Re: [R] PCA IN R

prcomp() in stats handles matrices with n < p well, IMO. -- 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] xeon processor and ATLAS

Jeffrey J. Hallman wrote: > I've been doing econometrics for nearly 20 years, and have not yet run across > a situation that called for looking at a 1000 x 1000 matrix. I tend not to > believe analyses with more than a dozen explanatory variables. In NIR spectroscopy, it is common to have at lea

Re: [R] Streamlining Prcomp Data

Try this result <- summary(prcomp(USArrests)) names(result) M <- result$importance M[2,] The "labels" are the dimnames of the "importance" matrix. They only "show up" when the matrix is printed. If you wish, you can remove them with dimname

Re: [R] about R, RMSEP, R2, PCR

CV, or train). The objects returned by these functions have a plot method, som plot(RMSEP(...)) does "what you'd expect". See ?R2 for details about the returned objects. To get R (I presume you mean the correlation between predicted and measured values), yo

Re: [R] R-About PLSR

res Regression in R; Journal of Statistical Software 18(2), 1--24. <http://www.jstatsoft.org/v18/i02/v18i02.pdf> -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the post

Re: [R] About PLR

>From within R, you can give the command > install.packages("pls") and R will download and install it for you (as long as you have access to the Internet). To install an already downloaded package, you can use R CMD INSTALL pls_2.0-0.tar.gz in a terminal window. -- B

Re: [R] PCA (prcomp) details info.

e: M <- matrix(rnorm(900*100), ncol = 900) pca <- prcomp(M, scale = TRUE) S <- scale(M) %*% pca$rotation all.equal(S, pca$x) ## => TRUE -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-h

[R] [R-pkgs] pls version 2.0-0

cumulative' has been removed. - A new data set 'gasoline' has been included. - The 'NIR' and 'sensory' data sets have been renamed to 'yarn' and 'oliveoil'. See the file CHANGES in the sources for all changes. -- Bjørn-Helge Mevik __

Re: [R] Why the factor levels returned by cut() are not ordered?

x27; is 'TRUE', the factor levels are assumed to be ordered. > ... The help file for factor() probably doesn't tell you much about how cut() works. :-) -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat

Re: [R] Look for a R Package to locate peak data point in one dimensional data set

I think the Bioconductor package PROcess has functions for that. -- 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] can lm() automatically take in the independent variables without knowing the names in advance

ataframe) (i.e. with no formula!) will use the first column as response and the rest as predictors. -- 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://w

Re: [R] A statement over multiple lines (i.e. the ... feature in Matlab)

ning 3 and -3, respectively), while 1 + 2 - 3 will be interpreted as a single command (returnig 0). -- 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:/

[R] [R-pkgs] New package ffmanova for 50-50 MANOVA released

er jejuni under environmental conditions, Applied and Environmental Microbiology, 71, 2086-2094. -- Bjørn-Helge Mevik and Øyvind Langsrud ___ R-packages mailing list R-packages@stat.math.ethz.ch https://stat.ethz.ch/mailman/list

Re: [R] Adding Grid lines

Perhaps ?grid will help you. -- 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 and provide commented, minimal, self

Re: [R] princomp and eigen

t; sqrt(eX$values) [1] 1.2931924 1.0215069 0.8346836 0.5828707 > sqrt(9/10 * eX$values) [1] 1.2268300 0.9690865 0.7918504 0.5529597 -- 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] problem with "code/documentation mismatch"

Just an idea: how about using the \usage for the formal syntax, and \synopsis for the "user syntax", i.e. x/y ? Not sure it will work, but it might be worth a try... :-) -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing

Re: [R] R ``literal'' comand

capture.output(...) If you want a single string, with newlines: paste(capture.output(...), collapse = "\n") -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the pos

Re: [R] Status of "data.table" package

Liaw, Andy wrote: > I don't see it on CRAN, either, nor could I find mention of it in the R News > you cited. p. 66 -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] PLS

ter off using an existing implementation, for instance Barry Wise's chemometric toolbox. -- 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] Keeping scientific format on assignment

format p-values in different ways using format.pval(), which returns a string with the formatted value. E.g., > format.pval(2e-14) [1] "2e-14" -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/lis

[R] [R-pkgs] pls package: bugfix release 1.2-1

of (R)MSEP and R2 - A simple multiplicative scatter correction (msc) implementation - Functions for plotting predictions, validation statistics, coefficients, scores, loadings, biplots and correlation loadings. -- Bjørn-Helge Mevik ___ R-packages

Re: [R] Question about PLS regression

Andris Jankevics wrote: > But I have a sligthy different results with my real data. Where can the > problem be? I think you have to supply some details for anyone to be able to answer. At least what you did (the code), what you got (the results) and what you expected to get. -- Bjørn

Re: [R] question about Principal Component Analysis in R?

