[R] function for cumulative occurrence of elements

[Mrs Karen Kotschy]

Hi Steven

Are you aware of the package "vegan" for community ecology? There is a
function in this package called specaccum, which calculates species
accumulation curves for you. Various methods can be specified, including
"random".

I must admit I have not used this particular function (yet!) but it seems
like it could be useful to you.

Regards
Karen

-------
Karen Kotschy
Centre for Water in the Environment
University of the Witwatersrand
Johannesburg
South Africa


On Tue, 28 Jun 2005, Steven K Friedman wrote:

>
> Hello,
>
> I have a data set with 9700 records, and 7 parameters.
>
> The data were collected for a survey of forest communities.  Sample plots
> (1009) and species (139) are included in this data set. I need to determine
> how species are accumulated as new plots are considered. Basically, I want
> to develop a species area curve.
>
> I've included the first 20 records from the data set.  Point represents the
> plot id. The other parameters are parts of the information statistic H'.
>
> Using "Table", I can construct a data set that lists the occurrence of a
> species at any Point (it produces a binary 0/1 data table). From there it
> get confusing, regarding the most efficient approach to determining the
> addition of new and or repeated species occurrences.
>
> ptcount <-  table(sppoint.freq$species, sppoint.freq$Point)
>
>  From here I've played around with colSums to calculate the number of species
> at each Point.  The difficulty is determining if a species is new or
> repeated.  Also since there are 1009 points a function is needed to screen
> every Point.
>
> Two goals are of interest: 1) the species accumulation curve, and 2) an
> accumulation curve when random Points are considered.
>
> Any help would be greatly appreciated.
>
> Thank you
> Steve Friedman
>
>
>  Point        species frequency point.list point.prop   log.prop
> point.hprime
> 1      7   American elm         7         27 0.25925926 -1.3499267
> 0.3499810
> 2      7          apple         2         27 0.07407407 -2.6026897
> 0.1927918
> 3      7   black cherry         8         27 0.29629630 -1.2163953
> 0.3604134
> 4      7      black oak         1         27 0.03703704 -3.2958369
> 0.1220680
> 5      7    chokecherry         1         27 0.03703704 -3.2958369
> 0.1220680
> 6      7         oak sp         1         27 0.03703704 -3.2958369
> 0.1220680
> 7      7 pignut hickory         1         27 0.03703704 -3.2958369
> 0.1220680
> 8      7      red maple         1         27 0.03703704 -3.2958369
> 0.1220680
> 9      7      white oak         5         27 0.18518519 -1.6863990
> 0.3122961
> 10     9   black spruce         2         27 0.07407407 -2.6026897
> 0.1927918
> 11     9    blue spruce         2         27 0.07407407 -2.6026897
> 0.1927918
> 12     9        missing        12         27 0.44444444 -0.8109302
> 0.3604134
> 13     9  Norway spruce         8         27 0.29629630 -1.2163953
> 0.3604134
> 14     9   white spruce         3         27 0.11111111 -2.1972246
> 0.2441361
> 15    12          apple         2         27 0.07407407 -2.6026897
> 0.1927918
> 16    12   black cherry         1         27 0.03703704 -3.2958369
> 0.1220680
> 17    12   black locust         1         27 0.03703704 -3.2958369
> 0.1220680
> 18    12   black walnut         1         27 0.03703704 -3.2958369
> 0.1220680
> 19    12          lilac         3         27 0.11111111 -2.1972246
> 0.2441361
> 20    12        missing         2         27 0.07407407 -2.6026897
> 0.1927918
>
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