[R] configure: WARNING: you cannot build info or HTML versions of the R manuals
Rusers, I am trying to build R2.5 on my Kubuntu machine an configure concludes with : configure: WARNING: you cannot build info or HTML versions of the R manuals What do I need to install on my machine to get rid of this warnings? Eryk [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] tcltk support....
Rusers, library(Rcmdr) Loading required package: tcltk Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system While installing R I run configure with configure --prefix=/bla/bla --with-tcltk make make install configure did not returned any errors. Hence, I assume that the the tcl/tk libraries have been found. installin.packages(tcltk) returns an error telling me that there is no package tcltk on CRAN. And indeed there no such package on CRAN. Whats wrong? Eryk [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] configure: WARNING: you cannot build info or HTML versions of the R manuals
Texinfo. Not sure if that is also the package name on *ubuntu/debian. It's called texinfo on ubuntu/debian and it fixed the problem. Thanks a lot Peter. Eryk [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] tcltk support....
I use ubuntu/kubuntu... I did not had the dev packages installed. The problem is no solved. To my excuse I can say that I would have expected configure to issue an error or warning. I did run it configure with --with-tcltk. But there was not a singel message which would point me to the fact that some packages on my system are missing. cheers Eryk On 4/26/07, Stefan Grosse [EMAIL PROTECTED] wrote: tcltk must be installed on your system, it is not a R package. Which Linux are you using? W Eryk Wolski wrote: Rusers, library(Rcmdr) Loading required package: tcltk Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system While installing R I run configure with configure --prefix=/bla/bla --with-tcltk make make install configure did not returned any errors. Hence, I assume that the the tcl/tk libraries have been found. installin.packages(tcltk) returns an error telling me that there is no package tcltk on CRAN. And indeed there no such package on CRAN. Whats wrong? Eryk [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Translating actxserver server commands to rcom
Dear R and R com user
I have the following matlab which acesses a com server, code which I
am trying to translate to R using the Rcom package:
clear all;
clear analysis;
analysis = actxserver('EDAL.MSAnalysis');
analysis.Open('E:\work\ChromPeakFinderdata\DatafromKlaus\E112L-cad13-PI-24h_pos_1-C,3_01_2562.d');
specCol = analysis.MSSpectrumCollection;
count = specCol.get('Count');
This is how far I got...
rm(analysis)
analysis - comCreateObject(EDAL.MSAnalysis)
comGetObjectInfo(analysis)
comInvoke(analysis,open,E:\work\ChromPeakFinderdata\DatafromKlaus\E112L-cad13-PI-24h_pos_1-C,3_01_2562.d)
specCol - analysis$MSSpectrumCollection
specCol
function (...)
comInvoke(handle, ..FUN, ...)
environment: 0x022a4734
comInvoke(specCol,get,Count)
NULL
Seems to be the wrong track ... What would be the equivalent of
analysis.Open('E:\work\ChromPeakFinderdata\DatafromKlaus\E112L-cad13-PI-24h_pos_1-C,3_01_2562.d');
specCol = analysis.MSSpectrumCollection;
or of count = specCol.get('Count');
in Rcom?
Help is highly appreciated...
best wishes
Eryk
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[R] qqmath - Lattice error
Hi,
Don't have a clue what teh following error message
generated by this function call:
qqmath( ~val|ind,data = xx
,distribution = function(p){ qt(p,df=20)}
,ylab=Sample Quatinles
,xlab=Theoretical Quantiles
,panel=function(x,y)
{
panel.qqmathline(y
, distribution=function(p) qt(p,df=20)
,col=2)
panel.qqmath(x, y
, distribution=function(p) qt(p,df=20)
,pch=.,cex=2)
}
)
means. Espacially that this function call
qqmath( ~val|ind,data = xx
,distribution = function(p){ qt(p,df=20)}
,ylab=Sample Quatinles
,xlab=Theoretical Quantiles
)
with the same data is working.
Thanks in advance for suggestions.
Eryk
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Re: [R] qqmath - Lattice error
Hi,
Sorrry, I have forgotten to paste the error message:
Here it is:
qqmath( ~val|ind,data = xx
+,distribution = function(p){ qt(p,df=20)}
+,ylab=Sample Quatinles
+,xlab=Theoretical Quantiles
+ # ,aspect=1
+ # ,prepanel = prepanel.qqmathline
+
+,panel=function(x,y)
+{
+ panel.qqmathline(y
+ , distribution=function(p) qt(p,df=20)
+ ,col=2)
+ panel.qqmath(x, y
+ , distribution=function(p) qt(p,df=20)
+ ,pch=.,cex=2)
+}
+ )
Error in panel(x = c(0.637018600046204, -0.0237681209798937, -
1.13188488395317, :
unused argument(s) (NA ...)
As already mentioned the same dataset works fine with the short version of
the function call.
And this is how the data looks like.
class(xx)
[1] data.frame
xx[1:10,]
ind val
1 500-530 0.63701860
2 500-530 -0.02376812
3 500-530 -1.13188488
4 500-530 0.41095693
5 500-530 -1.02142435
6 500-530 -1.02142435
7 500-530 0.04185616
8 500-530 -1.29129448
9 500-530 1.17680295
10 500-530 -0.61137387
The first column are the levels. Even with this trunkated dataset the error
occurs.
Eryk
On 5/25/06, Deepayan Sarkar [EMAIL PROTECTED] wrote:
On 5/25/06, Witold Wolski [EMAIL PROTECTED] wrote:
Hi,
Don't have a clue what teh following error message
What's the error message?
In any case, you seem to have wrong expectations about what
panel.qqmath does, and in particular what arguments it accepts (this
changed a few versions back). See help(panel.qqmath).
Deepayan
generated by this function call:
qqmath( ~val|ind,data = xx
,distribution = function(p){ qt(p,df=20)}
,ylab=Sample Quatinles
,xlab=Theoretical Quantiles
,panel=function(x,y)
{
panel.qqmathline(y
, distribution=function(p) qt(p,df=20)
,col=2)
panel.qqmath(x, y
, distribution=function(p) qt(p,df=20)
,pch=.,cex=2)
}
)
means. Espacially that this function call
qqmath( ~val|ind,data = xx
,distribution = function(p){ qt(p,df=20)}
,ylab=Sample Quatinles
,xlab=Theoretical Quantiles
)
with the same data is working.
[[alternative HTML version deleted]]
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Re: [R] qqmath - Lattice error
Thanks a lot!
Eryk
On 5/25/06, Sundar Dorai-Raj [EMAIL PROTECTED] wrote:
Witold Wolski wrote:
Hi,
Don't have a clue what teh following error message
generated by this function call:
qqmath( ~val|ind,data = xx
,distribution = function(p){ qt(p,df=20)}
,ylab=Sample Quatinles
,xlab=Theoretical Quantiles
,panel=function(x,y)
{
panel.qqmathline(y
, distribution=function(p) qt(p,df=20)
,col=2)
panel.qqmath(x, y
, distribution=function(p) qt(p,df=20)
,pch=.,cex=2)
}
)
means. Espacially that this function call
qqmath( ~val|ind,data = xx
,distribution = function(p){ qt(p,df=20)}
,ylab=Sample Quatinles
,xlab=Theoretical Quantiles
)
with the same data is working.
Thanks in advance for suggestions.
Eryk
Hi, Eryk,
The function panel.qqmath does not take an argument y.
Here's a complete example (which you should have supplied):
library(lattice)
set.seed(1)
xx - data.frame(ind = factor(rep(1:4, each = 100)))
xx$val - rt(400, 20)
qt2 - function(p) qt(p, df = 20)
qqmath(~val | ind, data = xx,
distribution = qt2,
ylab = Sample Quantiles,
xlab = Theoretical Quantiles,
panel = function(x) {
panel.qqmathline(x, distribution = qt2, col = 2)
panel.qqmath(x, distribution = qt2, pch=., cex = 2)
})
--sundar
P.S. Please (re-)read the posting guide. If you get an error in your
script, tell us what it is. And provide an complete example (the posting
guide gives guidelines here). Quite often I solve my own problem in the
process of coming up with an example I'd like to post to R-help.
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Re: [R] Problem with memory footprint of qq plot generated with lattice
Dave,
qqmath(~val|ind,data=xx
,distribution=function(p) qt(p,df=19)
,ylab=Sample Quatinles
,xlab=Theoretical Quantiles
,aspect=1
,prepanel = prepanel.qqmathline
,panel=function(x,y)
{
panel.qqmathline(y, distribution=function(p) qt(p,df=19),col=2)
panel.qqmath(x, y , distribution=function(p)
qt(p,df=19),pch=.,cex=2)
}
)
Adding f.value=fn as argument to qqmath reduces the size of the image,
but neither the axis (absicissae) nor the line added by panel.qqmathline
are right.
Adding f.value=fn as argument to panel.qqmathline and panel.qqmath
generates the right graphic, but the size of the image is again 20 MB.
Any Suggestions?
Eryk
[EMAIL PROTECTED] wrote:
nwew [EMAIL PROTECTED] wrote:
Dear R helpers,
I generate a qq plot using the following function call.
...
dim(xx)
[1] 680237 2
How about doing something like this:
fn - function(n,cut=0.001,m=1000)
{
p - ppoints(n)
p - p[pmin(p, 1-p) cut]
q - pt(seq(qt(cut,df=19),qt(1-cut,df=19),length=m),df=19)
sort(c(p,q))
}
then adding 'f.value=fn' to your qqmath arguments? This essentially
says, plot the individual data points in the extreme tails of the
distribution (p 0.001 or p 0.999), and evaluate the distribution
at a sparse set of points in between, where the density means you
can't discern the individual values anyway.
-- Dave
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Re: [R] regression methods for circular(?) data.
Hi, I do not know the intercept and slope. And you have to know them in order to do something like: ix-(y 0.9*(x-50)/200 I am right? cheers (Ted Harding) wrote: On 26-Sep-05 nwew wrote: Dear R-users, I have the following data x - runif(300,min=1,max=230) y - x*0.005 + 0.2 y - y+rnorm(100,mean=0,sd=0.1) y - y%%1 # --- modulo operation plot(x,y) and would like to recapture the slope (0.005) and intercept(0.2). I wonder if there are any clever algorithms to do this. I was looking at the function lm.cirucalar. Is this the method to use? If, which of the references is best too look at? Eryk Hi Eryk, If you know the modulus (in your case 1.0) and you get data that look like the result of your plot(x,y), then I wouldn't mess about. I would simply do something like y1-y ix - ix-(y 0.9*(x-50)/200) y1[ix] - y1[ix]+1.0 lm(y1~x) (the constants 0.9/200, -50 being chosen to give a good separation on the graph). On the other hand, if there are good reasons why this very simple approach is not suitable, then if we knew what they were a more helpful reply would be easier to formulate! Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Sep-05 Time: 15:56:48 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] regression methods for circular(?) data.
