问题
I have used the specaccum() command to develop species accumulation curves for my samples.
Here is some example data:
site1<-c(0,8,9,7,0,0,0,8,0,7,8,0)
site2<-c(5,0,9,0,5,0,0,0,0,0,0,0)
site3<-c(5,0,9,0,0,0,0,0,0,6,0,0)
site4<-c(5,0,9,0,0,0,0,0,0,0,0,0)
site5<-c(5,0,9,0,0,6,6,0,0,0,0,0)
site6<-c(5,0,9,0,0,0,6,6,0,0,0,0)
site7<-c(5,0,9,0,0,0,0,0,7,0,0,3)
site8<-c(5,0,9,0,0,0,0,0,0,0,1,0)
site9<-c(5,0,9,0,0,0,0,0,0,0,1,0)
site10<-c(5,0,9,0,0,0,0,0,0,0,1,6)
site11<-c(5,0,9,0,0,0,5,0,0,0,0,0)
site12<-c(5,0,9,0,0,0,0,0,0,0,0,0)
site13<-c(5,1,9,0,0,0,0,0,0,0,0,0)
species_counts<-rbind(site1,site2,site3,site4,site5,site6,site7,site8,site9,site10,site11,site12,site13)
accum <- specaccum(species_counts, method="random", permutations=100)
plot(accum)
In order to ensure I have sampled sufficiently, I need to make sure the curve of the species accumulation plot reaches an asymptote, defined as a slope of <0.3 between the last two points (ei between sites 12 and 13).
results <- with(accum, data.frame(sites, richness, sd))
Produces this:
sites richness sd
1 1 3.46 0.9991916
2 2 4.94 1.6625403
3 3 5.94 1.7513054
4 4 7.05 1.6779918
5 5 8.03 1.6542263
6 6 8.74 1.6794660
7 7 9.32 1.5497149
8 8 9.92 1.3534841
9 9 10.51 1.0492422
10 10 11.00 0.8408750
11 11 11.35 0.7017295
12 12 11.67 0.4725816
13 13 12.00 0.0000000
I feel like I'm getting there. I could generate an lm with site vs richness and extract the exact slope (tangent?) between sites 12 and 13. Going to search a bit longer here.
回答1:
Streamlining your data generation process a little bit:
species_counts <- matrix(c(0,8,9,7,0,0,0,8,0,7,8,0,
5,0,9,0,5,0,0,0,0,0,0,0, 5,0,9,0,0,0,0,0,0,6,0,0,
5,0,9,0,0,0,0,0,0,0,0,0, 5,0,9,0,0,6,6,0,0,0,0,0,
5,0,9,0,0,0,6,6,0,0,0,0, 5,0,9,0,0,0,0,0,7,0,0,3,
5,0,9,0,0,0,0,0,0,0,1,0, 5,0,9,0,0,0,0,0,0,0,1,0,
5,0,9,0,0,0,0,0,0,0,1,6, 5,0,9,0,0,0,5,0,0,0,0,0,
5,0,9,0,0,0,0,0,0,0,0,0, 5,1,9,0,0,0,0,0,0,0,0,0),
byrow=TRUE,nrow=13)
Always a good idea to set.seed() before running randomization tests (and let us know that specaccum is in the vegan package):
set.seed(101)
library(vegan)
accum <- specaccum(species_counts, method="random", permutations=100)
Extract the richness and sites components from within the returned object and compute d(richness)/d(sites) (note that the slope vector is one element shorter than the origin site/richness vectors: be careful if you're trying to match up slopes with particular numbers of sites)
(slopes <- with(accum,diff(richness)/diff(sites)))
## [1] 1.45 1.07 0.93 0.91 0.86 0.66 0.65 0.45 0.54 0.39 0.32 0.31
In this case, the slope never actually goes below 0.3, so this code for finding the first time that the slope falls below 0.3:
which(slopes<0.3)[1]
returns NA.
来源：https://stackoverflow.com/questions/38754612/find-where-species-accumulation-curve-reaches-asymptote