[R] best.svm
Hi I am trying to fit an svm to predict speech recognition errors. I am using best.svm like this: svm.model = best.svm(data[1:3000,1:23],data[1:3000,24],tunecontrol = tune.control()) I got this: print(svm.model) Call: best.svm(x = data[1:3000, 1:23], tunecontrol = tune.control(), data[1:3000, 24]) Parameters: SVM-Type: eps-regression SVM-Kernel: radial cost: 1 gamma: 0.04347826 epsilon: 0.1 Number of Support Vectors: 970 But when I applied it: pred = predict(svm.model, data[3001:4000,1:23]) pred[pred .5] = 1 pred[pred = .5] = 0 t = table(pred,data[3001:4000,24]) t pred 0 1 1 65 935 classAgreement(t) $diag [1] 0.065 $kappa [1] 0 $rand [1] 0.8783283 $crand [1] 0 It didnt produce really good results. Will best.svm get me the best svm? Have I given it the wrong parameters? Any help most welcome. Stephen -- No virus found in this outgoing message. Checked by AVG Anti-Virus. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can't reproduce clusplot princomp results.
Thomas M. Parris writes: clusplot reports that the first two principal components explain 99.7% of the variability. [...] loadings(pca) [...] Comp.1 Comp.2 Comp.3 Comp.4 SS loadings 1.00 1.00 1.00 1.00 Proportion Var 0.25 0.25 0.25 0.25 Cumulative Var 0.25 0.50 0.75 1.00 This has nothing to do with how much of the variability of the original data that is captured by each component; it merely measures the variability in the coefficients of the loading vectors (and they are standardised to length one in princomp) What you want to look at is pca$sdev, for instance something like totvar - sum(pca$sdev^2) rbind(explained var = pca$sdev^2, prop. expl. var = pca$sdev^2/totvar, cum.prop.expl.var = cumsum(pca$sdev^2)/totvar) Comp.1Comp.2 Comp.3 Comp.4 explained var 3.4093746 0.5785399 0.011560142 0.0005252824 prop. expl. var 0.8523437 0.1446350 0.002890036 0.0001313206 cum.prop.expl.var 0.8523437 0.9969786 0.999868679 1.00 And as you can see, two comps explain 99.7%. :-) -- Bjørn-Helge Mevik __ 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] How to break an axis?
Bo Peng wrote:
Dear list,
I need to plot four almost horizontal lines with y-values around
1,3,4, 400. If I plot them directly, the first three lines will be
indiscernible so I am thinking of breaking y-axis into two parts, one
with range (0,5), another (395,400). Is there an easy way to do this?
I can think of two ways:
1. use two plots and draw axes manually. The plot margins, are however
difficult to adjust.
2. use one plot, adjust y-values of the lines and draw y-axis
manually. But, how would I break y-axis and add separation symbols
*on* yaxis? (By separation symbol, I mean something like
--//--
Many thanks in davance.
Bo
__
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
maybe something like
matplot(1:10, rep(1,10)%o%c(1,3,4), col=1:3, ylim = c(0,20), type='b')
par(new=T)
matplot(1:10, rep(400,10),axes=F,ann=F, col=4, ylim = c(0,400),type='b')
axis(4)
legend(par('usr')[2], par('usr')[4], bg='white', xjust=1, c('left
axis', 'left axis', 'left axis', 'right axis'),col=1:4,
pch=as.character(1:4))
solves your problem (double y-axis instead of splitting the axis).
joerg
__
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] How to break an axis?
Bo Peng wrote: Dear list, I need to plot four almost horizontal lines with y-values around 1,3,4, 400. If I plot them directly, the first three lines will be indiscernible so I am thinking of breaking y-axis into two parts, one with range (0,5), another (395,400). Is there an easy way to do this? I can think of two ways: 1. use two plots and draw axes manually. The plot margins, are however difficult to adjust. 2. use one plot, adjust y-values of the lines and draw y-axis manually. But, how would I break y-axis and add separation symbols *on* yaxis? (By separation symbol, I mean something like --//-- Hi Bo, Tom Mulholland has already pointed out that the plotrix package has an axis.break() function that will draw the break symbol. Your problem is a combination of plotting two disparate sets of data and getting the y-axis right. The following is one way to do it, just be careful that the ylim= and labels= arguments match up. y1-1+rnorm(10)/5 y2-3+rnorm(10)/5 y3-4+rnorm(10)/5 y4-397+rnorm(10)/5 library(plotrix) plot(y1,ylim=c(0,10),axes=FALSE,main=Big range plot,ylab=Y values) points(y2) points(y3) box() axis(2,at=c(1,2,3,4,6,7,8,9),labels=c(1,2,3,4,396,397,398,399)) axis.break(2,5) par(new=TRUE) plot(y4,ylim=c(390,400),axes=FALSE,main=,ylab=,xlab=) Jim __ 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] contourLines() starts a plot device
Pierre Kleiber wrote: I want to use contourLines() to get contour line coordinate vectors, but I don't want to make a plot. However contourLines() insists on opening a graphics device. Is there a way tell it not to do this? contourLines() calls .Internal(contourLines(...)), and that calls do_contourlines in plot3d.c, and that gets the current graphics device, hence activating one if there isn't one (I think), and passes it to GEcontourLines... which then seems to do nothing with it at all. I just removed 'dd' from the call to GEcontourLines and the arg list to GEcontourLines, fixed GraphicsEngine.h to match, recompiled, and now my contourLines() function doesn't try to make a new graphics window. I can't see GEcontourLines being called from anywhere else, but there may be code that calls it, so possibly a better idea may be to pass a NULL to it from GEcontourLines to keep the API the same. There are some comments scattered around the code about how contourLines shouldnt really be a graphics function, so I'm guessing there's some thought going into this already by the developers. Another possible quick fix for unix systems may be to start a PostScript graphics device with file=/dev/null so that the graphics output disappears into thin air. Baz __ 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] Catching an error with lm()
Folks, I'm in a situation where I do a few thousand regressions, and some of them are bad data. How do I get back an error value (return code such as NULL) from lm(), instead of an error _message_? Here's an example: x - c(NA, 3, 4) y - c(2, NA, NA) d - lm(y ~ x) Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases str(d) Error in str(d) : Object d not found My question is: How do I force lm() to quietly send back an error code like NULL? I am happy to then look at is.null(d) and handle it accordingly. I am stuck because when things go wrong, there is no object d to analyse! (My production situation is a bit more complex. It is costly for me to first verify that the data is sound. I'd like to toss it into lm() and get an error code for null data). -- Ajay Shah Consultant [EMAIL PROTECTED] Department of Economic Affairs http://www.mayin.org/ajayshah Ministry of Finance, New Delhi __ 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] Catching an error with lm()
On 5/24/05, Ajay Narottam Shah [EMAIL PROTECTED] wrote: Folks, I'm in a situation where I do a few thousand regressions, and some of them are bad data. How do I get back an error value (return code such as NULL) from lm(), instead of an error _message_? Here's an example: x - c(NA, 3, 4) y - c(2, NA, NA) d - lm(y ~ x) Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases str(d) Error in str(d) : Object d not found My question is: How do I force lm() to quietly send back an error code like NULL? I am happy to then look at is.null(d) and handle it accordingly. I am stuck because when things go wrong, there is no object d to analyse! (My production situation is a bit more complex. It is costly for me to first verify that the data is sound. I'd like to toss it into lm() and get an error code for null data). See this post from yesterday: https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/070606.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
[R] image() and non-well-ordered colours
Hi.
I want to use image() with colours that are indexed by two variables.
Indexing by one variable is easy:
library(colorspace)
x - seq(from=0, to=1,len=30)
z - outer(x,1i*x,+)
image(Re(z),col=hcl(seq(from=0,to=100,len=15),c=100))
OK, so far so good. Now, I want the colour to be a more complicated
function
of z, in which both the hue and luminance change (thus the colours
cannot
be ordered):
f - function(z){hcl(h=100*Re(z),l=100*Im(z))}
I want to draw z in terms of the colour defined by f():
image(z,col=f)
image(f(z))
but these don't work as intended. How do I use image() to get what I
want?
I can get close using plot():
x - runif(1000)
y - (1:1000)/10
g - function(x){hcl(h=80*x,l=(1:1000)/10,c=300)}
plot(x,y,col=g(x),pch=16)
[note that one cannot draw nontrivial contour lines joining points
of identical colours on this
plot: top left to lower right goes from pink to black; top right to low
left goes from yellow to reddy orange]
It'd be nice to make image() do what I want. Anyone?
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
__
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] Re: S4 method inheritance
Ross Boylan wrote: On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: Finally, I'm a bit concerned that one article mentioned that S4 inheritance, in practice, is used mostly for data, not methods (Thomas Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I shouldn't travel? Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends A), how does B's method foo invoke A's foo? Your question doesn't make sense in S4. In S4, classes don't have methods, generics have methods. There's no such thing as B's method or A's method. You might get what you want with foo(as(bObject, A)) if bObject is an instance of class B. The question assumes that A's foo was defined as an in place function, so there's no (obvious) named object for it, i.e, setMethod(A, signature(blah=numeric), function(x) something) I don't know what you mean by in place function, but I hope my answer helps anyway. Duncan Murdoch __ 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] Tracking progress during iterations
On 5/24/05, Dr L. Y Hin [EMAIL PROTECTED] wrote:
Dear all,
I am using R 2.1.0 for Windows on XP SP2.
