similar to: enhanced MDS

Hi all, I have relatively small dataset on which I would like to perform a PCA. I am interested about a package that would also combine a method for determining the number of components (I know there are plenty of approaches to this problem). Any suggestions about a package/function? thanks, Nick -- View this message in context:

Hi. I have data which i would want to assess the degree of agreement between two assays, e.g., to evaluate reproducibility or for inter-rater reliability. I have used the Pearson product-moment correlation coefficient. It looks good ranginging between 0.90 to 0.998. Though this looks good. I am told the Concordance correlation coefficient will give a better picture of how reproducible the assay

Dear helpRs Does anyone have an elegant way of doing the following: For a given numeric vector, e.g. vec <- c(3,2,6,4,7) Create a series of vectors where all but 1 of the values are replaced by 0's, e.g. vec.a <- c(3,0,0,0,0) vec.b <- c(0,2,0,0,0) vec.c <- c(0,0,6,0,0) vec.d <- c(0,0,0,4,0) vec.e <- c(0,0,0,0,7) I have looked at `replace', but can't think of a

Dear R list Would anyone be able to tell me whether it is possible to do "enhanced multidimensional scaling" (enhanced MDS) in R? In other words, something that goes beyond "cmdscale" by iteratively improving the fit between observed dissimilarities and inter-object distances, using the KYST algorithm (Kruskal, 1964). I have found several implementations of non-metric MDS

I'm in this situation: factorlabels <- c("School", "College", "Beyond") with data for 8 families: education.man <- c(1,2,1,2,1,2,1,2) # Note : no "3" values education.wife <- c(1,2,3,1,2,3,1,2) # 1,2,3 are all present. My goal is to create this table: School College Beyond

Dears, I'm a college student and In doing my statistics homework. I use R with SEM package as my tool for sem analysis, but my teacher told me AMOS is more suitable for such analysis. Could someone help tell me whether it is true that some commercial software is better accepted in academic fields? Sorry if I should not post such topics here. -- Best Regards, Reeyarn T. Lee Accounting

I work for a Investment group with a very extensive training program and we are having our new hires take a statistics course at University of Chicago where they have to complete some assignments with R. I was wondering if there are any online tutorials that exist where we could get our participants comfortable with R before the class itself? I appreciate any help at all. Thanks, Matt Maxon

Hello again I'm trying to put error bars onto a barplot. I've tried something that Bill Simpson suggested a while ago, ie: x<-c(1,2,3,4,5) y<-c(1.1, 2.3, 3.0, 3.9, 5.1) ucl<-c(1.3, 2.4, 3.5, 4.1, 5.3) lcl<-c(.9, 1.8, 2.7, 3.8, 5.0) plot(x,y, ylim=range(c(lcl,ucl))) arrows(x,ucl,x,lcl,length=.05,angle=90,code=3) #or segments(x,ucl,x,lcl) but I can't get it to work on a

Hi R users Does anyone out there have a better/quicker way of adding a factor column to a data frame based on levels of another factor? I have a (large) data frame consisting of records for individual plants, each represented by a unique ID number. The species of each plant is indicated in the column "species", which is a factor column with many different levels (species). There are

Hi everyone I'm trying to generate a vector of the form a <- c(1,2,3,4,1,2,3,1,2,1) where n = 5 in a general way, where n can be any positive integer. I've run out of ideas. Does anyone have any suggestions? Thanks Karen Karen Kotschy Centre for Water in the Environment University of the Witwatersrand Johannesburg Tel: 011 716-2218

Hi everyone I'm trying to generate a vector of the form a <- c(1,2,3,4,1,2,3,1,2,1) where n = 5 in a general way, where n can be any positive integer. I've run out of ideas. Does anyone have any suggestions? Thanks Karen Karen Kotschy Centre for Water in the Environment University of the Witwatersrand Johannesburg Tel: 011 716-2218

Dear help list Does anybody know if it is possible to somehow tell R to let LaTeX handle the fonts for postscript plots produced by R? It is for a thesis and I have MANY figures. These are created by R scripts dynamically as the document is compiled, using the Make system. I see that I can `manually' specify the font family each time I call the postscript device, but I am looking for a

Dear R community Have just recently got back into R after a long break and have been amazed at how much it has grown, and how active the list is! Thank you so much to all those who contribute to this amazing project. My question: I am trying to calculate Mahalanobis distances for a matrix called "fgmatrix" >dim(fgmatrix) [1] 76 15 >fg.cov <- cov.wt(fgmatrix)

Another question: Is it possible to move R objects from one directory to another without copying the whole .RData and .Rhistory files? (I'm running under Linux) Thanks Karen Kotschy Centre for Water in the Environment University of the Witwatersrand Johannesburg Tel: 011 716-2218 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

Hi, I need math function which is used in: isoMDS, Sammon and metaMDS method. Anybody know where I may find it? Any manual or webside? I would be very happy Thanks a lot ! -- View this message in context: http://n4.nabble.com/math-function-MDS-method-tp1008294p1008294.html Sent from the R help mailing list archive at Nabble.com.

Hi Could somebody please explain the following to me: If x is a 10x10 matrix, typing x[3] prints all 10 values of column 3, although the length of the vector =1. Why? x[,3] and x[[3]] both give all 10 values of column 3, length=10. What is the difference between these two, actually? Thanks Karen Kotschy Centre for Water in the Environment Department of Botany University of the Witwatersrand

Hi all, I'm trying to perform an MDS of some data that I have. When I use cmdscale everything is fine and I get some interesting results however, the tends to be low. What I wnat to do is compare this with the Non-Metric MDS using isoMDS or sammon. However, when I try using these I get the following message. Error in isoMDS(x.dist) : zero or negative distance between objects 2 and 4

Dear R users, I am using Sweave. I would like to use the width option for the graphics : \begin{figure}[h!] \centering \includegraphics[width=0.7\textwidth]{x} \end{figure} How do I get this ? Thank you very much, Randall [[alternative HTML version deleted]]

Dear all, I'm trying to get a two dimensional embedding of some data using different meythods, among which princomp(), cmds(), sammon() and isoMDS(). I have a problem with sammon() because the coordinates I get are all equal to NA. What does it mean? Why the method fails in finding the coordinates? Can I do anything to get some meaningful results? Thank you very much Domenico

Dear All, I am not familar with R. I want to use PCA (principal components analysis) and MDS (multidimensional scaling). Can someone tell me which R package I should use for PCA and MDS? I appreciate your help in advance. Ray