Re: [R] Is this my mistake or a bug?(K-S test and EVT)
Mu Tian wrote: Hi, I was doing a Kolmogrov test on x, y shown below. They are both 151 long. According to the help file, exact p-value is not available so I set exact = FALSE, but still got the warning. There are no duplicated values in either X or Y. But I'll wager that there are some Xs equal to Ys. Thank you for your tips. BTW, is there functions in R about Extreme value theory? Packages evd and evir and perhaps others. Peter Ehlers ks.test(x, y, exact=FALSE) Two-sample Kolmogorov-Smirnov test data: x and y D = 0.0199, p-value = 1 alternative hypothesis: two.sided Warning message: cannot compute correct p-values with ties in: ks.test(x, y, exact = FALSE) [snip] __ 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] a problem 'cor' function
Looks like another case of the most F of all FAQs: FAQ 7.31. See if the following makes sense to you: pl - iris[101:150, 3] all.equal(cor(pl,pl), 1) [1] TRUE cor(pl,pl) == 1 [1] FALSE sprintf(%1.22g, cor(pl, pl)) [1] 0.99989 sprintf(%1.22g, pl) [1] 6 5.0996 5.9004 etc Peter Ehlers Tao Shi wrote: Hi list, One of my co-workers found this problem with 'cor' in his code and I confirm it too (see below). He's using R 2.2.1 under Win 2K and I'm using R 2.3.0 under Win XP. === R.Version() $platform [1] i386-pc-mingw32 $arch [1] i386 $os [1] mingw32 $system [1] i386, mingw32 $status [1] $major [1] 2 $minor [1] 3.0 $year [1] 2006 $month [1] 04 $day [1] 24 $`svn rev` [1] 37909 $language [1] R $version.string [1] Version 2.3.0 (2006-04-24) data(iris) cor(iris[1:4]) Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length 1. -0.1176 0.8718 0.8179 Sepal.Width -0.1176 1. -0.4284 -0.3661 Petal.Length 0.8718 -0.4284 1. 0.9629 Petal.Width0.8179 -0.3661 0.9629 1. cor(iris[1:4])==1 Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length TRUE FALSEFALSE FALSE Sepal.Width FALSETRUEFALSE FALSE Petal.LengthFALSE FALSE TRUE FALSE Petal.Width FALSE FALSEFALSETRUE cor(iris[1:4], iris[1:4]) Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length 1. -0.1176 0.8718 0.8179 Sepal.Width -0.1176 1. -0.4284 -0.3661 Petal.Length 0.8718 -0.4284 1. 0.9629 Petal.Width0.8179 -0.3661 0.9629 1. cor(iris[1:4], iris[1:4])==1 Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length TRUE FALSEFALSE FALSE Sepal.Width FALSETRUEFALSE FALSE Petal.LengthFALSE FALSEFALSE FALSE Petal.Width FALSE FALSEFALSETRUE === The two ways of calculating correlation seem to generate the 'same' results, but the second one doesn't appear to be numerically stable (see the 3rd diagonal element of the last matrix). thanks, ...Tao _ Join the next generation of Hotmail and you could win the adventure of a lifetime __ 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 -- Peter Ehlers Chair, Division of Statistics and Actuarial Science Department of Mathematics and Statistics University of Calgary, 2500 University Dr. NW ph: 403-220-3936 Calgary, Alberta T2N 1N4, CANADA fax: 403-282-5150 email: [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] Vertical Line on Plot
Barry Rowlingson wrote: Peter Lauren wrote: I was wondering what would be the best way to put a vertical line on a graph made with plot(). I can get an horizontal line by plotting a vector where every element has the same value but it is not as clear how a vertical line should be done. abline(v=42) you can use it for horizontal lines too: abline(h=42) and several other things. See help(abline) for details. Barry I don't wish to discourage new R users from asking questions in this forum, but this seems like a good time to remind new R users of the existence of some _very_ useful documentation: 1. As has just recently been mentioned again by Berton Gunter in his periodic reminder, there exists a nice, concise ref-card at http://www.rpad.org/Rpad/Rpad-refcard.pdf This would have led to abline() almost immediately (page 3). 2. 'An Introduction to R' is installed with R. Again, it would have quickly led to abline() (section 12.2). The help pages are great when you know what function you need. The above two documents (and others on CRAN) help one to discover what function might be needed. Peter Ehlers __ 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] missed ylim from plot.default
Antonio, Fabio Di Narzo wrote: Hi all. On my R-2.3.0, calling: plot(1:5, rep(1,5), xlim=c(-0.5,7), ylim=c(-0.5,2.8), asp=1) gives to me a plot (tried pdf and X11) whose y axis goes from about -2 to about 4.5. What I've missed? How can I show some pre-specified x and y ranges from a plot (keeping fixed the aspect ratio)? Tnx all, Antonio, Fabio Di Narzo. [[alternative HTML version deleted]] Do you want a wide, but not very tall plot? If so, you could specify the width/height in your X11() call. Peter Ehlers __ 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 use lm.predict to obtain fitted values?
