gi0na / adjHelpR

R tools to build and deal with adjacency matrices

adjHelpR

The goal of adjHelpR is to provide tools to generate adjacency matrices from weighted edgelists, create weighted edgelists from edgelists with repeated edges, and handle these objects. It exploits dplyr and tibbles to deal efficiently with large edgelists, and Matrix sparse matrices to store adjacency matrices in sparse format.

Installation

You can install the released version of adjHelpR from CRAN with:

install.packages("adjHelpR")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("gi0na/adjHelpR")

Example

This is a basic example on how to generate a weighted adjacency matrix from an edge list:

library(adjHelpR)

el <- data.frame(from= c('a','b','b','c','d','d'),
                 to  = c('b','c','d','a','b','a'),
                 attr= c( 12, 6, 12 , 6 , 6 , 6 ))
(adj <- get_adjacency(el))
#> 4 x 4 sparse Matrix of class "dgCMatrix"
#>   a  b c  d
#> a . 12 .  .
#> b .  . 6 12
#> c 6  . .  .
#> d 6  6 .  .

(el_unweighted <- tibble::as_tibble(do.call(rbind, 
                        apply(el, 1, function(row) matrix(rep(row[1:2], each=as.integer(row[3])), ncol = 2))), 
                        .name_repair='minimal'))
#> # A tibble: 48 x 2
#>    ``    ``   
#>    <chr> <chr>
#>  1 a     b    
#>  2 a     b    
#>  3 a     b    
#>  4 a     b    
#>  5 a     b    
#>  6 a     b    
#>  7 a     b    
#>  8 a     b    
#>  9 a     b    
#> 10 a     b    
#> # … with 38 more rows
(adj <- get_adjacency(el_unweighted, multiedge = TRUE))
#> 4 x 4 sparse Matrix of class "dgCMatrix"
#>   a  b c  d
#> a . 12 .  .
#> b .  . 6 12
#> c 6  . .  .
#> d 6  6 .  .

Acknowledgements

The research and development behind adjHelpR is performed at the Chair of Systems Design, ETH Zürich.

Contributors

Giona Casiraghi

Christian Zingg

Copyright

adjHelpR is licensed under the GNU Affero General Public License.

c Copyright ETH Zürich, 2019-2021