extract beta.sim from dist type data (package betapart)
On Fri, Jul 19, 2013 at 5:12 AM, Elaine Kuo <elaine.kuo.tw at gmail.com> wrote:
Hello Sarah, Thank you for the help very much.
As already requested, please don't cross-post. Send your message to either the ecology list or the main help list, but NOT both.
Please kindly advise manuals dealing with the object list (or dist). In addition, I would like to show the beta diversity index in a map. Please kindly advise any other R package in need.
Every intro to R ever written talks about working with lists: they're a core class. You could try the one that came with your R installation and is on the main R website, or google for more options. Also note that in my original reply to the ecology list, I gave you a full working example. I can't answer your map question, because I don't have any idea what kind of spatial data you have to work with. GPS coordinates? Shapefiles? Raster? I can recommend the book Applied Spatial Data Analysis with R by Bivand, but I can't give concrete suggestions without a reproducible example. Sarah
Elaine On Wed, Jul 17, 2013 at 10:20 PM, Sarah Goslee <sarah.goslee at gmail.com> wrote:
Replied to on the R-sig-ecology list, with a request not to cross-post. Briefly, the output is a list with named components, so can be extracted as usual. Sarah On Wed, Jul 17, 2013 at 5:50 AM, Elaine Kuo <elaine.kuo.tw at gmail.com> wrote:
Dear List, This is Elaine. I am using beta.part to calculate the beta diversity index. The function of beta.part can generate three kinds of beta diversity indice at one time. However, it is Simpson index that I want. The calculation result is composed of three rows and N/A columns (dist class). I do not know how to extract one of the indice in the form of dist class. No relevant example is found the manual. (I tried as.vector as below but failed.) Please kindly help and thank you in advance. Elaine Code library(betapart) dist.sim<-beta.pair(dataR, index.family="sor") # Unfold distance matrices into vectors data.sim<-data.frame(as.vector(dist.sim))
Sarah Goslee http://www.functionaldiversity.org