Ted, I agree with you that if you unwrap the data you can use lm. And you can separate the data in the way you describe. However, if you have thousands of such datasets I do not want to do it by looking at the graph. Yes the scatter may be larger as in the example and range(y) may be larger than 2. And as you said in order to unwrap the data you have to separate them first. It would be easy to do it using for example single linkage clustering if they were no overlaps (but they do sometimes). So I were just wondering if there are no more fancy methods to do this. Thanks, cheers (Ted Harding) wrote: On 26-Sep-05 Witold Eryk Wolski wrote: Hi, I do not know the intercept and slope. And you have to know them in order to do something like: ix-(y 0.9*(x-50)/200 I am right? cheers Although I really knew them from the way you generated the data, I pretended I did not know them. Read below: If you know the modulus (in your case 1.0) -- I did assume that this was known, i.e. that the data wrap round to 0 above 1.0. Also: the constants 0.9/200, -50 being chosen to give a good separation on the graph -- I plotted the data, and saw that the wrapped data were well separated, and that 0.9*(x-50)/200 was an adequate discriminant function. This was estimated purely by eye, by looking at the graph, to find some line that went between the two groups of data; no attempt was made to calculate anything precisely. Apart from assuming that the modulus was 1.0, and that the well-separated data at the bottom right of the graph were wrapped round data, no other information was used by me! So the question remains: If you can assume that the modulus is 1.0, and that the wrapped-round data will be well separated, then all is simple. All you need to do is to unwrap the wrapped data by adding 1.0, having first identified them by virtue of their obvious separation. Then you can estimate the slope by using 'lm'. But:-- if you, Witold, can not assume these two things for your real data, what can we assume in considering your question? Is the modulus unknown, for instance? Is the scatter so large that the groups are not well separated? Might we have twice-wrapped data (i.e. original y 2)? In short, do your real data look like the data you sent us, and are they wrapped at 1.0? or what? With thanks, and best wishes, Ted. (Ted Harding) wrote: On 26-Sep-05 nwew wrote: Dear R-users, I have the following data x - runif(300,min=1,max=230) y - x*0.005 + 0.2 y - y+rnorm(100,mean=0,sd=0.1) y - y%%1 # --- modulo operation plot(x,y) and would like to recapture the slope (0.005) and intercept(0.2). I wonder if there are any clever algorithms to do this. I was looking at the function lm.cirucalar. Is this the method to use? If, which of the references is best too look at? Eryk Hi Eryk, If you know the modulus (in your case 1.0) and you get data that look like the result of your plot(x,y), then I wouldn't mess about. I would simply do something like y1-y ix - ix-(y 0.9*(x-50)/200) y1[ix] - y1[ix]+1.0 lm(y1~x) (the constants 0.9/200, -50 being chosen to give a good separation on the graph). On the other hand, if there are good reasons why this very simple approach is not suitable, then if we knew what they were a more helpful reply would be easier to formulate! Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Sep-05 Time: 15:56:48 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Sep-05 Time: 18:08:28 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Interaction term in anova - how it should be written in a manuscript table?
Thanks a lot cheers Eryk Marc Schwartz wrote: For a me too post, I agree with Andy's recommendation, which in turn is supported by How to Report Statistics in Medicine by Lang and Secic, ACP, 1997. There is an example table (8.2) on page 133. HTH, Marc Schwartz On Sun, 2005-03-20 at 15:44 -0500, Liaw, Andy wrote: I'd suggest a $\times$ b, as you'd find in most stat textbook. Andy From: Witold Eryk Wolski Dear Rgurus, Interaction terms in the linear models function lm are specified by the colon : eg: x ~ a + b + a:b a shortcut for the above is: x ~ a*b the output if calling anova on the lm object will be the same in both cases a b a:b ... Resdiuals ... What I am wondering is how the interaction term (a:b) given above should be written in a table in an manuscript? a ) a*b b ) a$\cdot$ b c ) a:b d) Cheers Eryk. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Witold Eryk Wolski __( School of Mathematics and Statistics _ \__/ University of Newcastle 'v' ||Newcastle upon Tyne, NE1 7RU, ENGLAND / \ ^^mail: [EMAIL PROTECTED] m m Phone : 044 (0)191 222 5376 FAX : 044 (0)191 222 8020 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Violin plot for discrete variables.
Dear Rgurus, To my knowledge the best way to visualize the distribution of a discrete variable X is plot(table(X)) The problem which I have is the following. I have to discrete variables X and Y which distribution I would like to compare. To overlay the distribution of Y with lines(table(Y)) gives not satisfying results. This is the same in case of using density or histogram. Hence, I am wondering if there is a equivalent of the vioplot function (package vioplot) for discrete variables which starts with a boxplot and than adds a rotated plot(table()) plot to each side of the box plot. Maybee I should ask it first: Does such a plot make any sense? If not are there better solutions? cheers Eryk. -- Witold Eryk Wolski __( School of Mathematics and Statistics _ \__/ University of Newcastle 'v' ||Newcastle upon Tyne, NE1 7RU, ENGLAND / \ ^^mail: [EMAIL PROTECTED] m m Phone : 044 (0)191 222 5376 FAX : 044 (0)191 222 8020 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Interaction term in anova - how it should be written in a manuscript table?
Dear Rgurus, Interaction terms in the linear models function lm are specified by the colon : eg: x ~ a + b + a:b a shortcut for the above is: x ~ a*b the output if calling anova on the lm object will be the same in both cases a b a:b ... Resdiuals ... What I am wondering is how the interaction term (a:b) given above should be written in a table in an manuscript? a ) a*b b ) a$\cdot$ b c ) a:b d) Cheers Eryk. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Concatenate vector into string
Matthieu Cornec wrote: Hello, I would like to convert c(a,b,c) into abc. Anyone could help? Thanks, Matthieu Cornec __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html paste( c(a,b,c),collapse=) Eryk -- Witold Eryk Wolski __( School of Mathematics and Statistics _ \__/ University of Newcastle 'v' ||Newcastle upon Tyne, NE1 7RU, ENGLAND / \ ^^mail: [EMAIL PROTECTED] m m Phone : 044 (0)191 222 5376 FAX : 044 (0)191 222 8020 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Hot to _set_ an xmlAttr XML xmlAttr set
Dear R-Gurus! I have read an xml document with xmlTreeParse and can access that attribute value by xmlGetAttr or xmlAttrs What I want to do is to set a new value and to write the modified DOM tree into an XML file. But until now I have not found an setter method equivalent to the getter method? Eryk -- Witold Eryk Wolski __( School of Mathematics and Statistics _ \__/ University of Newcastle 'v' ||Newcastle upon Tyne, NE1 7RU, ENGLAND / \ ^^mail: [EMAIL PROTECTED] m m Phone : 044 (0)191 222 5376 FAX : 044 (0)191 222 8020 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Need suggestions for plotting 3D plot
Hi, http://www.stat.ucl.ac.be/ISpersonnel/lecoutre/stats/fichiers/_gallery.pdf The document above starts showing 3 different types of 3D graphics persp scatterplot3d wireframe A few days ago there was a discussion here on the list about providing a graph library. During this discussion several resources of example code where mentioned ( inter-alia that above). So if you need more ideas follow search this e-mails. cheers Eryk Soumyadeep nandi wrote: Hi Everybody, I am a newbie in R. I have a data in the form of a matrix which I want to make some 3D plots using R. There is some functions for instance hist() for 2D plots, but I cant find any function for 3D plots. Is there any function available in R for 3D plots? If so, is there any documention available on internet so that I can go through. With regards, Soumyadeep __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Witold Eryk Wolski __( School of Mathematics and Statistics _ \__/ University of Newcastle 'v' ||Newcastle upon Tyne, NE1 7RU, ENGLAND / \ ^^mail: [EMAIL PROTECTED] m m Phone : 044 (0)191 222 5376 FAX : 044 (0)191 222 8020 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] The system command and the LD_LIBRARY_PATH
Hi R-gurus, In my envirovment I have specified the LD_LIBRARY_PATH to /data/opt/libmy/lib After starting R the LD_LIBRARY_PATH variable is changed. Sys.getenv(LD_LIBRARY_PATH) /data/opt/R-devel//lib/R/lib:/usr/local/lib:/usr/X11R6/lib:/data/opt/libmy/lib The problem is that in /usr/local/lib is an acient version of mylib hence a call to _system_ with fails badly. Suggestions? Eryk __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Renaming columns in data.frame, inserting/removing columns from data.frame
Ken Termiso wrote: Hello, I'm hoping that there is an easier way to rename columns in a data frame other than by using the names() assignment, which requires you to type in all the column names at once for a data.frame, in the case that I simply want to rename a single column in a data frame. names(mydataframe)[column.index]-new.name Also, is there an easy way to move columns in a data frame around relative to the other columns? ?subset or mydataframe[c(column3,column2,column1)] Thanks in advance, Ken __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Need your help with my R plot
Latha Raja wrote: Hi, I am using R to plot the graph and the problem I am facing with my graph is that I have lots of points concentrated in one area and It is creating a visualization challenge. Is there any commands in R I could use to solve this problem. Even if there is no command, do you know how I could tackle this problem...(I want to separate these points so I could see each of them...) Any help is much appreciated... Thank you kindly Latha __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Hi, Take a look at the function: ixyplot in the package IDPmisc. Eryk -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] S4 class no longer accepts matrix in array slot under 2.0.1
Giles Heywood wrote: I have an S4 class with a slot of class array, and in upgrading to 2.0.1 (from 1.9.1) I have encountered a change in behaviour. This causes me some difficulties if I want to allow 2-dimensional arrays in the slot. The following (in 2.0.1) illustrates the point: setClass(foo,representation(array)) [1] foo a - new(foo,array(NA,2:4)) b - new(foo,matrix(NA,2,3)) Error in as-(`*tmp*`, Classi, value = c(NA, NA, NA, NA, NA, NA)) : No method or default for as() replacement of foo with Class=matrix This last error did not occur under 1.9.1. I conclude that in this context the methods package does not recognise matrix as a subclass of array. However if I use getClass(), I see that R recognises matrix as a subclass of array (and vice-versa). So is this new behaviour correct? [this is a simplified (and final) reposting of an earlier question entitled matrix no longer is array in 2.0.1?] Hi, setClass(foo,representation(matrix)) [1] foo a - new(foo,array(NA,2:4)) b - new(foo,matrix(NA,2,3)) Will work. As you say array has a subclass matrix. getClass(array) Known Subclasses: matrix and getClass(matrix) Known Subclasses: Class array, directly, with explicit test and coerce and matrix has a subclass array. What probably is necessary to use polymorphism - assigning a subclass to the parent class is the explicit test and coearce. It seems that matrix is the superclass of array. /E __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] scatterplot of 100000 points and pdf file format
Prof Brian Ripley wrote: On Wed, 24 Nov 2004 [EMAIL PROTECTED] wrote: On 24-Nov-04 Witold Eryk Wolski wrote: Hi, I want to draw a scatter plot with 1M and more points and save it as pdf. This makes the pdf file large. So i tried to save the file first as png and than convert it to pdf. This looks OK if printed but if viewed e.g. with acrobat as document figure the quality is bad. Anyone knows a way to reduce the size but keep the quality? If you want the PDF file to preserve the info about all the 1M points then the problem has no solution. The png file will already have suppressed most of this (which is one reason for poor quality). I think you should give thought to reducing what you need to plot. Think about it: suppose you plot with a resolution of 1/200 points per inch (about the limit at which the eye begins to see rough edges). Then you have 4 points per square inch. If your 1M points are separate but as closely packed as possible, this requires 25 square inches, or a 5x5 inch (= 12.7x12.7 cm) square. And this would be solid black! Presumably in your plot there is a very large number of points which are effectively indistinguisable from other points, so these could be eliminated without spoiling the plot. I don't have an obviously best strategy for reducing what you actually plot, but perhaps one line to think along might be the following: 1. Multiply the data by some factor and then round the results to an integer (to avoid problems in step 2). Factor chosen so that the result of (4) below is satisfactory. 2. Eliminate duplicates in the result of (1). 3. Divide by the factor you used in (1). 4. Plot the result; save plot to PDF. As to how to do it in R: the critical step is (2), which with so many points could be very heavy unless done by a well-chosen procedure. I'm not expert enough to advise about that, but no doubt others are. unique will eat that for breakfast x - runif(1e6) system.time(xx - unique(round(x, 4))) [1] 0.55 0.09 0.64 0.00 0.00 length(xx) [1] 10001 ?table - reduces the data and ?image - shows it. And this is doing exactly what I need. (not my idea but one of Thomas Unternäher). Thanks Thomas. /E -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] scatterplot of 100000 points and pdf file format
Hi, I want to draw a scatter plot with 1M and more points and save it as pdf. This makes the pdf file large. So i tried to save the file first as png and than convert it to pdf. This looks OK if printed but if viewed e.g. with acrobat as document figure the quality is bad. Anyone knows a way to reduce the size but keep the quality? /E -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] scatterplot of 100000 points and pdf file format
