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

adjhelpr's Issues

rolling windows don't have extra edge weights

add functionality to track edge attributes to timestamped edgelists

Bug with mat2vec_ix when passing only number of nodes

package Matrix is not loaded, thus error when creating sparse object

interface with tidy graph

get_rolling_windows crashes with empty graphs

when using 'graph' out format

Error: Can't rename columns that don't exist.
x Column name doesn't exist.