similar to: Advice for calling a C function

Hello, I am a relatively new user of R. I have written a basic function to calculate the Gower similarity function. I was motivated to do so partly as an excercise in learning R, and partly because the existing option (vegdist in the vegan package) does not accept missing values. I think I have succeeded - my function gives me the correct values. However, now that I'm starting to use it with

I was wondering if someone can tell me the best way to search through a matrix and choose certain rows (based on certain conditions) to put into a separate matrix. What I have tried so far is very slow for a large dataset I'm working with. e.g., I have this piece of code to create a new matrix (newmat) based on my filtering conditions. Do I need to do this kind of thing where I keep

Hello I have 2 rows in a matrix and I want to calculate the Gower Distance between the 2 , how can I do it? I searched and found nothing that can help me, and my program doesn't know the gdist function and I couldn't find it on the R help site. Can anyone help me plz Thank u all [[alternative HTML version deleted]]

Dear R-Helpers, I am working on a dataset containing ca. 500 specimens of 17 different species. The data is three text columns, followed by ca 70 columns of binary data. I'm trying to write a function that will allow me to interactively exclude species using the inofrmation in the third text column. My function, matrix.slicer, appears to work as I intend. However, when I pass the

Hi I'm replacing my actual print server by a Linux server and I have everything else working except the following When I try to uplad tme printer drivers to the special Samba print$, I receive the following error Samba unable to install Windows 2000, intel driver I read an reread the how to an d differents books, without success Is it working to upload like they say in the How To ? (many

---------- Forwarded message ---------- From: <r-help-owner@r-project.org> Date: 2013/2/8 Subject: vegdist Error en double(N * (N - 1)/2) : tama?o del vector especificado es muy grande To: caro.bello58@gmail.com Message rejected by filter rule match ---------- Mensaje reenviado ---------- From: caro bello <caro.bello58@gmail.com> To: r-help@r-project.org Cc: Date: Fri, 8 Feb 2013

hello, i'd be happy if someone could provide help with the following problem: i have a dist.matrix that comes from vegdist() function of the vegan package. the used method = "horn" is not accepted as argument in hvcluster(...,dist.method="..."). is there a way to incorporate the method "horn" in hvcluster()? thanks in advance! yours, kay -- View this

Dear all, I am trying to get a PERMANOVA with quite large data set. I am reading a lot about this question, but I do not get the answer about it. Although I know that the R function is adonis () (vegan package), it does not work: adonis(Pha.env~SPha, data=Pha, permutations=10) The error message: Error: cannot allocate vector of size 334.2 Mb In addition: Warning messages: 1: In vegdist(lhs,

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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

Dear R community, I am analyzing plant communities with the function mvpart, using a dissimilarit matrix as input. The matrix is calculated with the funtion gdist. fit <- mvpart(gdist (ba12[,18:29], meth="maximum", full=TRUE, sq=F) ~ beers + slope_dem + elev_dem+ plc_dem + pr_curv+ +curv+max_depth+doc_rocks+ abandon+land_use+ca_old, data=ba12, xv="p") This

Hi! Thanks for providing great help in R-related statistics. Now, however I'm stuck. I'm not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16

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]]

Hi I am new to Cygwin and Linux. I installed R under Cygwin as part of the setup I chose "All" during installation, for all packages. So I have the FULL installlation of cygwin up and running, including gfortran. *Under Cygwin, how do I check and configure the path to the various libraries?* I am trying below command and it says, cannot find "lgfortran" But I have installed

Dear All, I would like to use the simprof function (clustsig package) but the available distances do not include Jaccard distance, which is the most appropriate for pres/abs community data. Here is the core of the function: > simprof function (data, num.expected = 1000, num.simulated = 999, method.cluster = "average", method.distance = "euclidean", method.transform =

I am curious if there is code developed to plot confidence regions in 3D. The scatterplot3d function generates the plot I want, but would like an 3D equivalent to the data.ellipse function. Any help in this direction would be appreciated, be it theoretical, graphical, or otherwise. Melanie Edwards Senior Statistician Exponent 15375 SE 30th PL, Suite 250 Bellevue, WA 98007 Tel: (425) 519-8714

Dear All, I wrote a function for cluster analysis to compute cophenetic correlations between dissimilarity matrices (using the VEGAN library) and cluster analyses of every possible clustering algorithm (SEE ATTACHED) http://old.nabble.com/file/p26288610/cor.coef.R cor.coef.R . As it is now, it is extremely long, and for the future I was hoping to find a more efficient way of doing this sort of

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Hello, I am attempting to assign significance levels to a UPGMA cluster analysis as part my doctoral research. The pvclust function works well but doesn't include the similarity index I need (morisita's) as an option for computing a distance matrix. Morisita's is available in vegdist in the VEGAN library but I am having a hard time getting the vegdist function to "direct

How to calculate sorensen (bray-curtis) distance by dist function within the vegan package? Cheers Duccio