similar to: lost in vegan package

I am currently testing species co-occurrence patterns using null models and the oecosimu() function within the vegan() package. My issue is that none of the methods appear to be the ones that I want. The methods listed are r0, r1, r2, r2dtable, swap, tswap. However, I want to know how to go about implementing fixed row algorithms, as suggested in Gotelli 2000 in Ecology. Also, the null models

Dear vegan team, Vegan development happens now completely in github. R-Forge repository is no more in sync with github. I tried to commit all github changes to R-Forge, but a week ago I got a conflict in file and I haven't had time to resolve that conflict. You can follow vegan development and vegan discussion also without signing to github. The system seems to be completely open and does not

Dear list, I would like to rename an object as follows: SimLUall <- matrix(c(0,1,0,0, 1,0,0,0, 0,0,1,0, 0,0,0,1),nrow=4, ncol=4) j <- 2 SimLUall2 <- SimLUall and j The value of j should be assigned automatically to SimLUall. How can I achieve this? Regards, Ulrich

Hi, I am trying to calculate a distance matrix on a binary data frame using dist.binary() {ade4}. This is the code I run and the error I get: > sjlc.dist <- dist.binary(as.data.frame(data), method=2) #D = (a+d) / (a+b+c+d) Error in if (any(df < 0)) stop("non negative value expected in df") : missing value where TRUE/FALSE needed I don't know if the problem are the

Dear all, I have 4 sites and want to determine how different they are from each other. For this I have decided to use R though it seems a bit daunting to learn. I have read data in from a CSV the structure is : Species1 Species2 Species3 Site1 4 4 7 Site2 3 1 0 Site3 0 99 6 Site4 75 3 33 There are many more species than shown above this is just an example. Here are the

Hi, I've been doing a lot of CA modeling lately and am now wanting to make some checkerboard plots in R. Let's say I have a matrix: > is.matrix(junk) [1] TRUE > junk [,1] [,2] [,3] [,4] [,5] [1,] 0 0 1 0 0 [2,] 0 1 1 1 0 [3,] 0 1 0 0 1 [4,] 0 1 1 1 1 [5,] 0 1 0 0 0 > and I want to make a

...as it was called on Phoronix forums. After this (http://forum.winehq.org/viewtopic.php?t=2066) discussion, I have decided to give the ATI/AMD fglrx drivers another go... and immediately remembered why I gave them up in the first place. That was version 8.5. Now, two versions after (yes, I've overslept a whole release, and I feel fascinatingly relaxed after that), the problem persists.

I have 4 very large species lists and I would like to compare them. I have the following results from running Sorenson’s dissimilarity tests: Norfolk Fens compared to Suffolk Coastal Fens: QS=0.583961142689298 Norfolk Fens compared to Breckland Edge Fens: QS=0.714896020281379 Norfolk Fens compared to Other Fens:

Hi All, is there a reasonably simple way of using a black and white chequer/checker board pattern as a colour: barplot(mydata, col = c('red', 'blue' 'checkerboard')) ? BW F -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli

Dear folks, I have been struggling to create what I fondly imagined would be a straightforward adaptation of the package's example to my own dataset, which looks at incidence of depression following the birth of initial and up to 3 subsequent children (4 children in all, with all subjects having a first child). I've regarded these as equivalent to tooth eruption and subsequent caries in

This is my current work.Now i am trying to use a function to do the normal distribution simulation. rm(list=ls()) t <- u<- mann<- rep(0, 45) Nsimulation<-function(S1,S2,Sds,nSims) { set.seed(1) for (sim in 1:nSims) { matrix_t <-matrix(0,nrow=nSims,ncol=3) matrix_u<-matrix(0,nrow=nSims,ncol=3)

Hi, I did a linear regression with 5 explanatory variables. Now, to see the contribution of each variable, I use varpart from vegan library. But varpart don?t accepts my 5 explanatory variables, it accept only 4. 1- How must I do to use my 5 explanatory variables? 2- Is it the sum of variance fraction of each variable must be equal to 1. Thanks for your help. Komine -- View this

Hi, Using Vegan package I was wondering if there's a way to use a distance matrix as an input for adonis (or any of the other similar hypothesis testing functions) instead of the usual species by sample table. Working in the field of microbial ecology, what I'm trying to do is to overcome the problem of having to use discrete units such as species or OTUs, which are problematic in

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

Hi List, I’m using the vegan function specaccum to produce a rarefaction curve. In the function’s help it says: “Function ‘specaccum’ finds species accumulation curves or the number of species for a certain number of sampled sites or individuals”. Well, I would like to finds this curve for individuals, but when I compute it the function (using the ‘rarefaction’ method) gives me Sites, Richness

Dear R folks While preparing figures of 'envfit' plots with vegan for publication, I ran into a layout problem, that I found no solution for in the literature or the help archive: The labels of the vectors that indicate correlations of environental variables sometimes overlap with each other or with other content of the figure. Hence, I would like to rearrange them. Is there a

I am using VEGAN ordistep function for stepwise model selection. By default the Pin and Pout values are set to .05 and .1 Is it appropriate to use a family wise correction ( such as bonferroni or one of the alternatives) to adjust these values where there are several (5-10), potentially correlated variables in the model selection process? -- Nevil Amos Molecular Ecology Research Group

Dear all at the R-project help list. I have run into a problem when it comes to getting values for "total inertia" and "R-squared" for my DCA using "decorana" in the package "vegan". I have tried the "goodness" function, but the reply indicates that it does not work with "decorana" class objects. In Canoco one gets the Total inertia in

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Dear List, I can'f figure how to add point labels in the next plot (example from ?taxondive help page, from vegan package): library(vegan) data(dune) data(dune.taxon) taxdis <- taxa2dist(dune.taxon, varstep=TRUE) mod <- taxondive(dune, taxdis) plot(mod) The points in this plot are diversity values of single sites, and I'd like to add a label to each one. The plot command don't