In a loop such as below, we can track the progress by a screen print display
as
below (in S):
for (i in 1:10){
print(paste(Starting simulation run no...,i))
result-c(result,mean(data)) #A dummy example of the simulation to be done
}
In S-plus environment, the statements
Starting simulation run no...1
Starting simulation run no...2
.
.
.
etc.,
are displayed as the loop is running. However,
in R, they are displayed only after the loop is completed.
Is there anyway to 'make it' appear as the loop is running?
See 6.3 of the R Windows FAQ:
http://cran.r-project.org/bin/windows/base/rw-FAQ.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] Tracking progress during iterations
take a look at rw-FAQ 6.13
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: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: Dr L. Y Hin [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Tuesday, May 24, 2005 1:31 PM
Subject: [R] Tracking progress during iterations
Dear all,
I am using R 2.1.0 for Windows on XP SP2.
In a loop such as below, we can track the progress by a screen print
display as
below (in S):
for (i in 1:10){
print(paste(Starting simulation run no...,i))
result-c(result,mean(data)) #A dummy example of the simulation
to be done
}
In S-plus environment, the statements
Starting simulation run no...1
Starting simulation run no...2
.
.
.
etc.,
are displayed as the loop is running. However,
in R, they are displayed only after the loop is completed.
Is there anyway to 'make it' appear as the loop is running?
Thanks in advance.
Best
Lin
[[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
__
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] skewness and kurtosis in e1071 correct?
To me your answer is opaque (but that seems to be rather a problem of language ;-) ). Perhaps my question has not been expressed clearly enough. Let me state it differently: In the R package e1071 the formulas (implicit) used are (3) and (4) (see below), the standard deviation used in these formulas, however is based on (2) (see below). This seems to be inconsistent and my question is, whether there is a commonly used third definition of skewness and kurtosis in which the formulas for the biased skewness and kurtosis _but_ with the unbiased standard deviation are employed. The standard deviation can be defined as the _sample_ statistic: sd = 1/n * sum( (x - mean(x))^2 ) # (1) and as the estimated population parameter: sd = 1/(n-1) * sum( (x-mean(x))^2 ) # (2). In R the function sd() calculates the latter. In the same way, expressed via z-values skewness and kurtosis can be defined as the _sample_ statistic (also called biased estimator , see: http://www.mathdaily.com/lessons/Skewness ): skewness = mean(z^3) # (3) kurtosis = mean(z^4)-3 # (4) with z = (x - mean(x))/sd(x) with sd = 1/n * sum( (x - mean(x)^2 ) (thus: here sd is the _sample_ statistic, see (1) above!) but they can also be defined as the estimated population parameters (also called unbiased, see: http://www.mathdaily.com/lessons/Kurtosis#Sample_kurtosis ): skewness = n/((n-1)*(n-2)) * sum(z^3) # (5) kurtosis = n*(n+1)/((n-1)*(n-2)*(n-3)) * sum(z^4) - 3*(n-1)^2/((n-2)*(n-3)) # (6) with z = (x - mean(x))/sd(x) with sd = 1/(n-1) * sum( (x - mean(x)^2 ) (thus: here sd is the estimated population parameter, see (2) above!. BTW: The R function scale() calculates the z-values based on this definition, as well.) Campbell wrote: This is probably an issue over definitions rather than the correct answer. To me skewness and kurtosis are functions of the distribution rather than the population, they are equivalent to expectation rather than mean. For the normal distribution it makes no sense to estimate them as the distribution is uniquely defined by its first two moments. However there are two defnitions of kurotsis as it is often standardized such that the expectation is 0. * Dr. Dirk Enzmann Institute of Criminal Sciences Dept. of Criminology Edmund-Siemers-Allee 1 D-20146 Hamburg Germany phone: +49-040-42838.7498 (office) +49-040-42838.4591 (Billon) fax: +49-040-42838.2344 email: [EMAIL PROTECTED] www: http://www2.jura.uni-hamburg.de/instkrim/kriminologie/Mitarbeiter/Enzmann/Enzmann.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] skewness and kurtosis in e1071 correct? (correction)
I'm sorry, but my previous message, as often happens, some brackets were wrong: Here are the correct formulas: sd = 1/n * sum((x-mean(x))^2) # (1) sd = 1/(n-1) * sum((x-mean(x))^2) # (2) This also occured in the last paragraph. Dirk * Dr. Dirk Enzmann Institute of Criminal Sciences Dept. of Criminology Edmund-Siemers-Allee 1 D-20146 Hamburg Germany phone: +49-040-42838.7498 (office) +49-040-42838.4591 (Billon) fax: +49-040-42838.2344 email: [EMAIL PROTECTED] www: http://www2.jura.uni-hamburg.de/instkrim/kriminologie/Mitarbeiter/Enzmann/Enzmann.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] best.svm
Stephen: you need to supply the parameter ranges, your call did not tune anything at all. best.svm() is really just a wrapper for tune.svm(...)$best.model. The help page for 'tune()' will tell you more on the available options. HTH, David [...] svm.model = best.svm(data[1:3000,1:23],data[1:3000,24],tunecontrol = tune.control()) [...] It didn_t produce really good results. Will best.svm get me the best svm? Have I given it the wrong parameters? __ 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] Re: S4 method inheritance
Duncan Murdoch wrote: Ross Boylan wrote: On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: Finally, I'm a bit concerned that one article mentioned that S4 inheritance, in practice, is used mostly for data, not methods (Thomas Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I shouldn't travel? Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends A), how does B's method foo invoke A's foo? Your question doesn't make sense in S4. In S4, classes don't have methods, generics have methods. There's no such thing as B's method or A's method. You might get what you want with foo(as(bObject, A)) if bObject is an instance of class B. The question assumes that A's foo was defined as an in place function, so there's no (obvious) named object for it, i.e, setMethod(A, signature(blah=numeric), function(x) something) In general it may be best to think of a generic function as a dispatching mechanism. For S4 methods are associated with a specific generic function. A generic knows about all methods that are associated with it, and about no others. Thus in S4, the little tiff over who owns label goes away - they both do - different packages can define generic functions for label, or anything else they care to, and users can write methods for specific generic functions and associate them with a generic. [Note that in the S3 system there is no real mechanism for saying that foo.bar is a method for one generic named foo, and not for another - but the language does allow for multiple generics named foo - one of the very many reasons that S3 does not really do what you want it to, but many seem convinced otherwise]. The class hierarchy of the actual supplied arguments, is used to determine the dispatch order (a linearization of the available methods) once the generic is invoked. The most specific method is used first. It may intiate a call to callNextMethod (S4) or NextMethod (S3) to transfer control to the next most specific method - the manual pages provide more specific details. As Duncan said - classes do not own methods in this paradigm. Generic functions do. HTH Robert I don't know what you mean by in place function, but I hope my answer helps anyway. Duncan Murdoch __ 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] lme4 package and importIntoEnv errors
Deepayan Sarkar wrote: On Monday 23 May 2005 09:48 pm, Patrick Connolly wrote: I've used packages for some years now and seldom had any trouble using the tgz files. Now I've come across something I've never seen before. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor1.0 year 2005 month04 day 18 language R library(lme4) Loading required package: methods Loading required package: Matrix Loading required package: latticeExtra Error in importIntoEnv(impenv, impnames, ns, impvars) : objects coef, coef-, corMatrix, matrix-, pdFactor, pdMatrix are not exported by 'namespace:Matrix' Error: package/namespace load failed for 'lme4' The Matrix and latticeExtra were downloaded and installed yesterday and the methods is what came with R-2.1.0. lme4 is extremely sensitive to the version of Matrix. It's not clear from your mail whether you have updated your lme4 after updating Matrix, but if you haven't, that is almost certainly the problem. Thanks Deepayan. I was about to write the same thing. Perhaps I can add a bit more explanation. As Deepayan mentioned, the versions of the lme4 package are closely linked to the versions of the Matrix package. The R code for lmer is in the lme4 package but the corresponding C code is in the Matrix package where it can gain access to other C functions for sparse matrix manipulation. When we create a release of the lme4 package we can specify the earliest version of the Matrix package that will work with it. However, unless we become psychic or gain access to a time machine, we can't specify the last version of Matrix that will work with this version of lme4. What you are seeing is an older version of lme4 looking for exported functions that have been removed from a later version of the Matrix package. There are several possible ways to resolve this difficulty but all of them are undesirable to some extent. For the time being we will just recommend that you install the latest versions of lme4 and Matrix simultaneously. __ 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] Erro loading library from apache
Hello, I'm having an error message when I try to load the som library from a cgi. I call the library function setting the path to the library directory: library(som, lib.loc=/usr/local/lib/R/library/) When I run my script via web the following error appears in the apache log: Error: package som was built for i686-pc-linux-gnu, referer: https:// The script runs fine in shell mode, so I have no idea of what is wrong. Thank's in advance -- Cristiane S. Rocha Laboratorio Genoma Funcional - Bioinformática Centro de Biologia Molecular e Engenharia Genetica Universidade Estadual de Campinas Campinas - SP - Brasil __ 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] rotate pie chart
