summary and node-based information of species in loops and simple paths
Source:R/topol_fac.R
topol_fac.Rdprovides summary and node-based information of number of species involved in loops of reciprocal facilitation or simple indirect facilitation linear paths from (or to) any given species.
Usage
topol_fac(int_data, cover_data, direction = c("in", "out"))Value
A list with two elements, one with the information of reciprocal facilitation loops and another with information of the simple linear indirect facilitation paths beginning of ending in each species.
The first element of the list loops provides the following information within two levels:
summary: A data frame with as many rows as SCC are present in the facilitation network (with more than one species, as autofacilitation is not considered) and in columns, an scc identifier scc_id and the number of species involved in that SCC n_nodos
nodes: a list with as many elements as SCCs found, each of them including a vector with the name of the species involved in that SCC The second element of the list simple, provides the following information within two levels:
summary: A data frame with as many rows as distinct simple linear indirect facilitation paths (i.e. their overlap in species composition is less than 75%) that begin ("from") or end ("to") in any species, including the linear versions of the SCCs. In columns, the species in which that distinct linear path begin or end nodo, and numeric index that identifies the paths within species path_index and the number of species involved in that path n_nodes_in_path which includes the focal species, independently of whether there is autofacilitation.
nodes: a list with as many elements as species in the facilitation network (either as nurse or facilitated), each of them including as many elements as distinct paths begin or ends in it, and in each of them, a vector with the name of the species involved in that simple indirect facilitation linear path. All arguments (options):
direction = c("in","out") Argument 1.
direction: Indicates the direction in which the indirect facilitation is assessed. Explanation of its options:
in: Estimates the paths based on the incoming links to each node, representing the set of nurse species from which a recruit species benefits, either directly (by enhancing its recruitment) or indirectly (by facilitating other nurse species that enhance its recruitment). Link direction is considered for both reciprocal and simple paths.
out: Estimates the paths based on the outgoing links from each nodes, representing the set of species that a nurse species benefits, either directly or indirectly (i.e. through other intermediate species). The direction of the links is applied to both reciprocal and simple paths
Examples
topol_fac(test_data$com,test_data$cov, direction="out")
#> $loops
#> $loops$summary
#> scc_id n_nodos
#> 4 1 3
#> 5 2 3
#>
#> $loops$nodes
#> $loops$nodes$`4`
#> [1] "E" "H" "K"