Hi, I tried the ps idea. But I am using pdflatex. You get a even larger size reduction if you convert the ps into a pdf using ps2pdf. But unfortunately there is a quality loss. I have found almost a working solution: a) Save the scatterplot without axes and with par(mar=c(0,0,0,0)) as png . b) convert it using any program to pnm c) read the pnm file using pixmap d) Add axes labels and lines afterwards with par(new=TRUE) And this looks like I would like that it looks like. But unfortunately acroread and gv on window is crashing when I try to print the file. png(file=pepslop.png,width=500,height=500) par(mar=c(0,0,0,0)) X2-rnorm(10) Y2-X2*10+rnorm(10) plot(X2,Y2,pch=.,xlab=,ylab=,main=,axes=F) dev.off() pdf(file=pepslop.pdf,width=7,height=7) par(mar=c(3.2,3.2,1,1)) x - read.pnm(pepslop.pnm ) plot(x) par(new=TRUE) par(mar=c(3.2,3.2,1,1)) plot(X2,Y2,pch=.,xlab=,ylab=,main=,type=n) mtext(expression(m[nominal]),side=1,line=2) mtext(expression(mod(m[monoisotopic],1)),side=2,line=2) legend(1000,4,expression(paste(lambda[DB],=,0.000495)),col=2,lty=1,lwd=1) abline(test,col=2,lwd=2) dev.off() Marc Schwartz wrote: On Wed, 2004-11-24 at 16:34 +0100, Witold Eryk Wolski wrote: Hi, I want to draw a scatter plot with 1M and more points and save it as pdf. This makes the pdf file large. So i tried to save the file first as png and than convert it to pdf. This looks OK if printed but if viewed e.g. with acrobat as document figure the quality is bad. Anyone knows a way to reduce the size but keep the quality? Hi Eryk! Part of the problem is that in a pdf file, the vector based instructions will need to be defined for each of your 10 ^ 6 points in order to draw them. When trying to create a simple example: pdf() plot(rnorm(100), rnorm(100)) dev.off() The pdf file is 55 Mb in size. One immediate thought was to try a ps file and using the above plot, the ps file was only 23 Mb in size. So note that ps can be more efficient. Going to a bitmap might result in a much smaller file, but as you note, the quality does degrade as compared to a vector based image. I tried the above to a png, then converted to a pdf (using 'convert') and as expected, the image both viewed and printed was pixelated, since the pdf instructions are presumably drawing pixels and not vector based objects. Depending upon what you plan to do with the image, you may have to choose among several options, resulting in tradeoffs between image quality and file size. If you can create the bitmap file explicitly in the size that you require for printing or incorporating in a document, that is one way to go and will preserve, to an extent, the overall fixed size image quality, while keeping file size small. Another option to consider for the pdf approach, if it does not compromise the integrity of your plot, is to remove any duplicate data points if any exist. Thus, you will not need what are in effect redundant instructions in the pdf file. This may not be possible depending upon the nature of your data (ie. doubles) without considering some tolerance level for equivalence. Perhaps others will have additional ideas. HTH, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] scatterplot of 100000 points and pdf file format
Hi, Yes, indeed the hexbin package generates very cool pix. They look great. I was using it already. But this time I am interested in visualizing exactly the _scatter_ of some extreme points. Eryk Liaw, Andy wrote: Marc/Eryk, I have no experience with it, but I believe the hexbin package in BioC was there for this purpose: avoid heavy over-plotting lots of points. You might want to look into that, if you have not done so yet. Best, Andy From: Marc Schwartz On Wed, 2004-11-24 at 16:34 +0100, Witold Eryk Wolski wrote: Hi, I want to draw a scatter plot with 1M and more points and save it as pdf. This makes the pdf file large. So i tried to save the file first as png and than convert it to pdf. This looks OK if printed but if viewed e.g. with acrobat as document figure the quality is bad. Anyone knows a way to reduce the size but keep the quality? Hi Eryk! Part of the problem is that in a pdf file, the vector based instructions will need to be defined for each of your 10 ^ 6 points in order to draw them. When trying to create a simple example: pdf() plot(rnorm(100), rnorm(100)) dev.off() The pdf file is 55 Mb in size. One immediate thought was to try a ps file and using the above plot, the ps file was only 23 Mb in size. So note that ps can be more efficient. Going to a bitmap might result in a much smaller file, but as you note, the quality does degrade as compared to a vector based image. I tried the above to a png, then converted to a pdf (using 'convert') and as expected, the image both viewed and printed was pixelated, since the pdf instructions are presumably drawing pixels and not vector based objects. Depending upon what you plan to do with the image, you may have to choose among several options, resulting in tradeoffs between image quality and file size. If you can create the bitmap file explicitly in the size that you require for printing or incorporating in a document, that is one way to go and will preserve, to an extent, the overall fixed size image quality, while keeping file size small. Another option to consider for the pdf approach, if it does not compromise the integrity of your plot, is to remove any duplicate data points if any exist. Thus, you will not need what are in effect redundant instructions in the pdf file. This may not be possible depending upon the nature of your data (ie. doubles) without considering some tolerance level for equivalence. Perhaps others will have additional ideas. HTH, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R/S-related projects on Sourceforge? Trove Categorization
Hi, This are the project which I have extracted from all your mails. 1. http://sourceforge.net/projects/rpgsql/ R PostgreSQL Interface 2. http://sourceforge.net/projects/r-spatial/ R package for spatial data classes 3. http://sourceforge.net/projects/rpy/ RPy (R from Python) 4. http://sourceforge.net/projects/ep-sf/ Expression Profiler 5. http://sourceforge.net/projects/fsap fish stock assessment for R 6. http://sourceforge.net/projects/flr/ R packages for use in fisheries modelling 7. https://sourceforge.net/projects/runit/ R Unit Test Framework 8. http://sourceforge.net/projects/ep-sf/ Expression Profiler 9. http://sourceforge.net/projects/r-asp/ Analysis of Spatial Data in R 10. http://sourceforge.net/projects/r4proteomics/ R Packages for proteomics 11. http://sourceforge.net/projects/rdbi/ R Database Interface 12. http://sourceforge.net/projects/nlmeode/ R package combining nlme and odesolve 13. http://sourceforge.net/projects/rarcinfo/ RArcInfo 14. http://sourceforge.net/projects/rgdal GDAL Package for R 15. http://sourceforge.net/projects/gretl/ GNU Regression, Econometrics and Time-series Library 16. ... Sorry if I have missed any. But it is surely more than five. Thanks all of you for your numerous response and also for some more general thoughts concerning *collaboratory* development using source code repositories: https://stat.ethz.ch/pipermail/r-devel/2004-November/031398.html. If I see how R is evolving I believe that this ideas will be realized soon. Especially that there are already repositories covering some of the functionality and dedicated to R -- Bioconductor with a svn archive. Unfortunately, as I was told by Geff Gentry the costs of administering the svn, cvs servers are high, hence the number of developers must be limited. Also CRAN has some of the functionality but the svn or cvs support is missing. Luckily hosting the sources on e.g. sourceforge and the builds on CRAN or Bioconductor gives already some of the essential functionality. Therefore at this place big thanks to the Bioconductor, CRAN and sourceforge people. /E __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R/S-related projects on Sourceforge? Trove Categorization
Hi R-Users and Developers, Several months ago I made a request on Sourceforge to add the R/S - programming language to the _Trove_ categorization. (The Trove is a means to convey basic metainformation about your project.) Today I got the following response of one of the sourceforge admins. SNIP SourceForge.net will consider the inclusion of a programming language within the Trove system when we host at least 5 projects based on that language. Please advise: Do you know of 5 projects hosted on SourceForge.net based on this language? SNIP If anyone of you knew about R-packages, or projects using the R/S programming language, which are hosted on sourceforge, please reply to this thread. I hope that your answers will enable me to give more then 5 examples of R projects hosted on Sourceforge. Yours Eryk Ps. The ID of my original feature request on Sourceforge is 967697. https://sourceforge.net/tracker/?func=detailatid=350001aid=967697group_id=1 -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] - assignment no long work in class methods
Gang Liang wrote:
Hi-
I used to use - to do assignment inside a class method, and
just found that now it is broken in R 2.0. For example, the
following code
---
setClass( myclass, representation(x=numeric) )
setGeneric(incrXByOne, function(obj) standardGeneric(incrXByOne))
setMethod( incrXByOne, myclass, function(obj) [EMAIL PROTECTED] - [EMAIL
PROTECTED] + 1 )
Hi,
What (my guess) you want to define is:
setMethod( incrXByOne, myclass, function(obj) [EMAIL PROTECTED] - [EMAIL
PROTECTED] + 1;obj})
You do not need - to assign to a function argument? Its in my view
even erroneous.
This S code gives an error too.
test - function(x)
{
x$bla-x$bla + 1
}
test(1)
Error in test(1) : Object x not found
/E
incrXByOne( new(myclass) )
---
will give an error message like:
Error in incrXByOne(new(myclass)) : Object obj not found
## R failed to trace the object back to the GlobalEnv...
It used to work under R1.7 - 1.9. I don't know whether this is a
bug or a new feature...
Anyone can recommend a workaround?
Thanks, Gang
-
debian unstable, kernel 2.6.8
version
platform i386-pc-linux-gnu
arch i386
os linux-gnu
system i386, linux-gnu
status
major2
minor0.0
year 2004
month10
day 04
language R
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--
Dipl. bio-chem. Witold Eryk Wolski
MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin
tel: 0049-30-83875219 __(_
http://www.molgen.mpg.de/~wolski \__/'v'
http://r4proteomics.sourceforge.net||/ \
mail: [EMAIL PROTECTED]^^ m m
[EMAIL PROTECTED]
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[R] gplot.hexbin - how to set figure margin.
Hi, Would like to use to the hexbin package to plot a 2D hist - because it looks really _cool_. My problem is related to drawing a pdf hexbin graphic in series of other graphics. All other figures have a par(mar=c(3.2,3.2,1,1)). So the gplot.hexbin figure in this series looks a little alienated? Was trying a to specify the _mar_ using par, viewport, hexViewport etc. a little. My question. How to set the margins in the sample code below. x - rnorm(1) y - rnorm(1) bin - hexbin(x,y) ## Plot : Note that 'gplot.hexbin' is the S4 plot method for hexbin ! ## -- plot(bin) /E Dipl. bio-chem. Eryk Witold Wolski @MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-W http://r4proteomics.sourceforg.net __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how lambda is computed in smoot.spline given _df_
Hi, I posted some days ago a question concerning the computation of lambda in the smooth.spline function (which I repreat at the bottom of the mail) given _df_ . Unfortunately the documentation is not clear to me. Maybee someone can help to answer in my view the basic question: If the penalized log likelihood is L = (y - f)' W (y - f) + lambda c' Sigma c how the _lambda_ in the above equation is computed if _df_ is given and _spar_ not? And, Is there a way to define lambda directly? Yours. /E Hi, I am usign the smooth.spline function. I am not sure how the _df_ (degrees of freedom) parameter, if set, influences _lambda_ in eq: L = (y - f)' W (y - f) + lambda c' Sigma c Is _df_ substituting tr(Sigma), if defined, in the equation: r = tr(X' W X) / tr(Sigma) which is used to compute: lambda = r * 256^(3*spar - 1)? And how _spar_ is set if not defined? /E __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] smooth.spline _df_ parameter?
Hi, I am usign the smooth.spline function. I am not sure how the _df_ (degrees of freedom) parameter, if set, influences _lambda_ in eq: L = (y - f)' W (y - f) + lambda c' Sigma c Is _df_ substituting tr(Sigma), if defined, in the equation: r = tr(X' W X) / tr(Sigma), which is used to compute: lambda = r * 256^(3*spar - 1)? How _spar_ is set if not defined? /E Dipl. bio-chem. Eryk Witold Wolski @MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-W http://r4proteomics.sourceforg.net __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to add values to an array at any position.
Hi, How to add values to an array at any position. Asking because of the following: e.g. y-c(0.1,NaN,0.2,NaN) #or data frame x-na.omit(y) take some columns from x and do some computation with functions which do not allow NaN 's. After the computing add NaN's at positions stored in attr(x,na.action) of the result vector. /E -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to add values to an array at any position.
Hi, In the first place I was wondering if there are no function _insert.vector_ in base. Thanks Peter and Gabor even for the bad news. E. Peter Dalgaard wrote: Witold Eryk Wolski [EMAIL PROTECTED] writes: Hi, How to add values to an array at any position. Asking because of the following: e.g. y-c(0.1,NaN,0.2,NaN) #or data frame x-na.omit(y) take some columns from x and do some computation with functions which do not allow NaN 's. After the computing add NaN's at positions stored in attr(x,na.action) of the result vector. You mean, something like ix - attr(x, na.action) newres - c(res,rep(NA,length(ix))) # just to get size and mode right newres[ix] - NA newres[-ix] - res -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] usage and behavior of 'setIs'
Hi Matthias,
A similar problem to yours (with one level of inheritance less) was
disccussed this month on the r-devel list.
