[R-sig-eco] [R] extract beta.sim from dist type data (package betapart)

[Sarah Goslee]

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