Count 3-nodes motifs and positions for unipartite networks.
So far, this package includes motif_census(), a function that counts the
different positions occupied by the different species in all the 3 species
motifs of a given unipartite network. Also, motif_census_triplet() return
details for all triplets.
Note that count_motif() in igraph counts motifs of
size 3 and 4 of different kind networks, but does not account for the different
positions occupied within a motif.
install.packages("remotes")
install_github("Ecosystem-Assessments/motifscensus")R> library(motifcensus)
R> # Network net: 4->3->1 & 4->3->2 & 1<-3->2 ; meaning 2 linear chains
R> # (motif 2 in Milo (2002)) and 1 exploitative exploitation (motif 1)
R> net <- rbind(c(0,0,0,0), c(0,0,0,0), c(1,1,0,0), c(0,0,1,0))
net
[,1] [,2] [,3] [,4]
[1,] 0 0 0 0
[2,] 0 0 0 0
[3,] 1 1 0 0
[4,] 0 0 1 0
R> motif_census(net, unidirectional = TRUE)
$motifs
1 2 3 4 5
2 0 1 0 0
$motifs_node
1 2 3 4 5
[1,] 1 0 1 0 0
[2,] 1 0 1 0 0
[3,] 2 0 1 0 0
[4,] 2 0 0 0 0
$positions
[1] 2 2 2 0 0 1 2 0 0 0 0
$positions_node
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 0 0 1 0 0 0 1 0 0 0 0
[2,] 0 0 1 0 0 0 1 0 0 0 0
[3,] 0 2 0 0 0 1 0 0 0 0 0
[4,] 2 0 0 0 0 0 0 0 0 0 0
R> motif_census(net) # net is treated as bidirectional network
$motifs
1 2 3 4 5 6 7 8 9 10 11 12 13
1 2 0 0 0 0 0 0 0 0 0 0 0
$motifs_node
1 2 3 4 5 6 7 8 9 10 11 12 13
[1,] 1 1 0 0 0 0 0 0 0 0 0 0 0
[2,] 1 1 0 0 0 0 0 0 0 0 0 0 0
[3,] 1 2 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 2 0 0 0 0 0 0 0 0 0 0 0
$positions
[1] 1 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
$positions_node
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 0 1 0 0 1 0 0 0 0 0 0
[2,] 0 1 0 0 1 0 0 0 0 0 0
[3,] 1 0 0 2 0 0 0 0 0 0 0
[4,] 0 0 2 0 0 0 0 0 0 0 0
[,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0 0 0 0
[,22] [,23] [,24] [,25] [,26] [,27] [,28] [,29] [,30]
[1,] 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0 0 0
R> motif_census_triplet(net)
n i j k i_to_j j_to_i i_to_k k_to_i j_to_k k_to_j pos_i pos_j pos_k sum_pos motif name_uni
1 0 0 1 3 FALSE FALSE FALSE FALSE FALSE FALSE 0 0 0 0 i j + i k + j k
2 34 0 2 3 FALSE TRUE FALSE FALSE FALSE TRUE 5 4 3 12 i<--j + i k + j<--k linear chain
3 34 1 2 3 FALSE TRUE FALSE FALSE FALSE TRUE 5 4 3 12 i<--j + i k + j<--k linear chain
4 40 0 1 2 FALSE FALSE FALSE TRUE FALSE TRUE 2 2 1 5 i j + i<--k + j<--k exploitative competition
R> head(bidirectional_motifs3)
mid i_to_j j_to_i i_to_k k_to_i j_to_k k_to_j pid_i pid_j pid_k psum motif name_uni
1 0 FALSE FALSE FALSE FALSE FALSE FALSE 0 0 0 0 i j + i k + j k
2 1 TRUE FALSE FALSE FALSE FALSE FALSE 0 0 0 0 i-->j + i k + j k
3 2 FALSE TRUE FALSE FALSE FALSE FALSE 0 0 0 0 i<--j + i k + j k
4 3 TRUE TRUE FALSE FALSE FALSE FALSE 0 0 0 0 i<->j + i k + j k
5 4 FALSE FALSE TRUE FALSE FALSE FALSE 0 0 0 0 i j + i-->k + j k
6 5 TRUE FALSE TRUE FALSE FALSE FALSE 1 2 2 5 i-->j + i-->k + j k exploitative competition