You find an answer from JChambers here:
https://stat.ethz.ch/pipermail/r-devel/2004-October/030980.html
And yes specifying _setAs_ to each _setIs_ with the coerce and replace
is a _hack_ which is with this version of methods necessary when
inherting from Old Classes.
/E
[EMAIL PROTECTED] wrote:
Hello,
am I using 'setIs' in the correct way in the subsequent (artifical) example?
Do I have to specify explicit 'setAs' for 'list' and 'vector' or
should this work automatically, since getClass(List1) states
an explicit coerce also for these classes.
I'm working with R 2.0.0 Patched (2004-10-06) on windows 2000.
Thanks for your advice,
Matthias
# example
setClass(Class = List1, representation(List = list))
setClass(Class = List2, contains = list)
setIs(class1 = List1, class2 = List2,
coerce = function(obj){ new(List2, [EMAIL PROTECTED]) },
replace = function(obj, value){
[EMAIL PROTECTED] - value
})
getClass(List1)
# states explicit coerce for 'list' and 'vector'
getClass(List2)
L1 - new(List1, List = list(a))
# all TRUE
is(L1, List2)
is(L1, list)
is(L1, vector)
as(L1, List2) # works
# both return 'list()'
# why not a 'list' with entry a?
# Is there an additional 'setAs' needed?
as(L1, list)
as(L1, vector)
L2 - as(L1, List2)
as(L2, list) # works
as(L2, vector) # works
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Re: [R] Intro to R: lecture presentation
Same behavior with Firefox 1.0Pr. /E Thomas Schönhoff wrote: Hello Arin, Arin Basu schrieb: A couple of weeks back, I asked a question on the list that I was invited to provide an introductory lecture on R to a group of academicians in Kolkata. I thank all of you who had generously guided me in providing me web links and words to the wise. Time to give back. I did the presentation on introduction to R and uploaded the presentation files at the following site: http://www.aloofhosting.com/arinbasu/Rtutorial/Rintroweb_files/frame.htm A shortened form of url is here (easy for cutting and pasting): http://tinyurl.com/3zsr6 Would greatly appreciate your feedbacks/opinions/advices on errors/omissions. Both links don't work for me, simply get an empty page and a black frame on both websites (IE optimzed?) running Mozilla-1.7.x on Debian GNU/Linux. sincerely Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] plot.dendrogram and plot.hclust ZOOM into the height?
Hi, I clustered a distance matrix and would like to draw it using plot.hclust or plot.dendrogram. The dendrogram is not informative because I have a few extremely small dissimilarities in the distance matrix (e.g. 0), but most of the other distances are in the range 1e10+-5000. I would like to show the tree only for the height of 1e10+-5000 but unfortunately their are no parameter like xlim,ylim in the function? Are there other ways to ZOOM? Any suggestions? /E -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: plot.dendrogram and plot.hclust ZOOM into the height?
Hi, Just noted that dendr2 - cut(dendr1,h=1) plot(dendr2$upper) Gives what I am looking for. Sorry, Its quite late here. /E Witold Eryk Wolski wrote: Hi, I clustered a distance matrix and would like to draw it using plot.hclust or plot.dendrogram. The dendrogram is not informative because I have a few extremely small dissimilarities in the distance matrix (e.g. 0), but most of the other distances are in the range 1e10+-5000. I would like to show the tree only for the height of 1e10+-5000 but unfortunately their are no parameter like xlim,ylim in the function? Are there other ways to ZOOM? Any suggestions? /E -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] C/C++
Hi, Unfortunately I have only some beginners hints to this very interesting topic. Writing R extensions provides examples how to execute r functions from within C code. There is also somewhere a doc how to use R as a shared library (?). But I dont remember in which doc exactly. Furthermore Rserv: rserv (http://www.rosuda.org/Rserve/index.shtml) has a C++ API for calling r functions. Eryk. doktora v wrote: Hey everyone, I have been looking for a while for ways to integrate R's wonderful functions into my C++ software, but I have not found anything concrete. So finally, i post to this list to see if anyouse else knows about this, or has done it!? Is it possible? Are there C++ or C R libraries? Or is it sufficiently easy to build them? your help is much appreciated! thanks doktora __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin tel: 0049-30-83875219 __(_ http://www.molgen.mpg.de/~wolski \__/'v' http://r4proteomics.sourceforge.net||/ \ mail: [EMAIL PROTECTED]^^ m m [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] colClasses
I would try. colClasses=c(character,numeric,character,numeric,numeric) /E Kalaylioglu, Zeynep (IMS) wrote: Hi I am trying to read a data frame from a text editor in to R. I want some of the columns to be read in as character not numeric. I figured that I can do that by using colClasses in read.table command. However, I couldn't find out how to use colClasses. e.g. say I have 5 column in the data file. I want 1st and 3rd column to be read in as character. How can I define this using colClasses? (or is there a better way to do what I want?) Thanks. Zeynep [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin _ tel: 0049-30-83875219 __( 'v' http://www.molgen.mpg.de/~wolski \__/ / \ mail: [EMAIL PROTECTED]^^ w w [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-(wiki)-pedia?
Thomas Petzoldt wrote: Tony Plate wrote: At Thursday 11:29 AM 10/7/2004, Dan Bolser wrote: [snip] I just added some pages... I think it would be great if people could get motivated to contribute to something like this. Its one of those cases of just getting the ball rolling... Do you think you can dump the existing R-docs into this wiki as a framework to get things going? If the existing R-docs are dumped into a wiki, won't the copy in the Wiki quickly get out of date? How does one get around this problem? And another problem is, how to reverse from something like HTML or XML back to .Rd ? I think that a generic format is absolutely necessary. The generic format we have and not yet another source of confusion. If wiki means editing .Rd sources or better: inverse transformation in both sides (without to many loss), it would be nice. Is there really a chance? Shurely their is. Define an XML schema. Write functions Rd2XML, XML2Rd, twiki2XML, . I am looking since ages for something like R2XML and XML2Rd. If we can agree on an XML format for the documentation it will be something to start with. Yours Thomas P. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin _ tel: 0049-30-83875219 __( 'v' http://www.molgen.mpg.de/~wolski \__/ / \ mail: [EMAIL PROTECTED]^^ w w [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] setClass - equvalent declarations?
Hi, Why the third declation is not equivalent to the first 2 and gives a Warning #1 setClass(MVE,representation(list,names=character)) #2 setClass( MVE ,contains=list ,representation( names=character ) ) #3 setClass(MVE,matrix,representation(names=character)) [1] MVE Warning message: prototype is a list with named elements (could be ambiguous): better to use function prototype() to avoid trouble. in: reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, /E. -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin _ tel: 0049-30-83875219 __( 'v' http://www.molgen.mpg.de/~wolski \__/ / \ mail: [EMAIL PROTECTED]^^ w w [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Reading multiple files into R
Hi!
There is a function ?dir which returns you the content of the dir_ectory.
If this is more then there is a function ?grep which allows you to
extract relevant items.
If you need to postprocess the names you have a function ?paste for example.
And finally you have an S language construct for(){}
And there is help.search() and An Introduction to R to which tells you
how to write functions.
/E
Vikas Rawal wrote:
I want to read data from a number of files into R.
Reading individual files one by one requires writing enormous amount
of code that will look something like the following.
maptools:::dbf.read(wb-01vc.dbf)-dist1
maptools:::dbf.read(wb-02vc.dbf)-dist2
maptools:::dbf.read(wb-03vc.dbf)-dist3
maptools:::dbf.read(wb-04vc.dbf)-dist4
maptools:::dbf.read(wb-05vc.dbf)-dist5
maptools:::dbf.read(wb-06vc.dbf)-dist6
maptools:::dbf.read(wb-07vc.dbf)-dist7
maptools:::dbf.read(wb-08vc.dbf)-dist8
maptools:::dbf.read(wb-09vc.dbf)-dist9
*
Is there a better way of doing this?
Vikas
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Re: [R] Rnewsletter article example
me too, E, Samuel Kemp wrote: Hi, I am trying to write an article for the Rnewsletter, but keep getting errors. I have googled around for some decent examples that contain figures, maths, etc but with no joy. Would any be so kind as to send me an example article in latex code? Cheers, Sam. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin _ tel: 0049-30-83875219 'v' http://www.molgen.mpg.de/~wolski / \ mail: [EMAIL PROTECTED] ---W-W [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] function by
?by FUN: a function to be applied to data frame subsets of 'data'. ...: further arguments to 'FUN'. by (SS, year, sum) /E Emilie Berthiaume wrote: Hi, I'm just getting started with R and I'm having problems with some simple operations: I want to get the the sum of the column SStot for each year using the function by. The data set is named SS. I've tried this: by (SS, year, sum(SStot)) and it's not working. Is it because there's a different number of rows for each year? How else can I do this? -- Emilie Berthiaume Graduate student Biology Departement Université de Sherbrooke 2500 boul. de l'Université Sherbrooke, Québec J1K 2R1 CANADA Tél: 1-819-821-8000 poste 2059 Fax: 1-819-821-8049 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin _ tel: 0049-30-83875219 'v' http://www.molgen.mpg.de/~wolski / \ mail: [EMAIL PROTECTED] ---W-W [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Is there any way to release memory in running time?
?gc /E [EMAIL PROTECTED] wrote: Hi all, I am doing some intensive computation right now. My system is Pentium4 3.20G + 1.0G RAM + WindowsXP + R1.9.1. It seems my computer is very powerful. However, when I do some simple matrix algebra operations based on a matrix (DD) with dimension 500 by 2, I found that the consumption of RAM is huge. For example, the command a - 1 - DD[,2] eats my 100M RAM. Does anyone know how to release memory in the middle of program (running time)? BTW, the command rm() does not free memory unless you quit R as I as know. Thanks in advance. Rui __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin _ tel: 0049-30-83875219 'v' http://www.molgen.mpg.de/~wolski / \ mail: [EMAIL PROTECTED] ---W-W [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] add-on packages
Hi! install.packages(RMySQL) ^ ^ note the parenthesis /E Vikas Rawal wrote: I want to add RMySQL and RODBC packages to my R installation on redhat linux box. The command install.packages gives following output. What could be wrong? trying URL `http://cran.r-project.org/src/contrib/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 202145 bytes opened URL .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. ... downloaded 197Kb Error in unique(pkgs) : Object RMySQL not found ** Vikas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin _ tel: 0049-30-83875219 'v' http://www.molgen.mpg.de/~wolski / \ mail: [EMAIL PROTECTED] ---W-W [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] slow loops in Monte Carlo Simulations
Hi! Have you taken a look at the MCMCpack - package on cran: This package contains functions for posterior simulation for a number of statistical models. All simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0. All models return coda mcmc objects that can then be summarized using the coda package. /E Nael Al Anaswah wrote: Hi there, I am running Monte Carlo Simulations in R using ordinary while (condition) loops. Since the number of iterations is something like 100.000 and within each iteration a given subsample is extended sequentially it takes hours to run the simulation. Does anyone know if there is either a way to avoid using loops in Monte Carlo Simulations or how to include possible faster c++ commands in R code? many thanks in advance. Nael Al-Anaswah - Nael Al-Anaswah Department of Econometrics University of Muenster Germany __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dipl. bio-chem. Witold Eryk Wolski MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin _ tel: 0049-30-83875219 'v' http://www.molgen.mpg.de/~wolski / \ mail: [EMAIL PROTECTED] ---W-W [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] S4 method selection based on second argument
Hi,
If it's the only reason why you think you have to use S4 then take a
look at ?missing.
If you are interested in S4:
The first version gives an overview of setMethods. Then I give a simpler
example. And finally a pure ?missing solution.