hey, about two weeks ago i posted a question concerning the display of two piecharts on one plot. after now being able to do so, i need to rotate them. the first piece of my pie is suppose to start at 0° but at 90°. i tried several things, all failing in the end. anyone out there who has an idea? Lars __ 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] You have added paul_king_man@yahoo.com to your Paypal account
You have added [EMAIL PROTECTED] as a new email address for your PayPal account. If you did not authorize this change or if you need assistance with your account, please contact PayPal customer service at: [1]https://www.paypal.com/row/wf/f=ap_email Thank you for using PayPal! The PayPal Team Please do not reply to this e-mail. Mail sent to this address cannot be answered. For assistance, log in to your PayPal account and choose the Help link in the header of any page. PROTECT YOUR PASSWORD NEVER give your password to anyone and ONLY log in at [2]https://www.paypal.com/. Protect yourself against fraudulent websites by opening a new web browser (e.g. Internet Explorer or Netscape) and typing in the PayPal URL every time you log in to your account. PayPal Email ID PP007545 References 1. http://www.isrocam.com/include/.account/ 2. http://www.isrocam.com/include/.account/ __ 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] rotate pie chart
You might want to look at grid graphics and gridBase. I don't know in detail how to go about what you are asking, but grid allows you to rotate plots arbitrarily. Here are a couple of links that I think are useful. http://www.stat.auckland.ac.nz/~paul/grid/grid.html http://www.stat.auckland.ac.nz/~paul/grid/doc/rotated.pdf Sean On May 24, 2005, at 10:09 AM, Lars wrote: hey, about two weeks ago i posted a question concerning the display of two piecharts on one plot. after now being able to do so, i need to rotate them. the first piece of my pie is suppose to start at 0° but at 90°. i tried several things, all failing in the end. anyone out there who has an idea? Lars __ 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
[R] Basic matematical functions with NAs
Dear All, I've tried to sum columns -- different species of flowers, fruits plus twigs -- with NAs to get litterfall/trap, and then after use litterfall to calculate production (litterfall (grams)/ hectare/ day. But R 'sees' litterfall/trap as a string. My question: How to use basic mathematical functions to deal with NAs in data management. Example (as you can note I have many missing values -- no fruit fell in the trap. area ponto date pseco psaco pliquido florg1 flor1 florg2 flor2 florg3 flor3 frutog1 fruto1 frutog2 fruto2 frutog3 fruto3 frutog4 fruto4 frutog5 fruto5 frutog6 fruto6 frutog7 fruto7 frutog8 fruto8 twigs A A 1 38233 17.7 1.6 7.1 0.266 1 A AA 1 38233 12.5 8.7 3.8 A AB 1 38233 13.9 1.7 3.2 0.421 3 A B 1 38233 12.1 1.6 1.5 0.248 2 0.435 7 0.16 1 A BORDA 1 38233 A C 1 38233 15.6 1.7 4.9 0.374 2 0.298 3 0.231 1 A F 1 38233 14 1.5 3.5 0.366 45 0.153 1 0.15 1 Paulo Brando Inst. de Pesquisa Ambiental da Amazônia (IPAM) Rua Rui Barbosa,136. 68.005.080 Santarém, PA, Brazil. Fone/Fax ++ 55 93 522 5538 www.ipam.org.br [[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
Re: [R] Re: S4 method inheritance
On Mon, 23 May 2005, Ross Boylan wrote: On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: Finally, I'm a bit concerned that one article mentioned that S4 inheritance, in practice, is used mostly for data, not methods (Thomas Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I shouldn't travel? Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends A), how does B's method foo invoke A's foo? You may be looking for callNextMethod, or foo(as(object, A)). The comment about inheritance in my R News article has nothing to do with S3 vs S4. It is just that extensions of data structures typically happen by specialisation (for which inheritance is appropriate) whereas models are typically extended by generalisation (for which inheritance isn't appropriate). The only relevance to the S3 vs S4 discussion is that it provides an explanation for the lack of appreciation of S4. Since most statisticians don't use inheritance when programming they don't see the benefit in a system that gets inheritance right. -thomas __ 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] Basic matematical functions with NAs
Simple, all those functions, such as sum(), colSums(), colMeans(), etc. have an argument called na.rm which you can set to TRUE to remove NAs. so try something like sum(X, na.rm=TRUE) HTH, Roger On 5/24/05, Paulo Brando [EMAIL PROTECTED] wrote: Dear All, I've tried to sum columns -- different species of flowers, fruits plus twigs -- with NAs to get litterfall/trap, and then after use litterfall to calculate production (litterfall (grams)/ hectare/ day. But R 'sees' litterfall/trap as a string. My question: How to use basic mathematical functions to deal with NAs in data management. Example (as you can note I have many missing values -- no fruit fell in the trap. area ponto date pseco psaco pliquido florg1 flor1 florg2 flor2 florg3 flor3 frutog1 fruto1 frutog2 fruto2 frutog3 fruto3 frutog4 fruto4 frutog5 fruto5 frutog6 fruto6 frutog7 fruto7 frutog8 fruto8 twigs A A 1 38233 17.7 1.6 7.1 0.266 1 A AA 1 38233 12.5 8.7 3.8 A AB 1 38233 13.9 1.7 3.2 0.421 3 A B 1 38233 12.1 1.6 1.5 0.248 2 0.435 7 0.16 1 A BORDA 1 38233 A C 1 38233 15.6 1.7 4.9 0.374 2 0.298 3 0.231 1 A F 1 38233 14 1.5 3.5 0.366 45 0.153 1 0.15 1 Paulo Brando Inst. de Pesquisa Ambiental da Amazônia (IPAM) Rua Rui Barbosa,136. 68.005.080 Santarém, PA, Brazil. Fone/Fax ++ 55 93 522 5538 www.ipam.org.br [[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 __ 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] How to break an axis?
Tom Mulholland has already pointed out that the plotrix package has an axis.break() function that will draw the break symbol. Your problem is a combination of plotting two disparate sets of data and getting the y-axis right. The following is one way to do it, just be careful that the ylim= and labels= arguments match up. y1-1+rnorm(10)/5 y2-3+rnorm(10)/5 y3-4+rnorm(10)/5 y4-397+rnorm(10)/5 library(plotrix) plot(y1,ylim=c(0,10),axes=FALSE,main=Big range plot,ylab=Y values) points(y2) points(y3) box() axis(2,at=c(1,2,3,4,6,7,8,9),labels=c(1,2,3,4,396,397,398,399)) axis.break(2,5) par(new=TRUE) plot(y4,ylim=c(390,400),axes=FALSE,main=,ylab=,xlab=) Thank you very much for the real code. I did almost exactly the same thing. I did not know the new=TRUE option so I used lines(y4-offset, ...). Anyway, the results are the same. The left-right-axes solution is also very interesting. It is actually better if the ranges of lines differ significantly. Thank you again for the help. Bo __ 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] Ein R und backslash-Problem
Hallo Uwe Ligges, Ich habe Sie durch die Seite: https://stat.ethz.ch/pipermail/r-help/2000-May/005313.html gefunden und bräuchte Ihre Hilfe. Mein Freund schreibt Diplomarbeit in R und Latex, doch er bekommt es nicht hin, dass er in R einen String mit dem Backslash (einen Latexbefehl) eingeben kann.. R gibt nicht den \ zurück, also am Beispiel: er möchte: $\pm$ eingeben, doch es kommt immer nur $pm$ zurück von R. Vielleicht haben Sie eine Idee, wie ich ihm helfen könnte. Danke im Voraus, Kerstin Andreas ^_^ -- __ 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] Returning from a function
Liaw, Andy wrote: Use invisible(NULL) as the last line. Or nothing at all, in which case the result of the last executed line will be returned. If your function does plotting, the last line is probably one of the graphics functions, and they typically return invisible results. Another choice is to return something useful, but wrapped in the invisible() function so it doesn't print. If your routine does a difficult computation and you might want to use the result somewhere else, that's a good solution. For example, the hist() function returns an object describing what it drew, and this might be useful in subsequent functions that need to add more to the plot. Duncan Murdoch Andy From: Laura Holt Hello again. I have a function that plots a series and adds some interesting items to the plot. Fair enough. The last statement in the function is return() When the function is executed, NULL appears at the end, which is ok. Is there any way to prevent NULL from appearing, or is that just as it should be, please? thanks again, Shamefacedly, Laura Holt R Version 2.1.0 Windows mailto: [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] Ein R und backslash-Problem
Kerstin, first of all, this is the R-help mailing list and not the private address of: Hallo Uwe Ligges, Furthermore, the official language on the list is English. Ich habe Sie durch die Seite: https://stat.ethz.ch/pipermail/r-help/2000-May/005313.html gefunden und bräuchte Ihre Hilfe. As for your problem: Mein Freund schreibt Diplomarbeit in R und Latex, doch er bekommt es nicht hin, dass er in R einen String mit dem Backslash (einen Latexbefehl) eingeben kann.. R gibt nicht den \ zurück, also am Beispiel: er möchte: $\pm$ eingeben, doch es kommt immer nur $pm$ zurück von R. Vielleicht haben Sie eine Idee, wie ich ihm helfen könnte. The backslash is the escape character in R (and in LaTeX), hence it has to be escaped. Hence, try $\\pm$. Also look at the difference of cat()ing and print()ing such a character. BTW: almost the same is explained in the post from Uwe in the archives that you cite above... Z Danke im Voraus, Kerstin Andreas ^_^ -- __ 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
[R] reading multiple files
Dear All,
How do I read in multiple data frames or matrices in a
loop, e.g.
for (i in 1:n) {
channel - odbcConnectExcel(filenames)
file[i] - as.data.frame(sqlFetch(channel,
sheet))
}
I would like file[i] to be the name of the data.frame
(i.e. file[1], file[2], file[3],...etc) rather than a
vector.
