search for: labdsv

I am trying to install labdsv from CRAN binaries (or source) to use with R 2.3.0 from Mac OS X, but the package fails to install properly. Here is the message that I receive from R when I type library(labdsv): Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Framewo...

I am trying to install labDSV from http://labdsv.nr.usu.edu/ into R-Windows 1.5.0. It only comes as a TAR file which extracts into folders that seem to match those for other libraries DATA, MAN, R and SRC. I have manually copied these folders into a folder called labDSV under the Library directory under R. However when I...

Hi everyone, I am doing PCA with labdsv package. I was trying to create a biplot graphs in order to observe arrows related to my variables. However when I run the script for this graph, the console just keep saying: *Error in nrow(y) : element 1 is empty; the part of the args list of 'dim' being evaluated was: (x)* could...

Hi everybody, I am doing Indicator species analysis using the function "indval" from the package "labdsv". For further analysis I need the values "Number of Significant Indicators" and "Sum of Indicator Values" that is calculated from the summary on my indval object. indication3<-indval(Veg,caver3,numitr=4999) summary(indication3) cluster indicator_value probability...

Hi, I'm trying to find out what threshold of indicator value in labadsv should be used to accept a specie as an indicator one? So far I assumed that indval=0.5 is high enough to avoid any mistakes but it was based only in my intuition. I'd be greatful for any advise best regards Agnieszka

...DS solution such as each point in the plot has a label. This is what I did: data <- read.table('c:/multivariate/mds/colour.txt',header=FALSE) similarity <- as.dist(data) distance <- 1-similarity result.nmds <- nmds(distance) plot(result.nmds) (nmds and plot.nmds as defined at labdsv.nr.usu.edu/splus_R/lab8/lab8.html; nmds simply calls isoMDS) Colour.txt, containing the similaity matrix, reads as follows: 1.0 .86 .42 .42 .18 .06 .07 .04 .02 .07 .09 .12 .13 .16 .86 1.0 .50 .44 .22 .09 .07 .07 .02 .04 .07 .11 .13 .14 .42 .50 1.0 .81 .47 .17 .10 .08 .02 .01 .02 .01 .05 .03 ....

I have a general question about using thin plate splines in the surf and ordisurf routines. My rudimentary knowledge of a gam is that with each predictive variable there is a different smooth for each one and then they are added together with no real interaction term (because they don't handle this well?). Now, If I have two variables that have a high D^2 score and a low GCV score (I am

...> First - you need to transpose the matrix to have species as > columns. You can do > this with: > > d2 = data.frame(t(Test[,-1])) > colnames(d2) = Test[,1] #now use d2 > > > >> Now I try to perform a similarity analysis with the dsvdis function >> of the labdsv package with the sorensen-Index. >> >> My first question is if all zeros in my table are seen as missing >> values and if it islike that how can I change without turning zero >> into other numbers? > > no - the zeros are valid observations. the na's are missing da...

...0 1 0 0 0 1 0 0 0 0 1 0 0 1 All columns are binary coded characters. The Import was done by this Test<-read.table("TestRFemMalBivariat1.csv",header = TRUE, sep = ";") Now I try to perform a similarity analysis with the dsvdis function of the labdsv package with the sorensen-Index. My first question is if all zeros in my table are seen as missing values and if it islike that how can I change without turning zero into other numbers? Secondly I tried to perform the analysis as simple as possible, after changing the characterstates into 1...

Hello, We are trying to find a function to compute "stress" in our multidimensional scaling analysis of a dissimilarity matrix. We've used "dist()" to create the matrix and "cmdscale()" for the scaling. In order to determine the number of dimensions we would like to plot stress vs. dimensions. However, we cannot find a pre-made command. It seems that other

Hi, I need to run a PCoA (PCO) for a data set wich has both positive and negative values for variables. I  could not find any distancecoefficient other than euclidean distace running for the data set. Are there any other coefficient works with negtive values.Also I cannot get summary out put (the eigen values) for PCO as for PCA.   Thanks. Dilshan [[alternative HTML version deleted]]

...ce for a taxa is included or a boolean (presence/absence) for the taxa in a given plot. Im new to such analyses in R, but before writing it myself hope or suspect that such a function or library is out there (although I dont see it after some quick searching in things like Vegan or BiodivesityR or labdsv). Thanks billy

...estion: I have to rank all values in a matrix from 0 to X, [1] [2] [3] [4] [1] 0.1 2 0 3 [2] 50 3 3 1 [3] 100 1 1 0 [4] 100 2 2 0 0->0 0.1->1 2->2 3->3 50->4 100->5 (X=5) is there any function for this? i have looked in several packages (vegan, labdsv etc.) because I am working with species by site tables, but without success. perhaps I looked for the wrong terms (rank matrix etc.) thank you for your help regards, Jens -- +++++++++++++++++++++++++++++++++++++++++ Dipl.Biol. Jens Oldeland University of Hamburg Biocentre Klein Flottbek and Bo...

Colleagues, I have a routine in package labdsv that calls a FORTRAN subroutine. Recently, I was informed that it sometimes gives different results on a PC and Mac, and that the PC version is clearly wrong. I tested it on linux (because I don't have a PC), and I get the same (incorrect) behavior as the PC. Simply by inserting debug WRI...

Dear friends, I cannot load the pachkages labdsv...which i do not understand is linked to 'mgcv' package. Anyway neither the last is loadable in my new R 2.10 version. Th emessage on the screen is the following: This is mgcv 1.6-1. For overview type `help("mgcv-package")'. Error in runif(1) : .Random.seed is not an integ...

Dear R developers and users! I have calculated metric MDS by cmdscale from matrix of distances (dissimilarities). I would like to ask you how can I estimate how well this new mapping represents characteristic features of my data set? Thank you for any suggestions. Best, tomek

Dear R-users: Im trying (using gam package) to develop a stepwise analysis. My gam object contains five pedictor variables (a,b,c,d,e,f). I define the step.gam: step.gam(gamobject, scope=list("a"= ~s(a,4), "b"= ~s(b,4), "c"= ~s(c,4), "d"= ~s(d,4), "e"= ~s(e,4), "f"= ~s(f,4))) However, the result shows a formula containing the whole

...h as it is now. So if I am interested in vegetation analysis or environmental analysis but I never did it before I go to that category and see which packages are more geared towards that particular subject. For example it was by chance alone and some GOOGLE search that I discovered that the package labdsv has anything to do with vegetation analysis since first of course I looked at any package which might have ?veg? or ?env? in the title. I also realize that this might mean a lot of work, but R develops so rapidly that soon I think it will be unmanageable to just peruse the list of packages and re...

Hi, I've just started using R and am having some problems with CCA using vegan. I'm looking at abundance p/m2 (hence decimals) vs environmental variables and have been using http://ecology.msu.montana.edu/labdsv/R/labs/lab12/lab12.html to guide me through. My organism data looks like this: Sample "Species_1" "Species_2" "Species_3" etc Sample_1 0 0.12432 0.3456 etc and is in a .csv file My environment data (.csv again) looks like...

hello all R experts, how do I calculate the reliability between the two groups using the ICCs? I'll appreciate your reply, Thanks Sincerely, Supreet kaur, Biomedical research engineer, Nationwide Childrens Hospital, Columbus, OH (614)355-3509 [[alternative HTML version deleted]]