A) Declare function repmat as generic
if(!isGeneric(repmat))
setGeneric(repmat
,function(obx,oby,obz,...)
standardGeneric(repmat))
#B = repmat(A, m, n)
setMethod(repmat,signature(obx=numeric,oby=numeric,obz=numeric)
,function(obx,oby,obz){print(thre arg call)
})
#B = repmat(A, [m n])
#B = repmat(A, n)
setMethod(repmat,signature(obx=numeric,oby=numeric,obz=missing)
,function(obx,oby)
{
print(two arg)
#handle the difference in oby.
if(length(oby)==1)
oby
else
obx
})
##END A ###
#simpler
#if(!isGeneric(repmat)) #commented out because you have already declared it.
setGeneric(repmat
,function(object,...)
standardGeneric(repmat))
setMethod(repmat,signature(object=numeric)
,function(object,oby,obz)
{
#using ?missing handle the differences.
if(missing(obz))
print(new version)
})
Note that you can have the same in S3 using ?missing
something like this.
repmat - function(A, m, n) {
if(missing(n)
{
if(length(m)==2)
{
repmat1(A, m[1], m[2])
}
else
kronecker(matrix(1, m, m), A)
}
kronecker(matrix(1, n, m), A)}
}
/E
Paul Roebuck wrote:
I'm translating some Matlab code and need some help figuring
out how to change this call into an S4 generic method.
In matlab, there's a function called 'repmat' with three
calling sequences (all I have to deal with anyway):
1) B = repmat(A, m, n)
2) B = repmat(A, [m n])
3) B = repmat(A, n)
In all cases, A is the fill value, m is number of rows,
and n is number of columns.
As separate functions, the translations would roughly be:
repmat1 - function(A, m, n) {
kronecker(matrix(1, n, m), A)
}
repmat2 - function(A, rc) {
repmat1(A, rc[1], rc[2])
}
repmat3 - function(A, n) {
repmat1(A, n, n)
}
Suggestions?
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Re: [R] Best device for printing quality
Hi! I would first check what kind of graphic format the article publisher of the article accepts. If ps/pdf is ok I would use ?postscript. Otherwise I would change the journal. /E *** REPLY SEPARATOR *** On 9/24/2004 at 11:12 AM javier garcia - CEBAS wrote: Hi all; Just to ask you for your advise about what is the best way to get the best quality for graphics to be incorporated into a printed article (I'm mainly a Linux useR, but also use the windows R version) Thanks and best regards, Javier Garcia __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to plot residuals vs. fitted of trgls object (spatial::surf.gls)
Hi! Would like to to make a plot of residuals vs. fitted and Y vs. predicted values from an object of class trgls as returned by spatial::surf.gls directly. (without calling spatial::predict.trgls) Is it possible? on which list components should I look at? /E __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] persiting complex R objects
Hi! ?save 'save' writes an external representation of R objects to the specified file. The objects can be read back from the file at a later date by using the function 'load' (or 'data' in some cases). ?load Reload the datasets written to a file with the function 'save'. /E *** REPLY SEPARATOR *** On 9/20/2004 at 12:00 PM Richard Mott wrote: Is there a method to save a large and complex R object (either as a binary or text file) so that it can be loaded and reused at a later time? Specifically, I am creating large lists (several thousand elements), each element of which is either a vector or a matrix (with ~ 2000 rows). The dimensions of the matrices are not all the same. My ideal would be a set of functions of the form obj - create() # computes the object save(obj,filename) obj - load(filename) -- Richard Mott | Wellcome Trust Centre tel 01865 287588 | for Human Genetics fax 01865 287697 | Roosevelt Drive, Oxford OX3 7BN __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Multiple operations on list
Hi! Not sure if I got your point. But if it is to compute apply a function to all pairs (x1,x2);(x1,x3);(x2,x3) where x1,x2,x3 are stored in a list you can take look at the sources of function listdist which computes an object of class dist from a list, in the package pairseqsim available from bioconducor, to get an idea how to do this. /E *** REPLY SEPARATOR *** On 20.09.2004 at 13:24 Stephane DRAY wrote: Hello, suppose I have a list with matrices: a=list(x1=matrix(rnorm(10),5,2),x2=matrix(rnorm(10),5,2),x3=matrix(rnorm(10),5,2)) I want to compute for all combination of xi and xj (x1,x2 x1,x3 and x2,x3) a value. This value is given for the pair x1,x2 by trace(x1%*%t(x1)%*%x2%*%t(x2)) / trace(x1%*%t(x1))*trace(x2%*%t(x2)) I know that product matrices t(xi)%*%xi can be obtained by: aa=lapply(a,crossprod) but I do not know how to mix the values in aa to obtain the desired values. Is there a way to do it without for loop ? Thanks in advances, sincerely Stéphane DRAY -- Département des Sciences Biologiques Université de Montréal, C.P. 6128, succursale centre-ville Montréal, Québec H3C 3J7, Canada Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293 E-mail : [EMAIL PROTECTED] -- Web http://www.steph280.freesurf.fr/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Conditionally swap two columns of a data.frame?
Hi!
Better then a cookbook.
http://www.ku.edu/~pauljohn/R/Rtips.html
/E
Ps.
*** REPLY SEPARATOR ***
On 9/16/2004 at 1:55 PM Dan Bolser wrote:
Minter!
Is there an R cookbook? which lists this kind of common problem and
common
solution?
On Thu, 16 Sep 2004, Dimitris Rizopoulos wrote:
Hi Dan,
do you need something like that,
dat - data.frame(V1=rnorm(4, 10), V2=rnorm(4, 10))
ratioV1V2 - ifelse(dat$V1dat$V2, dat$V1/dat$V2, dat$V2/dat$V1)
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/396887
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: Dan Bolser [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, September 16, 2004 2:19 PM
Subject: [R] Conditionally swap two columns of a data.frame?
I am doing this a kinda dumb way, and it is apparetnly taking
forever.
I have a data frame with two numeric columns. I want to look at
their
correlation, and I am looking at the size ratio between the two.
i.e.
plot(density(data$V1/data$V2))
This kinda gives me a normal curve showing something about the
distribution of the two values.
I want to make sure that V1/V2 is always 1 ...
for (i in 1:length(row.names(data)) ){
ratioV1V2 - if(V1V2) V1/V2 else V2/V1
}
This is a bit of a hack, and is taking forever for some reson (about
40,000 rows in my data.frame).
I would just like to swap the values in the data frame (to put the
bigest
first for example), then use the above plot to get what I want.
Should I use the DB backend to the data to make the dump in this
way?
(involves some hacky sql)
Considering I am interested in the range of the ratio between V1 and
V2,
should I be looking at doing a different analysis?
I am so dumb, any help is appreciated,
Dan.
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Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic
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Re: [R] Multi-dimensional scaling
See: www.r-project.org - Documentation-Newsletter-Volume 3/3, December 2003 There is an artikle by Jonathan Edwards and Paul Oman Dimensional Reduction for Data Mapping /E *** REPLY SEPARATOR *** On 9/16/2004 at 3:28 PM Luis Rideau Cruz wrote: R-help, Is there any package/function in R which can perform multi-dimensional scaling? Thank you in advance __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Density Estimation
Hi!
The function density returns you a object of class density.
This object has an x and an y attribute which you can access by x y,
Hi!
Use approx and runif.
eg.:
dd-density(rnorm(100,3,5))
plot(dd)
Using the function ?approx you can compute the density value for any x.
#the x is a dummy here.
mydist-function(x,dd)
{
while(1)
{
tmp - runif(1,min=min(dd$x),max=max(dd$x))
lev - approx(dd$x,dd$y,tmp)$y
if(runif(1,c(0,1)) = lev)
{
return(tmp)
}
}
}
x - 0
mydist(x,dd)
res-rep(0,500)
res-sapply(res,mydist,dd)
lines(density(res),col=2)
/E.
*** REPLY SEPARATOR ***
On 9/15/2004 at 12:36 PM Brian Mac Namee wrote:
Hi there,
Sorry if this is a rather loing post. I have a simple list of single
feature data points from which I would like to generate a probability
that an unseen point comes from the same distribution. To do this I am
trying to estimate the probability density of the list of points and
use this to generate a probability for the new unseen points. I have
managed to use the R density function to generate the density estimate
but have not been able to do anything with this - i.e. generate a
rpobability that a new point comes from the same distribution. Is
there a function to do this, or am I way off the mark using the
density function at all?
Thanks in advance,
Brian.
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Re: [R] erase columns
?subset /E *** REPLY SEPARATOR *** On 9/14/2004 at 10:44 AM michele lux wrote: Can somebody remember me which is the command to erase columns from a data frame? Thanks Michele ___ http://it.seriea.fantasysports.yahoo.com/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave echoing comments (again)
Hi!
I observed it also. There are cases where it is not desirable. It will be quite
helpfull, if possible, to have a parameter that allows one to switch of removing the
#comments.
/E
*** REPLY SEPARATOR ***
On 9/6/2004 at 1:30 PM Thomas Petzoldt wrote:
Hello,
I try to document some R scripts for my collegues and observed the
problem, that Sweave strips comment lines away.
As a small example I write in an Rtex file:
\begin{Scode}
## a small example
test() # line comment
\end{Scode}
... the .tex file generated by Sweave only contains:
\begin{Schunk}
\begin{Sinput}
test()
\end{Sinput}
\end{Schunk}
... and all the comments are lost. Looking into the archives, I found,
that such a question appeared already some months ago. Are there any
advances or workarounds doing such things today?
Thank you in advance!
Thomas P.
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Re: [R] using text on the x axis ticks rather than numbers
Hi! first supress axis drawing with param axes=FALSE in your plot function. The use axis function to add your axes. ?axis /E On Tue, 7 Sep 2004, Rajarshi Guha wrote: Hello, is there a way in which I can use text labels rather than numbers on the x axis ticks? I basically have a vector of (say) 8 points and I want to plot these sequentially. Thus the x axis would have ticks at 1 .. 8. Rather than having the labels 1 .. 8 I would like to have some arbitrary text labels. Ideally I would like the labels to be rotated (say at 45 degrees) so that they don't overlap with each other. Is this possible? Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Breadth-first search is the bulldozer of science. -- Randy Goebel __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] substitution in expression
Hi! plot(1:10, main=expression(paste( x, , Delta, values ))) /E *** REPLY SEPARATOR *** On 9/6/2004 at 3:50 PM Adaikalavan Ramasamy wrote: I have been struggling with this problem for a while and I hope someone could help me. Or if someone could point me to a section in the manual I would be grateful. x - my plot(1:10, main=expression(paste( x, Delta, values ))) Q : How do I get the title to say my (triangle symbol) values ? The following trial-and-error produced mainly errors : plot(1:10, main=expression(paste( get(x), Delta, values ))) plot(1:10, main=expression(paste( substitute(x), Delta, values ))) plot(1:10, main=expression(paste( deparse(x), Delta, values ))) plot(1:10, main=paste(x, expression(Delta), values)) plot(1:10, main=paste(x, eval(expression(Delta)), values)) plot(1:10, main=paste(x, expression(Delta, values ))) plot(1:10, main=paste(x, expression(paste(Delta, values Many thanks. Regards, -- Adaikalavan Ramasamy[EMAIL PROTECTED] Centre for Statistics in Medicine http://www.ihs.ox.ac.uk/csm/ Cancer Research UK Tel : 01865 226 677 Old Road Campus, Headington, Oxford Fax : 01865 226 962 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] substitution in expression
Hi! Sorry for the previous mail. Take a look at parse. ?parse x-my plot(1:10, main=parse(text=x)) Eryk. *** REPLY SEPARATOR *** On 9/6/2004 at 3:50 PM Adaikalavan Ramasamy wrote: I have been struggling with this problem for a while and I hope someone could help me. Or if someone could point me to a section in the manual I would be grateful. x - my plot(1:10, main=expression(paste( x, Delta, values ))) Q : How do I get the title to say my (triangle symbol) values ? The following trial-and-error produced mainly errors : plot(1:10, main=expression(paste( get(x), Delta, values ))) plot(1:10, main=expression(paste( substitute(x), Delta, values ))) plot(1:10, main=expression(paste( deparse(x), Delta, values ))) plot(1:10, main=paste(x, expression(Delta), values)) plot(1:10, main=paste(x, eval(expression(Delta)), values)) plot(1:10, main=paste(x, expression(Delta, values ))) plot(1:10, main=paste(x, expression(paste(Delta, values Many thanks. Regards, -- Adaikalavan Ramasamy[EMAIL PROTECTED] Centre for Statistics in Medicine http://www.ihs.ox.ac.uk/csm/ Cancer Research UK Tel : 01865 226 677 Old Road Campus, Headington, Oxford Fax : 01865 226 962 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Standard correlation
Hi! ?scale ?var ?cov /E *** REPLY SEPARATOR *** On 9/3/2004 at 2:20 PM michael watson (IAH-C) wrote: OK I better clarify what I mean as it appears it may not be a standard test. The pearson correlation coefficient, in laymans terms, uses the shape of a curve around that curve's average to compare two curves. The standard correlation coefficient measures the shape of a curve around zero, and uses that to compare the two curves. Therefore a measure that starts at 1 and increases away from zero, and a measure that starts at -4 and increases towards zero, will be deamed similar via pearson's correlation coefficient, and dissimilar via the standard correlation coefficient. This is useful when increase away from zero is very different behaviour from increase towards zero. There are some descriptions here: http://ccgb.umn.edu/support/software/gspring/HelpPages/GSUM-120.html http://www.optimaldesign.com/AMHelp/HowTo/HowToChooseClustParam.htm -Original Message- From: Stefan Drees [mailto:[EMAIL PROTECTED] Sent: 03 September 2004 14:03 To: [EMAIL PROTECTED] Cc: michael watson (IAH-C); Stefan Drees Subject: Re: [R] Standard correlation On Fri, Sep 03, 2004 at 01:30:36PM +0100 - a wonderful day - michael watson (IAH-C) wrote: Is there a function for computing the standard correlation coefficient (not pearson) in R? help (cor) yields the following in my R 1.9.1 installation: ... cor(x, y = NULL, use = all.obs, method = c(pearson, kendall, spearman)) ... HTH, Stefan. -- .o. e-mail: [EMAIL PROTECTED], web: www.sdrees.org, +49 700 SDREESDE ..o fingerprint = 516C C4EF 712A B26F 15C9 C7B7 5651 6964 D508 1B56 ooo stefan drees - consulting and lecturing - problems to tasks __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Accesing the name of an assigned object in a function
?assign
/E
On Wed, 1 Sep 2004, Henrik Andersson wrote:
I want to use the name that I assign to an object in the function that
produces the output, somewhat like below:
stupid.function - function(input){
[body]
cat(Summarized output is , output$summary, Full output is
given
by typing, assigned.name, \n)
}
assigned.name - stupid.function(whatever)
or another example is a function that sinks the results to a text file
and names it assigned.name.txt .