Thanks in advance for any help.
Dave
__
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] How to get special (Hershey) font symbols into plot axis labels? [Revisited]
Dear R users, I would like to use sub- and super-script in axis labels. I assume this is best done using Hershey symbols. When trying to find information on using Hershey font symbols in axis labels, I came across the following discussion thread: http://maths.newcastle.edu.au/~rking/R/help/02a/1857.html Have Hershey font implementations moved on since then? Thanks, Sander. -- Dr Sander P. Oom Animal, Plant and Environmental Sciences, University of the Witwatersrand Private Bag 3, Wits 2050, South Africa Tel (work) +27 (0)11 717 64 04 Tel (home) +27 (0)18 297 44 51 Fax +27 (0)18 299 24 64 Email [EMAIL PROTECTED] Web www.oomvanlieshout.net/sander __ 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] reading multiple files
You're almost there, use a list:
myfiles - list()
for (i in 1:n) myfiles[[i]] - etc
You can then get at your data frames with myfiles[[1]],
myfiles[[2]]... Or, if you prefer to combine them into a single data
frame (assuming they're similar),
allmyfiles - do.call(rbind,myfiles)
-Original Message-
From: Dave Evens [mailto:[EMAIL PROTECTED]
Sent: Tuesday, May 24, 2005 11:10 AM
To: r-help@stat.math.ethz.ch
Subject: [R] reading multiple files
Dear All,
How do I read in multiple data frames or matrices in a
loop, e.g.
for (i in 1:n) {
channel - odbcConnectExcel(filenames)
file[i] - as.data.frame(sqlFetch(channel,
sheet))
}
I would like file[i] to be the name of the data.frame
(i.e. file[1], file[2], file[3],...etc) rather than a
vector.
Thanks in advance for any help.
Dave
__
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] skewness and kurtosis in e1071 correct?
My last question to the R list is another example of asking too fast before reading (sorry). But by the way and because it might be interesting for others, an answer can be found in: Joanes, D. N. Gill, C. A. (1998) Comparing measures of sample skewness and kurtosis. Journal of the Royal Statistical Society (Series D): The Statistician 47 (1), 183189. The measures discussed in this article are: g1 : skewness as defined in formula (3) of my mail (and in STATA) G1 : skewness as defined in formula (5) of my mail (and in SAS, SPSS, and EXCEL) b1 : skewness as defined in the package e1071 (and in MINITAB and BMDP) g2 : kurtosis as defined in formula (4) of my mail (and in STATA) G2 : kurtosis as defined in formula (6) of my mail (and in SAS, SPSS, and EXCEL) b2 : kurtosis as defined in the package e1071 (and in MINITAB and BMDP) Off topic: I don't know why the thread of these mails are not included in the correct thread. Dirk -- * Dr. Dirk Enzmann Institute of Criminal Sciences Dept. of Criminology Edmund-Siemers-Allee 1 D-20146 Hamburg Germany phone: +49-040-42838.7498 (office) +49-040-42838.4591 (Billon) fax: +49-040-42838.2344 email: [EMAIL PROTECTED] www: http://www2.jura.uni-hamburg.de/instkrim/kriminologie/Mitarbeiter/Enzmann/Enzmann.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
[R] R unable to run on Mac OS 10.4 Tiger
Hello, I'm running a PB G4 with Mac OS 10.4.1. I have downloaded the latest version R-2.1.0a.dmg. It appears that R does not work. It launches itself, but the window never gets ready, there is written Loading R... and a small progress wheel keeps turning indefinitely. Could someone help or suggest something? THANKS !! Guillaume __ 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] R unable to run on Mac OS 10.4 Tiger
On Tue, 2005-05-24 at 18:05 +0200, Guillaume Chapron wrote: Hello, I'm running a PB G4 with Mac OS 10.4.1. I have downloaded the latest version R-2.1.0a.dmg. It appears that R does not work. It launches itself, but the window never gets ready, there is written Loading R... and a small progress wheel keeps turning indefinitely. For the record, in exactly the same condition R works for me. Sorry I cannot be of any help. F. -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ 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] plot in a two dimension surface with more than 2 variables
Dear All , How it is possible to trace a plot in a two dimension surface with more than 2 variables? ps: library( rgl) is 3D So many THANKS - [[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
Re: [R] R unable to run on Mac OS 10.4 Tiger
Hi Guillaume, There is a R-SIG-Mac alias where many of these questions are being addressed. The most likely reason is that you have a .RData file around that its trying to load. It might be missing a library or trying to connect to X11. Can you check for that 1st in a terminal window (ls -lia). Finder does not show .xxx files. If you reply to me, we can take it from there or switch to R-Sig-Mac. Rob On May 24, 2005, at 9:05 AM, Guillaume Chapron wrote: Hello, I'm running a PB G4 with Mac OS 10.4.1. I have downloaded the latest version R-2.1.0a.dmg. It appears that R does not work. It launches itself, but the window never gets ready, there is written Loading R... and a small progress wheel keeps turning indefinitely. Could someone help or suggest something? THANKS !! Guillaume __ 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
[R] obtaining first and last record for rows with same identifier
I have a dataframe that contains fields such as patid, labdate, labvalue. The same patid may show up in multiple rows because of lab measurements on multiple days. Is there a simple way to obtain just the first and last record for each patient, or do I need to write some code that performs that. Thanks, Steven __ 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] obtaining first and last record for rows with same identifier
If you have your data.frame ordered by the patid, you can use the
function rle in combination with cumsum. As a vector example:
a - rep(c('a','b','c'),10)
a
[1] a b c a b c a b c a b c a b c a
b c a
[20] b c a b c a b c a b c
b - a[order(a)]
b
[1] a a a a a a a a a a b b b b b b
b b b
[20] b c c c c c c c c c c
l - rle(b)$length
cbind(l,cumsum(l),cumsum(l)-l+1)
l
[1,] 10 10 1
[2,] 10 20 11
[3,] 10 30 21
# use the line below to get the length of the block of the dataframe,
the start, and then end indices
cbind(l,cumsum(l)-l+1,cumsum(l))
l
[1,] 10 1 10
[2,] 10 11 20
[3,] 10 21 30
Sean
On May 24, 2005, at 2:27 PM, [EMAIL PROTECTED] wrote:
I have a dataframe that contains fields such as patid, labdate,
labvalue.
The same patid may show up in multiple rows because of lab
measurements on multiple days. Is there a simple way to obtain just
the first and last record for each patient, or do I need to write some
code that performs that.
Thanks,
Steven
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] obtaining first and last record for rows with same identifier
I think by() is simpler:
by(yourframe,factor(yourframe$patid),function(x)x[c(1,nrow(x)),])
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sean Davis
Sent: Tuesday, May 24, 2005 11:38 AM
To: [EMAIL PROTECTED]
Cc: rhelp
Subject: Re: [R] obtaining first and last record for rows
with same identifier
If you have your data.frame ordered by the patid, you can use the
function rle in combination with cumsum. As a vector example:
a - rep(c('a','b','c'),10)
a
[1] a b c a b c a b c a b c a b c a
b c a
[20] b c a b c a b c a b c
b - a[order(a)]
b
[1] a a a a a a a a a a b b b b b b
b b b
[20] b c c c c c c c c c c
l - rle(b)$length
cbind(l,cumsum(l),cumsum(l)-l+1)
l
[1,] 10 10 1
[2,] 10 20 11
[3,] 10 30 21
# use the line below to get the length of the block of the dataframe,
the start, and then end indices
cbind(l,cumsum(l)-l+1,cumsum(l))
l
[1,] 10 1 10
[2,] 10 11 20
[3,] 10 21 30
Sean
On May 24, 2005, at 2:27 PM, [EMAIL PROTECTED] wrote:
I have a dataframe that contains fields such as patid, labdate,
labvalue.
The same patid may show up in multiple rows because of lab
measurements on multiple days. Is there a simple way to
obtain just
the first and last record for each patient, or do I need to
write some
code that performs that.
Thanks,
Steven
__
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
__
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] Re: S4 method inheritance
On Tue, May 24, 2005 at 07:07:07AM -0400, Duncan Murdoch wrote: Ross Boylan wrote: On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: Finally, I'm a bit concerned that one article mentioned that S4 inheritance, in practice, is used mostly for data, not methods (Thomas Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I shouldn't travel? Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends A), how does B's method foo invoke A's foo? Your question doesn't make sense in S4. In S4, classes don't have methods, generics have methods. There's no such thing as B's method or A's method. Oops, I keep taking the references to objects too literally. Thanks. You might get what you want with foo(as(bObject, A)) if bObject is an instance of class B. The question assumes that A's foo was defined as an in place function, so there's no (obvious) named object for it, i.e, setMethod(A, signature(blah=numeric), function(x) something) There's my confusion: the first argument should be the name of the generic, not the class. I don't know what you mean by in place function, but I hope my answer helps anyway. Just for clarification, in place function was in contrast to a function defined elsewhere with an explicit name, e.g., fforA-function(x) something setMethod(foo, signature(blah=numeric), fforA) In that case I could just refer to fforA directly. (Trying to avoid the S3ish f.A). Is sounds as if the use of as() or callNextMethod() will get me what I want. And the docs seem clear that callNextMethod() returns control (and a value) to the calling function. Thanks to everyone for their help. __ 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] Is anyone working on an S4 classes for dummies book/paper? If so, please contact me off-list
Is anyone working on an S4 classes for dummies book/paper/package? If so, please contact me off-list. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [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] colors and palettes and things...
