Steven K Friedman
2005-Jul-18 20:11 UTC
[R] Package Vegan: species accumlumation functions
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.poolrichness.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.