Larry Howe wrote: I have had a similar issue recently, and looking at the archives of this list, I see other cases of it as well. It took me a while to figure out that the variable name in the data frame must be identical to the variable name in the model. I don't see this mentioned in the documentation of predict.lm, and R issues no warning in this case. How would I go about officially requesting that this is mentioned, either in the documentation, or as a warning? Sincerely, Larry Howe Here's what I would do before officially requesting anything: read 'An Introduction to R', especially section 11.3: predict(object, newdata=data.frame) The data frame supplied must have variables specified with the same labels as the original. Seems pretty explicit. As well, the predict.lm help page has, under Arguments: newdata An optional data frame in which to look for variables with which to predict. That, too, seems unambiguous; i.e. you can't predict with values of z when z is not in your formula. Peter Ehlers On Friday May 19 2006 13:26, Prof Brian Ripley wrote: data.frame(x=newData) will not have any entries called x: You supplied newdata, so assuming you means newdata, data.frame(x=newdata) x.1 x.2 x.3 x.4 x.5 x.6 1 1 1 1 1 1 1 has 6 columns none of which is labelled x. If you read the help for lm, it does not mention having a matrix on the rhs of a formula, and the help for data.frame does explain how it works. predict(model, data.frame(x=I(newData))) might work. On Fri, 19 May 2006, Richard Lawn wrote: I am writing a function to assess the out of sample predictive capabilities of a time series regression model. However lm.predict isn't behaving as I expect it to. What I am trying to do is give it a set of explanatory variables and have it give me a single predicted value using the lm fitted model. model = lm(y~x) newdata=matrix(1,1,6) pred = predict.lm(model,data.frame(x=newData)); Warning message: 'newdata' had 6 rows but variable(s) found have 51 rows. pred = predict.lm(model,data.frame(newData)); Warning message: 'newdata' had 6 rows but variable(s) found have 51 rows. y is a vector of length 51. x is a 6x51 matrix newdata is a matrix of the explanatory variables I'd like a prediction for. The predict.lm function is giving me 51 (=number of observations I had) numbers, rather than the one number I do want - the predicted value of y, given the values of x I have supplied it. Many thanks, R __ 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 there be a cd command?