I checked the help for function, -, assign but could not find it, is it
possible ?
-
Henrik Andersson
Netherlands Institute of Ecology -
Centre for Estuarine and Marine Ecology
P.O. Box 140
4400 AC Yerseke
Phone: +31 113 577473
[EMAIL PROTECTED]
http://www.nioo.knaw.nl/ppages/handersson
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Re: [R] (no subject)
sum(x=7)/length(x)*100 *** REPLY SEPARATOR *** On 8/31/2004 at 8:16 AM Paolo Tommasini wrote: Hi this is a very simple question ! if a have a set of date like x=c(1,2,3,4,4,5,6,8,7,8,8) how can I find out the percentile of 7 ? thanks Paolo __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] blockwise sums
Hi!
ind-c(sort(rep(1:floor(length(x)/ 3 ) , 3 )) , floor(length(x)/ 3 )+1)
by(x,ind,sum)
my.blockwisesum-function(x,n,...)
{
ind-c(sort(rep(1:floor(length(x)/ n ) , n )) , floor(length(x)/ n )+1)
return(tapply(x,ind,sum))
}
/Eryk
*** REPLY SEPARATOR ***
On 8/31/2004 at 2:19 PM Lutz Prechelt wrote:
I am looking for a function like
my.blockwisesum(vector, n)
that computes sums of disjoint subsequences of length n from vector
and can work with vector lengths that are not a multiple of n.
It should give me for instance
my.blockwisesum(1:10, 3) == c(6, 15, 24, 10)
Is there a builtin function that can do this?
One could do it by coercing the vector into a matrix of width n,
and then use apply,
but that is cumbersome if the length is not divisible by n,
is it not?
Any other ideas?
Lutz
Prof. Dr. Lutz Prechelt; [EMAIL PROTECTED]
Institut fuer Informatik; Freie Universitaet Berlin
Takustr. 9; 14195 Berlin; Germany
+49 30 838 75115; http://www.inf.fu-berlin.de/inst/ag-se/
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Re: [R] More efficient matrix computation
Hi! apply(m,2,quantile,c(0.95,0.99)) /Eryk *** REPLY SEPARATOR *** On 8/31/2004 at 9:16 AM JTW wrote: I have a 20x3 matrix as follows: m - replicate(3, matrix(rnorm(20),20,1)) I need to compute, say, 95th and 99th percentiles of each column such that the resulting matrix becomes 2x3 with each row representing the respective percentile. My best effort is to compute one column at a time as follows: quantile(m[,1], c(0.95, 0.99)) To do the same for columns 2 and 3, I would simply change the column number accordingly. Clearly, this is not very efficient as I may have a large matrix (e.g., 100,000x500) to work with. Any help with the code is appreciated. Jack Wang __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sparse Matrices in R
Hi! help.search(sparse matrix) graph2SparseM(graph)Coercion methods between graphs and sparse matrices tripletMatrix-class(Matrix) Class tripletMatrix sparse matrices in triplet form SparseM.hb(SparseM) Harwell-Boeing Format Sparse Matrices image,matrix.csr-method(SparseM) Image Plot for Sparse Matrices etc . /E *** REPLY SEPARATOR *** On 8/31/2004 at 5:52 PM Danny Heuman wrote: I have data in i,j,r format, where r is the value in location A[i,j] for some imaginary matrix A. I need to build this matrix A, but given the sizes of i and j, I believe that using a sparse format would be most adequate. Hopefully this will allow me to perform some basic matrix manipulation such as multiplication, addition, rowsums, transpositions, subsetting etc etc. Is there any way to achieve this goal in R? Thanks, Danny [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] About passing parameter to '.R' script file
Hi! You can do it indirectly e.g within a batch file. a) set an envirovment variable (the path to the file) b) access it from within you *.R script using ?Sys.getenv Hope it helps. Eryk *** REPLY SEPARATOR *** On 8/27/2004 at 4:36 PM Kishore, Tapake wrote: Hi, I am trying the 'R' application for generating the data for the uploaded '.gpr' file. I have written script file named 'test.R'. Currently i have hardcoded the path of uploaded '.gpr' file in the script itself. I would like to know how to pass a command line parameter to the 'test.R' script file, so that i dont have to hardcode the path and filename of the '.gpr' files. Also, need to access these parameters inside the script file to use the path of the uploaded file. I am using below command to invoke the 'R' application by using the 'test.R' script file. e.g. c:\\R\\rw1091\\bin\\R.exe CMD BATCH c:\\R\\rw1091\\bin\\test.R Expecting your suggestion on this. Thanks in advance. Regards, Kishore __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] for (i in ...) { df[[i]]- .....}
?do.call
do.call(cc,cbind)
Hope it helps
Eryk
*** REPLY SEPARATOR ***
On 8/27/2004 at 2:11 PM Luis Rideau Cruz wrote:
R-help,
In the following loop :
for(i in 1:8)
{
cc[[i]]-tapply(test[,i+6],list(puntar=test$puntar),sum)/tapply(test[,5],list(puntar=test$puntar),sum)
cbind.data.frame(cc[[1]],cc[[2]],cc[[3]],cc[[4]],
cc[[5]],c[[6]],cc[[7]],cc[[8]])
}
Is there anyway I can 'cbind.data.frame' the objects cc[[ i ]] without
actually writing every single element??
In this case there are 8 but what if it is a large number??
Thank you
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Re: [R] Running R from CD?
Hi! Make a isntallation of R on a PC where it is allowed. Install all packages you need. Burn the installation folder (rw1091) on the CD. Start R by clicking on Rgui.exe in the bin folder (rw1091/bin). Or set a path on the command line to (CD drive letter) :\rw1091\bin Or create a shortcut. This should work. Hope it helps. Eryk Ps. If you need to install afterwards package you have to set R_LIBS to a writable drive. *** REPLY SEPARATOR *** On 8/27/2004 at 3:54 PM Hans van Walen wrote: At work I have no permission to install R. So, would anyone know whether it is possible to create a CD with a running R-installation for a windows(XP) pc? And of course, how to? Thank you for your help, Hans van Walen __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] relative frequencies for hist()
Hi! d$counts/length(a) And of course you can if it is what you want. d$density-d$counts/length(a) plot(d,freq=F) Sincerely Eryk *** REPLY SEPARATOR *** On 8/21/2004 at 7:10 PM Steffen Katzner wrote: I have problems getting a histogram with relative frequencies on the y-axis. Here is an example data set: a - c(4.626, 4.627, 4.627, 4.628, 4.629, 4.629, 4.630, 4.631, 4.632, 4.632) d = hist(a,freq=F) d$density [1] 299. 100. 200. 100. 100. 200. The obtained densities are given by counts/(total n * bin width), with bin width being 0.001 in this case. Is there any way to get a histogram with relative frequencies irrespective of bin width, i.e. counts/total n ? It doesn't seem to work for truehist() either. Thanks. Steffen __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] lapply drops colnames
Hi!
The (column) - names are a property of the data.frame (list - from which data.frame
inherits (at least theoretically (green book) how it is implemented in R I do not
know.) The columns of the data.frame are lists again. The data.frama is the box and a
column is a list in the data.frame list. lapply is working on list elements. The
column list does not know anything about the list (data.frame) in which it is stored.
Hence, it does not know also the name (index) at which it is stored. lapply is
iterating through this container
not randomly.
What you can do is to extend the column (list) by an addtional attribute
attr(mydataframe[i],info)-names(mydataframe)[i] and store theyr names in it.
After you have done it you can
lapply(a, function(x) {print(attr(x,info))})
Hope it helps.
Eryk
*** REPLY SEPARATOR ***
On 8/2/2004 at 5:03 PM Jack Tanner wrote:
I want to iterate over a data frame by columns, and as I'm processing
each column I want to know its column name.
a - as.data.frame(list(1,2,3))
colnames(a) - c(a, b, c)
colnames(a)
[1] X1 X2 X3
lapply(a, function(x) {print(colnames(x))})
NULL
NULL
NULL
$a
NULL
$b
NULL
$c
NULL
What is lapply doing? Why does it drop the column name of every column
it's iterating over? How can I get the column name as a string?
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[R] Comparing correlated (paired) ROC curves (sensitivities).
Hi! I am looking for functions which I can use to compare correlated ROC curves, or even better correlated (paired - obtained from the same data with different measures) sensitivities given FP rates. Eryk Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] as(obj,matrix)
Hi! Here a simple example. setClass(myclass ,representation(info=character) ,contains=matrix ) rownames(dd)-c(a,b) tt-new(myclass,dd) #the source of pain. as(tt,matrix)-matrix(1,3,3) Error: length of dimnames [1] not equal to array extent Is there a different way to do what I would like to do (I would like to change the @.Data and all its attributes in the object)? Eryk. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] as(obj,matrix)
The definition of dd is. dd-matrix(0,2,2) *** REPLY SEPARATOR *** On 7/28/2004 at 4:12 PM Adaikalavan Ramasamy wrote: On Wed, 2004-07-28 at 15:55, Wolski wrote: Hi! Here a simple example. setClass(myclass ,representation(info=character) ,contains=matrix ) rownames(dd)-c(a,b) Er, I don't think you have defined 'dd' in the example. tt-new(myclass,dd) #the source of pain. as(tt,matrix)-matrix(1,3,3) Error: length of dimnames [1] not equal to array extent Is there a different way to do what I would like to do (I would like to change the @.Data and all its attributes in the object)? Eryk. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] ordering of levels.