): d1=scale(test_data, center=pca$center, scale=FALSE) %*% pca$rotation; -- 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

[R] [R-pkgs] pls version 1.2-0

scoreplot() are now generic. See the file CHANGES in the sources for all changes. -- Ron Wehrens and Bjørn-Helge Mevik ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages _

Re: [R] Using R to process spectroscopic data

cients in significance tests. (I don't have any reference or implementation, sorry. :-) The correlation loadings can also give valuable information about which variables that might be important for the regression. See ?corrplot in the pls package. -- Bjørn-Helge Mevik ___

Re: [R] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice

Why don't you test it yourself? E.g., set.seed(42) bob1 <- rnorm(1000,0,1) set.seed(42) bob2 <- rnorm(500,0,1) bob3 <- rnorm(500,0,1) identical(bob1, c(bob2, bob3)) I won't tell you the answer. :-) -- Bjørn-Helge Mevik __ R-hel

Re: [R] 'all' inconsistent?

> > any(logical(0)) > [1] FALSE But they are, all none of them: > all(!logical(0)) [1] TRUE :-) And there aren't any FALSE values either: > any(!logical(0)) [1] FALSE so it is only logical that all none of them are TRUE. I love the empty set! :-) -- Bjørn-Helge Mevik

[R] [R-pkgs] New package lspls

-- Sincerely, Bjørn-Helge Mevik ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] modifying code in contributed libraries - changes from versions 1.* to 2.*

is changed by R CMD build, is DESCRIPTION. All .R and .Rd files are untouched (even the modification dates are unchanged). (This is on a Linux system, I don't know how it works on MS/Mac.) -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.

Re: [R] changing figure size in Sweave

Bjørn-Helge Mevik wrote: > Or use \documentclass[nogin,...]{...}. Then the 'Gin' will have no > effect, and the size of the plots in the document will not be changed > from the size given as <<...,height=??,width=??>> (i.e. the size > produced by R). A s

Re: [R] changing figure size in Sweave

ocument will not be changed from the size given as <<...,height=??,width=??>> (i.e. the size produced by R). -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] Insightful Announces: "R and S-PLUS- Panel Discussion" at 9th Annual 2005 User Conference

Michael O'Connell wrote: > tools to make it easy to convert R packages to S-PLUS. Not the other way around as well? -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

Re: [R] ISO R-programming docs/refs

y) quickly have led you to manuals such as "the R Language Definition", "Writing R Extensions" and "R Data Import/Export", and given references to books on programming S and/or R. -- Bjørn-Helge Mevik __ R-help@stat.math.

[R] [R-pkgs] pls version 1.1-0

`varnames' in coefplot, to label the x tick marks with the variable names. - loadingplot, coefplot and plot.mvrVal can now display legends, with the argument 'legendpos'. See CHANGES in the sources for all changes. -- Bjørn-Helge Mevik

Re: [R] Help: PLSR

tvar = 16562, Because the Xtotvar is the "total X variation", measured by sum(X^2) (where X has been centered). With 14 variables, scaled to sd == 1, and 1200 observations, you should get Xtotvar == 14*(1200-1) == 16786. (Maybe you have 1184 observations: 14*1183 == 16562.)

