Description Usage Arguments Details Value Examples
View source: R/05_bipartite_rank.R
Estimate bipartite ranks (centrality scores) of nodes from an edge list or adjacency matrix. Functions as a wrapper for estimating rank based on a number of normalizers (algorithms) including HITS, CoHITS, BGRM, and BiRank. Returns a vector of ranks or (optionally) a list containing a vector for each mode.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  bipartite_rank(
data,
sender_name = NULL,
receiver_name = NULL,
weight_name = NULL,
rm_weights = FALSE,
duplicates = c("add", "remove"),
normalizer = c("HITS", "CoHITS", "BGRM", "BiRank"),
return_mode = c("rows", "columns", "both"),
return_data_frame = TRUE,
alpha = 0.85,
beta = 0.85,
max_iter = 200,
tol = 1e04,
verbose = FALSE
)

data 
Data to use for estimating rank. Must contain bipartite graph data, either formatted as an edge list (class data.frame, data.table, or tibble (tbl_df)) or as an adjacency matrix (class matrix or dgCMatrix). 
sender_name 
Name of sender column. Parameter ignored if data is an adjacency matrix. Defaults to first column of edge list. 
receiver_name 
Name of sender column. Parameter ignored if data is an adjacency matrix. Defaults to the second column of edge list. 
weight_name 
Name of edge weights. Parameter ignored if data is an adjacency matrix. Defaults to edge weights = 1. 
rm_weights 
Removes edge weights from graph object before estimating rank. Parameter ignored if data is an edge list. Defaults to FALSE. 
duplicates 
How to treat duplicate edges if any in data. Parameter ignored if data is an adjacency matrix. If option "add" is selected, duplicated edges and corresponding edge weights are collapsed via addition. Otherwise, duplicated edges are removed and only the first instance of a duplicated edge is used. Defaults to "add". 
normalizer 
Normalizer (algorithm) used for estimating node ranks (centrality scores). Options include HITS, CoHITS, BGRM, and BiRank. Defaults to HITS. 
return_mode 
Mode for which to return ranks. Defaults to "rows" (the first column of an edge list). 
return_data_frame 
Return results as a data frame with node names in the first column and ranks in the second column. If set to FALSE, the function just returns a named vector of ranks. Defaults to TRUE. 
alpha 
Dampening factor for first mode of data. Defaults to 0.85. 
beta 
Dampening factor for second mode of data. Defaults to 0.85. 
max_iter 
Maximum number of iterations to run before model fails to converge. Defaults to 200. 
tol 
Maximum tolerance of model convergence. Defaults to 1.0e4. 
verbose 
Show the progress of this function. Defaults to FALSE. 
If input data is an edge list, this function returns ranks ordered by the unique values in the supplied edge list. Data inputted as an edge list are always assumed to contain named vertex IDs rather than to reflect an index of vertex positions in a network matrix. Users who wish for their edge lists to reflect vertex indices are recommended to input their data as a matrix or as a sparse matrix.
Network isolates are assigned a value of (1  alpha) / (n\_columns) or (1  beta) / (n\_rows) depending on their mode in the network. These values will always be smaller than the minimum value assigned to nonisolated nodes in the given mode. However, estimates on network isolates are nonmeaningful. Users are advised to treat isolates with caution.
For information about the different normalizers available in this function, see the descriptions for the HITS, CoHITS, BGRM, and BiRank functions. However, below outlines the key differences between the normalizers, with K_d and K_p representing diagonal matrices with generalized degrees (sum of the edge weights) on the diagonal (e.g. (K_d)_{ii} = ∑_j w_{ij} and (K_p)_{jj} = ∑_i w_{ij}).
Transition matrix  S_p  S_d 
     
HITS  W^T  W 
CoHITS  W^T K_d^{1}  W K_p^{1} 
BGRM  K_p^{1} W^T K_d^{1}  K_d^{1} W K_p^{1} 
BiRank  K_p^{1/2} W^T K_d^{1/2}  K_d^{1/2} W K_p^{1/2} 
A dataframe containing each node name and node rank. If return_data_frame changed to FALSE or input data is classed as an adjacency matrix, returns a vector of node ranks. Does not return node ranks for isolates.
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