non-iterative and that solve mentioned equations exists? As far as I know, we don't even have the quadratic... They can't be hard to implement, though. However, you may need to take care that non-iterative solutions are not necessarily more precise or even faster than iterative ones. There may be cancellation issues and the closed-form expressions can be complicated and involve slow function calls. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] The output of script is hidden in console
Hi everyone, I execute a script with source(filename) The script has effect but i don't see the output on console screen.Why? I'm a newbie. Thanks :handshake: -- View this message in context: http://n4.nabble.com/The-output-of-script-is-hidden-in-console-tp999095p999095.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 session in Compstat' 2010
Dear members of the R user community, I am pleased to inform you that the Compstat'2010 conference (19th conference on Computational statistics) will take place in Paris from the 22 to the 27th of august. An R session can be organized during this conference. People have to submit a full paper before the 10th of January or a single abstract before 23rd of May (you can indicate that you want to be in the R session). For more information, you can visit the website : http://www.compstat2010.fr/ Francois Husson __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] The output of script is hidden in console
There are probably numerous ways, but one is to add print() to the functions that you wish to display in the console. For example, in your source file, Instead of summary(x) try print(summary(x)) This should do the trick. Tom Fletcher -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of vtvdung Sent: Tuesday, January 05, 2010 9:42 AM To: r-help@r-project.org Subject: [R] The output of script is hidden in console Hi everyone, I execute a script with source(filename) The script has effect but i don't see the output on console screen.Why? I'm a newbie. Thanks :handshake: -- View this message in context: http://n4.nabble.com/The-output-of-script-is-hidden-in-console-tp999095p 999095.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data replacement
Lisa wrote: I have a dataset that looks like this: data idcode1code2 1 114 2 123 3 244 .. I want to change some numbers in the columns of “code1” and “code2” based on “indx” as below indx [[1]] code 1 1 2 3 3 4 For example, for the first ten records (rows) of my dataset, I want to change 2 to 3, 3 to 4, 4 to 6, and 5 to 8 in both “code1” and “code2”, while for the last ten records, I want to change 3 to 4 and 4 to 6. You might check for recode, for example in package car, or for transform. You could also do it the quick and dirty way, good to learn indexing. Be careful if you have NA in your data, or data out of the recode range. Dieter data = data.frame(code1=sample(1:5,10,TRUE),code2=sample(1:5,10,TRUE)) data = rbind(data,data.frame(code1=sample(1:4,10,TRUE),code2=sample(1:4,10,TRUE))) # The recode table as in your example #indx = list(data.frame(code=c(1,3,4,6,8)),data.frame(code=c(1,2,4,6))) #easier to read recode1 = c(1,3,4,6,8) recode2 = c(1,2,4,6) data$code1T[1:10] = recode1[data$code1[1:10]] data$code2T[1:10] = recode1[data$code2[1:10]] data$code1T[11:20] = recode2[data$code1[11:20]] data$code2T[11:20] = recode2[data$code2[11:20]] -- View this message in context: http://n4.nabble.com/Data-replacement-tp999060p999176.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] Negative binomial
On Jan 5, 2010, at 9:38 AM, Stefani Mallia wrote: Hi, I'm trying to fit a glm with a negative binomial error distribution and a log link, using the example found in the paper Stochastic Claims Reserving In General Insurance by England and Verrall. I am attaching a pdf since it is more difficult to write equations in here. So to hopefully explain myself better I wrote a pdf, where I'm explaining what I need to do and where I got stuck. (I tried to be clear as possible). In your attachment you suggest (I think) that the ordering of levels of the dev factor may be the problem. The methods of rearranging those levels in R has always been a bit of a mystery to me, but you may get useful information with: levels(mack$dev) and you may need to do something like: mack$dev - relevel(mack$dev, ref=dev1) Thanks in advance for any help Stefani Microsoft Word - Negative Binomial.pdf David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Negative binomial
On Jan 5, 2010, at 12:20 PM, David Winsemius wrote: On Jan 5, 2010, at 9:38 AM, Stefani Mallia wrote: Hi, I'm trying to fit a glm with a negative binomial error distribution and a log link, using the example found in the paper Stochastic Claims Reserving In General Insurance by England and Verrall. I am attaching a pdf since it is more difficult to write equations in here. So to hopefully explain myself better I wrote a pdf, where I'm explaining what I need to do and where I got stuck. (I tried to be clear as possible). In your attachment you suggest (I think) that the ordering of levels of the dev factor may be the problem. The methods of rearranging those levels in R has always been a bit of a mystery to me, but you may get useful information with: levels(mack$dev) and you may need to do something like: mack$dev - relevel(mack$dev, ref=dev1) Actually that is probably wrong, since I was reading the level label off the output of the model which is not how htat factor is constructed. So it is more likely to work correctly with: mack$dev - relevel(mack$dev, ref=1) # still untested -- David Thanks in advance for any help Stefani Microsoft Word - Negative Binomial.pdf David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] mean for subset
Hello, does anyone know how to take the mean for a subset of observations? For example, suppose my data looks like this: OBS NAME SCORE 1 Tom 92 2 Tom 88 3 Tom 56 4 James85 5 James75 6 James32 7 Dawn 56 8 Dawn 91 9 Clara 95 10Clara 84 Is there a way to get the mean of the SCORE variable by NAME but only when the number of observations is equal to 3? In other words, is there a way to get the mean of the SCORE variable for Tom and James, but not for Dawn and Clara? Thank you. -- Geoffrey Smith Visiting Assistant Professor Department of Finance W. P. Carey School of Business Arizona 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.