Re: [R] Reference manual is not available in the help menu of the rgui

The payoff came in the section giving the meaning of the C library error codes: EGREGIOUS means `You did *what*?'. :-) -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do re

Re: [R] PLSR: model notation and reliabilities

l), but you would have to build the "inner model" (the constructs) with other tools, such as prcomp/princomp or other factor analyses (see e.g. ?factanal and ?varimax). Alternatively, there is an R package "sem" that implements structured equation models. You might want t

Re: [R] help: pls package

ge currently doesn't estimate se of cross-validated MSEPs. There is also the question of what the estimated should be conditioned on: for leave-one-out cross-validation, sd(MSEP | trainData) = 0. [If someone knows how to calculate unbiased estimates of cross-validated MSEPs, plea

Re: [R] PLS: problem transforming scores to variable space

dings) %*% t$projection) [1] TRUE (A tip: Since 't' is used for transposing, it is usually a Good Thing(TM) to avoid using it as a varable name.) -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/lis

Re: [R] add transformed columns into a matrix

Supposing 'inmatrix' is a matrix with coloumn names 'x1', 'x2' and 'x3'; how about something like model.matrix(~ (x1 + x2 + x3)^2 + log(x1) + log(x2) + log(x3) + sqrt(x1) + sqrt(x2) + sqrt(x3) - 1, as.data

Re: [R] Pca loading plot lables

One way is to use the loadingplot() function in the package `pls': molprop.pc <- princomp(whatever) library(pls) loadingplot(molprop.pc, scatter = TRUE, labels = "names") (If you want comp 2 vs. comp 1: loadingplot(molprop.pc, comps = 2:1, scatter = TRUE, labels = "na

Thanks! (Was: Re: [R] R-2.1.0 is released)

I'd like to thank the developers in the Core Team for their great work! R has become an invaluable and indispensible tool for (at least) me, much thanks to the hard and good work of the Core Team. -- Bjørn-Helge Mevik __ R-help@stat.math.et

Re: [R] Journal Quality R Graphs?

Werner Wernersen writes: > the graphs look nice on the screen but when printed in black and > white every color apart from black doesn't look very nice. My advice is: If you want a black-and-white or grayscale printout, don't plot in colors. -- B

Re: [R] How to set up number of prin comp.

rst loadings (The loadings can also be extracted with loadings(pc)[,1:4] .) -- 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] using 'nice' with R

Roger D. Peng writes: > On a Unix like system you can do `nice +19 R' or perhaps `nice +19 R > CMD BATCH commands.R'. At least on Suse (9.1) and Debian (3.0) Linux, the syntax is `nice -19 R' (i.e. with `-', not `+'.) -- Bjørn-Helge Mevik __

Re: [R] Setting the width and height of a Sweave figure

I haven't found any other solution than using <> theCode() @ (but of course that doesn't have any effect when theCode() is used interactively). -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/ma

[R] http://bugs.r-project.org down?

I haven't been able to connect to http://bugs.r-project.org the last few days. Is there a problem with the site (or am I having a problem :-) ? -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help P

Re: [R] Combined variable names

ree that the regularity of R (or S) is part of what makes it so much better than for instance Matlab. At least for me.) -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] LDA with previous PCA for dimensionality reduction

lacing the PCA "outside" the cross-validation. (The same for any resampling-based validation.) -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

Re: [R] Recovering R Workspace

file format and use a binary editor to extract/repair objects in the file -- and even then, if the file was compressed, you may be out of luck). -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLE

Re: [R] R-2.0: roadmap? release statements? plans?

Well, you could download the latest beta-release and look in the NEWS file there. -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting

Re: [R] Sparse Matrices in R

u already have packages such as SparseM, Matrix and graph installed on your system. If you don't, help.search("sparse matrix") returns no matches. :-) -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

Re: [R] Precision in R

Since you didn't say anything about _what_ you did, either in SAS or R, my first thought was: Have you checked that you use the same parametrization of the models in R and SAS? -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list

Re: [R] center or scale before analyzing using pls.pcr

s spectroscopic data. > and whether the dependent variable should be scaled. There is no need for scaling the dependent variable. -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] Stepwise Regression and PLS

he covariance with the response, the first few components are usually more correlated to the response than PCs. For spectroscopists, the PLSR loadings are often very interpretable, and are much used to qualitatively validate the model. -- Bjørn-Helge Mevik _

