COMDYN was developed to estimate parameters associated with community dynamics
using presence/absence data from 2 locations or time periods. The basic
estimator for species richness underlying all estimators is the jackknife
estimator proposed by Burnham and Overton (1978, Biometrika 65:625-633;
1979, Ecology 60:927-936).
Application of this estimator to species richness estimation is described and
justified by Boulinier, Nichols, Sauer, Hines, and Pollock
(1998, Ecology 79:1018-1028)
The estimators
for community-dynamic parameters and their variances are presented by Nichols,
Boulinier, Hines, Pollock, and Sauer
("
Inference methods for spatial variation in species richness and community
composition when not all species are detected,
Conservation Biology, in press;
Estimating rates of local species extinction, colonization and turnover in
animal communities, Ecological Applications, in press).
Terminology and Notation for Input Data
Sample-1 : the first of 2 locations or times over which change is to be estimated
Sample-2 : the second of 2 locations or times over which change is to be estimated
Subset-A: Subset of species which were observed in both samples:
f(i) and n(i) data come from Sample 2,
Subset-B: Subset of species which were observed in both samples:
f(i) and n(i) data come from Sample 1,
f(i) = number of species observed at exactly i sites/occasions
n(i) = number of species observed at site/occasion i
Sample data
Sample 1 f(i)
13
18
9
6
9
Sample 1 n(i)
26
36
26
29
28
Sample 2 f(i)
19
9
13
7
8
Sample 2 n(i)
23
35
22
33
31
Subset A f(i)
8
8
12
7
8
Subset A n(i)
21
30
18
29
30
Subset B f(i)
5
15
9
5
9
Subset B n(i)
22
31
21
27
26
Nichols 1998 data
Sample 1 f(i)
13
13
8
7
16
Sample 1 n(i)
28
36
35
32
35
Sample 2 f(i)
19
15
17
13
5
Sample 2 n(i)
36
34
34
37
33
Subset A f(i)
7
9
16
13
5
Subset A n(i)
33
32
30
25
28
Subset B f(i)
8
11
8
7
16
Subset B n(i)
27
33
34
32
31
Note: If number of sites/occasions are different between sample 1 and sample 2, enter '.' for missing sites/occasions.
Sample 1 f(i)
Sample 1 n(i)
Sample 2 f(i)
Sample 2 n(i)
Subset A f(i)
Subset A n(i)
Subset B f(i)
Subset B n(i)
Enter the number of iterations for the bootstrap variance estimation:
Definitions
R1 : Number of species observed in Sample 1
R2 : Number of species observed in Sample 2
fi : Observed frequencies - number of species observed at exactly i sites/occasions
f'i : Observed frequencies - number of species observed at i sites where sites are in groups of 10
ni : Observed species- number of species observed at the ith site/occasion
N1 : Estimated number of species present in Sample 1
N2 : Estimated number of species present in Sample 2
M2R1 : Estimated number of species present in Sample 2 which were observed in Sample 1
M1R2 : Estimated number of species present in Sample 1 which were observed in Sample 2
φ : Estimated complement of extinction probability - proportion of Sample 1 species still present in Sample 2
γ : Estimated complement of species turnover - proportion of Sample 2 species present in Sample 1
λ : Estimated rate of change of species richness estimated as N2/N1
altλ : Estimated rate of change of species richness estimated using alternate method,R2/R1
β : Estimated local colonizing species - number of species not present in Sample 1, but present in Sample 2
p1 : Estimated species detection probability in Sample 1
p2 : Estimated species detection probability in Sample 2
Note: 95% confidence interval computed by ordering bootstrap replicate estimates and using the values ranked at 2.5% and 97.5%.