Thank you Jari for a fast reply! I will try the vegan function asap as it seems to work smoothly. I am still wondering what causes the problem in the PCNM () function though... If anyone else knows, then please let me know.
Best Emma -----Ursprungligt meddelande----- Från: Jari Oksanen [mailto:jari.oksa...@oulu.fi] Skickat: den 5 oktober 2011 12:46 Till: Emma Gothe Kopia: r-sig-ecology@r-project.org Ämne: Re: [R-sig-eco] Help PCNM analysis On Wed, 2011-10-05 at 10:25 +0200, Emma Gothe wrote: > Dear list members! > > I am trying to perform a PCNM analysis with function PCNM() (binary package > provided by the provided by project Spatial ecological data analysis with R). > I recently ran into a problem. I have a triangular distance matrix based on > the shortest distance between my sampling points which I am using in the PCNM > function instead of geographic coordinates. When I tried to perform the > analysis on this distance matrix I got an error message (see below) that says > I have "empty neighbor sites". I have used the same code and the exactly same > type of distance matrices before and I did not have any problem. I have also > searched my distance matrix for ev. missing values/other obvious errors and > tried to search for a solution online but without any luck. > > The file "Eucl stream order1.txt" is attached and my code is: > > > dist.matr <- read.delim("Eucl stream order1.txt",row.names=1) > > dist <- as.dist(dist.matr) > > PCNM.auto=PCNM(dist) > Truncation level = 1092.48 > Error in as.matrix(listw2sn(nb2listw(nb))[, 1:2]) : > error in evaluating the argument 'x' in selecting a method for function > 'as.matrix': Error in nb2listw(nb) : Empty neighbour sets found > Timing stopped at: 0.01 0 0.02 > > If anyone could help me to figure this out, and have suggestions for a > solution I would be very greatful! > Emma, I don't know about the PCNM package, but the matrix goes smoothly true vegan::pcnm: > library(vegan) Loading required package: permute This is vegan 2.0-0 > dist.matr <- read.delim("Eucl stream order1.txt",row.names=1) > dist <- as.dist(dist.matr) > p <- pcnm(dist) > str(p) List of 4 $ vectors : num [1:30, 1:19] -0.2245 -0.2239 -0.2249 -0.2907 -0.0212 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:30] "A2" "A3" "A4" "A5" ... .. ..$ : chr [1:19] "PCNM1" "PCNM2" "PCNM3" "PCNM4" ... $ values : num [1:29] 71640230 66080002 58129580 29179643 16447538 ... $ weights : num [1:30] 1 1 1 1 1 1 1 1 1 1 ... $ threshold: num 1092 - attr(*, "class")= chr "pcnm" Cheers, Jari Oksanen _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