Re: [R] mean for subset
Have a look at this post and the rest of that thread: https://stat.ethz.ch/pipermail/r-help/2010-January/223420.html On Tue, Jan 5, 2010 at 1:29 PM, Geoffrey Smith g...@asu.edu wrote: Hello, does anyone know how to take the mean for a subset of observations? For example, suppose my data looks like this: OBS NAME SCORE 1 Tom 92 2 Tom 88 3 Tom 56 4 James 85 5 James 75 6 James 32 7 Dawn 56 8 Dawn 91 9 Clara 95 10 Clara 84 Is there a way to get the mean of the SCORE variable by NAME but only when the number of observations is equal to 3? In other words, is there a way to get the mean of the SCORE variable for Tom and James, but not for Dawn and Clara? Thank you. -- Geoffrey Smith Visiting Assistant Professor Department of Finance W. P. Carey School of Business Arizona 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] mean for subset
On 05/01/2010 1:29 PM, Geoffrey Smith wrote: Hello, does anyone know how to take the mean for a subset of observations? For example, suppose my data looks like this: OBS NAME SCORE 1 Tom 92 2 Tom 88 3 Tom 56 4 James85 5 James75 6 James32 7 Dawn 56 8 Dawn 91 9 Clara 95 10Clara 84 Is there a way to get the mean of the SCORE variable by NAME but only when the number of observations is equal to 3? In other words, is there a way to get the mean of the SCORE variable for Tom and James, but not for Dawn and Clara? Thank you. You probably want to do it in two steps: first, find which names have 3 observations, and take that subset of the dataset; then do the mean on all groups. This is one way: counts - table(dataset$NAME) keep - names(counts)[counts == 3] subset - dataset[ dataset$NAME %in% keep,] tapply(subset$SCORE, subset$NAME, mean) Clara DawnJames Tom NA NA 64.0 78.7 Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] mean for subset
On Tue, 5 Jan 2010, Geoffrey Smith wrote: Hello, does anyone know how to take the mean for a subset of observations? For example, suppose my data looks like this: OBS NAME SCORE 1 Tom 92 2 Tom 88 3 Tom 56 4 James85 5 James75 6 James32 7 Dawn 56 8 Dawn 91 9 Clara 95 10Clara 84 Is there a way to get the mean of the SCORE variable by NAME but only when the number of observations is equal to 3? In other words, is there a way to get the mean of the SCORE variable for Tom and James, but not for Dawn and Clara? Thank you. You can use tapply() together with a custom function that returns NA if the condition is not satisfied, e.g. ## read data dat - read.table(textConnection( OBS NAME SCORE 1 Tom 92 2 Tom 88 3 Tom 56 4 James85 5 James75 6 James32 7 Dawn 56 8 Dawn 91 9 Clara 95 10Clara 84 ), header = TRUE) ## use tapply() with custom function with(dat, tapply(SCORE, NAME, function(x) if(length(x) == 3) mean(x) else NA) ) Alternatively you could look at mymean - with(dat, tapply(SCORE, NAME, mean)) mylength - with(dat, tapply(SCORE, NAME, length)) mymean[mylength == 3] etc. hth, Z -- Geoffrey Smith Visiting Assistant Professor Department of Finance W. P. Carey School of Business Arizona 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Weigths in lm and kruskal_test
Is it correct that the weights argument in lm and kruskal_test from package coin have different meanings? Example: library(coin) set.seed(29) x - gl(3, 10) y - rnorm(length(x), mean = c(0, 0, 1)[x]) d - data.frame(y = y, x = x) w - rep(2, nrow(d)) ### double each obs ### all the same kruskal_test(y ~ x, data = rbind(d, d)) kruskal_test(y ~ x, data = d[rep(1:nrow(d), w),]) kruskal_test(y ~ x, data = d, weights = ~ w) anova(lm(y ~ x, data = d[rep(1:nrow(d), w),])) anova(lm(y ~ x, data = d, weights = w)) -- Armin Goralczyk -- http://www.gwdg.de/~agoralc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] mean for subset
Here is the solution using sqldf which can do it in one statement: # read in data Lines - OBS NAME SCORE + 1 Tom 92 + 2 Tom 88 + 3 Tom 56 + 4 James85 + 5 James75 + 6 James32 + 7 Dawn 56 + 8 Dawn 91 + 9 Clara 95 + 10Clara 84 DF - read.table(textConnection(Lines), header = TRUE) # run library(sqldf) sqldf(select NAME, avg(SCORE) from DF group by NAME having count(*) = 3) NAME avg(SCORE) 1 James 64.0 2 Tom 78.7 On Tue, Jan 5, 2010 at 2:03 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Have a look at this post and the rest of that thread: https://stat.ethz.ch/pipermail/r-help/2010-January/223420.html On Tue, Jan 5, 2010 at 1:29 PM, Geoffrey Smith g...@asu.edu wrote: Hello, does anyone know how to take the mean for a subset of observations? For example, suppose my data looks like this: OBS NAME SCORE 1 Tom 92 2 Tom 88 3 Tom 56 4 James 85 5 James 75 6 James 32 7 Dawn 56 8 Dawn 91 9 Clara 95 10 Clara 84 Is there a way to get the mean of the SCORE variable by NAME but only when the number of observations is equal to 3? In other words, is there a way to get the mean of the SCORE variable for Tom and James, but not for Dawn and Clara? Thank you. -- Geoffrey Smith Visiting Assistant Professor Department of Finance W. P. Carey School of Business Arizona 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] mean for subset
Try this: with(split(DF, with(DF, ave(SCORE, NAME, FUN = length)))[['3']], tapply(SCORE, NAME[,drop = TRUE], FUN = mean)) Or: with(DF, tapply(SCORE, NAME, mean))[table(DF$NAME) == 3] On Tue, Jan 5, 2010 at 4:29 PM, Geoffrey Smith g...@asu.edu wrote: Hello, does anyone know how to take the mean for a subset of observations? For example, suppose my data looks like this: OBS NAME SCORE 1 Tom 92 2 Tom 88 3 Tom 56 4 James 85 5 James 75 6 James 32 7 Dawn 56 8 Dawn 91 9 Clara 95 10 Clara 84 Is there a way to get the mean of the SCORE variable by NAME but only when the number of observations is equal to 3? In other words, is there a way to get the mean of the SCORE variable for Tom and James, but not for Dawn and Clara? Thank you. -- Geoffrey Smith Visiting Assistant Professor Department of Finance W. P. Carey School of Business Arizona 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] variable three dimensional array
I am using R for my bioinformatics research. I am dealing with a graph in
which I need to find all possible path. I was looking for some package that
solve my purpose
but all in vain. There are available algorithms but most of them find
shortest path that ignore other paths So I decided to write my own from
scratch.
I need to create a two dimensional matrix of size nXn.
The element of each entry may contain (node,edge) pair in the form of
bit-vector.
eg. (mat is the matrix)
mat[1,1] = NULL
mat[1,2] = {1, 1100} #first entry is node vector and second
entry is edge vector
mat[1,3] = {{01000, 01001000}, {00100, 0110}} #Here there are two
node-edge pair. There can be more also, so it is variable.
In other sense it can be said that, the matrix is a 3-d matrix with a
variable third dimension.
I tried the problem with list but I was partially succesful.
Any suggestion in this regard will be highly appreciated.
thanks
---Fahim
Louisville, KY, USA
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[R] Usage of weights in kruskal_test from package coin
With this email I will be following up on this (some months old) post: http://tolstoy.newcastle.edu.au/R/e7/help/09/06/0799.html From this I would assume that the following is also valid: set.seed(29) x - gl(3, 10) y - rnorm(length(x), mean = c(0, 0, 1)[x]) d - data.frame(y = y, x = x) # w - rep(2, nrow(d)) ### double each obs w - rep(c(1,5), nrow(d)/2) kruskal_test(y ~ x, data = d[rep(1:nrow(d), w),]) # should be the same as kruskal_test(y ~ x, data = d, weights = ~ w) But the tests are not the same. Am I wrong somewhere here? -- Armin Goralczyk -- http://www.gwdg.de/~agoralc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Unwanted association between a function and a namespace
On Thu, 24-Dec-2009 at 02:14PM +1300, Patrick Connolly wrote:
ly way I found to get round the problem was to make an
| additional function Summarize in the same place. It involves editing
| any old scripts/functions before they work, but work they do.