Rolf Turner wrote: Duncan Murdoch wrote (amongst other things): Statistical computing is not easy, so how could R be? Who has ever claimed it is? Any package that makes statistical computing appear to be easy is probably giving you wrong answers half the time, or is extremely limited in scope. Well expressed, Duncan! (A slam Dunc, one might say. :-) ) cheers, Rolf I agree - well said! The only thing Duncan missed is that the volume is high partly because there are quite a few people who want to use R without reading any documentation. But is it just my imagination or is that type of post on the decrease? Peter Ehlers __ 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] 3D pie
This discussion of 3-d pie charts comes at an opportune time. I have just formulated a new theory of graphical information transfer which is particularly simple in the case of 3-d pie charts. Let theta denote the angle between the normal to the pie cylinder and the pie-eyed line (connecting eye and centre of pie). Then the information transmitted from pie to viewer is K * (pi/2 - theta)^3 for theta in [0, pi/2]. The normalizing constant may be written in the obvious manner as K = 8 * I_0 / pi^3. I conjecture that I_0 is not large, but I'm still waiting to hear from Microsoft regarding my application for funding to allow me to conduct extensive testing. I'm also working on higher-dimensional generalizations, but even the 4-d case does not seem to be simple. Peter Ehlers Frank E Harrell Jr wrote: Rolf Turner wrote: Gabor Grothendieck wrote: Since everyone else wimped out with a tedious you-do-not-want-to-do-that, here is a solution that uses R to control Excel and create a 3d chart. . . . People really ***should not*** be encouraged or abetted in wrong-headedness. Excel is terrible. Pie charts are terrible. Don't mess with them. Period. cheers, Rolf Turner [EMAIL PROTECTED] I second that. Helping people do things known to have major problems with the approaches can actually hurt others in the long run. 2-D pie charts are terrible. That makes 3-D pie charts terrible to the 3/2 power. Excel has serious errors and is not a good model for reproducible research. __ 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] About poisson distribution fitting and testing
Does fitdistr() in package MASS help? Peter Ehlers Linda Lei wrote: Hi All, I have a sequence of positive integers, which is right skewed. The mean value is 6 and variance is 11. I suspect it can be fitted by poisson distribution. But I'm not familiar with the function to fit distribution. Could you please help me with it? Also, once I fit the poisson distribution, how can I check the good-ness of this fitting? Thank you! [[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] Unfound objects in function
Colin,
Did you use correction = trans in Kinhom in the past? I think
Ki$trans will contain a number of NAs. Try
diff- sum (Ki$theo - Ki$trans, na.rm = TRUE)
Peter Ehlers
Colin Beale wrote:
A couple of my functions that were working last week seem to have been
changed over the weekend and no longer work, but I can't understand why
not: it seems that objects defined at the start of the function are not
located further on in the function, when this worked fine before. An
example follows at the end, using the package spatstat, though the
problem seems more general. My only guess is that I've accidentally
changed something to do with the environment that functions are
searching in to exclude themselves, but if so I've no idea how I did or
how I can cancel it!
Thanks in advance,
Colin
library (spatstat)
kernelEst - function (data, max.r = 10, edge = TRUE) {
if (!is.ppp (data)) stop (data must be a point process object)
i - 0.1
diff- 1
smo - 1
while (diff 0) {
olddiff - diff
oldsmo - smo
smo - density.ppp (data, sigma = 2 * i, edge = edge)
lambda - smo[data]
Ki - Kinhom (data[,data$window], lambda = lambda, r = seq (0,
max.r, length = 100), correction = trans)
diff- sum (Ki$theo - Ki$trans)
i - i + 0.1
if (i max.r) stop (no suitable kernel found within 0.2 to
max.r)
}
if (abs (olddiff) abs (diff)) return (smo) else return (oldsmo)
}
data (simdat)
test - kernelEst (simdat)
Error in while (diff 0) { : missing value where TRUE/FALSE needed
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major2
minor2.1
year 2005
month12
day 20
svn rev 36812
language R
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Re: [R] installation of package randomForest failed
Ruth, Does your R know about the library C://Programme//R//rw2011//library//randomForest ? I suspect that you want lib = C://Programme//R//rw2011//library in your install.packages() call. Or you could just leave the 'lib=' argument at its default. Peter Ehlers Ruth Meili wrote: Hello I'd like to try out some functions in the package randomForest. Therefore, I did install this package. However, it is not possible to load the library, although I have R-Version 2.1.1 (i.e. later than 2.0.0). The commands I used and the Answers/Error from R is as follows: install.packages(C://Programme//R//rw2011//library//randomForest_4.5-16.zip, lib=C://Programme//R//rw2011//library//randomForest,repos = NULL) package 'randomForest' successfully unpacked and MD5 sums checked updating HTML package descriptions library(randomForest) Fehler in library(randomForest) : 'randomForest' ist kein gültiges Paket -- vor 2.0.0 installiert? I run in this problem for the first time. Until now, I used to install new packages by copying the*.zip-file to the library-directory in the rw2011-directory. This seam not to work anymore. So I tried using the function install.package(), but I did not success. Does anybody know the Problem? I did not find any hints in the NEWS. Thanks anyway. Ruth ** This footnote confirms that this email message has been swept by MIMEsweeper for the presence of computer viruses. www.clearswift.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-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 terms in formula of lm or glm