#>
#> $loops$nodes$`5`
#> [1] "B" "I" "J"
#>
#>
#>
#> $simple
#> $simple$summary
#> nodo path_index n_nodes_in_path
#> 1 B 1 3
#> 2 B 2 3
#> 3 C 1 2
#> 4 D 1 1
#> 5 E 1 5
#> 6 E 2 3
#> 7 G 1 1
#> 8 H 1 4
#> 9 H 2 4
#> 10 H 3 3
#> 11 I 1 5
#> 12 J 1 4
#> 13 J 2 3
#> 14 K 1 6
#> 15 A 1 4
#> 16 A 2 4
#> 17 F 1 2
#>
#> $simple$nodes
#> $simple$nodes$B
#> $simple$nodes$B[[1]]
#> [1] "B" "C" "D"
#>
#> $simple$nodes$B[[2]]
#> [1] "B" "I" "J"
#>
#>
#> $simple$nodes$C
#> $simple$nodes$C[[1]]
#> [1] "C" "D"
#>
#>
#> $simple$nodes$D
#> $simple$nodes$D[[1]]
#> [1] "D"
#>
#>
#> $simple$nodes$E
#> $simple$nodes$E[[1]]
#> [1] "E" "H" "B" "C" "D"
#>
#> $simple$nodes$E[[2]]
#> [1] "E" "H" "K"
#>
#>
#> $simple$nodes$G
#> $simple$nodes$G[[1]]
#> [1] "G"
#>
#>
#> $simple$nodes$H
#> $simple$nodes$H[[1]]
#> [1] "H" "B" "C" "D"
#>
#> $simple$nodes$H[[2]]
#> [1] "H" "B" "I" "J"
#>
#> $simple$nodes$H[[3]]
#> [1] "H" "K" "E"
#>
#>
#> $simple$nodes$I
#> $simple$nodes$I[[1]]
#> [1] "I" "J" "B" "C" "D"
#>
#>
#> $simple$nodes$J
#> $simple$nodes$J[[1]]
#> [1] "J" "B" "C" "D"
#>
#> $simple$nodes$J[[2]]
#> [1] "J" "B" "I"
#>
#>
#> $simple$nodes$K
#> $simple$nodes$K[[1]]
#> [1] "K" "E" "H" "B" "C" "D"
#>
#>
#> $simple$nodes$A
#> $simple$nodes$A[[1]]
#> [1] "A" "B" "C" "D"
#>
#> $simple$nodes$A[[2]]
#> [1] "A" "B" "I" "J"
#>
#>
#> $simple$nodes$F
#> $simple$nodes$F[[1]]
#> [1] "F" "G"
#>
#>
#>
#>
topol_fac(test_data$com,test_data$cov, direction="in")
#> $loops
#> $loops$summary
#> scc_id n_nodos
#> 4 1 3
#> 5 2 3
#>
#> $loops$nodes
#> $loops$nodes$`4`
#> [1] "E" "H" "K"
#>
#> $loops$nodes$`5`
#> [1] "B" "I" "J"
#>
#>
#>
#> $simple
#> $simple$summary
#> nodo path_index n_nodes_in_path
#> 1 B 1 4
#> 2 B 2 3
#> 3 B 3 2
#> 4 C 1 5
#> 5 C 2 4
#> 6 C 3 3
#> 7 D 1 6
#> 8 E 1 3
#> 9 G 1 2
#> 10 H 1 3
#> 11 I 1 5
#> 12 I 2 3
#> 13 I 3 3
#> 14 J 1 6
#> 15 K 1 3
#> 16 A 1 1
#> 17 F 1 1
#>
#> $simple$nodes
#> $simple$nodes$B
#> $simple$nodes$B[[1]]
#> [1] "B" "H" "E" "K"
#>
#> $simple$nodes$B[[2]]
#> [1] "B" "J" "I"
#>
#> $simple$nodes$B[[3]]
#> [1] "B" "A"
#>
#>
#> $simple$nodes$C
#> $simple$nodes$C[[1]]
#> [1] "C" "B" "H" "E" "K"
#>
#> $simple$nodes$C[[2]]
#> [1] "C" "B" "J" "I"
#>
#> $simple$nodes$C[[3]]
#> [1] "C" "B" "A"
#>
#>
#> $simple$nodes$D
#> $simple$nodes$D[[1]]
#> [1] "D" "C" "B" "H" "E" "K"
#>
#>
#> $simple$nodes$E
#> $simple$nodes$E[[1]]
#> [1] "E" "K" "H"
#>
#>
#> $simple$nodes$G
#> $simple$nodes$G[[1]]
#> [1] "G" "F"
#>
#>
#> $simple$nodes$H
#> $simple$nodes$H[[1]]
#> [1] "H" "E" "K"
#>
#>
#> $simple$nodes$I
#> $simple$nodes$I[[1]]
#> [1] "I" "B" "H" "E" "K"
#>
#> $simple$nodes$I[[2]]
#> [1] "I" "B" "J"
#>
#> $simple$nodes$I[[3]]
#> [1] "I" "B" "A"
#>
#>
#> $simple$nodes$J
#> $simple$nodes$J[[1]]
#> [1] "J" "I" "B" "H" "E" "K"
#>
#>
#> $simple$nodes$K
#> $simple$nodes$K[[1]]
#> [1] "K" "H" "E"
#>
#>
#> $simple$nodes$A
#> $simple$nodes$A[[1]]
#> [1] "A"
#>
#>
#> $simple$nodes$F
#> $simple$nodes$F[[1]]
#> [1] "F"
#>
#>
#>
#>