In case anyone was following this thread, I solved the problem by
overwriting the summarize function with the Summarize function.
summarize - Summarize
Then copied that to the appropriate directory. Now all my previous
code still works unmodified. End of problem -- though I'm still
mystified as to how it arose in the first place.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) . Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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Re: [R] The output of script is hidden in console
R FAQ 7.16. R Newbies should read this first (+the FAQ for Windows, if appropriate) _before_ posting questions to the list. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tom Fletcher Sent: Tuesday, January 05, 2010 9:15 AM To: vtvdung; r-help@r-project.org Subject: Re: [R] The output of script is hidden in console There are probably numerous ways, but one is to add print() to the functions that you wish to display in the console. For example, in your source file, Instead of summary(x) try print(summary(x)) This should do the trick. Tom Fletcher -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of vtvdung Sent: Tuesday, January 05, 2010 9:42 AM To: r-help@r-project.org Subject: [R] The output of script is hidden in console Hi everyone, I execute a script with source(filename) The script has effect but i don't see the output on console screen.Why? I'm a newbie. Thanks :handshake: -- View this message in context: http://n4.nabble.com/The-output-of-script-is-hidden-in-console-tp999095p 999095.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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Naming functions for the purpose of profiling
Hi all, I have some long-running code that I'm trying to profile. I am seeing a lot of time spent inside the Anonymous function. Of course, this can in fact be any of several functions, but I am unable to see how I could use the information from Rprof.out to discern which function is taking the most time. An example line from my Rprof.out is: rbernoulli Anonymous runOneRound FUN lapply sfLapply doTryCatch tryCatchOne tryCatchList tryCatch try eval.with.vis eval.with.vis source In my case, the Anonymous functions seem to be any of several work-horse functions, that are part of a list, and different cases are dispatched to different functions. I could of course get them all out of the list and rewrite the dispatch code, but that does not seem like a neat way do address this. So I am wondering if there is any way to explicitly set the name of a function in a way that leads to it being picked up by the profiler? The same problem seems to apply to Anonymous functions that are generated on the fly in an apply call or elsewhere. Of course, having source files and line numbers included in the profiling output would solve this issue, but it seems to me that R probably does not have any awareness of where a function was written down (and of course, even the text of a function can be constructed dynamically within a program). So I guess that is not a viable approach. Thanks in advance for any help on this, and any pointers on the best references for advanced profiling issues would be appreciated as well (I know of summaryRprof of course, but it can be difficult to get the full picture from the summaryRprof output if the calling structure is complicated). Best, Magnus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data replacement
Thank you for your kind help. Your R script works well. Lisa Dieter Menne wrote: Lisa wrote: I have a dataset that looks like this: data idcode1code2 1 114 2 123 3 244 .. I want to change some numbers in the columns of “code1” and “code2” based on “indx” as below indx [[1]] code 1 1 2 3 3 4 For example, for the first ten records (rows) of my dataset, I want to change 2 to 3, 3 to 4, 4 to 6, and 5 to 8 in both “code1” and “code2”, while for the last ten records, I want to change 3 to 4 and 4 to 6. You might check for recode, for example in package car, or for transform. You could also do it the quick and dirty way, good to learn indexing. Be careful if you have NA in your data, or data out of the recode range. Dieter data = data.frame(code1=sample(1:5,10,TRUE),code2=sample(1:5,10,TRUE)) data = rbind(data,data.frame(code1=sample(1:4,10,TRUE),code2=sample(1:4,10,TRUE))) # The recode table as in your example #indx = list(data.frame(code=c(1,3,4,6,8)),data.frame(code=c(1,2,4,6))) #easier to read recode1 = c(1,3,4,6,8) recode2 = c(1,2,4,6) data$code1T[1:10] = recode1[data$code1[1:10]] data$code2T[1:10] = recode1[data$code2[1:10]] data$code1T[11:20] = recode2[data$code1[11:20]] data$code2T[11:20] = recode2[data$code2[11:20]] -- View this message in context: http://n4.nabble.com/Data-replacement-tp999060p999342.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] Multivariate Poisson GLM??
Dear R Users, I'm working on a problem where I have a multivariate response vector of counts and a continuous predictor. I've thought about doing this the same way you would do a Multvariate regression model with normally distributed data, but since these data are counts, they are probably better modeled with a Poisson distribution. For example y1-rpois(100,3.5) y2-rpois(100,1.5) y3-rpois(100,.09) x-rnorm(100, mean=25, sd=10) dat-data.frame(y1, y2, y3, x) #Get the Multivariate linear model assuming normality fit-lm(cbind(y1,y2,y3)~x, data=dat) fit.0-update(fit, ~1) #Calculate Pillai's trace for global model test anova(fit, fit.0) But, if I try this approach with glm() instead of lm(), I get the error indicating that a multivariate response vector isn't allowed in glm fit.pois-glm(cbind(y1,y2,y3)~x, data=dat, family=poisson) Error: (subscript) logical subscript too long If anyone has experience with a multivariate Poisson response vector I would gladly appreciate any suggestions. Corey Sparks -- Corey Sparks Assistant Professor Department of Demography and Organization Studies University of Texas at San Antonio 501 West Durango Blvd Monterey Building 2.270C San Antonio, TX 78207 210-458-3166 corey.sparks 'at' utsa.edu https://rowdyspace.utsa.edu/users/ozd504/www/index.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] why is object.size is more for constant numeric vector?
Hi All, I ran the following lines in R: print(object.size(a - rep(1,10^6)),units=Mb) print(object.size(a - rep(3.542,10^6)),units=Mb) print(object.size(b - rep(x,10^6)),units=Mb) print(object.size(b - rep(xyzxyz xyz,10^6)),units=Mb) print(object.size(b - 1:10^6),units=Mb) print(object.size(b - rep(1:10,each=10^5)),units=Mb) print(object.size(b - rep(TRUE,10^6)),units=Mb) The object size from first two lines is 7.6 MB, but from the last five it is 3.8 MB, although the length of vector is same. Apparently, the size of any vector of a given length is twice if the vector is numeric constant than if it is not. Why is it so? Is my observation wrong? Or, is there some catch with 'object.size'? Thanks in advance. Regards Utkarsh [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] why is object.size is more for constant numeric vector?