Luke, A really useful thing to do would be to read section 11.1 of An Introduction to R, which comes with your R installation. Peter Ehlers Luke wrote: Thanks, Christos. Another relevant question: If I want to include the interaction term consisting of V2 and V3 (they are numeric vectors), should I use: y ~ 1 + V2:V3 or y ~ 1 + I(V2*V3) or both are good? -Luke On 4/17/06, Christos Hatzis [EMAIL PROTECTED] wrote: If you want the quadratic term, you need to pass it as an argument in function I(): y ~ 1 + V1 + V3 + I(V3^2) This is documented in ?formula -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Luke Sent: Monday, April 17, 2006 12:08 AM To: R-help@stat.math.ethz.ch Subject: [R] interaction terms in formula of lm or glm I would like to include pairwise interaction terms for lm(). For example, I want to include the quadratic term of variable V3. my.formula y ~ 1 + V1 + V3 + V3:V3 my.data y V1 V2 V3 1 31 1 42 140 2 32 0 43 120 3 33 0 57 150 4 34 0 55 132 foo - lm(my.formula, data = my.data) foo$coefficients (Intercept) V1 V3 29.47368421 -2.15789474 0.02631579 Why do the foo coefficients not include V3:V3 ? I thought that the variable V3:V3 has the values of squares of V3 elements, that is, V3:V3 140*140 120*120 Am I wrong? If I specify a fouth varaible V4 with square values of V3, and the formula is y ~ 1 + V1 + V3 + V4, it seems that the foo will give me different in and out-sample predictions. -Luke [[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 [[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] subset a matrix
Assuming that you want odd-numbered rows/cols, the seq() function is handy, as in: mat - matrix(1:(20*30), nr = 20) mat1 - mat[seq(1, 19, by = 2), seq(1, 29, by = 2)] Peter Ehlers zhijie zhang wrote: Dear friends, I have a (20*30) matrix,and want to get a subset of it like the following: The original matrix: rows:1,2,3,20; columns:1,2,3,30 I want to get my subset of The original matrix and delete others: rows:1,3,5,7,...19; columns:1,3,5.29 -- Kind Regards,Zhi Jie,Zhang ,PHDDepartment of EpidemiologySchool of Public HealthFudan UniversityTel:86-21-54237149 [[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] TukeyHSDs function (pgirmess package)
Rune Vejen Petersen wrote: Dear R-help, I have been trying to use the TukeyHSDs function in the pgirmess package to quickly extract all significant pairwise comparisons in an aov object. However, it seems that this function isn't working as intended when only the two last populations means being tested are significant. An example of this can be seen below: numbers-c(464,482,453,434,495,487) group-gl(3,2,label=c(A,B,C)) testobject-aov(numbers~group) result-TukeyHSD(testobject,conf.level=0.95) error-TukeyHSDs(result) error$group[,1] Error in error$group[, 1] : incorrect number of dimensions To illustrate the normal function, the data set below can be used. numbers-c(845,829,682, 689,581,495) Is there something wrong with this function? Or is there a better way to extract significant comparisons from a tukey test? It looks like the line res[[1]] - x[y, ] in TukeyHSDs() should be replaced with res[[1]] - x[y, , drop = FALSE] Peter Ehlers Cheers, Rune --- Rune Vejen Petersen, M.Sc.Eng. Statens Serum Institute Dept. of Infectious Disease Immunology Artillerivej 5, 81/344 DK-2300 Copenhagen [[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] a statistics question
It sounds as though 'logic regression' might help. See Ruczinski I, Kooperberg C, LeBlanc ML (2003). Logic Regression, Journal of Computational and Graphical Statistics, 12, 475-511. and the LogicReg package. Peter Ehlers Weiwei Shi wrote: Hi there, I have a statistics question on a classification problem: Suppose I have 1000 binary variables and one binary dependent variable. I want to find a way similar to PCA, in which I can find a couple of combinations of those variables to discriminate best according to the dependent variable. It is not only for dimension reduction, but more important, for finding best way to construct features. This is NOT CDA since the explanatory variables are NOT continuous. I knew the existence of that method since I consulted before with a professor but I forgot the name of the method.. sigh... I am also wondering if R has already some function or package addressing this kind of problem. Thanks -- Weiwei Shi, Ph.D Did you always know? No, I did not. But I believed... ---Matrix III [[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 run stepAIC starting with NULL model?
