similar to: Obtaining translated, rotated and scaled matrics in procrustes analysis

Hi, I have been trying to create a function to generate a Procrustes plot, generated from package "vegan" in lattice. standard vegan code as follows library(vegan) pro=protest(P1, P8, permutations=4999,choices=1:4) plot(pro) Now, here is the code for the function that I have failed to get to work properly. panel.procrustes=function(x,y) }Pro=protest(x,y,permutations=4999,choices=1:4)

Dear All, I would like to ask how to customize the graph corresponding to a procrustes analysis. I have to distance matrices, that I transform to two set of coordinates by means of muti dimensional scaling: library(mva) c1<-cmdscale(mat.dist1) c2<-cmdscale(mat.dist2) I vant to rotate c2 on c1, and I use the "procrustes" analysis from the {vegan} library. library(vegan)

Hello This is a simple question but I couldn't google an answer. In the procrustes function of the vegan package, one uses plot(procrustes_object, kind=2) to obtain a plot of the residual differences. For instance: data(varespec) vare.dist <- vegdist(wisconsin(varespec)) library(MASS) mds.null <- isoMDS(vare.dist, tol=1e-7) mds.alt <- isoMDS(vare.dist,

Dear All, I am using a Procrustes analysis to compare two NMDS ordinations for the same set of sites. One ordination is based on fish data, the other is based on invertebrate data. Ordinations were derived using metaMDS() from the {vegan} library as follows: fish.mds<-metaMDS(fish.data, distance="bray", k=3, trymax=100, wascores=TRUE, trace=TRUE, zero="add")

Hi, I am trying to create 3 mds plots: one with axis 1 vs axis 2, one with axis 2 vs axis 3, and one with axis 1 vs axis 3. When inputting my code, I only end up with one diagram and when inputting mdsg.mds$dims, the program returns 2 for 2 dimensions. How can I create the other two plots? Any help would be greatly appreciated, Calla Carbone The table I use is number of each taxa on each

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Dear List, I am writing a custom panel function and xyplot method to plot the results of a procrustes analysis from the vegan package. I am having trouble getting the call to panel.arrows to work as I wish when conditioning. The attached file contains the function definitions for the xyplot method and the custom panel and prepanel functions I am using. This example, using data and functions from

An updated version of the package plink has been uploaded to CRAN. This is a major revision that now includes multidimensional models and methods. plink is a package for conducting unidimensional and multidimensional IRT-based test linking using separate calibration methods for multiple groups for single-format or mixed-format common items. The package supports sixteen IRT models and eleven

An updated version of the package plink has been uploaded to CRAN. This is a major revision that now includes multidimensional models and methods. plink is a package for conducting unidimensional and multidimensional IRT-based test linking using separate calibration methods for multiple groups for single-format or mixed-format common items. The package supports sixteen IRT models and eleven

Dear all, Is there anyway too generate MA plot for 2 qPCR assays (an array of 2x 400). -- View this message in context: http://r.789695.n4.nabble.com/Bioconductor-MA-plot-for-qPCR-array-tp4182805p4182805.html Sent from the R help mailing list archive at Nabble.com.

Hi! How can I fit a loess curve to an array (384 x 2). How can I obtain the equation for thi fi? Thanks in advance. -- View this message in context: http://r.789695.n4.nabble.com/How-to-it-a-loess-curve-and-obtain-the-equation-in-R-tp3927622p3927622.html Sent from the R help mailing list archive at Nabble.com.

Hi every one, How is it possible to create a matrix with 3 dimensions from several 2 dimensional matrice? Is it possible that each of "elementary/building block" matrices could be called by its corresponding original name? Thanks alot. -- View this message in context:

Hi everyone. Newbie to statistics. I have 40 matrices of ~400 values. how may I determine whether the distribution follows zips law? response <-sample (1:20,400*4, replace= TRUE) Thank you vry much. -- View this message in context: http://r.789695.n4.nabble.com/A-introductory-question-about-Zips-law-Newbie-to-statistics-tp4521190p4521190.html Sent from the R help mailing list archive at

Hi all, I want to do this: B.list$aa= (a loop containing My.fun acting on the reults of second function on a A.list$aa)) or, overally B.list$aa = function (A.list$aa) B.list and A.list has many sublists aa, ab and.... Is there a way I can apply the function and loop on all sublists of A.list and get B.list? Thanks in advance. -- View this message in context:

Suppose I have two sets of (x,y) points like this: x1<-runif(n=10) y1<-runif(n=10) A<-cbind(x1,y1) x2<-runif(n=10) y2<-runif(n=10) B<-cbind(x2,y2) I would like to measure how similar the two sets of points are. Something like a correlation coefficient, where 0 means the two patterns are unrelated, and 1 means they are identical. And in addition I'd like to be able to

Dear all community, My issue is related to the R package (made4) that permits me to calculate the RV coefficient of co-inertia. However, it is a theoretical question. And if I am not mistaken, the list Usenet groups sci.stat.consult is not currently active. Let me explain briefly: Through different microbiota datasets, I have plotted PCoA, db-RDA and sPLS-DA using 3 different types of

Hi, I'm very new to R. I want to know if there is any way to write only the lower half of a distance matrix created in R to a csv file for example. I get the 'cannot coerce class "dist" into a data.frame' message when I try. I have used as.matrix and can write to a file this way, but as a full matrix. The reason I only want the lower half is that I've been doing some

Hi I have just (finally) started to poke around in R and wanted to analyse a stream fish dataset with 28 sites and 18 species. When trying to follow the Vegan manual to run nmds from distance measures calculated by the vegdist function it turns out that I have two sites (streams) with the exactly the same four species (I have used pres-abs data in this case). When I try to run isoMDS I get an

I am trying to apply a permuation-based MANOVA (Anderson 2001) to a set of morphological data from three ecomorphs of fish reared under two different conditions and measured at two points during ontogeny. I will supply a distance matrix based on Procrustes distances calculated outside of vegan. I have not found an example of a design such as this for adonis. However, I have designed my factors

Dear R users, I am pleased to announce the release of the new BiplotGUI package on CRAN. Biplots are graphs in which the samples and all the variables of a data matrix are represented simultaneously. They can be very useful for exploring multivariate data. The BiplotGUI package allows users to construct and interact with biplots as they are described in "Biplots" (Gower and Hand,