similar to: Re creating Procrustes Plot in Lattice

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)

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")

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

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,

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

Hi all, I wondered how I can get the translated, rotated and scaledmatrix in a procrustes analysis. This does not help: ############################## library (vegan) #defining the target matrix: a= cbind (c (1,2,3,4), c( 10,12,14,16)) #defining the matrix to be rotated: b= a; b[,2]= c(9,11,15,16) c=procrustes (a,b); g=fitted (c) # trying to get to the procrustes matrices: d= t

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Hi R experts, I'm looking for some help with plotting vectors from envfit in vegan, onto a 3d plot using ordiplot3d. So far I have data.mds <- metaMDS(data, k=3,trace = FALSE) vect_data<-envfit(data.mds,vegdata[,3:21],choices=1:3,permu=9999) ordiplot3d(data.mds,envfit=vect_data) ordixyplot(data.mds,pch=pts,envfit=vect_data) (my data's not really called data, I thought it might be

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

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

Hi R-experts, I am using the envfit function over an ordination of floristic data. The problem is that every time that I run it changes the results. Sometimes dramatically, selecting variables that the first time were not significant. I do not get what could be the problem or if is normal given the permutations are different. # the NMDS ordination gap_flor_NMDS_chord <- metaMDS(gaps_flor,

hi, I have a matrix (representing original data) that looks e.g. like this (consider it beeing x,y,z coords): 441 447 0 265 407 0 374 223 0 288 574 0 669 309 0 591 195 0 595 475 0 424 351 0 I get a second matrix (subject data) that is similiar to the above matrix but it is scaled, translated and rotated (and of course a little inprecise). Also I have an

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

I've been unable to find a R package that provides the means of performing Clarke & Ainsworth's BIO-ENV procedure or something comparable. Briefly, they describe a method for comparing two separate sample ordinations, one from species data and the second from environmental data. The analysis includes selection of the 'best' subset of environmental variables for explaining

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,

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,

Hi to all the people again, I was writting a simply function in R, and wish to collect the results in a excel file. The work goes as follows, Ciervos<-function(K1, K0, A, R,M,Pi,Hembras) {B<-(K1-K0)/A T1<-(R*Pi*Hembras-M*Pi+B)/(Pi-M*Pi+R*Pi*Hembras) P1<-Pi-B R1<-P1*Hembras*R M1<-P1*M T2<-(R1-M1+B)/(P1-M1+R1) P2<-P1-B R2<-P2*Hembras*R M2<-P2*M