Joshua B Robins wrote: Hello, I'm trying to figure out how to run the stepAIC function starting with the NULL model. I can call the null model (e.g., lm(y ~ NULL)), but using this object in stepAIC doesn't seem to work. I don't know what doesn't seem to work means here, but your null model is equivalent to lm(y ~ 1) and stepAIC handles both just fine for me. Did you specify 'scope' with an 'upper' component? Peter Ehlers The objective is to calculate AICc. This can be done if stepAIC can be run starting with the NULL model; the (2p(p-1)/(n-p-1))to get AICc would be added to the final step AIC value. Can anyone suggest how to run stepAIC beginning with the NULL model, and sequentially adding and removing variables (essentially a bottom-up approach)? Thanks, Josh Robins School of Fisheries and Ocean Sciences University of Alaska Fairbanks Juneau Center (206) 331-8633 [EMAIL PROTECTED] http://students.washington.edu/jbrobins __ 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] Correlation of coefficients?
If you're talking about regression models, then I'm puzzled that this occurs frequently in R, since the summary.lm() function defaults to 'correlation = FALSE'. S-PLUS defaults to TRUE. Can you give an example where R gives you the correlations of coefficients? Anyway, parameter estimators are correlated random variables and, in the case of regression, summary(model, correlation = TRUE) gives the estimated correlation matrix. This must be somewhere in MASS, the book; any decent linear models text should will have a discussion, e.g. Draper and Smith, Applied Regression Analysis. Peter Ehlers asako Ishii wrote: Hi R users! One thing I cannot understand with R is the frequently appearing Correlation of coefficients. I do not find a through going explanation of this concept either on the help pages of R or on the internet. A Google search has shown many examples of R/S-Plus outputs but no explanations of meaning. I am afraid this turns out to be a silly and unworthy question. Would anyone be kind enough to show relevant literature or a text book to a layperson studying on his/her own? Thanks in advance. __ 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] S-PLUS 8 beta program [repost]
I have to come to the defence of Insightful here. In my experience, they have been one of the better software companies I've dealt with. (Try getting Microsoft to fix something.) I think that their new packages initiative is an excellent idea. Peter Ehlers eugene dalt wrote: In addition, I think people should always explore ways to repackage exclusive S-Plus facilities and libraries into R. By rewritting them or using GPL loopholes. It seems to me that Insightful is very good at protecting whatever they create and the same time feels very comfortable taking R stuff to keep they clients happy. In essence they are selling free stuff. --- Spencer Graves [EMAIL PROTECTED] wrote: Correct: I'm not an attorney, but I've read the GPL. It clearly says that if you have software that has functionality independent of GPL code, the GPL applies to the code you use to connect to GPL code not to your original code. Thus, Insightful would have to make publicly available anything special they do to link to GPL code that they can't reasonably claim works for other purposes. However, they are not required to reveal other parts of their source code. hope this helps, spencer graves Philippe Grosjean wrote: David Smith wrote: The GPL code is available as separately-downloaded packages for S-PLUS, as has been done for many years. My own Oswald library for S-PLUS was published under the GPL in 1997, for example, and many other authors produce open-source libraries for S-PLUS under a variety of licenses. The only difference is that they will be packaged as, well, packages rather than libraries. # David Smith Thank you for the explanation. The fact that GPL code is distributed *separately* from S-PLUS is the key point here. PhG __ 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
Re: [R] calcualtign a trailing 12 column mean in a dataframe?