Note this: class(rep(1, 3)) [1] numeric class(1:3) [1] integer On Tue, Jan 5, 2010 at 3:16 PM, Utkarsh Singhal utkarsh@gmail.com wrote: Hi All, I ran the following lines in R: print(object.size(a - rep(1,10^6)),units=Mb) print(object.size(a - rep(3.542,10^6)),units=Mb) print(object.size(b - rep(x,10^6)),units=Mb) print(object.size(b - rep(xyzxyz xyz,10^6)),units=Mb) print(object.size(b - 1:10^6),units=Mb) print(object.size(b - rep(1:10,each=10^5)),units=Mb) print(object.size(b - rep(TRUE,10^6)),units=Mb) The object size from first two lines is 7.6 MB, but from the last five it is 3.8 MB, although the length of vector is same. Apparently, the size of any vector of a given length is twice if the vector is numeric constant than if it is not. Why is it so? Is my observation wrong? Or, is there some catch with 'object.size'? Thanks in advance. Regards Utkarsh [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] solving cubic/quartic equations non-iteratively
quote: There are certainly formulas for solving polynomials numerically up to 4th degree non-iteratively, but you will almost certainly get better results using iterative methods. endquote I must be missing something here. Why not use the analytic formulas for polynomials below 5th degree? Once you do so, your answer is as precise as the level of precision you enter for the coefficients. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] bootstrapping a matrix and calculating Pearson's correlation coefficient
Hi All, I have got matrix 'data' of dimension 22000x600. I want to make 50 independent samples of dimension 22000x300 from the original matrix 'data'. And then want to calculate pearsons CC for each of the obtained 50 matrices. It seems it is possible to do this using 'boot' function from library boot but I am not able to figure out how? I am really stuck. Please help! Best Lee [[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] model simplification using Crawley as a guide
So here is some information that I hope gets criticized by the higher-intelligences that posted on this topic. Beware that I'm not a statistician and I'm just saying about what I think is correct. First, before fitting any model, check the distribution of your data, in some cases a simple anova is way better than a very complicated model, after you tried some data transformations or simply realizing that you can't fit the model because it has a unique distribution then you might consider more complicates options such as general linear models or mixed models, in that case Hadley's information comes handy, check your residuals, plot your models and see what kind of insight you get from it, this way you can move to more complicated models. After you find a model that fits your data then you can start thinking about simplifying it. Crawley's approach of simplifying your model by dropping the non-significant interactions has been slammed here but quite honestly it is still used (I'm not saying it is correct though) and I don't see how drop1 from Peter Dalgaard is much better (again I'm not saying that it isn't but I just lack the knowledge to explain the benefits). Ben Bolker et al wrote a very good paper on how to make model simplication (check Trends in Ecology Evolution 24:3). At least in ecology AIC seems to be the most used methodology for model simplication. Meaning that people simplify their overparameterized models (with all co-variables they could get) just looking at AIC and then report the p-values. How is that any different from a stepwise approach I don't know and probably that is the reason why Crawley's approach is heavily criticized. Often times people mix the AIC approach with the traditional frequentist approach (p values). If I get it right from the workshop that I took with David Anderson this approach is considered to be wrong and if you decide to simplify your models based on AIC then you should use model averaging instead of just reporting what was significant. My impression is that you are usually better off using a simple analysis that you understand what is going on have enough scientific background to support your statistical inference than using a super elaborated model with lots of variables and fancy stats that you don't master all the shortcomings of analysis. Sometimes less is more, but hey studying harder (especially stats) can pay off (better publications). PS: I wish there was a book on Ecological Experiments (I am sure there is) explaining more modern approaches to analyze factorial experiments, Crawley's book is a good start but it is too simplistic sometimes, I haven't seen Bolker's book yet so I'm not sure it cover's experiments, it certainly would be awesome if he made his course on Modeling Ecological data available on the youtube. Jim Lemon wrote: Peter Dalgaard wrote: ... That'll be anti-hist()-amine, I presume? I would think p-necillin a more appropriate treatment. 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. -- View this message in context: http://n4.nabble.com/model-simplification-using-Crawley-as-a-guide-tp858580p999459.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] zero-fill absent data
Hello, I have a set of data frames, generated by an SQL query that I am working with. Because of the way the query was written, zero values for the dependent variable (V2 in the example) are not recorded. Up until now this has not been a problem. I would like to be able to fill all absent data with 0. Current state of data (e.g.): frame-as.data.frame(cbind(c(1:2,5:7),c(0.5,0.2,1,1.6,2))) frame V1 V2 1 1 0.5 2 2 0.2 3 5 1.0 4 6 1.6 5 7 2.0 So that frame returns: V1 V2 1 1 0.5 2 2 0.2 3 3 0.0 4 4 0.0 5 5 1.0 6 6 1.6 7 7 2.0 Since absent data may be beyond the last recorded point I'd like to be able to use a terminating 0 frame-as.data.frame(cbind(c(1:2,5:7,10),c(0.5,0.2,1,1.6,2,0))) frame V1 V2 1 1 0.5 2 2 0.2 3 5 1.0 4 6 1.6 5 7 2.0 6 10 0.0 So that values 7V110 are zero filled. Can anyone suggest a method to do this? thank you for your time. Dan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] xyplot - help with multiple Y's vs. X of a member data in multiple panels
Hi.. thanks for the tips.. that variation works. How can I control pch, lty and col for each member (gp1) in the group (paste(gp2, gp3))? Regards,Santosh On Tue, Jan 5, 2010 at 2:15 AM, Felix Andrews fe...@nfrac.org wrote: You should reshape the data into a long format, and an easy way to do that is to use the 'reshape' package: library(reshape) mdat - melt(dat, measure.vars = c(y1, y2, y3)) I'm still not sure what you want in the plot. Confusingly, your last example dropped the ID you referred to earlier, and appears to use grp1 in the same role. Maybe something like this: xyplot(value ~ x | paste(gp2, gp3), mdat, groups = paste(variable, gp1), type = l, auto.key = list(lines = TRUE, columns = 3), par.settings = simpleTheme(col = 1:8, lty = rep(1:3, each = 8))) 2010/1/5 Santosh santosh2...@gmail.com: Thanks for your email.. Yes, I am looking for lattice version of matplot... Attached are some codes for simplicity for rapid testing..Any suggestions would be highly appreciated... library(lattice) dat - data.frame(x = rep(1:10,2), y1 = rnorm(20), y2=rnorm(20,sd=1.3), y3=rnorm(20,sd=0.3), gp1 = rep(letters[1:8],each=10), gp2=rep(LETTERS[1:4],each=20), gp3=rep(c(P,Q),each=40)) pset - simpleTheme(lty = c(0,1,2), col=c(blue,red,green)) xyplot(y1+y2+y3~x|factor(gp3)+factor(gp2), data=dat, groups=gp1, allow.multiple=T, panel=panel.superpose, distribute.type=T, type=c(b,l,l), par.settings=pset, strip=strip.custom(strip.names=F,strip.levels=T)) Thanks.. Santosh On Mon, Jan 4, 2010 at 11:16 PM, Dennis Murphy djmu...@gmail.com wrote: Hi: I think Santosh wants a Lattice version of matplot. I didn't find anything with help.search(), though... Dennis On Mon, Jan 4, 2010 at 8:14 PM, Santosh santosh2...