search for: procrustes

...mds<- metaMDS(sp.rich) Error in metaMDS(sp.rich) : object 'sp.rich' not found > mdsg.mds<- metaMDS(mdsg) Square root transformation Wisconsin double standardization Run 0 stress 10.62813 Run 1 stress 14.73774 Run 2 stress 11.19939 Run 3 stress 10.61520 ... New best solution ... procrustes: rmse 0.005646588 max resid 0.009332332 Run 4 stress 10.61520 ... New best solution ... procrustes: rmse 0.0001009763 max resid 0.0001754211 *** Solution reached > mdsg.mds.ALT<- metaMDS(mdsg, distance="euclidean", k=3, trymax=50, autotransform=FALSE) Run 0 stress 3.020817 Ru...

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,...

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...

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 t...

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 (appl...

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.di...

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=10...

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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

...eralized partial credit model -Nominal response model, MD nominal response model -Multiple-choice model, MD multiple-choice model Unidimensional Calibration Methods: -Mean/Mean -Mean/Sigma -Haebara -Stocking-Lord Multidimensional Calibration Methods: -Reckase-Martineau (least squares with oblique procrustes rotation) -MD Haebara -MD Stocking-Lord --For the later two methods there are three dilation approaches - Oshima-Davey-Lee (oblique rotation) - Li-Lissitz (orthogonal procrustes rotation with a single dilation parameter) - Min (orthogonal procrustes rotation with multiple dilation parameters)...

...eralized partial credit model -Nominal response model, MD nominal response model -Multiple-choice model, MD multiple-choice model Unidimensional Calibration Methods: -Mean/Mean -Mean/Sigma -Haebara -Stocking-Lord Multidimensional Calibration Methods: -Reckase-Martineau (least squares with oblique procrustes rotation) -MD Haebara -MD Stocking-Lord --For the later two methods there are three dilation approaches - Oshima-Davey-Lee (oblique rotation) - Li-Lissitz (orthogonal procrustes rotation with a single dilation parameter) - Min (orthogonal procrustes rotation with multiple dilation parameters)...

...cs. I have seen methods that, for each point, search in some neighbourhood around it and then compute the correlation as a function of search radius. That is not what I am looking for. I would like a single number that summarises the strength of the relationship between the two patterns. I will do procrustes on the two point sets first, so that if A is just a rotated, translated, scaled, reflected version of B the two patterns will superimpose and the statistic I'm looking for will say there is perfect correspondence. Thanks very much for any help in finding such a statistic and calculating it usi...

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

...alization methods (Total sum of squares, cumulative sum of squares and rarefaction). For each dataset and multivariate analysis (PCoA, db-RDA or sPLS-DA) in order to easily interpret if the different normalization strategies creates me different or equivalent PCoA for example, I have calculated the Procrustes sum of squares and the RV coefficient of co-inertia. However, for the RV coefficient of co-inertia, I have obtained the value 1 (perfect equivalence) for the PCoA comparisons amongst the 3 methods of normalization, and also for the db-RDA. For the sPLS-DA I have not obtained 1 for all the compariso...

...ple. 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 Mantel correlations with distance matrices (of Procrustes distances) generated by other (geometric morphometric) software that are in this format. However, I'm needing to use an alternative such as R to calculate distance matrices of Fourier coefficients which the other software can't do. So far, the Mantel correlations calculated from these two...

...between objects 14 and 15 i.e. the two sites with the same fish species. I can run the decorana function with "sensible" results so the dataset seems to be ok. My next step would be to compare the results of the fish ordination with some other datasets from the same sites (i.e. through procrustes rotation) - so I wouldn?t like to remove one of the "twin" sites. Any suggestion on how to circumvent this or am I simply using the wrong method? Best wishes, Leonard -- Dr. Leonard Sandin Department of Environmental Assessment / Milj?analys Swedish University of Agricultural Science...

Hi Now a more theoretical question. I have two correlation matrices - one of a set of variables under a particular condition, the other of the same set of variables under a different condition. Is there a statistical test I can use to see if these correlation matrices are "different"? Thanks Mick

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 for this test which hopefully will work. This design is just to understand the principals of this test, my real data set is comprised of over a thousand spec...

...ns are similar to ordinary scatter plots, but with all the variables represented at one time. Version 0.0-2 of the package has the following features: * A graphical user interface (GUI), making it easy to use * Support for different types of biplots (PCA, covariance/correlation, CVA, regression, Procrustes, circular non-linear), both interpolative and predictive * Support for different scaling techniques (PCO, metric MDS, non-metric MDS, semi-metric MDS) * Various data transformations and distance metrics * Additional descriptors (convex hulls, alpha-bags, point densities, classification regions) * I...