While we wait for others to provide the best way, here's one way (if I understand your question correctly): numrows - 10 x - rnorm(25 * numrows) dat - as.data.frame(matrix(x, nc = 25)) newdat - as.data.frame(matrix(0, nr = numrows, nc = 14)) for(j in 1:14) newdat[, j] - rowMeans(dat[, j:(j + 11)], na.rm = TRUE) Peter Ehlers r user wrote: I have a dataframe of 25 columns and 100,000 rows called “testdf”. I wish to build a new dataframe, with 14 columns and 100,000 rows. I wish the new dataframe to have the “trailing 12 column” mean. That is, I want column 1 of the new dataframe to have soemthing like: “( mean(testdf[,1:12],na.rm=T)” What is the best way to accomplish this? __ 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] Welch test for equality of variance
Peter, I don't know the Welch test for variances, but you might consider using the Fligner-Killeen test (fligner.test) or one of the Levene test variations (package:car). A useful reference is WJ Conover, ME Johnson, MM Johnson. 1981. Technometrics 23:351 with a minor correction in Technometrics 26:302. Peter Ehlers Peter Flom wrote: Hello Using R 2.2.1 on a Windows machine. Has anyone programmed the Welch test for equality of variances? I tried RSiteSearch, but this gave references to t test and oneway.test, which are not quite what I need.I need the Welch test itself, for use in a meta-analysis (to determine if variances are equal). TIA Peter Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St http://cduhr.ndri.org www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) __ 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 -- Department of Mathematics and Statistics University of Calgary, 2500 University Dr. NW ph: 403-220-3936 Calgary, Alberta T2N 1N4, CANADA fax: 403-282-5150 __ 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] install local packages
Where did you get mclust.zip? CRAN shows mclust_2.1-11.zip. Why not just let R install mclust directly from the CRAN mirror at SFU? Use the menu: Packages Install package(s). As to your install.packages(), you need forward slashes, contriburl=, and you probably want a different destdir (or just leave the default NULL). Peter Ehlers [EMAIL PROTECTED] wrote: Hello all, I'm trying to install the local package under window system. Two ways I've tried: 1. using the menupackages install package(s) from local zip files My .zip file is mclust.zip. But it shows Errors which are: Error in gzfile(file,r): unable to open connection In addition: Warning messages: 1.error -1 in extracting from zip file 2.cannot open compressed file 'mclust/DESCRIPTION' 2. using function install.packages. the command I use is install.packages(mclust.zip,D:\sfu\BC project\clustering project\stuff from Jeffrey\flowCytometryClustering,repos=NULL,destdir=C:\Program Files\R\rw2011\library) But error is object mclust.zip not found. Could you please help me how I can install the local packages? Thanks a lot! __ 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] RGui: windows-record and command history
Duncan Murdoch wrote: On 3/23/2006 7:35 AM, Thomas Steiner wrote: a) How can I set the recording of all windows()-history forever to true? I want something like windows(record = TRUE) but not just for the window that opens then, but for all windows I will open ever. options(graphics.record=TRUE) will make that happen for the rest of the session. To really make it happen forever, you need to put this line in your Rprofile (see ?Rprofile for where that comes from). Watch out though: the graphics history is stored in your current workspace in memory, and it can get big. You might find you're running out of memory if you store everything, and you'll find your .RData files quite large if you save your workspace. On my todo list (but not for 2.3.0) is the possibility of setting a default history length, perhaps defaulting to saving the last 2 or 3 pages. [snip] Duncan, This may be asking too much, but would it be possible to consider implementing selective graph removal from the graph history? I use graph.record=TRUE frequently for comparing graphs, but often find that I'd like to kill one of the graphs while keeping others in memory. Peter Ehlers __ 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] RGui: windows-record and command history
Paul Murrell wrote: Hi Duncan Murdoch wrote: On 3/23/2006 10:46 AM, Gabor Grothendieck wrote: On 3/23/06, Duncan Murdoch [EMAIL PROTECTED] wrote: On 3/23/2006 10:29 AM, Gabor Grothendieck wrote: On 3/23/06, Duncan Murdoch [EMAIL PROTECTED] wrote: On 3/23/2006 7:35 AM, Thomas Steiner wrote: a) How can I set the recording of all windows()-history forever to true? I want something like windows(record = TRUE) but not just for the window that opens then, but for all windows I will open ever. options(graphics.record=TRUE) will make that happen for the rest of the session. To really make it happen forever, you need to put this line in your Rprofile (see ?Rprofile for where that comes from). Watch out though: the graphics history is stored in your current workspace in memory, and it can get big. You might find you're running out of memory if you store everything, and you'll find your .RData files quite large if you save your workspace. On my todo list (but not for 2.3.0) is the possibility of setting a default history length, perhaps defaulting to saving the last 2 or 3 pages. Would it be feasible to have history on disk or perhaps the last m in memory and the last n (possibly Inf) on disk? The history is just another R object. Saving big R objects on disk might be