sp.pair: Species association between each pair of species

In helixcn/spaa: SPecies Association Analysis

Description

Compute species association between each pair of species.

Usage

sp.pair(matr)

Arguments

matr	Standard community matrix, with rows representing sites and columns representing species.

Details

If a, b, c, d denote the co-occurrence the two species A and B, where:

a = number of plots occupied both by A and B.

b = number of plots only have A.

c = number of plots only have B.

d = number of plots without A or B.

N = a+b+c+d

Then, it is possible to compute:

Chi square (Yate's correction): chi^{2}=((((a*d-b*c)-0.5*N)^2)*N)/(a+b)*(a+c)*(b+d)*(c+d)

V ratio: V = ((a+d)-(b+c))/(a + b + c + d)

Jaccard index: Jaccard =a/(a + b + c)

Ochiai index: Ochiai = a/sqrt((a+b)*(a+c))

Dice index: Dice = 2*a/(2*a + b + c)

The Association Coefficient(AC):

if a*d >= b*c:

AC = (a*d - b*c)/((a+b)*(b+d))

if a*d < b*c and a <= d:

AC = (a*d - b*c)/((a+b)*(a+c))

if a*d < b*c and a > d:

AC = (a*d - b*c)/((b+d)*(c+d))

Point correlation coefficient

(PCC):

PCC = {a*d-b*c}/{(a+b)*(a+c)*(c+d)*(b+d)}

Value

chisq	Chi Square matrix
V	V positive or negative association
Ochiai	Ochiai's index
Dice	Dice's index
Jaccard	Jaccard's index
Pearson	Pearson's correlation coefficient
Spearman	Spearman's rank correlation coefficient
PCC	Point correlation coefficient
AC	Association coefficient

Author(s)

Jinlong Zhang [e-mail]

References

HURLBERT, S. H. (1969). A coefficient of interspecific association. Ecology, 50(1), 1-9.

WANG, B. S., & PENG S. L. (1985). Studies on the Measuring Techniques of Interspecific Association of Lower-Subtropical Evergreen-Broadleaved Forests. I. The Exploration and the Revision on the Measuring Formulas of Interspecific Association. Chinese Journal of Plant Ecology, 9(4), 274-285.

JIAN, M. F., LIU, Q. J., ZHU, D., & YOU, H. (2009). Inter-specific correlations among dominant populations of tree layer species in evergreen broad-leaved forest in Jiulianshan Mountain of subtropical China. Chinese Journal of Plant Ecology, 33(4), 672-680.

ZHOU, X. Y., WANG, B. S., LI, M. G., & ZAN, Q. J. (2000). An analysis of interspecific associations in secondary succession forest communities in Heishiding Natural Reserve, Guangdong Province. Chinese Journal of Plant Ecology, 24(3), 332-339

See Also

See Also as sp.assoc for computing association for all the species.

Examples

data(testdata)
spmatrix <- data2mat(testdata)
result <- sp.pair(spmatrix)

helixcn/spaa documentation built on Aug. 13, 2021, 3:21 a.m.