Etienne, Thank you so much for your help. I have managed to get the values I wanted after your advice!
Best /Emma _______________________________________ Emma Göthe, PhD-student Department of Aquatic Sciences and Assessment Swedish University of Agricultural Sciences Box 7050 750 07 Uppsala Tel: +46-(0)18-673138 Fax: +46-(0)18-673156 E-mail: [email protected] ________________________________________ Från: Etienne Laliberté [[email protected]] Skickat: den 1 juni 2010 21:22 Till: Emma EG. Gothe Kopia: [email protected] Ämne: Re: [R-sig-eco] Multivariate dispersion and SE Emma, betadisper returns a list, from which you can extract the individual distances to group centroids. You can then compute whatever you want from them (means, variances, etc). Example: data(varespec) ## Bray-Curtis distances between samples dis <- vegdist(varespec) ## First 16 sites grazed, remaining 8 sites ungrazed groups <- factor(c(rep(1,16), rep(2,8)), labels = c("grazed","ungrazed")) ## Calculate multivariate dispersions mod <- betadisper(dis, groups) mod ## Compute mean distance to centroid per group tapply(mod$distances, groups, mean) ## Same, but variance instead tapply(mod$distances, groups, var) Cheers Etienne Le mardi 01 juin 2010 à 14:25 +0200, Emma EG. Gothe a écrit : > Dear All, > > I am trying to calculate values of SE from an analysis of multivariate > homogeneity of groups dispersions (betadisper {vegan})? > > With function betadisper() I get values of the average distance to > centroid/group and it is also possible to draw a boxplot with function > boxplot() with variance information but I cant find a way to tell R to > caclulate SE. > > I realise it is possible to calulate (by hand) from the formula for the > distance from a point to its centroid: > > z[ij]^c = sqrt(Delta^2(u[ij]^+, c[i]^+) - Delta^2(u[ij]^-, c[i]^-)) > > given in the R documentation, by using the scores of the different points and > centroids that can be obtained by using function scores (). But before I go > there I thought Id ask if there is an easier way to obtain the variance > information (in my case SE). > > I am greatful for any help/advice I can get. > > /Emma > _______________________________________ > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Etienne Laliberté ================================ School of Forestry University of Canterbury Private Bag 4800 Christchurch 8140, New Zealand Phone: +64 3 366 7001 ext. 8365 Fax: +64 3 364 2124 www.elaliberte.info _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