@gmail.com wrote: Hi, Thanks for your email.. Each panel (in a multiple panel) is identified by DS1, DS2 DS3 in the dataset sent earlier. I would like an overlay of Y1, Y2 Y3 (each by different lines) for each ID in the group. Each ID in the group is represented by a color. Regards Thanks, Santosh On Mon, Jan 4, 2010 at 5:07 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Can you clarify how many curves you want in each panel? You have 3 Ys and your original email indicated at least 7 ID values. Do you really want 21 curves in each panel? Or do you want separate panels for the Ys? Re your code: note that, regarding a formula of the type y1 + y2 ~ x, ?xyplot says: This feature cannot be used in conjunction with the groups argument. -Peter Ehlers Santosh wrote: Hi Jim and others, I tried suggestions and somehow the graphs do not seem to be aligned on X-axis (i.e. they appear to be shifted on x-axis).. I guess panel.xyplot or panel.superpose is needed? I am not sure what the group variable be panel.xyplot, whether it is the ID or the newFactor. I tried panel.xyplot(x,y,) with group=ID and group=newFactor and it did not work. Your suggestions would be highly appreciated!! Regards, Santosh On Thu, Dec 31, 2009 at 6:59 PM, jim holtman jholt...@gmail.com wrote: I am not too sure if this is what you are after, but I just created a new factor for the panel: # create a new factor d1$newFactor - factor(paste(d1$DS1, +, d1$DS2, +, d1$DS3)) xyplot(Y1+Y2+Y3~X1|newFactor,data=d1,group=ID) On Thu, Dec 31, 2009 at 6:25 AM, Santosh santosh2...@gmail.com wrote: Dear R experts, Wish you all a HAPPY NEW YEAR! How do I go about plotting (using lattice) overlays of an ID (group=ID) observed, fitted data in each panel of a multiple panel plot (each panel identified by DS1 + DS2 + DS3)? x variable is X1 in the accompanying section of a dataset. each individual is identified by color and Y's are identified by pch or lty. I guess the code goes something like the one below, but could not get the proper use of panel functions xyplot(Y1+Y2+Y3~X1|DS1+DS2+DS3,data=d1,group=ID,...)... [[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 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
Re: [R] bootstrapping a matrix and calculating Pearson's correlation coefficient
Hello On 1/5/10, Lee William leeon...@gmail.com wrote: I have got matrix 'data' of dimension 22000x600. I want to make 50 independent samples of dimension 22000x300 from the original matrix 'data'. And then want to calculate pearsons CC for each of the obtained 50 matrices. It seems it is possible to do this using 'boot' function from library boot but I am not able to figure out how? I am really stuck. Please help! Initially consider constructing the bootstrap function on a much smaller scale, with dummy data. For a dummy example on bootstrapping, see one of my old posts [1]. Also, check this Quick-R page [2] and the links at the bottom of the page for various explanations on the procedure. Liviu [1] http://www.mail-archive.com/r-help@r-project.org/msg65667.html [2] http://www.statmethods.net/advstats/bootstrapping.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] zero-fill absent data
Tena koe Dan On approach - create a fullFrame with all your observations and merge with the frame: frame - as.data.frame(cbind(c(1:2,5:7,10),c(0.5,0.2,1,1.6,2,0))) fullFrame - as.data.frame(min(frame[,1]):max(frame[,1])) # Create fullFrame fullFrame min(frame[, 1]):max(frame[, 1]) 11 22 33 44 55 66 77 88 99 10 10 fullFrame - merge(fullFrame, frame, by=1, all.x=T) # Merge with frame fullFrame[is.na(fullFrame[,2]),2] - 0 # Replace NAs with 0s fullFrame min(frame[, 1]):max(frame[, 1]) V2 11 0.5 22 0.2 33 0.0 44 0.0 55 1.0 66 1.6 77 2.0 88 0.0 99 0.0 10 10 0.0 HTH ... Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Dan Kortschak Sent: Wednesday, 6 January 2010 11:40 a.m. To: r-help@r-project.org Subject: [R] zero-fill absent data Hello, I have a set of data frames, generated by an SQL query that I am working with. Because of the way the query was written, zero values for the dependent variable (V2 in the example) are not recorded. Up until now this has not been a problem. I would like to be able to fill all absent data with 0. Current state of data (e.g.): frame-as.data.frame(cbind(c(1:2,5:7),c(0.5,0.2,1,1.6,2))) frame V1 V2 1 1 0.5 2 2 0.2 3 5 1.0 4 6 1.6 5 7 2.0 So that frame returns: V1 V2 1 1 0.5 2 2 0.2 3 3 0.0 4 4 0.0 5 5 1.0 6 6 1.6 7 7 2.0 Since absent data may be beyond the last recorded point I'd like to be able to use a terminating 0 frame-as.data.frame(cbind(c(1:2,5:7,10),c(0.5,0.2,1,1.6,2,0))) frame V1 V2 1 1 0.5 2 2 0.2 3 5 1.0 4 6 1.6 5 7 2.0 6 10 0.0 So that values 7V110 are zero filled. Can anyone suggest a method to do this? thank you for your time. Dan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] zero-fill absent data
The zoo package's merge.zoo routines has a fill=0 argument so: create an expanded index, ix, and then in the next line create zoo objects from the data and the expanded index and merge them together. Finally in the last line convert back to a data frame. library(zoo) ix - with(frame, seq(min(V1), max(V1))) z - with(frame, merge(zoo(V2, V1), zoo(, ix), fill = 0)) data.frame(V1 = time(z), V2 = coredata(z)) On Tue, Jan 5, 2010 at 5:39 PM, Dan Kortschak dan.kortsc...@adelaide.edu.au wrote: Hello, I have a set of data frames, generated by an SQL query that I am working with. Because of the way the query was written, zero values for the dependent variable (V2 in the example) are not recorded. Up until now this has not been a problem. I would like to be able to fill all absent data with 0. Current state of data (e.g.): frame-as.data.frame(cbind(c(1:2,5:7),c(0.5,0.2,1,1.6,2))) frame V1 V2 1 1 0.5 2 2 0.2 3 5 1.0 4 6 1.6 5 7 2.0 So that frame returns: V1 V2 1 1 0.5 2 2 0.2 3 3 0.0 4 4 0.0 5 5 1.0 6 6 1.6 7 7 2.0 Since absent data may be beyond the last recorded point I'd like to be able to use a terminating 0 frame-as.data.frame(cbind(c(1:2,5:7,10),c(0.5,0.2,1,1.6,2,0))) frame V1 V2 1 1 0.5 2 2 0.2 3 5 1.0 4 6 1.6 5 7 2.0 6 10 0.0 So that values 7V110 are zero filled. Can anyone suggest a method to do this? thank you for your time. Dan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] prefixing values in a table
Hi, I have generated a table of counts, and now need to add a prefix to the counts. #count KO occurrences KO_occur = table(groupKOIDs) #where groupKOIDs is a vector of characters e.g., if groupKOIDs = c(A, A, B, A) then KO_occur would look like this: A B 3 1 and I need to add a W to the front of the counts: A B W3 W1 If anyone has ideas for me as to how to approach this, I'd be very grateful! cheers, Laura __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] xyplot: problems with column names legend
Anybody? Frustrating to be unable to solve this silly little
problem...
On Jan 3, 12:48 pm, Jay josip.2...@gmail.com wrote:
Thanks, the backtickes got the code working. However, now I cant get
it to draw the legend/key.
For example, look at this
figure:http://osiris.sunderland.ac.uk/~cs0her/Statistics/xyplot5.png
My graph is similar, but instead of 1,2,...,8 as the names of the
series I want it to say Data one (a string with spaces) and so on.
On Jan 3, 10:58 am, baptiste auguie baptiste.aug...@googlemail.com
wrote:
Hi,
Using backticks might work to some extent,
library(lattice)
`my variable` = 1:10
y=rnorm(10)
xyplot(`my variable` ~ y)
but if your data is in a data.frame the names should have been converted,
make.names('my variable')
[1] my.variable
HTH,
baptiste
2010/1/3 Jay josip.2...@gmail.com:
Hello!
one more question about xyplot. If I have data which have space in the
column names, say xyz 123. How do I create a working graph where
this text is displayed in the legend key?
Now when I try something like xyplot(xyz 123 ~ variable1, data =
mydata, ...) I get nothing.
Also, is it possible to genrate the graph with xyplot(mydata[,1] ~
variable1, data = mydata, ...) and then later in the code specify
the names that should be displayed in the legend?
Thank you!
__
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guidehttp://www.R-project.org/posting-guide.html
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listhttps://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multivariate Poisson GLM??