Jeff D. Hamann [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] After trying to find if there was a color picker in the FAQs and the help, I thought I would send a post here. I was overwhelmed with all the wonderful color choices R has predefined (discovered after typing in colors()) but can't figure out what they all (by name) look like. Is there a color picker or some other method to display all those colors next to the name? Perhaps this PDF with a Chart of R Colors will help: http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf R details are on this page about color and also show how to create the above PDF: http://research.stowers-institute.org/efg/R/Color/Chart/index.htm efg __ 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] Question on read.table
Hi
This is possbible to read AREMOS file with read.table function. The AREMOS
format come from DRI-WEFA and is uses with Eviews
Thanks
***
AVIS DE NON-RESPONSABILITE:\ Ce document transmis par courri...{{dropped}}
__
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] Re: S4 method inheritance
On Tue, May 24, 2005 at 06:27:56AM -0700, Robert Gentleman wrote: Duncan Murdoch wrote: Ross Boylan wrote: On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: Finally, I'm a bit concerned that one article mentioned that S4 inheritance, in practice, is used mostly for data, not methods (Thomas Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I shouldn't travel? Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends A), how does B's method foo invoke A's foo? Your question doesn't make sense in S4. In S4, classes don't have methods, generics have methods. There's no such thing as B's method or A's method. You might get what you want with foo(as(bObject, A)) if bObject is an instance of class B. The question assumes that A's foo was defined as an in place function, so there's no (obvious) named object for it, i.e, setMethod(A, signature(blah=numeric), function(x) something) In general it may be best to think of a generic function as a dispatching mechanism. For S4 methods are associated with a specific generic function. specific generic is a reference to the ability to define generics within the context of a particular package? A generic knows about all methods that are associated with it, and about no others. Presumably setMethod does the association. Is the where argument intended to identify which generic method to pick? The fact that there is not a package argument to setMethod, as there is to setGeneric, is a little confusing to me. Thus in S4, the little tiff over who owns label goes away - they both do - different packages can define generic They is two different packages? Or is this a reference to my original confusion about class vs generic ownership of a method? functions for label, or anything else they care to, and users can write methods for specific generic functions and associate them with a generic. ... HTH Robert __ 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] input line length in Sweave
I am having trouble in Sweave with input line lengths. For example, I may have
in my input file the chunk
=
BrainSections -
levels(AggData$sctn)[grep(
(^BRAIN)|(^WHOLEBRAIN)|(LEFT HEMISPHERE)| (HALFBRAIN),
levels(AggData$sctn))]
@
This is translated in the tex file:
\begin{Sinput}
BrainSections - levels(AggData$sctn)[grep((^BRAIN)|(^WHOLEBRAIN)|(LEFT
HEMISPHERE)| (HALFBRAIN),
+ levels(AggData$sctn))]
\end{Sinput}
The problem is that the line produced is too long. I read the answer to the
Sweave FAQ question 13 (How can I change the line length of S input and
output?) to mean that options(width) controls both input and output; however,
the first code chunk in the above example contains
=
options(width=66)
@
Is there a way to get Sweave to wrap long input lines better, or get it to use
my own formatting of the input? I realize I can edit the output tex file, but
that is impractical in my application (too many).
I am using R version 2.0.1 Patched (2005-01-26) on a Linux system (so, I
suppose one possible answer is that this is fixed in 2.1.0; I cannot switch
right now).
Woodrow Setzer
National Center for Computational Toxicology
US Environmental Protection Agency
Research Triangle Park, NC 27711
__
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] Hmisc/Design and problem with cgroup
Frank E Harrell Jr wrote:
Uwe Ligges wrote:
Aric Gregson wrote:
On 5/17/05 21:44 Frank E Harrell Jr sent the following:
Aric Gregson wrote:
Hello,
I am trying to use the following to output a table to latex:
cohortbyagesummary - by(data.frame(age,ethnicity), cohort, summary)
w - latex.default(cohortbyagesummary,caption=Five Number Age
Summaries by Cohort,
label=agesummarybycohort,cgroup=c('hello','goodbye','hello'),
colheads=c(Age,Ethnicity),
extracolheads=c('hello','goodbye'),greek=TRUE,
ctable=TRUE)
I am not able to get the major column headings of cgroup to work. I
receive the error:
Object cline not found
See if a modified version at
http://biostat.mc.vanderbilt.edu/cgi-bin/cvsweb.cgi/Hmisc/R/latex.s
fixes your problem.
Dr. Harrell,
Thanks for your help. I have downloaded latex.s, but am unable to figure
out where it should go. How do I ensure that it is called when I load
Hmisc? Do I patch it against R/Hmisc?
I have a local directory structure in ~/Library/R/library/Hmisc/:
-rw-r--r-- 1 user user 594 12 May 19:20 CITATION
-rw-r--r-- 1 user user 989 12 May 19:20 DESCRIPTION
drwxr-xr-x 3 user user 102 12 May 19:20 Meta/package.rds
drwxr-xr-x 3 user user 102 12 May 19:20 R/Hmisc
drwxr-xr-x 3 user user 102 12 May 19:20 libs/Hmisc.so
Thanks for your patience.
Your directory structure is from an installed binary package. You need
to replace the file in the *source* package and *install* the source
package after that.
Uwe Ligges
A better approach is just to source( ) in the new version after
library(Hmisc) is issued. You can put latex.s anywhere, just put that
path in the source( ). A new version of Hmisc will include the fix.
Please note that this does now work generally if a NAMESPACE is involved
(which seems not to be the case here).
Uwe
Frank
aric
__
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
__
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] How to use fixed-width fonts such as courier in R
Hi, I am trying to use Arial bold for labelling (font.lab =2), and use the fixed-width Courier bold for axis. I will export the plot to .ps format. I have been trying to use font.axis = 11, but that doesn't work when I exported the plot to a .ps file. I have been trying hard to read the help page of postscript these few days, but didn't get the courier font yet. Can you please help me figure out how I should use postscript? Thanks! Best Sean __ 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] Missing Data Line Type?
I have a general question. Is there a setting that can be used for a multiple line type? The situation is that I want a solid line between x and y points but if the y point is missing, I want a dashed line type to the next point. In other words, if point 1 to 2 exists, make that line solid, otherwise, make it dashed up to the next existing x/y point. Additionally, what plot type would you recommend for a plot with two Y points per X? The two points would be joined by a vertical line. The average of the two is the dual type line described above. mailto:[EMAIL PROTECTED] Kenneth Ray Hobson, P.E. Oklahoma DOT - QA IAS Manager 200 N.E. 21st Street Oklahoma City, OK 73105-3204 (405) 522-4985, (405) 522-0552 fax Visit our website at: http://www.okladot.state.ok.us/materials/materials.htm __ 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] Table Help
Reply to sender Reply to all Reply to folder Forward Move/Copy Delete Read previous item Read next item Get help information on the current window From: McMurtry, Benjamin G. To: '[EMAIL PROTECTED]' Cc: Subject:Table Help Sent: 5/24/2005 4:33 PM Importance: Normal I have a very large table that I want to add some of the certain rows. The table is as follows: Username1 2 Username1 4 Username2 6 Username2 10 Username3 12 Username3 10 Username3 16 Etc The data is sorted by Column 1 (Ie the username) then by columm 2 (The numbers). I want to combine the rows so it would be as follows: Username1 6 Username2 16 Username3 38 Is there easy way using a feature like bind to sum all of collumn two where column 1 is the same? Thanks! Ben __ 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] Plot range resizing when adding additiona lines
Hi -- I have searched the documentation and archives on graphing
capabilities in R for the past couple of hours, but I haven't been able
to find anything directly related to my problem.
I want to create a plot with several lines displayed on it. I want each
line to be displayed in a different color, so it seems the only way to
do this is to create a plot and then use the lines() function. However,
once i create the original plot, when I add new lines to the plot, the
axes range stays the same, and the new lines often extend beyond the
range of the original axes, cutting off the data of the added lines.
Is there any way to force the plot to resize it's axes range when new
lines are added, or is there some other optional way of implementing
this? Thanks.
DISCLAIMER: This e-mail message and any attachments are inte...{{dropped}}
__
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] Table Help
I have a very large table that I want to add some of the certain rows. The table is as follows: Username1 2 Username1 4 Username2 6 Username2 10 Username3 12 Username3 10 Username3 16 Etc The data is sorted by Column 1 (Ie the username) then by columm 2 (The numbers). I do not know how many of each username I will have. I want to combine the rows so it would be as follows: Username1 6 Username2 16 Username3 38 Is there easy way using a feature like bind to sum all of collumn two where column 1 is the same? Thanks! Ben __ 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] lme4 package and importIntoEnv errors
On Tue, 24-May-2005 at 08:40AM -0500, Douglas Bates wrote: | Perhaps I can add a bit more explanation. As Deepayan mentioned, the | versions of the lme4 package are closely linked to the versions of the | Matrix package. The R code for lmer is in the lme4 package but the | corresponding C code is in the Matrix package where it can gain access | to other C functions for sparse matrix manipulation. Thanks for that explanation. I was curious to know why it's so different from other packages I've had no trouble with. My problem did, indeed, arise from using an older version of lme4 with a new version of Matrix. Douglas's post explains why lme4_0.95-8.tar.gz is so much smaller than lme4_0.8-2.tar.gz. I feel much less confused now. Thank you Renaud Lancelot and Deepayan Sarkar also. -- Patrick Connolly HortResearch Mt Albert Auckland New Zealand Ph: +64-9 815 4200 x 7188 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ I have the world`s largest collection of seashells. I keep it on all the beaches of the world ... Perhaps you`ve seen it. ---Steven Wright ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ __ 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] output of mars() in package mda; how do I read the pairwise interaction terms from the output?