desirable, but it would be a big change, so I'd call it infeasible. I wouldn't want to get into special-casing this particular R object: that way lies madness. However, since it is just an R object, it's available for R code to work with, so someone who was interested in doing this could write a contributed package that did it. Are there R-level facilities to manipulate the history, not just the top? Sure, it's a regular R object. You will need to read the source to know how to interpret it, and since it's undocumented there's a risk of changes in future R versions, but it's not very complicated. See my message to Peter. Be careful with this. The objects that are recorded on the display list are calls to graphics functions PLUS state information in a raw binary format. The display list was originally intended for reuse within the same R session (for redrawing the screen). If you try to save it and use it between sessions or (worse) between versions of R you could run into some nasty problems. For example, what if the graphics function interface has changed? what if the raw binary state information format has changed? what if the required packages are not installed? At best, your saved object produces errors; at worst it becomes completely useless and is unrecoverable. Paul Paul, If I read your comments correctly, the problem with manipulating the graph history is with saved histories across sessions/versions. Is there any reason not to manipulate it *within* a session? I never save plots for re-use in R. Re-running code is usually best for me. But I would find it handy to fiddle with the display list in a session. Peter Ehlers __ 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] RGui: windows-record and command history
Thanks, Paul, that's useful information. Peter Paul Murrell wrote: Hi Peter Ehlers wrote: Paul Murrell wrote: Hi Duncan Murdoch wrote: On 3/23/2006 10:46 AM, Gabor Grothendieck wrote: On 3/23/06, Duncan Murdoch [EMAIL PROTECTED] wrote: On 3/23/2006 10:29 AM, Gabor Grothendieck wrote: On 3/23/06, Duncan Murdoch [EMAIL PROTECTED] wrote: On 3/23/2006 7:35 AM, Thomas Steiner wrote: a) How can I set the recording of all windows()-history forever to true? I want something like windows(record = TRUE) but not just for the window that opens then, but for all windows I will open ever. options(graphics.record=TRUE) will make that happen for the rest of the session. To really make it happen forever, you need to put this line in your Rprofile (see ?Rprofile for where that comes from). Watch out though: the graphics history is stored in your current workspace in memory, and it can get big. You might find you're running out of memory if you store everything, and you'll find your .RData files quite large if you save your workspace. On my todo list (but not for 2.3.0) is the possibility of setting a default history length, perhaps defaulting to saving the last 2 or 3 pages. Would it be feasible to have history on disk or perhaps the last m in memory and the last n (possibly Inf) on disk? The history is just another R object. Saving big R objects on disk might be desirable, but it would be a big change, so I'd call it infeasible. I wouldn't want to get into special-casing this particular R object: that way lies madness. However, since it is just an R object, it's available for R code to work with, so someone who was interested in doing this could write a contributed package that did it. Are there R-level facilities to manipulate the history, not just the top? Sure, it's a regular R object. You will need to read the source to know how to interpret it, and since it's undocumented there's a risk of changes in future R versions, but it's not very complicated. See my message to Peter. Be careful with this. The objects that are recorded on the display list are calls to graphics functions PLUS state information in a raw binary format. The display list was originally intended for reuse within the same R session (for redrawing the screen). If you try to save it and use it between sessions or (worse) between versions of R you could run into some nasty problems. For example, what if the graphics function interface has changed? what if the raw binary state information format has changed? what if the required packages are not installed? At best, your saved object produces errors; at worst it becomes completely useless and is unrecoverable. Paul Paul, If I read your comments correctly, the problem with manipulating the graph history is with saved histories across sessions/versions. Is there any reason not to manipulate it *within* a session? I never save plots for re-use in R. Re-running code is usually best for me. But I would find it handy to fiddle with the display list in a session. That is *one* problem with the display list. Messing directly with the display list *within a session* is *less* dangerous, but R's behaviour if you do that is undefined. The display list is technically an internal structure for R's internal use. We can't stop you playing with it, but I do not encourage it and it is not officially supported. There are a number of simple things that you could do to the display list that should work, but providing proper support for general manipulations of the display list would require a significant amount of (re)design of the R graphics code. Paul p.s. These comments apply to the display list in R's graphics engine. The 'grid' package also maintains a display list, and that has been designed to support more general manipulations. __ 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