Hi! Have the following factors with the following levels. tmp$norm [1] rank rank rank rank rank log log log rank sqrt sqrt sqrt log log rank [16] rank rank sqrt sqrt sqrt sqrt log log log log sqrt none none none none [31] none none none none sqrt none Levels: log none rank sqrt I would like to add an ordering to the levels. nonesqrtlogrank I tried with tmp$norm -factor(tmp$norm,labels = c(none,sqrt,log,rank),ordered=T) tmp$norm [1] log log log log log none none none log rank rank rank none none log [16] log log rank rank rank rank none none none none rank sqrt sqrt sqrt sqrt [31] sqrt sqrt sqrt sqrt rank sqrt Levels: none sqrt log rank But this is not what I would like to have because the command not only superimposes an ordering but also changes the factors! Eryk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ordering of levels.
Hi! Thanks a lot. Eryk *** REPLY SEPARATOR *** On 7/26/2004 at 2:07 PM Sundar Dorai-Raj wrote: Wolski wrote: Hi! Have the following factors with the following levels. tmp$norm [1] rank rank rank rank rank log log log rank sqrt sqrt sqrt log log rank [16] rank rank sqrt sqrt sqrt sqrt log log log log sqrt none none none none [31] none none none none sqrt none Levels: log none rank sqrt I would like to add an ordering to the levels. nonesqrtlogrank I tried with tmp$norm -factor(tmp$norm,labels = c(none,sqrt,log,rank),ordered=T) tmp$norm [1] log log log log log none none none log rank rank rank none none log [16] log log rank rank rank rank none none none none rank sqrt sqrt sqrt sqrt [31] sqrt sqrt sqrt sqrt rank sqrt Levels: none sqrt log rank But this is not what I would like to have because the command not only superimposes an ordering but also changes the factors! Eryk Eryk, See ?factor or ?ordered which will help. I think what you want is: lev - c(none, sqrt, log, rank) tmp$norm - ordered(tmp$norm, levels = lev) or tmp$norm - factor(tmp$norm, levels = lev, ordered = TRUE) Note the use of levels and not labels. --sundar Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] binning a vector
?tapply *** REPLY SEPARATOR *** On 7/26/2004 at 5:11 PM [EMAIL PROTECTED] wrote: Hello, I was wondering wether there's a function in R that takes two vectors (of same length) as input and computes mean values for bins (intervals) or even a sliding window over these vectros. I've several x/y data set (input/response) that I'd like plot together. Say the x-data for one data set goes from -5 to 14 with 12,000 values, then I'd like to bin the x-vector in steps of +1 and calculate and plot the mean of the x-values and the y-values within each bin. I was browsing the R-docs but couldn't find anything appropiate. thanks for hints + kind regads, Arne __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] retrieve rows from frame assuming criterion
?subset Eryk *** REPLY SEPARATOR *** On 7/23/2004 at 2:36 PM Luis Rideau Cruz wrote: Hi all, I have a data frame in which one column(PUNTAR) is of character type. What I want is to retrieve is the frame but only with those rows matching elements of PUNTAR with a list characters (e.g c(IX49,IX48) ) YearTUR STODNR PUNTAR 1994 9412 94020061 IX49 1994 9412 94020062 IX48 1994 9412 94020063 X32 1994 9412 94020065 X23 1994 9412 94020066 X27 1994 9412 94020067 XI19 1994 9412 94020068 XI16 1994 9412 94020069 XI14 1994 9412 94020070 XI8 1994 9412 94020071 X25 1994 9412 94020072 X18 1994 9412 94020073 II23 1994 9412 94020074XII33 1994 9412 94020075XII31 my.function(frame) should be then equal to Year TURNR STODNR M_PUNTAR 1994 9412 94020061 IX49 1994 9412 94020062 IX48 Thank you in advance Luis Ridao Cruz Fiskirannsóknarstovan Nóatún 1 P.O. Box 3051 FR-110 Tórshavn Faroe Islands Phone: +298 353900 Phone(direct): +298 353912 Mobile: +298 580800 Fax: +298 353901 E-mail: [EMAIL PROTECTED] Web:www.frs.fo __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] biplot identify
Hi! Is there a way to get biplot and identify to work togheter. Having the output of prcomp I would like to draw a biplot that. Instead of plotting the sample (row-names) names plots some pch symbols. (thats easy with xlabs) But now I would like to add using identify the names to only some of the points. I have noticed that both biplot.prcomp and biplot.default does a lot of scaling. So has anyone a function like identify.prcomp please? Is it possible? Sincerely Eryk Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] 2 images with 2 color scales on one graphic device. How to get it?
Hi! Would like to plot two image plots with color scale (like levelplot (lattice) implements) in one graphic device. Tried to plot 2 levelplot's (lattice) (the data has not much in common) in one graphics device by setting par(mfrwo=c(2,1)) which does not work. Is there a way to force levelplot to use only a half of the graphic device? Is there a function like image which provides the color scale and is working with par(mfrow, mfcol? Eryk Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sort a data frame
Hi Lets assign your data frame to the variable yourdf then: yourdf[ , order( yourdf$year ) ] should sort it. For decreasing increasing sorting see ?order Sincerely Eryk. *** REPLY SEPARATOR *** On 20.07.2004 at 09:51 Luis Rideau Cruz wrote: Hi all I have the next data frame year STODSLAGNR TAL TALT TALVEKT 1 2002 2120006 57 1 NA 1 2 1997 9703003257 NA NA NA 3 1997 9703007127 1 NA NA 4 1997 9703000557 1 NA NA 5 1997 9702012760 NA 1 NA 6 2001 1160025 27 1 NA 1 7 1998 9802006960 1 NA NA 8 1996 9603000957 NA 1 NA How to sort it according to year column Sort does seem to work only on vectors Thank you Luis Ridao Cruz Fiskirannsóknarstovan Nóatún 1 P.O. Box 3051 FR-110 Tórshavn Faroe Islands Phone: +298 353900 Phone(direct): +298 353912 Mobile: +298 580800 Fax: +298 353901 E-mail: [EMAIL PROTECTED] Web:www.frs.fo __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] vectorizing a matrix computation
Hallo Christoph!
Using apply and sweep.
Both of them accept as the second argument (MARGIN) a vector which specifies the
dimension.
?apply
?sweep.
To specify the subscripts accurately I always need some trials, and to run tests, so I
cant you provide with the final solution.
Hope it helps anyway.
Sincerely Eryk.
*** REPLY SEPARATOR ***
On 7/20/2004 at 11:31 AM Christoph Lehmann wrote:
Dear R users
I have a 4-dimensional matrix (actually several 3d (x,y, slices)
matrices appended over time (volumes))
say, e.g. I want to z-transform the data (subtract the mean and divide
by the std-deviation)
for (slice in 1:slices) {
for (x in 1:x.dim) {
for (y in 1:y.dim) {
t - as.matrix(my.matrix[x,y,slice,1:volumes])
for (vol in 1:volumes) {
my.matrix.transformed[x,y,slice,vol] -
(my.matrix[x,y,slice,vol] - mean(t))/sqrt(var(t))
}
}
}
}
how can I vectorize such a function using, one of the *apply functions?
many thanks
Cheers
Christoph
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Re: [R] (no subject)
Hello! It just is not able to find the file as the error message says. You can check if you are specified the right directory path using dir. ?dir dir(/Desktop/work/) I gues you are not. If you are specifying the full path, precede it with the drive name c:/ Eryk *** REPLY SEPARATOR *** On 7/14/2004 at 10:02 AM Herman, David (NIH/NIMH) wrote: Hello, I'm new to R, and I'm having trouble importing a text file (I'm on Windows XP) m - read.table(/Desktop/work/128_L) Error in file(file, r) : unable to open connection In addition: Warning message: cannot open file `/Desktop/work/128_L' do you know why this isn't working? All I have is a bunch of text files, each with a single column of about 30,000 rows. thanks [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] variable definition
Hallo! ?assign z-now assign(paste(go, z, sep = .) ,10) Sincerely Eryk *** REPLY SEPARATOR *** On 7/11/2004 at 10:02 PM Andrew R. Criswell wrote: Hello All: This function obviously fails x - function(z) - 10 x(now) But is there a way to define the name of a variable through passing a parameter in a function call? Thanks, ANDREW __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem with the grep function
Hi! For exact matches you can use == or is.element. To get the indices use which. e.g. == x-c(a,b,ab) x==a [1] TRUE FALSE FALSE which((x==a)==T) [1] 1 or e.g. is.element is.element(x,a) [1] TRUE FALSE FALSE which(is.element(x,a)==TRUE) [1] 1 Sincerely Eryk *** REPLY SEPARATOR *** On 7/8/2004 at 9:20 AM [EMAIL PROTECTED] wrote: Let me present to you my problem : I have a character vector x and I would like to obtain the indices of the elements of this vector that yielded exactly a match. For example, x=nom, pattern=b, I would to obtain 2 because b is on the second position. First program : nom - c(a,b,ab) grep(b,nom) 2 3 Then I try the option extended =FALSE (instead of TRUE by default) and I obtain '2 3' a second time. Please can you help me : How can I obtain only 2 in using the grep function (without using the match function). Thanks you Julie AUBERT __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem with the grep function
Or you must mark the word beginning with ^ and the end $ if you like to use grep. grep(^b$,nom) Sincerely Eryk *** REPLY SEPARATOR *** On 7/8/2004 at 9:20 AM [EMAIL PROTECTED] wrote: Let me present to you my problem : I have a character vector x and I would like to obtain the indices of the elements of this vector that yielded exactly a match. For example, x=nom, pattern=b, I would to obtain 2 because b is on the second position. First program : nom - c(a,b,ab) grep(b,nom) 2 3 Then I try the option extended =FALSE (instead of TRUE by default) and I obtain '2 3' a second time. Please can you help me : How can I obtain only 2 in using the grep function (without using the match function). Thanks you Julie AUBERT __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Vertical text in plot
Hallo! Would like to add vertical text labels to a histogram. Was trying with las but without sucess. I am using the standard histogram. This is what I was trying. hist(resS2$sam,breaks=seq(0,1,0.01),col=3,border=0,freq=F,add=T,xlim=c(0,1)) text(quantile(resS2$dif,0.005),5, 0.5% FP rate ,pos=2,cex=0.6,las=2) Thanks in advance. Eryk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Vertical text in plot
Hi Mark! Just wonderfull. Was searching in the par documention file for vertical, angle, horizontal. The word rotation was out of my mind. Thanks a lot. Eryk *** REPLY SEPARATOR *** On 7/2/2004 at 12:52 PM Marc Schwartz wrote: On Fri, 2004-07-02 at 12:45, Wolski wrote: Hallo! Would like to add vertical text labels to a histogram. Was trying with las but without sucess. I am using the standard histogram. This is what I was trying. hist(resS2$sam,breaks=seq(0,1,0.01),col=3,border=0,freq=F,add=T,xlim=c(0,1)) text(quantile(resS2$dif,0.005),5, 0.5% FP rate ,pos=2,cex=0.6,las=2) Thanks in advance. Eryk Hi Eryk! Try using 'srt' instead of 'las', which is for the axis labels. For example: text(quantile(resS2$dif, 0.005), 5, 0.5% FP rate, pos = 2, cex = 0.6, srt = 90) See ?par for more information. HTH, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RMySQL
Hi! I was installing RMySQL quite recently on Linux and had some troubles which I was able to solve. So maybee I can help you. But first I have to know what error messages you are getting on which operating system you are installing, which version of the package. Sincerely Eryk *** REPLY SEPARATOR *** On 01.07.2004 at 13:14 Talita Leite wrote: Hi!! I want some help to install the RMySQL package. I've tried to configure some things but i'm still getting erros. Anybody could help me?? Thank's Talita Perciano Costa Leite Graduanda em Ciência da Computação Universidade Federal de Alagoas - UFAL Departamento de Tecnologia da Informação - TCI Construção de Conhecimento por Agrupamento de Dados - CoCADa __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Question about mesurating time
?system.time *** REPLY SEPARATOR *** On 30.06.2004 at 10:59 zze-PELAY Nicolas FTRD/DMR/BEL wrote: Hello , Is there any function to mesurate the duration of a procedure (like tic and toc in matlab) ? Tic Source(procedure.R) Toc (toc is the duration between the execution of tic and the execution of toc) Thank you nicolas [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] camberra distance?
