similar to: how to add a new dataset to default R distributions

I've tried a few things both with prcomp(), and rda() and its friends in vegan (including biplot.rda and ordiplot), but can't find a solution. I'd like to associate subsets of the points in a resulting biplot ("sites" in the rda object) with different plotting colors/text styles to emphasize certain sets of points. I can't figure out how to keep the arrows (for

Dear all, I did a RDA and when I looked to the signification of the test with permutest, the output was non-significant. But when I used the envfit function, some of the vectors are significant. All the test's conditions are respected. What it means? Is it an error in the script? Commands and output: > permutest(rda.ind, perm=999, first=TRUE) Permutation test for rda  Call:

hello, I am doing PCA in R using some habitat factors, and I used the function result1=rda() and result2=princomp(),then pick up scores of the result1 and result2 using scores(),but the scores are significantly different,i do not know the meaning of it. Best wishes! Cheng

Our Query: Actually while opening R console and R commander we see some packages like car and datasets. In these packages we have default datasets. For example: "Women" and "Prestige" so on. Now we created a "Sales" dataset importing either from excel, xml or text file. Now we are trying to store that dataset permanently in any one of the packages mentioned above

Hi I'm having a problem with model.frame, encapsulated in this example: y1 <- matrix(c(3,1,0,1,0,1,1,0,0,0,1,0,0,0,1,1,0,1,1,1), nrow = 5, byrow = TRUE) y1 <- as.data.frame(y1) rownames(y1) <- paste("site", 1:5, sep = "") colnames(y1) <- paste("spp", 1:4, sep = "") y1 model.frame(~ y1) Error in model.frame(formula, rownames,

Hello I am using Jari Oksanen's CCA routine from the Vegan package on some estuary data, following a technique applied in (Anderson, M.J. & Gribble, N.A., 1998, Partitioning the variation among spatial, temporal and environmental components in a multivariate data set, Australian Journal of Ecology 23, 158-167). Some steps in the process require that the dependent matrix be constrained by

Dear r-Community, Step1: I would like to calculate a NMDS (package vegan, function metaMDS) with species data. Step2: Then I want to plot environmental variables over it, using function envfit. The Problem: One of these environmental variables is cos(EXPOSURE). But for flat releves there is no exposure. The value is missing and I can't call it 0 as 0 stands for east and west. Therefore I

After some investigation I found out that constrained ordination is working fine under R version 6.5.0 and 6.5.1 but not under any of newer versions. Is it posible to repair/make something in for example newest version of R 7.0 lito enble correct using of constrained ordination under BiodiversityRGUI environment? [[alternative HTML version deleted]]

Hello to all, I'm new to R so I have a lot of problems with it, but I'll only ask the main one. I have clustered an environmental matrix with 2 different methods, and I'd like to plot them in a PCA and a db-RDA. I mean, I want see these clusters in the plots like points of differents colours, together with the rest information of the plot, but I don't know how to do this.

Hi Listers, I am trying to reflect a PCA biplot in the x-axis (i.e. PC1) but am not having much success. In theory I believe all I need to do is multiply the site and species scores for the PC1 by -1, which would effectively flip the biplot. I am creating a blank plot using the plot command and accessing the results from a call to rda. I then use the calls to scores to obtain separate site and

Hi Listers, This has a simple answer but it has been eluding me nonetheless. I have been building a PCA plot from scratch with the ability to plot predefined groups in different colors. This has worked fine but when I try to get a polygon drawn around each of the groups it is not recognising my colour file correctly and is only printing the first colour in the file....code is below

Hi All, Can anyone point me a hint (package) how to draw a 3D plot using the first 3 components from PCA? Thanks a lot, FD [[alternative HTML version deleted]]

Hi all, I am using the vegan package to run a prcincipal components analysis on forest structural variables (tree density, basal area, average height, regeneration density) in R. However, I could not find out how to extract factor loadings (correlations of each variable with each pca axis), as is straightforwar in princomp. Do anyone know how to do that? Moreover, do anyone knows

Hi all, I have site data with plant species cover and am looking for trends. I'm kind of new to this, but have done lots of reading and can't find an answer. I tried decorana (I know it's been replaced by ca.) and see a trend, but I'm not sure what it means. Is there a way to get the loadings/eigenvectors of the axes (like in PCA)? Is there a way to do this with rda() too? How

Hi, I find it a bit annoying that aggregate.default forces the returned object to loose the 'name' of the variable aggregated, replacing it with 'x'. A brief example: > dat <- data.frame(A = runif(100), B = rnorm(100), + Group = gl(4, 25)) > with(dat, aggregate(A, by = list(Group = Group), FUN = mean)) Group x 1 1 0.6523228 2 2

Dear List, A student in the Department where I work would like to produce a graphic similar to this one: http://image.guardian.co.uk/sys-files/Guardian/documents/2009/09/16/Public_spending_160909.pdf Does anyone know if the figure in the pdf can be generated in a specific software application for example? Any suggestions would be most gratefully received by the student concerned. Many thanks,

The eurodist dataset (my favorite for mds) is malformed. Instead of a standard distance matrix, it's a data frame. The rownames have gotten 'bumped' to a new anonymous dimension "X". It's possible to fix the data, but it messes up a lot of example code out there. X Athens Barcelona Brussels Calais ... 1 Athens 0 3313 2963 3175 2 Barcelona

Hi all, Is there any chance that readRDS and saveRDS might one day become read.rds and write.rds? That would make them more consistent with the other reading and writing functions. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/

Dear List, In one of my packages on R-Forge I have a custom panel function for Lattice graphics. In the Rd file for this panel function I want to provide links to some lattice functions (in package lattice). My first instinct was to use: \code{\link[lattice]{panel.xyplot}} for example. However, I missed a few references to lattice functions and just marked them up as \code{\link{panel.xyplot}}.

Hello there, I'm trying to plot vectors with p<0.1 in a NMDS ordination plot using p.max. Below the scripts I'm using. I guess I'm missing something! could you please give me a hand? species<-metaMDS(species_matrix)ef<-envfit(species,environmentaldata_file,permu=999,na.rm=TRUE)efplot(species, dis="sites")plot(ef,p.max=0.1) Error in plot.envfit(ef, p.max = 0.1) :