[R] Package Vegan: species accumlumation functions

From: Steven K Friedman <friedm69_at_msu.edu>
Date: Tue 19 Jul 2005 - 06:11:18 EST

Hi everyone,

I am working with a data frame consisting of 1009 sampling locations, 138 species incidence and abundance data, and eight forest community types.

My goal is to develop species acumulation curves and extrapolated estimates for each community type.

I am using the following approach:
attach(forest_plots)
library(vegan)
# calcuate species abundance and species incidence (presence/absence)per plot
# where Point_ID = plot sample unit.

sp.abund <- table(forest_plots$Latin_Name, forest_plots$Point_ID) sp.incid <- matrix(ifelse(sp.abund > 0, 1, sp.abund))

## now quantify richness using community type as "pool"

richness.pool <- specpool(sp.incid, type)

> richness.pool

richness.pool

  Species     Chao  Chao.SE   Jack.1 Jack1.SE   Jack.2     Boot  Boot.SE   n
5       NA       NA       NA       NA       NA       NA       NA       NA  
52
8      546 718.3939 28.70646 787.3462 139.0467 858.6446 662.9829 97.92155  
26
9       NA       NA       NA       NA       NA       NA       NA       NA  
93
10      NA       NA       NA       NA       NA       NA       NA       NA 
126
11      NA       NA       NA       NA       NA       NA       NA       NA  
36
13      NA       NA       NA       NA       NA       NA       NA       NA 
122
15      NA       NA       NA       NA       NA       NA       NA       NA  
36
18     364 687.1809 55.49003 591.5556 135.2185 722.6111 463.3126 83.16079   
9

Ok, I do not understand this output. Why is NA reported for all community types other than type 8 and 18?

Thanks for helping.
Steve F.



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