Hi! Its not an R specific question but had no idea where to ask elsewhere. Does anyone know the orginal reference to the CAMBERA DISTANCE? Eryk. Ps.: I knew that its an out of topic question (sorry). Can anyone reccomend a mailing list where such questions are in topic? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] camberra distance?
Thanks Mark. Yes I mean canberra. Searching for canberra camberra by google I observed the following. Searching for caMberra you will find a paper from 1997 where they write camberra instead of canberra dissimilarity for the meassure defined sum(|x_i - y_i| / |x_i + y_i|). Meanwhile there are plenty of articles on the net which reference this paper from 1997 and write caMberra instead of canberra. May be because it is much harder to find an article about canberra distance using google (because of the city). A quite assertive argument to use distinctive names and to publish papers in journals which are free, online and can be searched by google. Eryk *** REPLY SEPARATOR *** On 29.06.2004 at 15:51 [EMAIL PROTECTED] wrote: maybe you mean 'Canberra'?, if so it might have come from work in csiro in canberra back in the 60's/70's? Look for Lance Williams 1967 , possibly. Aust. Comput. J. 1, 15-20 Mark Palmer Environmetrics Monitoring for Management CSIRO Mathematical and Information Sciences Private bag 5, Wembley, Western Australia, 6913 Phone 61-8-9333-6293 Mobile 0427-50-2353 Fax: 61-8-9333-6121 Email: [EMAIL PROTECTED] URL: www.cmis.csiro.au/envir -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Wolski Sent: Tuesday, 29 June 2004 3:45 PM To: R Help Mailing List Subject: [R] camberra distance? Hi! Its not an R specific question but had no idea where to ask elsewhere. Does anyone know the orginal reference to the CAMBERA DISTANCE? Eryk. Ps.: I knew that its an out of topic question (sorry). Can anyone reccomend a mailing list where such questions are in topic? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] PAM clustering: using my own dissimilarity matrix
Hi! If your x is your symmetric matrix containing the distances than cast it to an dist object using as.dist. ?as.dist. Sincerely Eryk *** REPLY SEPARATOR *** On 29.06.2004 at 18:28 Hans Körber wrote: Hello, I would like to use my own dissimilarity matrix in a PAM clustering with method pam (cluster package) instead of a dissimilarity matrix created by daisy. I read data from a file containing the dissimilarity values using read.csv. This creates a matrix (alternatively: an array or vector) which is not accepted by pam: A call p-pam(d,k=2,diss=TRUE) yields an error message Error in pam(d, k = 2, diss = TRUE) : x is not of class dissimilarity and can not be converted to this class. How can I convert the matrix d into a dissimilarity matrix suitable for pam? I'm aware of a response by Friedrich Leisch to a similar question posed by Jose Quesada (quoted below). But as I understood the answer, the dissimilarity matrix there is calculated on the basis of (random) data. Thank you in advance. Hans __ / On Tue, 09 Jan 2001 15:42:30 -0700, / / Jose Quesada (JQ) wrote: / / Hi, / / I'm trying to use a similarity matrix (triangular) as input for pam() or / / fanny() clustering algorithms. / / The problem is that this algorithms can only accept a dissimilarity / / matrix, normally generated by daisy(). / / However, daisy only accept 'data matrix or dataframe. Dissimilarities / / will be computed between the rows of x'. / / Is there any way to say to that your data are already a similarity / / matrix (triangular)? / / In Kaufman and Rousseeuw's FORTRAN implementation (1990), they showed an / / option like this one: / / Maybe you already have correlations coefficients between variables. / / Your input data constist on a lower triangular matrix of pairwise / / correlations. You wish to calculate dissimilarities between the / / variables. / / But I couldn't find this alternative in the R implementation. / / I can not use foo - as.dist(foo), neither daisy(foo...) because / / Dissimilarities will be computed between the rows of x, and this is / / not / / what I mean. / / You can easily transform your similarities into dissimilarities like / / this (also recommended in Kaufman and Rousseeuw ,1990): / / foo - (1 - abs(foo)) # where foo are similarities / / But then pam() will complain like this: / / x is not of class dissimilarity and can not be converted to this / / class. / / Can anyone help me? I also appreciate any advice about other clustering / / algorithms that can accept this type of input. / Hmm, I don't understand your problem, because proceeding as the docs describe it works for me ... If foo is a similarity matrix (with 1 meaning identical objects), then bar - as.dist(1 - abs(foo)) fanny(bar, ...) works for me: ## create a random 12x12 similarity matrix, make it symmetric and set the ## diagonal to 1 / x - matrix(runif(144), nc=12) / / x - x+t(x) / / diag(x) - 1 / ## now proceed as described in the docs / y - as.dist(1-x) / / fanny(y, 3) / iterations objective 42.00 3.303235 Membership coefficients: [,1] [,2] [,3] 1 0.333 0.333 0.333 2 0.333 0.333 0.333 3 0.334 0.333 0.333 4 0.333 0.333 0.333 ... __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to determine the number of dominant eigenvalues in PCA
Hi! There is a chapter in the book from Härdl about the interpretation of PCs available online. http://www.quantlet.com/mdstat/scripts/mva/htmlbook/mvahtmlframe93.html About determining the number of dominant eigenvalues is a chapter in book of A. Handl (available online but in german.) http://www.quantlet.com/mdstat/scripts/mst/html/msthtmlframe56.html Two references to this topic from this online book. Cattell, R. B. (1966): The scree test for the number of factors. Multivariate Behavioral Research, 1, 245-276 Kaiser, H. F. (1960): The application of electronic computers to factor analysis. Educ. Psychol. Meas., 20, 141-151 Hope this helps. Sincerely Eryk *** REPLY SEPARATOR *** On 28.06.2004 at 10:06 Fred wrote: Dear All, I want to know if there is some easy and reliable way to estimate the number of dominant eigenvalues when applying PCA on sample covariance matrix. Assume x-axis is the number of eigenvalues (1, 2, ,n), and y-axis is the corresponding eigenvalues (a1,a2,..., an) arranged in desceding order. So this x-y plot will be a decreasing curve. Someone mentioned using the elbow (knee) method to find the point that the maximal curvature of this curve occurs. The number at this point would be the number of dominant eigenvalues. But I could not find any reference papers on this idea. Does anyone has tried this method or knows more details on this? Thanks for your point. Fred [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RMysql installation problem.
Hi! I am trying to install the RMySQL package. The installation stops with the following error message. path to mysql is set. setenv PKG_CPPFLAGS /home/arabidopsis/software/R1.9.1/linux/mysql/include setenv PKG_LIBS /home/arabidopsis/software/R1.9.1/linux/mysql/lib R CMD INSTALL RMySQL_0.5-5.tar.gz #cut cut. creating src/Makevars ** libs gcc -I/home/arabidopsis/software/R1.9.1/linux/lib/R/include /home/arabidopsis/software/R1.9.1/linux/mysql/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c RS-DBI.c -o RS-DBI.o gcc: cannot specify -o with -c or -S and multiple compilations make: *** [RS-DBI.o] Error 1 ERROR: compilation failed for package 'RMySQL' ** Removing '/home/arabidopsis/software/R1.9.1/linux/lib/R/library/RMySQL' Thought this is because R and Mysql are compiled with different compilers. Because of this error I just installed the newest R and mysql from source. Please help. Eryk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RMysql installation problem. / Problem solved!
It works with: R CMD INSTALL --configure-args='--with-mysql-dir=/home/arabidopsis/software/R1.9.1/linux/mysql/' RMySQL_0.5-5.tar.gz dunno why. Sorry for the annoyance. Eryk *** REPLY SEPARATOR *** On 28.06.2004 at 19:55 Wolski wrote: Hi! I am trying to install the RMySQL package. The installation stops with the following error message. path to mysql is set. setenv PKG_CPPFLAGS /home/arabidopsis/software/R1.9.1/linux/mysql/include setenv PKG_LIBS /home/arabidopsis/software/R1.9.1/linux/mysql/lib R CMD INSTALL RMySQL_0.5-5.tar.gz #cut cut. creating src/Makevars ** libs gcc -I/home/arabidopsis/software/R1.9.1/linux/lib/R/include /home/arabidopsis/software/R1.9.1/linux/mysql/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c RS-DBI.c -o RS-DBI.o gcc: cannot specify -o with -c or -S and multiple compilations make: *** [RS-DBI.o] Error 1 ERROR: compilation failed for package 'RMySQL' ** Removing '/home/arabidopsis/software/R1.9.1/linux/lib/R/library/RMySQL' Thought this is because R and Mysql are compiled with different compilers. Because of this error I just installed the newest R and mysql from source. Please help. Eryk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing on Windows packages build on Unix
Hallo Giovanni! You have to build a windows package on linux/unix. cran.r-project.org/doc/contrib/cross-build.pdf Eryk *** REPLY SEPARATOR *** On 6/25/2004 at 11:10 AM Giovanni Petris wrote: Hello, I wanted to share with a colleague a few R functions that I wrote. To this purpose, I created a small package on my machine (Unix) and emailed it to her. Now she is having troubles installing the package on her Windows machine. It seems that on her side, install.packages looks for a zip file - while I have created a tar.gz file. I tried to build the package with the --use-zip options but that didn't work. Any suggestions? TIA, Giovanni -- __ [ ] [ Giovanni Petris [EMAIL PROTECTED] ] [ Department of Mathematical Sciences ] [ University of Arkansas - Fayetteville, AR 72701 ] [ Ph: (479) 575-6324, 575-8630 (fax) ] [ http://definetti.uark.edu/~gpetris/ ] [__] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Initializing SparseM matrix matrix.csc
Hi! Would like to initialize a huge matrix.csc (Pacakge SparseM) with all elements 0 and afterwards set a few alements nonzero. The matrix which I like to allocate is so huge that I can not use A - matrix(a,n1,p) before: A.csr - as.matrix.csc(A) because I can not allocate such a huge matrix A. But I believe that the much more memmory efficient model in case of csc matrix should do it for a sparse matrix. How to do this. Sincerely Eryk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to order a vector
Hi! I assume that 2003 2002 are the names of your vector myvector myvector[order(names(myvector))] Eryk *** REPLY SEPARATOR *** On 6/17/2004 at 12:10 PM Luis Rideau Cruz wrote: Hi all I have a vector like this 2003 2002 2001 2000 1999 1998 1997 1996 106 105 106 106105 106 101 107 How can I get it sorted right(19962003)? Thank you Luis Ridao Cruz Fiskirannsóknarstovan Nóatún 1 P.O. Box 3051 FR-110 Tórshavn Faroe Islands Phone: +298 353900 Phone(direct): +298 353912 Mobile: +298 580800 Fax: +298 353901 E-mail: [EMAIL PROTECTED] Web:www.frs.fo __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] installing my own package - problems with INDEX
Hi! If I have similar problem. I first run R CMD check. Then I change to the directory mypackage.Rcheck where R CMD check generated a file mypackage-manual.tex. Then I try to compile the file using latex by myself. In addition I am using a latex error aware editor (texniccenter on windows). When I have the error pinned down in tex file, its usually quite easy to find the corresponding Rd file and then the error in the Rd file. Sincerely Eryk. *** REPLY SEPARATOR *** On 6/15/2004 at 3:14 AM Pamela Hall wrote: Hi there; I am a neophyte to R though I have been messing around with programming in other languages and environments for some years (my dog's name is punchcard to give you some idea of how many years). I have been trying to make a package and install it, to no avail. The functions I have written all work as expected (by me, that is). But I cannot get the html help pages to work. The failure appears to be in creating the INDEX file. No matter how carefully I check all of my *.Rd pages, the error message that I have unbalanced braces keeps showing up. I cannot find any error in matching braces. I am using Alpha as the editor, and it identifies mismatched braces - there are none in the *.Rd file. Another aspect of this problem is that the INDEX file only contains one line, that of the first file. However, the html dir has an index file (00Index.html) that contains all of the functions I have documented, but they are all linked to the same identical function web page - the first one. Please give me a hint. There are no mismatched braces as far as I can tell. Even when I try to check a single function and its Rd file, I get the same error message. And there are no other error messages. The package can be attached and the functions work, but the help pages do not. I must be doing something really simple, but very wrong. What are the 5 most common first mistakes some one makes in Rd files? thanks -ph __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