Hi,
I have run mars() with the default degree=1, and have constructed
splines which are similar to what I would get from Salford System's
MARS. I then use these splines as potential predictors, along with
rpart( ) terminal nodes and other potential predictors, in logistic
regression in SAS. The output of mars() and the splines I created are
shown below (pardon the lengthy output):
names(pchresp)
[1] ord_flag OI_lodlrsize_cnt DI_diff_wo_arch
DI_Days_s_2l_wo
[5] DI_wo_rec_count DH_diff_wo_arch DH_Days_s_l_wo
DH_tot_loss_amt
[9] DH_wo_rec_count DH_Avg_loss_amt DA_diff_wo_arch DA_max_loss
[13] DA_Days_s_l_wo DA_Days_s_2l_wo DA_wo_rec_count CZ_cen65
[17] CZ_cen78 CZ_cen86 CZ_cen98 CZ_cen99
[21] CZ_cen132CZ_cen232CZ_cen236CZ_cen247
[25] CZ_cen272CZ_cen274CZ_cen287CZ_cen335
[29] CZ_cen337CZ_cen370CZ_cen371CZ_cen373
[33] CZ_cen377CZ_cen419CZ_cen509CZ_cen569
[37] CZ_cen638CZ_cen695CZ_cen696CZ_cen698
[41] CZ_cen700CZ_cen701CZ_cen702DZ9_rec
[45] log25DZ5_rec DZ5_str DZ1_pob
[49] alor ihcfbalratio cgsbalratio cgsbalpaid
[53] oxlogit_new nslogit_new sclogit_new hit
[57] II_Find_Income2 II_SESI2
y - pchresp[, c(1)]
x - pchresp[, -c(1)]
m1 - mars(x, y)
showcuts - function(obj)
+ {
+ tmp - obj$cuts[obj$sel, ]
+ dimnames(tmp) - list(NULL, dimnames(x)[[2]])
+ tmp
+ }
showcuts(m1)
OI_lodlrsize_cnt DI_diff_wo_arch DI_Days_s_2l_wo DI_wo_rec_count
[1,]0 0 0 0
[2,]0 0 0 0
[3,]0 0 0 0
[4,]0 0 0 1
[5,]0 0 0 0
[6,]0 0 0 0
[7,]0 0 0 0
[8,]0 0 0 0
[9,]0 0 0 0
[10,]0 0 0 0
[11,]0 0 0 0
[12,]0 0 0 0
[13,]0 0 0 0
[14,]0 0 0 0
[15,]0 0 0 0
[16,]0 0 0 0
[17,]0 0 0 0
[18,]0 0 0 0
[19,]0 0 0 0
[20,]0 0 0 0
[21,]0 0 0 0
[22,]0 0 0 0
DH_diff_wo_arch DH_Days_s_l_wo DH_tot_loss_amt DH_wo_rec_count
[1,] 0 0 0 0
[2,] 0 0 0 0
[3,] 0 0 0 0
[4,] 0 0 0 0
[5,] 0 0 0 0
[6,] 0 0 0 0
[7,] 0 0 0 0
[8,] 0 0 0 0
[9,] 0 0 0 0
[10,] 0 0 0 0
[11,] 0 0 0 0
[12,] 0 0 0 0
[13,] 0 0 0 0
[14,] 0 0 0 0
[15,] 0 0 0 0
[16,] 0 0 0 0
[17,] 0 0 0 0
[18,] 0 0 0 0
[19,] 0 0 0 0
[20,] 0 0 0 0
[21,]1917 0 0 0
[22,] 0 1735 0 0
DH_Avg_loss_amt DA_diff_wo_arch DA_max_loss DA_Days_s_l_wo
[1,] 0 0 0 0
[2,] 0 0 0 0
[3,] 0 0
Re: [R] Table Help
see ?aggregate Sean On May 24, 2005, at 4:39 PM, McMurtry, Benjamin G. wrote: Is there easy way using a feature like bind to sum all of collumn two where column 1 is the same? __ 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] in other words Re: How to use fixed-width fonts such as courier in R
the problem is how to use both courier bold font for axis and arial bold font for labelling. If I use familiy = courier in postscript, everything will become courier fonts .. I noticed that in postscirpt help page, we can customize a family such as family = c(CM_regular_10.afm,CM_boldx_10.afm, cmti10.afm, cmbxti10.afm, CM_symbol_10.afm; However, I tried many times, and just don't know the symbol used in R for courier bold or arial bold, etc. Hi, I am trying to use Arial bold for labelling (font.lab =2), and use the fixed-width Courier bold for axis. I will export the plot to .ps format. I have been trying to use font.axis = 11, but that doesn't work when I exported the plot to a .ps file. I have been trying hard to read the help page of postscript these few days, but didn't get the courier font yet. Can you please help me figure out how I should use postscript? Thanks! Best Sean __ 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] Plot range resizing when adding additiona lines
In traditional, or base graphics, see matplot, which does exactly what
you describe.
You can also look at lattice graphics, which will give you flexibility to
plot in a single panel or multiple panels.
Hope this helps,
Matt Wiener
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Hikel, Jerry
Sent: Tuesday, May 24, 2005 4:41 PM
To: R-help@stat.math.ethz.ch
Subject: [R] Plot range resizing when adding additiona lines
Hi -- I have searched the documentation and archives on graphing
capabilities in R for the past couple of hours, but I haven't been able
to find anything directly related to my problem.
I want to create a plot with several lines displayed on it. I want each
line to be displayed in a different color, so it seems the only way to
do this is to create a plot and then use the lines() function. However,
once i create the original plot, when I add new lines to the plot, the
axes range stays the same, and the new lines often extend beyond the
range of the original axes, cutting off the data of the added lines.
Is there any way to force the plot to resize it's axes range when new
lines are added, or is there some other optional way of implementing
this? Thanks.
DISCLAIMER: This e-mail message and any attachments are inte...{{dropped}}
__
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] Plot range resizing when adding additiona lines
Hikel, Jerry wrote:
Hi -- I have searched the documentation and archives on graphing
capabilities in R for the past couple of hours, but I haven't been able
to find anything directly related to my problem.
I want to create a plot with several lines displayed on it. I want each
line to be displayed in a different color, so it seems the only way to
do this is to create a plot and then use the lines() function. However,
once i create the original plot, when I add new lines to the plot, the
axes range stays the same, and the new lines often extend beyond the
range of the original axes, cutting off the data of the added lines.
Is there any way to force the plot to resize it's axes range when new
lines are added, or is there some other optional way of implementing
this? Thanks.
DISCLAIMER: This e-mail message and any attachments are inte...{{dropped}}
__
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
You can check the range of all items to plot and take the minimum and
maximum value across all items. Then draw the plot with the axis range
explicitely set to 'minimum'-'maximum'!
That is assuming you know the items you are drawing before hand.
Sander.
--
Dr Sander P. Oom
Animal, Plant and Environmental Sciences,
University of the Witwatersrand
Private Bag 3, Wits 2050, South Africa
Tel (work) +27 (0)11 717 64 04
Tel (home) +27 (0)18 297 44 51
Fax +27 (0)18 299 24 64
Email [EMAIL PROTECTED]
Web www.oomvanlieshout.net/sander
__
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] Plot range resizing when adding additiona lines
That's what i wound up doing -- i am totally new to R, so i wasn't sure
if there were an easy way of getting the min and max values of a data
frame, but i tried that and it worked out well. Thanks.
-Original Message-
From: Sander Oom [mailto:[EMAIL PROTECTED]
Sent: Tuesday, May 24, 2005 5:04 PM
To: Hikel, Jerry
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Plot range resizing when adding additiona lines
Hikel, Jerry wrote:
Hi -- I have searched the documentation and archives on graphing
capabilities in R for the past couple of hours, but I haven't been
able to find anything directly related to my problem.
I want to create a plot with several lines displayed on it. I want
each line to be displayed in a different color, so it seems the only
way to do this is to create a plot and then use the lines() function.
However, once i create the original plot, when I add new lines to the
plot, the axes range stays the same, and the new lines often extend
beyond the range of the original axes, cutting off the data of the
added lines.
Is there any way to force the plot to resize it's axes range when new
lines are added, or is there some other optional way of implementing
this? Thanks.
DISCLAIMER: This e-mail message and any attachments are
inte...{{dropped}}
__
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
You can check the range of all items to plot and take the minimum and
maximum value across all items. Then draw the plot with the axis range
explicitely set to 'minimum'-'maximum'!
That is assuming you know the items you are drawing before hand.
Sander.