You could have a look at the VGAM (vector glm /gam models) at CRAN. Kjetil On Tue, Jan 5, 2010 at 5:59 PM, Corey Sparks corey.spa...@utsa.edu wrote: Dear R Users, I'm working on a problem where I have a multivariate response vector of counts and a continuous predictor. I've thought about doing this the same way you would do a Multvariate regression model with normally distributed data, but since these data are counts, they are probably better modeled with a Poisson distribution. For example y1-rpois(100,3.5) y2-rpois(100,1.5) y3-rpois(100,.09) x-rnorm(100, mean=25, sd=10) dat-data.frame(y1, y2, y3, x) #Get the Multivariate linear model assuming normality fit-lm(cbind(y1,y2,y3)~x, data=dat) fit.0-update(fit, ~1) #Calculate Pillai's trace for global model test anova(fit, fit.0) But, if I try this approach with glm() instead of lm(), I get the error indicating that a multivariate response vector isn't allowed in glm fit.pois-glm(cbind(y1,y2,y3)~x, data=dat, family=poisson) Error: (subscript) logical subscript too long If anyone has experience with a multivariate Poisson response vector I would gladly appreciate any suggestions. Corey Sparks -- Corey Sparks Assistant Professor Department of Demography and Organization Studies University of Texas at San Antonio 501 West Durango Blvd Monterey Building 2.270C San Antonio, TX 78207 210-458-3166 corey.sparks 'at' utsa.edu https://rowdyspace.utsa.edu/users/ozd504/www/index.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.
[R] Anybody can suggest a better method to build a package while ignoring some functions
Hi, Say i have three functions in a new package, a,b and c. I only want the one function a to be exported for use. b and c are not very stable. If i specify to export all the three functions in the NAMESPACE file (export(a,b,c)), no errors appeared after checking the package. And i am sure there should be no errors. But if i only export the one function a by specifying it in the NAMESPACE file(export(a)), one error appeared. See below. Error ### * checking examples ... ERROR Running examples in 's-Ex.R' failed. The error most likely occurred in: ### * b flush(stderr()); flush(stdout()) ### Name: b ### Title: Compute inverse cosine with angle given in degrees ### Aliases: ab ### Keywords: array ### ** Examples b(theta=30) Error: could not find function acos_d Execution halted Anybody knows where the problem is and how to solve this? Is there better method to obtain what i want? Thanks -- - Jane Chang Queen's [[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] chi-squared test
I would like to do a chi-squared test on the following matrix: CP-matrix(c(26,17,9,27,8,9,9,8,29,9,6,17,81,7,43,36,2,4,3,0,5,1,0,12,29,9,12,19,0,0),nrow=3) dimnames(CP) - list(c(less10,bt10and50,more50),c(T10,T9,T8,T7,T6,T5,T4,T3,T2,T1)) I want to set the expected values as 26, 17, 9 (ie. the data from T10). How do assign expected values and complete the Chi-squared test? Cheers [[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] The output of script is hidden in console
If you are using windows, In windows console. Rgui.exe filename.R -The command does not work at all. You have open Rgui.exe first, retrieve filename.R then run the script. Noli On 1/5/10, vtvdung vtvdung.in...@yahoo.com wrote: Hi everyone, I execute a script with source(filename) The script has effect but i don't see the output on console screen.Why? I'm a newbie. Thanks :handshake: __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data Frame Transpose
Hi John
Thanks for your reply. I think I was posting properly the problem.
Here are the error, R script and console errors below.
Thanks. Noli
~~~
The error:
~~
Error in data.frame(CROP_ID = x[1, 1], CROPTYPE = x[1, 2], name =
colnames(x)[4:5], :
subscript out of bounds
~~~
I have a dynamic subscripts for the Period, as result of linear
programming (LP) model run. How I generalise this line. Right now it
has 3 index only.
x01=y[,1], x02=y[,2], x03=y[,3])
This is sample the data.
PERIOD
1
1
1
1
2
2
2
2
3
3
3
4
4
5
5
5
5
5
6
6
6
6
6
6
7
8
9
10
10
10
10
R script:
harvest.dat - read.dbf('C:\\Down2\\R_forestmgt\\Carbon\\forest_cut_m.dbf')
names(harvest.dat) = c(CROP_ID, CROPTYPE, PERIOD,CUT_AGE, AREA_CUT)
# Transpose 5 columns
fn - function(x) {
y - t(x[,4:5])
data.frame( CROP_ID=x[1,1], CROPTYPE=x[1,2], name=colnames(x)[4:5],
x01=y[,1], x02=y[,2], x03=y[,3])
}
harvest.dat - do.call( rbind,
lapply(split(harvest.dat,list(harvest.dat$CROP_ID,harvest.dat$CROPTYPE)),fn)
)
write.csv(harvest.dat, forest_cut3.csv)
~
Scite console with r package
~
Rscript --vanilla --slave
C:\Down2\R_forestmgt\Carbon\ForestCarbon_1_F_Clean7_transpose.R
[1] C:/Down2/R_forestmgt/Carbon
Loading required package: foreign
Loading required package: sp
Loading required package: methods
Loading required package: lattice
Warning messages:
1: package 'maptools' was built under R version 2.10.1
2: package 'foreign' was built under R version 2.10.1
3: package 'sp' was built under R version 2.10.1
Error in data.frame(CROP_ID = x[1, 1], CROPTYPE = x[1, 2], name =
colnames(x)[4:5], :
subscript out of bounds
Calls: do.call - lapply - FUN - data.frame
Execution halted
Exit code: 1Time: 2.128
~
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Re: [R] svm
Hi, On Tue, Jan 5, 2010 at 7:01 PM, Amy Hessen amy_4_5...@hotmail.com wrote: Hi, I understand from help pages that in order to use a data set with svm, I have to divide it into two files: one for the dataset without the class label and the other file contains the class label as the following code:- This isn't exactly correct ... look at the examples in the ?svm documentation a bit closer. library(e1071) x- read.delim(mydataset_except-class-label.txt) y- read.delim(mydataset_class-labell.txt) model - svm(x, y, cross=5) summary(model) but I couldn’t understand how I add “formula” parameter to it? Does formula contain the class label too?? Using the first example in ?svm attach(iris) model - svm(Species ~ ., data = iris) The first argument in the function call is the formula. The Species column is the class label. `iris` is a data.frame ... you can see that it has the label *in it*, look at the output of head(iris) and what I have to do to use testing set when I don’t use “cross” parameter. Just follow the example in ?svm some more, you'll see training a model and then testing it on data. The example happens to be the same data the model trained on. To use new data, you'll just need a data matrix/data.frame with as many columns as your original data, and as many rows as you have observations. The first step separates the labels from the data (you can do the same in your data -- you don't have to have separate test and train files that are different -- just remove the labels from it in R): attach(iris) x - subset(iris, select = -Species) y - Species model - svm(x, y) # test with train data pred - predict(model, x) Hope that helps, -steve -- 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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] xyplot: problems with column names legend
You have not said what the problem is, i.e. what you have tried and
what you expect. Please post a small, reproducible example if you want
help.
Regards
-Felix
2010/1/6 Jay josip.2...@gmail.com:
Anybody? Frustrating to be unable to solve this silly little
problem...
On Jan 3, 12:48 pm, Jay josip.2...@gmail.com wrote:
Thanks, the backtickes got the code working. However, now I cant get
it to draw the legend/key.
