Since igraph has delete the function 'as_adjacency_matrix()'

This is incorrect. This function was not removed, and will not be removed from igraph.

from braingraph.

Yeah, you are right. I'm sorry for my unclear words.
The function 'as_adjacency_matrix()' was no longer to support attributions of character in version 2.0.0 (https://r.igraph.org/news/index.html).
I reports this function because when I install the brainGraph 3.0.0 in the R 4.4.0 with my ubuntu 20.04 system, the R terminal reminds me errors of using 'as_adjacency_matrix()' which can't be worked in igraph upper version 2.0.0.
Therefore, I recommend the following code to run brainGraph with new version of R:

'# remotes::install_version("igraph", version = "1.6.0")'
'library(igraph) # 1.6.0'
'packageVersion("igraph") # 1.6.0'

from braingraph.

Results comparison between GRETNA and brainGraph:

computation config

GRETNA (weighted)

GRETNA (binary)

brainGraph

Results Comparison

GRETNA (weighted)

GRETNA (binary)

brainGraph

Conclusion

(1) Density in brainGraph = Network Sparsity in GRETNA = rate threshold (contrast with fixed threshold)
(2) Results of brainGraph are same to GRETNA
(3) In brainGraph, the indicator with ‘wt’ represents ‘weighted’ and without ‘wt’ represents ‘binary’
(4) I recommend to use brainGraph rather than GRETNA

from braingraph.