--
Dr Sander P. Oom
Animal, Plant and Environmental Sciences, University of the
Witwatersrand Private Bag 3, Wits 2050, South Africa
Tel (work) +27 (0)11 717 64 04
Tel (home) +27 (0)18 297 44 51
Fax +27 (0)18 299 24 64
Email [EMAIL PROTECTED]
Web www.oomvanlieshout.net/sander
-
DISCLAIMER: This e-mail message and any attachments are inte...{{dropped}}
__
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] Missing Data Line Type?
The dashed line can be added to the plot with a call to lines after removing the NAs from your x/y vectors (I'm assuming 'missing' means NA). plot(x,y,type='l') lines(x[!is.na(y)],y[!is.na(y)],lty=2) Vertical lines can be accomplished with segments. norm -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, May 24, 2005 1:39 PM To: r-help@stat.math.ethz.ch Subject: [R] Missing Data Line Type? I have a general question. Is there a setting that can be used for a multiple line type? The situation is that I want a solid line between x and y points but if the y point is missing, I want a dashed line type to the next point. In other words, if point 1 to 2 exists, make that line solid, otherwise, make it dashed up to the next existing x/y point. Additionally, what plot type would you recommend for a plot with two Y points per X? The two points would be joined by a vertical line. The average of the two is the dual type line described above. mailto:[EMAIL PROTECTED] Kenneth Ray Hobson, P.E. Oklahoma DOT - QA IAS Manager 200 N.E. 21st Street Oklahoma City, OK 73105-3204 (405) 522-4985, (405) 522-0552 fax Visit our website at: http://www.okladot.state.ok.us/materials/materials.htm __ 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] rotate pie chart
Hi
gridBase won't help here (grid can't rotate traditional graphics output).
I think you have to get your hands dirty on this one, but it's not too
hard. Here's a function pie90() which is a tiny modification of pie().
Does that do the trick?
pie90 - function (x, labels = names(x), edges = 200, radius = 0.8,
density = NULL,
angle = 45, col = NULL, border = NULL, lty = NULL, main = NULL,
...)
{
if (!is.numeric(x) || any(is.na(x) | x = 0))
stop('x' values must be positive.)
if (is.null(labels))
labels - as.character(1:length(x))
x - c(0, cumsum(x)/sum(x))
dx - diff(x)
plot.new()
pin - par(pin)
xlim - ylim - c(-1, 1)
if (pin[1] pin[2])
xlim - (pin[1]/pin[2]) * xlim
else ylim - (pin[2]/pin[1]) * ylim
plot.window(xlim, ylim, , asp = 1)
nx - length(dx)
if (is.null(col))
col - if (is.null(density))
c(white, lightblue, mistyrose, lightcyan,
lavender, cornsilk)
else par(fg)
col - rep(col, length.out = nx)
border - rep(border, length.out = nx)
lty - rep(lty, length.out = nx)
angle - rep(angle, length.out = nx)
density - rep(density, length.out = nx)
for (i in 1:nx) {
n - max(2, floor(edges * dx[i]))
# modified line below
t2p - 2 * pi * seq(x[i], x[i + 1], length = n) + pi/2
xc - c(cos(t2p), 0) * radius
yc - c(sin(t2p), 0) * radius
polygon(xc, yc, density = density[i], angle = angle[i],
border = border[i], col = col[i], lty = lty[i])
# modified line below
t2p - 2 * pi * mean(x[i + 0:1]) + pi/2
xc - cos(t2p) * radius
yc - sin(t2p) * radius
if (!is.na(lab - labels[i]) lab != ) {
lines(c(1, 1.05) * xc, c(1, 1.05) * yc)
text(1.1 * xc, 1.1 * yc, lab, xpd = TRUE, adj = ifelse(xc
0, 1, 0), ...)
}
}
title(main = main, ...)
invisible(NULL)
}
Paul
Sean Davis wrote:
You might want to look at grid graphics and gridBase. I don't know in
detail how to go about what you are asking, but grid allows you to
rotate plots arbitrarily. Here are a couple of links that I think are
useful.
http://www.stat.auckland.ac.nz/~paul/grid/grid.html
http://www.stat.auckland.ac.nz/~paul/grid/doc/rotated.pdf
Sean
On May 24, 2005, at 10:09 AM, Lars wrote:
hey,
about two weeks ago i posted a question concerning the display of two
piecharts on one plot. after now being able to do so, i need to rotate
them. the first piece of my pie is suppose to start at 0° but at 90°.
i tried several things, all failing in the end. anyone out there who
has an idea?
Lars
__
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
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
__
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] in other words Re: How to use fixed-width fonts such as courier in R
Great. Thanks a lot. That is exactly what I need. Xiang On Wed, 25 May 2005, Paul Murrell wrote: Hi Does this do what you want? postscript(example.ps, fonts=c(sans, mono)) plot(1:10, axes=FALSE, ann=FALSE) par(family=sans) # By default Helvetica which is like Arial title(xlab=sans serif axis label) title(ylab=bold sans serif axis label, font.lab=2) par(family=mono) # By default Courier axis(1, at=seq(2, 8, 2), label=c(mono, space, tick, labels)) axis(2, at=seq(2, 10, 2), label=c(bold, mono, space, tick, labels), font.axis=2) box() dev.off() You might also want to take a look at the article Fonts, lines, and transparency ... in R News 4/2 http://cran.stat.auckland.ac.nz/doc/Rnews/Rnews_2004-2.pdf Paul Xiang Li wrote: the problem is how to use both courier bold font for axis and arial bold font for labelling. If I use familiy = courier in postscript, everything will become courier fonts .. I noticed that in postscirpt help page, we can customize a family such as family = c(CM_regular_10.afm,CM_boldx_10.afm, cmti10.afm, cmbxti10.afm, CM_symbol_10.afm; However, I tried many times, and just don't know the symbol used in R for courier bold or arial bold, etc. Hi, I am trying to use Arial bold for labelling (font.lab =2), and use the fixed-width Courier bold for axis. I will export the plot to .ps format. I have been trying to use font.axis = 11, but that doesn't work when I exported the plot to a .ps file. I have been trying hard to read the help page of postscript these few days, but didn't get the courier font yet. Can you please help me figure out how I should use postscript? Thanks! Best Sean __ 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 -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 [EMAIL PROTECTED] http://www.stat.auckland.ac.nz/~paul/ __ 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] Contingency tables from data.frames
Dear list,
I'm trying to do a set of generic functions do make contingency tables from
data.frames. It is just running nice (I'm learning R), but I think it can be
better.
I would like to filter the data.frame, i.e, eliminate all not numeric variables.
And I don't know how to make it: please, help me.
Below one of the my functions ('er' is a mention to EasieR, because I'm trying
to do a package for myself and the my students):
#2. Tables from data.frames
#2.1---er.table.df.br (User define breaks and right)
er.table.df.br - function(df,
breaks = c('Sturges', 'Scott', 'FD'),
right = FALSE) {
if (is.data.frame(df) != 'TRUE')
stop('need data.frame data')
dim_df - dim(df)
tmpList - list()
for (i in 1:dim_df[2]) {
x - as.matrix(df[ ,i])
x - na.omit(x)
k - switch(breaks[1],
'Sturges' = nclass.Sturges(x),
'Scott' = nclass.scott(x),
'FD' = nclass.FD(x),
stop('breaks' must be 'Sturges', 'Scott' or 'FD'))
tmp - range(x)
classIni - tmp[1] - tmp[2]/100
classEnd - tmp[2] + tmp[2]/100
R- classEnd-classIni
h- R/k
# Absolut frequency
f - table(cut(x, br = seq(classIni, classEnd, h), right = right))
# Relative frequency
fr - f/length(x)
# Relative frequency, %
frP - 100*(f/length(x))
# Cumulative frequency
fac - cumsum(f)
# Cumulative frequency, %
facP - 100*(cumsum(f/length(x)))
fi - round(f, 2)
fr - round(as.numeric(fr), 2)
frP - round(as.numeric(frP), 2)
fac - round(as.numeric(fac), 2)
facP - round(as.numeric(facP),2)
# Table
res - data.frame(fi, fr, frP, fac, facP)
names(res) - c('Class limits', 'fi', 'fr', 'fr(%)', 'fac', 'fac(%)')
tmpList - c(tmpList, list(res))
}
names(tmpList) - names(df)
return(tmpList)
}
To try the function:
#a) runing nice
y1=rnorm(100, 10, 1)
y2=rnorm(100, 58, 4)
y3=rnorm(100, 500, 10)
mydf=data.frame(y1, y2, y3)
#tbdf=er.table.df.br (mydf, breaks = 'Sturges', right=F)
#tbdf=er.table.df.br (mydf, breaks = 'Scott', right=F)
tbdf=er.table.df.br (mydf, breaks = 'FD', right=F)
print(tbdf)
#b) One of the problems
y1=rnorm(100, 10, 1)
y2=rnorm(100, 58, 4)
y3=rnorm(100, 500, 10)
y4=rep(letters[1:10], 10)
mydf=data.frame(y1, y2, y3, y4)
tbdf=er.table.df.br (mydf, breaks = 'Scott', right=F)
print(tbdf)
Could anyone give me a hint how to work around this?
PS: Excuse my bad English ;-)
--
Jose Claudio Faria
Brasil/Bahia/UESC/DCET
Estatistica Experimental/Prof. Adjunto
mails:
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[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] Contingency tables from data.frames
On 5/24/05, Jose Claudio Faria [EMAIL PROTECTED] wrote:
Dear list,
I'm trying to do a set of generic functions do make contingency tables from
data.frames. It is just running nice (I'm learning R), but I think it can be
better.