For example, look at this
figure:http://osiris.sunderland.ac.uk/~cs0her/Statistics/xyplot5.png
My graph is similar, but instead of 1,2,...,8 as the names of the
series I want it to say Data one (a string with spaces) and so on.
On Jan 3, 10:58 am, baptiste auguie baptiste.aug...@googlemail.com
wrote:
Hi,
Using backticks might work to some extent,
library(lattice)
`my variable` = 1:10
y=rnorm(10)
xyplot(`my variable` ~ y)
but if your data is in a data.frame the names should have been converted,
make.names('my variable')
[1] my.variable
HTH,
baptiste
2010/1/3 Jay josip.2...@gmail.com:
Hello!
one more question about xyplot. If I have data which have space in the
column names, say xyz 123. How do I create a working graph where
this text is displayed in the legend key?
Now when I try something like xyplot(xyz 123 ~ variable1, data =
mydata, ...) I get nothing.
Also, is it possible to genrate the graph with xyplot(mydata[,1] ~
variable1, data = mydata, ...) and then later in the code specify
the names that should be displayed in the legend?
Thank you!
__
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guidehttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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listhttps://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
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--
Felix Andrews / 安福立
Postdoctoral Fellow
Integrated Catchment Assessment and Management (iCAM) Centre
Fenner School of Environment and Society [Bldg 48a]
The Australian National University
Canberra ACT 0200 Australia
M: +61 410 400 963
T: + 61 2 6125 4670
E: felix.andr...@anu.edu.au
CRICOS Provider No. 00120C
--
http://www.neurofractal.org/felix/
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Re: [R] prefixing values in a table
try this: x - c(A, A, B, A) x.t - table(x) x.t x A B 3 1 x.tw - paste(W, x.t, sep='') names(x.tw) - names(x.t) x.tw AB W3 W1 On Tue, Jan 5, 2010 at 6:38 PM, laura@utoronto.ca wrote: Hi, I have generated a table of counts, and now need to add a prefix to the counts. #count KO occurrences KO_occur = table(groupKOIDs) #where groupKOIDs is a vector of characters e.g., if groupKOIDs = c(A, A, B, A) then KO_occur would look like this: A B 3 1 and I need to add a W to the front of the counts: A B W3 W1 If anyone has ideas for me as to how to approach this, I'd be very grateful! cheers, Laura __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] chi-squared test
On Jan 5, 2010, at 8:53 PM, Xanthe Walker wrote: I would like to do a chi-squared test on the following matrix: CP- matrix (c (26,17,9,27,8,9,9,8,29,9,6,17,81,7,43,36,2,4,3,0,5,1,0,12,29,9,12,19,0,0 ),nrow=3) dimnames(CP) - list (c (less10 ,bt10and50 ,more50),c(T10,T9,T8,T7,T6,T5,T4,T3,T2,T1)) I want to set the expected values as 26, 17, 9 (ie. the data from T10). How do assign expected values and complete the Chi-squared test? You ought to look (more closely?) at the examples in chisq.test. Cheers -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] xyplot: adjusting the scale (min, max tick)
Hi, I'm terribly sorry but it seems it cannot figure this one out by myself so, please, if somebody could help I would be very grateful. So, when I plot with xyplot() I get an y-axis that is very ugly... starting from a random number and having so many ticks that it becomes unreadable. How do I tell xyplot how to draw the axis? E.g., start from 100, end at 200 with 25 units between ticks/labels? Can somebody give me an example? Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] debugging package
I am trying to debug a package to submit it to CRAN and am getting a bunch
of error messages. Most of the errors are because of the Rd files which
were automatically populated by the package.skeleton function. I find the
section on documentation to be pretty confusion in the R Extensions manual.
Any help on getting these errors fixed would be hugely appreciated. Thanks.
--Markus
* checking for working pdflatex ... OK
* using log directory '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck'
* using R version 2.9.2 Patched (2009-09-24 r50179)
* using session charset: UTF-8
* checking for file 'NFIRS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NFIRS' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package 'NFIRS' can be installed ... WARNING
Found the following significant warnings:
missing link(s): ~~fun~~ CLASSNAME-class
See '/Users/markus/Dropbox/NFIRS_S4/NFIRS.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... ERROR
Rd files with likely Rd problems:
Unaccounted top-level text in file 'NFIRS-class.Rd':
Following section 'note':
\n\n ~Make other sections like Warning with \\section{Warning }{}
~\n\n
Unaccounted top-level text in file 'NFIRS-package.Rd':
Following section 'references':
\n~~ Optionally other standard keywords, one per line, from file KEYWORDS
in the R documentation directory ~~\n
Rd files with missing or empty '\title':
NFIRS.summary.Rd
read.NFIRS.Rd
Rd files without 'description':
NFIRS.summary.Rd
read.NFIRS.Rd
Rd files without 'title':
NFIRS.summary.Rd
read.NFIRS.Rd
These entries are required in an Rd file.
Rd files with non-standard keywords:
as.data.frame-methods.Rd: ~~ other possible keyword(s)
head-methods.Rd: ~~ other possible keyword(s)
NFIRS.summary.Rd: ~kwd1 ~kwd2
read.NFIRS.Rd: ~kwd1 ~kwd2
summary-methods.Rd: ~~ other possible keyword(s)
tail-methods.Rd: ~~ other possible keyword(s)
Each '\keyword' entry should specify one of the standard keywords (as
listed in file 'KEYWORDS' in the R documentation directory).
Rd files with duplicated alias 'as.data.frame,NFIRS-method':
as.data.frame-methods.Rd NFIRS-class.Rd
Rd files with duplicated alias 'head,NFIRS-method':
head-methods.Rd NFIRS-class.Rd
Rd files with duplicated alias 'summary,NFIRS-method':
NFIRS-class.Rd summary-methods.Rd
Rd files with duplicated alias 'tail,NFIRS-method':
NFIRS-class.Rd tail-methods.Rd
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
[[alternative HTML version deleted]]
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Re: [R] xyplot: problems with column names legend
Jay,
I don't recall the details of your original post so the
following may be entirely off the mark; nevertheless, here
goes:
thetext - paste('Data', 1:8)
# or: thetext - paste('Data', c('one', 'two', 'three', etc))
xyplot(decrease ~ treatment, OrchardSprays, groups = rowpos,
type = a,
auto.key =
list(text= thetext,
space = right,
points = FALSE,
lines = TRUE))
-Peter Ehlers
Jay wrote:
Anybody? Frustrating to be unable to solve this silly little
problem...
On Jan 3, 12:48 pm, Jay josip.2...@gmail.com wrote:
Thanks, the backtickes got the code working. However, now I cant get
it to draw the legend/key.
For example, look at this
figure:http://osiris.sunderland.ac.uk/~cs0her/Statistics/xyplot5.png
My graph is similar, but instead of 1,2,...,8 as the names of the
series I want it to say Data one (a string with spaces) and so on.
On Jan 3, 10:58 am, baptiste auguie baptiste.aug...@googlemail.com
wrote:
Hi,
Using backticks might work to some extent,
library(lattice)
`my variable` = 1:10
y=rnorm(10)
xyplot(`my variable` ~ y)
but if your data is in a data.frame the names should have been converted,
make.names('my variable')
[1] my.variable
HTH,
baptiste
2010/1/3 Jay josip.2...@gmail.com:
Hello!
one more question about xyplot. If I have data which have space in the
column names, say xyz 123. How do I create a working graph where
this text is displayed in the legend key?