Re: [R] MATLAB to R

n k1(J) = ... and k2(J) = ... > How do I write k2 in R? > k1 = f(t,y) > k2 = ? ## If f can take vector arguments: k1 <- f(tt[-M],y) k2 <- f(tt[-1], y+h*k1) ## Otherwise: for (J in 1:M) { k1[J] <- f(tt[J], y[J]) k2[J] <- f(tt[J+1], y[J] + h*k1[J]) } -- Hth, Bjørn-Helge Me

Re: [R] nameless functions in R

Rajarshi Guha <[EMAIL PROTECTED]> writes: > apply(x, c(2), funtion(v1,v2){ identical(v1,v2) }, v2=c(1,4,2)) > > The above gives me a syntax error. I also tried: No wonder! Try with `function' instead of `funtion'. -- Bjørn-Helge Mevik

Re: [R] /usr/lib/R/library vs /usr/local/lib/R/site-library

/cran.r-project.org/bin/linux/debian woody main' to /etc/apt/sources.list, to get the latest version of R.) -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help

Re: [R] disappointed (card model)

Don't be disappointed, be glad: It gives you the opportunity to contribute by writing one yourself! (Remember, R is developed by volunteers.) -- Sincerely, Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/ma

Re: [R] princomp with more coloumns than rows: why not?

Thanks for good suggestions for alternatives to princomp! My original question, though, was /why/ it was decided to disallow more coloumns than rows in princomp. (And also whether it would be possible to augment the result from prcomp with the coloumn means.) -- Bjørn-Helge Mevik

[R] princomp with more coloumns than rows: why not?

ed from the new data. Would it break conformance with S to let prcomp return the means as well? -- Sincerely, Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help

Re: [R] How to flip image?

Ernie Adorio <[EMAIL PROTECTED]> writes: > If not possible, is there any built-in R command to reverse the rows of a > matrix? How about Face[nrow(Face):1, ] ? -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://www.stat.

Re: [R] anova(lme object)

Spencer Graves <[EMAIL PROTECTED]> writes: > You need to say "library(nlme)" first. Of course. But since he has alreade used lme to fit the models, he must have loaded the library already. :-) -- Bjørn-Helge Mevik __ [EMAIL PROT

Re: [R] anova(lme object)

It is documented in ?anova.lme: > anova(res1, type="marginal") and > anova(res2, type="marginal") should give equivalent tables. -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help

Re: [R] Marginal (type II) SS for powers of continuous variables ina linear model?

Prof Brian D Ripley <[EMAIL PROTECTED]> writes: > On Tue, 12 Aug 2003, [iso-8859-1] Bjørn-Helge Mevik wrote: > >> Also, is this example (lm(y~x+I(x^2), Df)) really balanced? I think > > No, and I did not use summary,aov on it! And I didn't say you did! >> Th

[R] Marginal (type II) SS for powers of continuous variables in alinear model?

odel, i.e. it is no longer marginal. Using poly (x, 2) instead of x + I(x^2), one gets a marginal SS for the total effect of x, but not for the linear and quadratic effects separately. (summary.aov() has a 'split' argument that can be used to get separate SSs, but the

Re: [R] Marginal (type II) SS for powers of continuous variables ina linear model?

s that I think it would be nice if a function like Anova in the car package returned R(x | A, B, A:B) instead of R(x | A, B, A:B, x^2) as SS for x in a model such as the above. (I hope I've made myself clearer, and not insulted anyone by oversimplifying. :-) -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help

Re: [R] Mean Squares

Mona Riihimaki <[EMAIL PROTECTED]> writes: > I've done lme-analysis with R; [...] I'd need also the mean squares. AFAIK, lme doesn't calculate sum of squares (or mean squares). It maximises the likelihood (or restricted likelihood) and uses tests based on likelihood

Re: [R] PLS regression?

I'm writing a package for PLSR and PCR. It is not ready for "release" yet, but I could email you a copy if you want. -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help

Re: [R] Generating .R and .Rd files with Sweave/noweb?

the file, and in Rd-mode in a documentation part. I guess using two files and a shell script, as you do, might be the best solution. -- Bjørn-Helge Mevik __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help

[R] Generating .R and .Rd files with Sweave/noweb?

I'm writing a couple of related functions, and I'd like to generate a (single) .R file (containing the function definitions), and separate .Rd files (documenting each function). Would this be possible with Sweave/noewb? Has anyone tried something along this idea? -- Regards, Bjørn-H