I would like to filter the data.frame, i.e, eliminate all not numeric
variables.
And I don't know how to make it: please, help me.
Below one of the my functions ('er' is a mention to EasieR, because I'm trying
to do a package for myself and the my students):
#2. Tables from data.frames
#2.1---er.table.df.br (User define breaks and right)
er.table.df.br - function(df,
breaks = c('Sturges', 'Scott', 'FD'),
right = FALSE) {
if (is.data.frame(df) != 'TRUE')
stop('need data.frame data')
dim_df - dim(df)
tmpList - list()
for (i in 1:dim_df[2]) {
x - as.matrix(df[ ,i])
x - na.omit(x)
k - switch(breaks[1],
'Sturges' = nclass.Sturges(x),
'Scott' = nclass.scott(x),
'FD' = nclass.FD(x),
stop('breaks' must be 'Sturges', 'Scott' or 'FD'))
tmp - range(x)
classIni - tmp[1] - tmp[2]/100
classEnd - tmp[2] + tmp[2]/100
R- classEnd-classIni
h- R/k
# Absolut frequency
f - table(cut(x, br = seq(classIni, classEnd, h), right = right))
# Relative frequency
fr - f/length(x)
# Relative frequency, %
frP - 100*(f/length(x))
# Cumulative frequency
fac - cumsum(f)
# Cumulative frequency, %
facP - 100*(cumsum(f/length(x)))
fi - round(f, 2)
fr - round(as.numeric(fr), 2)
frP - round(as.numeric(frP), 2)
fac - round(as.numeric(fac), 2)
facP - round(as.numeric(facP),2)
# Table
res - data.frame(fi, fr, frP, fac, facP)
names(res) - c('Class limits', 'fi', 'fr', 'fr(%)', 'fac', 'fac(%)')
tmpList - c(tmpList, list(res))
}
names(tmpList) - names(df)
return(tmpList)
}
To try the function:
#a) runing nice
y1=rnorm(100, 10, 1)
y2=rnorm(100, 58, 4)
y3=rnorm(100, 500, 10)
mydf=data.frame(y1, y2, y3)
#tbdf=er.table.df.br (mydf, breaks = 'Sturges', right=F)
#tbdf=er.table.df.br (mydf, breaks = 'Scott', right=F)
tbdf=er.table.df.br (mydf, breaks = 'FD', right=F)
print(tbdf)
#b) One of the problems
y1=rnorm(100, 10, 1)
y2=rnorm(100, 58, 4)
y3=rnorm(100, 500, 10)
y4=rep(letters[1:10], 10)
mydf=data.frame(y1, y2, y3, y4)
tbdf=er.table.df.br (mydf, breaks = 'Scott', right=F)
print(tbdf)
Try this:
sapply(my.data.frame, is.numeric)
Also you might want to look up:
?match.arg
?stopifnot
?ncol
?sapply
?lapply
__
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] image() and non-well-ordered colours
Hi
Robin Hankin wrote:
Hi.
I want to use image() with colours that are indexed by two variables.
Indexing by one variable is easy:
library(colorspace)
x - seq(from=0, to=1,len=30)
z - outer(x,1i*x,+)
image(Re(z),col=hcl(seq(from=0,to=100,len=15),c=100))
OK, so far so good. Now, I want the colour to be a more complicated
function
of z, in which both the hue and luminance change (thus the colours cannot
be ordered):
f - function(z){hcl(h=100*Re(z),l=100*Im(z))}
I want to draw z in terms of the colour defined by f():
image(z,col=f)
image(f(z))
but these don't work as intended. How do I use image() to get what I want?
I can get close using plot():
x - runif(1000)
y - (1:1000)/10
g - function(x){hcl(h=80*x,l=(1:1000)/10,c=300)}
plot(x,y,col=g(x),pch=16)
[note that one cannot draw nontrivial contour lines joining points of
identical colours on this
plot: top left to lower right goes from pink to black; top right to low
left goes from yellow to reddy orange]
It'd be nice to make image() do what I want. Anyone?
How about a brute-force approach using rect() ... ?
x - seq(from=0, to=1,len=30)
z - outer(x,1i*x,+)
f - function(z){hcl(h=100*Re(z),l=100*Im(z))}
plot(x, x, type=n)
step - diff(x)[1]/2
xmid - rep(x, 30)
ymid - rep(x, each=30)
rect(xmid - step, ymid - step,
xmid + step, ymid + step,
col=f(z), border=NA)
box()
Paul
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
__
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] Re: S4 method inheritance
Ross Boylan wrote: On Tue, May 24, 2005 at 06:27:56AM -0700, Robert Gentleman wrote: Duncan Murdoch wrote: Ross Boylan wrote: On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: Finally, I'm a bit concerned that one article mentioned that S4 inheritance, in practice, is used mostly for data, not methods (Thomas Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I shouldn't travel? Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends A), how does B's method foo invoke A's foo? Your question doesn't make sense in S4. In S4, classes don't have methods, generics have methods. There's no such thing as B's method or A's method. You might get what you want with foo(as(bObject, A)) if bObject is an instance of class B. The question assumes that A's foo was defined as an in place function, so there's no (obvious) named object for it, i.e, setMethod(A, signature(blah=numeric), function(x) something) In general it may be best to think of a generic function as a dispatching mechanism. For S4 methods are associated with a specific generic function. specific generic is a reference to the ability to define generics within the context of a particular package? Well, more that you can identify one (either explicitly by its package [ie. fully-qualified name], or implicitly by the fact that it is first on the search path - the former being prefered). But the notion is that there is one and you have asked that your method be made available to that one generic function for dispatch. This is in contrast to S3 - where no such functionality exists - that I know of; under S3 any method is a method for all generic functions of the correct name and the programmer has no (easy) control. Under S4 methods are not really ordinary functions, should not be called directly and are invoked only via calls to the generic (you can of course break all of those rules). A generic knows about all methods that are associated with it, and about no others. Presumably setMethod does the association. Is the where argument intended to identify which generic method to pick? The fact that there is not a package argument to setMethod, as there is to setGeneric, is a little confusing to me. I believe that is the documented behavior. Yes the where argument should allow you complete specificity. I will leave it to the auther to clarify differences between the where and package arguments in the call to setGeneric (or you, if you care to explore the code). Thus in S4, the little tiff over who owns label goes away - they both do - different packages can define generic They is two different packages? Or is this a reference to my original confusion about class vs generic ownership of a method? It is the two packages. The S langauge allows for the same symbol to be bound to different values in different namespaces (in R that is becoming explicit, in SPlus it is less so, but still generally true). I can think of no good reason to treat generic functions, or any other first class object, differently. HTH, Robert functions for label, or anything else they care to, and users can write methods for specific generic functions and associate them with a generic. ... HTH Robert __ 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] obtaining first and last record for rows with same identifier
If you want to obtain a data frame you can use the functions head and tail
like:
dat=data.frame(id=rep(1:5,3),num=rnorm(15), num2=rnorm(15))#Creates data
frame with id
last=do.call(rbind,by(dat,dat$id,tail,1))#Selects the last observation for
each id
first=do.call(rbind,by(dat,dat$id,head,1))#Selects the first observation
for each id
newdat=rbind(first,last)#Joins data
newdat=newdat[order(newdat$id),]#sorts data by id
Notice that rownames will give you the original row location of the
observations selected
I hope this helps
Francisco
From: Berton Gunter [EMAIL PROTECTED]
To: 'Sean Davis' [EMAIL PROTECTED], [EMAIL PROTECTED]
CC: 'rhelp' r-help@stat.math.ethz.ch
Subject: RE: [R] obtaining first and last record for rows with same
identifier
Date: Tue, 24 May 2005 12:17:58 -0700
I think by() is simpler:
by(yourframe,factor(yourframe$patid),function(x)x[c(1,nrow(x)),])
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sean Davis
Sent: Tuesday, May 24, 2005 11:38 AM
To: [EMAIL PROTECTED]
Cc: rhelp
Subject: Re: [R] obtaining first and last record for rows
with same identifier
If you have your data.frame ordered by the patid, you can use the
function rle in combination with cumsum. As a vector example:
a - rep(c('a','b','c'),10)
a
[1] a b c a b c a b c a b c a b c a
b c a
[20] b c a b c a b c a b c
b - a[order(a)]
b
[1] a a a a a a a a a a b b b b b b
b b b
[20] b c c c c c c c c c c
l - rle(b)$length
cbind(l,cumsum(l),cumsum(l)-l+1)
l
[1,] 10 10 1
[2,] 10 20 11
[3,] 10 30 21
# use the line below to get the length of the block of the dataframe,
the start, and then end indices
cbind(l,cumsum(l)-l+1,cumsum(l))
l
[1,] 10 1 10
[2,] 10 11 20
[3,] 10 21 30
Sean
On May 24, 2005, at 2:27 PM, [EMAIL PROTECTED] wrote:
I have a dataframe that contains fields such as patid, labdate,
labvalue.
The same patid may show up in multiple rows because of lab
measurements on multiple days. Is there a simple way to
obtain just
the first and last record for each patient, or do I need to
write some
code that performs that.
Thanks,
Steven
__
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
__
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