Now when I try something like xyplot(xyz 123 ~ variable1, data =
mydata, ...) I get nothing.
Also, is it possible to genrate the graph with xyplot(mydata[,1] ~
variable1, data = mydata, ...) and then later in the code specify
the names that should be displayed in the legend?
Thank you!
__
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PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
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__
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PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
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PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
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--
Peter Ehlers
University of Calgary
403.202.3921
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[R] removing the rows with negative elements
Hello All, I would like to remove the entire row, if there is any negative element in that row. What is the best way to do that? For example, x-matrix(c(2,-1,-2,3,5,6,-3,7,4,2,1,0), 4, 3) the returning matrix should look like [,1] [,2] [,3] [1,] 2 5 4 [2,] 3 7 0 Thank you in advance, FM [[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] xyplot: adjusting the scale (min, max tick)
Have a look at the 'scales' argument. For example: # default plot xyplot(Sepal.Length ~ Petal.Length | Species, data = iris) # modified plot xyplot(Sepal.Length ~ Petal.Length | Species, data = iris, scales=list(y=list(at=c(-5,0,5,10), limits=c(-5,10 -Peter Ehlers Jay wrote: Hi, I'm terribly sorry but it seems it cannot figure this one out by myself so, please, if somebody could help I would be very grateful. So, when I plot with xyplot() I get an y-axis that is very ugly... starting from a random number and having so many ticks that it becomes unreadable. How do I tell xyplot how to draw the axis? E.g., start from 100, end at 200 with 25 units between ticks/labels? Can somebody give me an example? Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Ehlers University of Calgary 403.202.3921 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removing the rows with negative elements
x[-which(x 0, arr.ind=TRUE)[,1],] but I'm sure someone will suggest an easier way. Simon. On Wed, 2010-01-06 at 05:13 +, farida...@gmail.com wrote: Hello All, I would like to remove the entire row, if there is any negative element in that row. What is the best way to do that? For example, x-matrix(c(2,-1,-2,3,5,6,-3,7,4,2,1,0), 4, 3) the returning matrix should look like [,1] [,2] [,3] [1,] 2 5 4 [2,] 3 7 0 Thank you in advance, FM [[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. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. Statistics is the grammar of science - Karl Pearson __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removing the rows with negative elements
x[apply(x,1,function(x)all(x=0)),] -Peter Ehlers Simon Blomberg wrote: x[-which(x 0, arr.ind=TRUE)[,1],] but I'm sure someone will suggest an easier way. Simon. On Wed, 2010-01-06 at 05:13 +, farida...@gmail.com wrote: Hello All, I would like to remove the entire row, if there is any negative element in that row. What is the best way to do that? For example, x-matrix(c(2,-1,-2,3,5,6,-3,7,4,2,1,0), 4, 3) the returning matrix should look like [,1] [,2] [,3] [1,] 2 5 4 [2,] 3 7 0 Thank you in advance, FM [[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 Ehlers University of Calgary 403.202.3921 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removing the rows with negative elements
Thank you! On Jan 6, 2010 12:31am, Peter Ehlers ehl...@ucalgary.ca wrote: x[apply(x,1,function(x)all(x=0)),] -Peter Ehlers Simon Blomberg wrote: x[-which(x but I'm sure someone will suggest an easier way. Simon. On Wed, 2010-01-06 at 05:13 +, farida...@gmail.com wrote: Hello All, I would like to remove the entire row, if there is any negative element in that row. What is the best way to do that? For example, x7,4,2,1,0), 4, 3) the returning matrix should look like [,1] [,2] [,3] [1,] 2 5 4 [2,] 3 7 0 Thank you in advance, FM [[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 Ehlers University of Calgary 403.202.3921 [[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] seewave package:spectrogram resonance contour
Hi, I'd like to plot resonance contours on my spectrogram in the seewave package. Is this possible? -- Rajesh.J [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] why is object.size is more for constant numeric vector?
On Wed, 6 Jan 2010, Utkarsh Singhal wrote: Hi All, I ran the following lines in R: print(object.size(a - rep(1,10^6)),units=Mb) print(object.size(a - rep(3.542,10^6)),units=Mb) print(object.size(b - rep(x,10^6)),units=Mb) print(object.size(b - rep(xyzxyz xyz,10^6)),units=Mb) print(object.size(b - 1:10^6),units=Mb) print(object.size(b - rep(1:10,each=10^5)),units=Mb) print(object.size(b - rep(TRUE,10^6)),units=Mb) The object size from first two lines is 7.6 MB, but from the last five it is 3.8 MB, although the length of vector is same. Apparently, the size of any vector of a given length is twice if the vector is numeric constant than if it is not. Why is it so? Is my observation wrong? Or, is there some catch with 'object.size'? Your observation is faulty. The first two are type double, and a C double takes 8 bytes. The last three are type integer or logical with values stored in C int, 4 bytes each. Character strings are harder to compute storage for as identical strings share storage. On a 32-bit machine identical strings take an extra 4 bytes per string, on a 64-bit machine an extra 8 bytes. If you look at the values in bytes you will see that 'twice' is an approximation. So - the storage needed depends on the type of the vector as well as the length. - for character vectors it depends on the architecture and the content. Please do consult the R manuals rather than expect others to read them for you: this is all in the 'R Internals' manual. Thanks in advance. Regards Utkarsh [[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.
[R] MacOS X binary of package cairoDevice
Dear Michael and all R users, I find that there's no MacOS X binary of package cairoDevice on CRAN now. Can you or anybody else give me an older MacOS X edition for cairoDevice. Thank you. -- Wenjun [[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] removing the rows with negative elements
try also this: x - matrix(c(2,-1,-2,3,5,6,-3,7,4,2,1,0), 4, 3) x[!rowSums(x 0), ] Best, Dimitris farida...@gmail.com wrote: Hello All, I would like to remove the entire row, if there is any negative element in that row. What is the best way to do that? For example, x-matrix(c(2,-1,-2,3,5,6,-3,7,4,2,1,0), 4, 3) the returning matrix should look like [,1] [,2] [,3] [1,] 2 5 4 [2,] 3 7 0 Thank you in advance, FM [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removing the rows with negative elements
Another option is x[rowSums(x0)==0, ] but beware of floating point if your numbers can be near zero. Regards Petr r-help-boun...@r-project.org napsal dne 06.01.2010 06:52:48: Thank you! On Jan 6, 2010 12:31am, Peter Ehlers ehl...@ucalgary.ca wrote: x[apply(x,1,function(x)all(x=0)),] -Peter Ehlers Simon Blomberg wrote: x[-which(x but I'm sure someone will suggest an easier way. Simon. On Wed, 2010-01-06 at 05:13 +, farida...@gmail.com wrote: Hello All, I would like to remove the entire row, if there is any negative element in that row. What is the best way to do that? For example, x7,4,2,1,0), 4, 3) the returning matrix should look like [,1] [,2] [,3] [1,] 2 5 4 [2,] 3 7 0 Thank you in advance, FM [[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 Ehlers University of Calgary 403.202.3921 [[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.
