sp.pair: Species association between each pair of species

In spaa: SPecies Association Analysis

Description

Calculate species association between each pair of species.

Usage

sp.pair(matr)

Arguments

matr	Standard species matrix, with rows for plots and columns for species.

Details

Assume we have speciesA and speciesB, a, b, c, d that corresponding to the co-occurrence could be used to conduct the species association analysis between the two species.

a = number of plots both occupied by speciesA and speciesB.

b = number of plots only found speciesA.

c = number of plots only found speciesB.

d = number of plots without speciesA or speciesB.

N = a+b+c+d

This function are using the following formula:

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 b*c>= a*d and d>=a:

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

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

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

Point correlation coefficient

(PCC):

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

Value

chisq	chi square matrix
chisqass	chi square matrix information
V	V Value indicating species association is positive or negative
Ochiai	Ochiai's index
Dice	Dice's index
Jaccard	Jaccard's index
Pearson	Pearson's correlation
Spearman	Spearman's rank correlation
PCC	Point correlation coefficient
AC	Association coefficient

Author(s)

Jinlong Zhang [e-mail]

References

Zhang Qiaoying, Peng Shaolin, Zhang Sumei, Zhang Yunchun, Hou Yuping.(2008). Association of dormintant species in Guia hill Municipal Park of Macao. Ecology and Environment. 17:1541-1547

Zhou XY, Wang BS, Li MG, Zan QJ.(2000). An analysis of interspecific associations in secondary succession forest communities in Heishiding Nature Reserve, Guangdong Province. Acta Phytoecologica Sinica. 24:332-339.

JIAN Minfei, LIU qijing, ZHU du, YOU hai.(2009). Inter-specific correlations among dorminant populations of tree layer species in evergreen broad-leaved forest in Jiulianshan Mountain of subtropical China. Chinese Journal of Plant Ecology. 33: 672-680

See Also

See Also as sp.assoc for species association for total species.

Examples

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

Example output

spaa documentation built on May 2, 2019, 9:44 a.m.