search for: designdist

Hi R Helpers, I'm still new to R and i experience many difficulties..I'm using vegan package (R version 2.11) trying to calculate checkerboard units for each species pair of a matrix. I've prepared the function: pair.checker=function (dataset) {designdist (dataset, method="c("(A-J)x(B-J)", terms ="binary", abcd=FALSE)} to use with function oecosimu as follows: oecosimu(dataset, pair.checker, "tswap", nsimul=5000, burnin=0, thin=thin, statistic="pair.checker") It seemed to work but the output did not in...

...Would Bray-Curtis be a Percentage Similarity unlike the others? Here is an example of what happens when I run sorensons: #Compare Breckland with Other > a=table(breckland) > J=sum(breckland*other) > A=sum(breckland^2) > B=sum(other^2) > brecklandOther <- designdist(a,method=(A+B-2*J)/(A+B), terms = c("binary")) [1] 0.1750911 attr(,"call") designdist(x = a, method = (A + B - 2 * J)/(A + B), terms = c("binary")) attr(,"method") [1] "0.175091076893185 binary" I do not know why the following lines...

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

...just an example. Here are the questions. How do I read one row of data so as to load site2 into a variable called site2? Once I plot a graph using ordiplot how do I extract it from R so that I can put it into a Word for Windows document? Once I have the data in varables I hope to use designdist and Sørensen to discover diversity indices. I had a crack at this once but because I had sites as the columns it didn't work. Now that I think I have the data correct I can proceed. x Input data (this will be the whole data set that I read into my variable 'allSites' from a CSV.)?...

...been using it. I think R is brilliant. But using the formula... PS=3D2w/(a+b) where w=3Dminimum sum of individuals of species held in common between the samples being compared; a and b =3 the totals of individuals found in either region. I have had trouble working out from the help extract from designdist which of the methods is the percentage. What does it mean when someone says 'minimum sum of individuals of species held in common between samples? Is it the number of species where the count is exactly the same? So, if I collected 14 of A. curbitana from 'site a' and then 14 of A....