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Table 1 The network topological indexes used in this study

From: Molecular ecological network analyses

Indexes

Formula

Explanation

Note

Ref

Part I: network indexes for individual nodes

Connectivity

k i = ∑ j ≠ i a ij

a ij is the connection strength between nodes i and j.

It is also called node degree. It is the most commonly used concept for desibing the topological property of a node in a network.

[33]

Stress centrality

S C i = ∑ j k σ ( j , i , k )

σ ( j , i , k ) is the number of shortest paths between nodes j and k that pass through node i.

It is used to desibe the number of geodesic paths that pass through the ith node. High Stress node can serve as a broker.

[34]

Betweenness

B i = ∑ j k σ ( j , i , k ) σ ( j , k )

σ ( j , k ) is the total number of shortest paths between j and k.

It is used to desibe the ratio of paths that pass through the ith node. High Betweenness node can serve as a broker similar to stress centrality.

[34]

Eigenvector centrality

E C i = 1 λ ∑ j ∈ M ( i ) E C j

M(i) is the set of nodes that are connected to the ith node and λ is a constant eigenvalue.

It is used to desibe the degree of a central node that it is connected to other central nodes.

[35]

Clustering coefficient

C C i = 2 l i k i ' ( k i ' − 1 )

l i is the number of links between neighbors of node i and k i ’ is the number of neighbors of node i.

It desibes how well a node is connected with its neighbors. If it is fully connected to its neighbors, the clustering coefficient is 1. A value close to 0 means that there are hardly any connections with its neighbors. It was used to desibe hierarchical properties of networks.

[36, 37]

Vulnerability

V i = E − E i E

E is the global efficiency and E i is the global efficiency after the removal of the node i and its entire links.

It measures the deease of node i on the system performance if node i and all associated links are removed.

[38]

Part II: The overall network topological indexes

Average connectivity

a v g K = ∑ i = 1 n k i n

k i is degree of node i and n is the number of nodes.

Higher avgK means a more complex network.

[39]

Average geodesic distance

G D = 1 n ( n − 1 ) ∑ i ≠ j d ij

d ij is the shortest path between node i and j.

A smaller GD means all the nodes in the network are closer.

[39]

Geodesic efficiency

E = 1 n ( n − 1 ) ∑ i ≠ j 1 d ij

all parameters shown above.

It is the opposite of GD. A higher E means that the nodes are closer.

[40]

Harmonic geodesic distance

H D = 1 E

E is geodesic efficiency.

The reciprocal of E, which is similar to GD but more appropriate for disjoint graph.

[40]

Centralization of degree

C D = ∑ i = 1 n max ( k ) − k i

max(k) is the maximal value of all connectivity values and k i represents the connectivity of ith node. Finally this value is normalized by the theoretical maximum centralization score.

It is close to 1 for a network with star topology and in contrast close to 0 for a network where each node has the same connectivity.

[41]

Centralization of betweenness

C B = ∑ i = 1 n max ( B ) − B i

max(B) is the maximal value of all betweenness values and B i represents the betweenness of ith node. Finally this value is normalized by the theoretical maximum centralization score.

It is close to 0 for a network where each node has the same betweenness, and the bigger the more difference among all betweenness values.

[41]

Centralization of stress centrality

C S = ∑ i = 1 n max ( S C ) − S C i

max(SC) is the maximal value of all stress centrality values and SC i represents the stress centrality of ith node. Finally this value is normalized by the theoretical maximum centralization score.

It is close to 0 for a network where each node has the same stress centrality, and the bigger the more difference among all stress centrality values.

[41]

Centralization of eigenvector centrality

C E = ∑ i = 1 n max ( E C ) − E C i

max(EC) is the maximal value of all eigenvector centrality values and EC i represents the eigenvector centrality of ith node. Finally this value is normalized by the theoretical maximum centralization score.

It is close to 0 for a network where each node has the same eigenvector centrality, and the bigger the more difference among all eigenvector centrality values.

[41]

Density

D = l l exp = 2 l n ( n − 1 )

l is the sum of total links and l exp is the number of possible links.

It is closely related to the average connectivity.

[41]

Average clustering coefficient

a v g C C = ∑ i = 1 n C C i n

C C i is the clustering coefficient of node i.

It is used to measure the extent of module structure present in a network.

[36]

Transitivity

T r a n s = ∑ i = 1 n ( 2 l i ) ∑ i = 1 n k i ' ( k i ' − 1 )

l i is the number of links between neighbors of node i and k i ’ is the number of neighbors of node i.

Sometimes it is also called the entire clustering coefficient. It has been shown to be a key structural property in social networks.

[41]

Connectedness

C o n = 1 − W n ( n − 1 ) / 2

W is the number of pairs of nodes that are not reachable.

It is one of the most important measurements for summarizing hierarchical structures. Con is 0 for graph without edges and is 1 for a connected graph.

[42]