【3.14】vegdist(计算各种矩阵,包括Bray-Curtis similarity index)

vegdist {vegan}

Bray-Curtis similarity index

vegdist(x, method=“bray”, binary=FALSE, diag=FALSE, upper=FALSE,

    na.rm = FALSE, ...)

euclidean d[jk] = sqrt(sum(x[ij]-x[ik])^2)

binary: sqrt(A+B-2*J)

manhattan       d[jk] = sum(abs(x[ij] - x[ik]))

binary: A+B-2*J

gower       d[jk] = (1/M) sum(abs(x[ij]-x[ik])/(max(x[i])-min(x[i])))

binary: (A+B-2*J)/M,

where M is the number of columns (excluding missing values)

altGower d[jk] = (1/NZ) sum(abs(x[ij] - x[ik]))

where NZ is the number of non-zero columns excluding double-zeros (Anderson et al. 2006).

binary: (A+B-2*J)/(A+B-J)

canberra  d[jk] = (1/NZ) sum ((x[ij]-x[ik])/(x[ij]+x[ik]))

where NZ is the number of non-zero entries.

binary: (A+B-2*J)/(A+B-J)

bray          d[jk] = (sum abs(x[ij]-x[ik]))/(sum (x[ij]+x[ik]))

binary: (A+B-2*J)/(A+B)

kulczynski         d[jk] 1 - 0.5*((sum min(x[ij],x[ik])/(sum x[ij]) + (sum min(x[ij],x[ik])/(sum x[ik]))

binary: 1-(J/A + J/B)/2

morisita   d[jk] = 1 - 2*sum(x[ij]*x[ik])/((lambda[j]+lambda[k]) * sum(x[ij])*sum(x[ik])), where

lambda[j] = sum(x[ij]*(x[ij]-1))/sum(x[ij])*sum(x[ij]-1)

binary: cannot be calculated

horn Like morisita, but lambda[j] = sum(x[ij]^2)/(sum(x[ij])^2)

binary: (A+B-2*J)/(A+B)

binomial   d[jk] = sum(x[ij]*log(x[ij]/n[i]) + x[ik]*log(x[ik]/n[i]) - n[i]*log(1/2))/n[i],

where n[i] = x[ij] + x[ik]

binary: log(2)*(A+B-2*J)

cao   d[jk] = (1/S) * sum(log(n[i]/2) - (x[ij]*log(x[ik]) + x[ik]*log(x[ij]))/n[i]),where S is the number of species in compared sites and n[i] = x[ij] + x[ik]

参考资料:

http://cc.oulu.fi/~jarioksa/opetus/metodi/sessio3.pdf

help(vegdist)

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