Notably, should probably include in the front matter

vignette: >
  %\VignetteIndexEntry{Vignette Title}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}

We also need to make sure the correct package dependencies are going through.

1: Warning: @title [graph_match_methods.R#1]: requires a value
2: Warning: @description [graph_match_methods.R#1]: requires a value
3: Warning: @title [graph_match_methods.R#1]: requires a value
4: Warning: @description [graph_match_methods.R#1]: requires a value

Reference: r-lib/roxygen2#480

• Degree profile matching
• Unipartite to bipartite (Jesus Arroyo)
• Spectral/Filtering Approaches (Lin Li and [Fan et al])

Is this line correct?
https://github.com/dpmcsuss/iGraphMatch/blob/master/R/rlapjv.R#L64

The cost matrix transformation for lapjv looks like:

cost <- rbind(
  cbind(
    as.matrix(cost), 
    m + m * stats::runif(n)
  ),
  m + m * stats::runif(n + 1)
)

which adds a column to the left and a row to the bottom.

But the transformation for lapmod looks like:

cost <- rbind2(
  cbind2(
    cost, 
    sign * 1e5 * (m * ceiling(stats::runif(n))),
    c(pad_vec, - sign * 1e5 * m)
  )
)

which adds two columns to the left, and seems to call an rbind2 that doesn't do anything.

(I haven't yet dug into precisely what this transformation does, or the changes you made to lapmod, but figured I'd ask this first.)

Please add a parameter (e.g., "verbose") so that it can disable the console output!
Thanks!

splr indexing seems to fail when indexing a single row/column/entry.
This should return a vector

diag does not seem to compute correctly

If possible

• graph_match_ExpandWhenStuck
• graph_match_FW_multi (deprecated)
• graph_match_FW_multi_reward
• graph_match_PATH
• graph_match_soft_percolation

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Also, I want to verify that the output and behavior of gm_path matches that of gm_convex, gm_fw, etc in terms of outputting the same dimension matrices and the same type of match object.

Error1: object 'C_R_igraph_correlated_pair_game' not found
Error2: object 'C_R_igraph_finalizer' not found
Already require(igraph) in the function

After trying to install via devtools, I get the following error:

Error: package or namespace load failed for ‘iGraphMatch’ in namespaceExport(ns, exports):
 undefined exports: get_perm, graph_match_IsoRank, graph_match_Umeyama
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/iGraphMatch’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/iGraphMatch’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/var/folders/1j/1ft72mkd3cngwzhc1rs3l37m0000gs/T//RtmpTxFFkn/file1055e5f46d59/iGraphMatch_0.0.0.9000.tar.gz’ had non-zero exit status

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• Tweet
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I tried to run the example of "rds_sinkhorn_start" but it does not find the "check_soft_seeds" function. The information is as following:

rds_sinkhorn_start(nns=5, soft_seeds=as.data.frame(matrix(c(2,4,2,3),nrow=2)), distribution = "rnorm")
Error in rds_sinkhorn_start(nns = 5, soft_seeds = as.data.frame(matrix(c(2, :
could not find function "check_soft_seeds"

What I have tried: library(GraphMatch). check the R code in the package. I don't find the "check_soft_seeds" function code. Could you help me about this?

Matrix 1.6-2 defines additional methods for the %*% operator
that mask your four methods

     `%*%`(x=<matrix_list>, y=<ANY>)
     `%*%`(x=<ANY>, y=<matrix_list>)
     `%*%`(x=<graphMatch>, y=<ANY>)
     `%*%`(x=<ANY>, y=<graphMatch>)

where <ANY> inherits from virtual class Matrix. To ensure that your methods
continue to be dispatched, define four additional methods:

     `%*%`(x=<matrix_list>, y=<Matrix>)
     `%*%`(x=<Matrix>, y=<matrix_list>)
     `%*%`(x=<graphMatch>, y=<Matrix>)
     `%*%`(x=<Matrix>, y=<graphMatch>)

The new methods can be identical to the ones with <ANY> in the signature.

Please revise your package and test that it passes its checks under the latest
Matrix-devel, which you can install with

     install.packages("Matrix", repos = "http://r-forge.r-project.org/")

We anticipate releasing Matrix 1.6-2 in mid-October.

Please add to README.md

• How to install the package using devtools.
• How to compile the package.

Here is an error I'm getting with center_graph:

> A <- sample_correlated_gnp_pair(n = 10, corr = .5, p = .5)$graph1
> center_graph(A, scheme = "center")
Error in validObject(.Object) : 
  invalid class “splrMatrix” object: superclass "mMatrix" not defined in the environment of the object's class

and I got a similar error with gm:

> AB <- sample_correlated_gnp_pair(n = 10, corr = .5, p = .5)
> A = AB$graph1
> B = AB$graph2
> gm(A, B)
Error in validObject(.Object) : 
  invalid class “splrMatrix” object: superclass "mMatrix" not defined in the environment of the object's class

and this:

> gm(A, B, start='convex')
Error in validObject(.Object) : 
  invalid class “splrMatrix” object: superclass "mMatrix" not defined in the environment of the object's class

Maybe this is not directly related, but this option also gives an error:

> gm(A, B, start='rds_perm_bari')
Error in rds_perm_bari_start(nns, ns, soft_seeds, ...) : 
  unused arguments (A = new("dgCMatrix", i = c(2, 4, 5, 6, 9, 2, 3, 4, 5, 7, 8, 9, 0, 1, 3, 5, 6, 8, 1, 2, 4, 5, 6, 7, 0, 1, 3, 5, 8, 0, 1, 2, 3, 4, 6, 7, 9, 0, 2, 3, 5, 7, 1, 3, 5, 6, 8, 1, 2, 4, 7, 9, 0, 1, 5, 8), p = c(0, 5, 12, 18, 24, 29, 37, 42, 47, 52, 56), Dim = c(10, 10), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), B = new("dgCMatrix", 
    i = c(2, 4, 5, 7, 9, 2, 3, 4, 5, 7, 9, 0, 1, 3, 6, 7, 8, 1, 2, 6, 7, 9, 0, 1, 5, 6, 8, 9, 0, 1, 4, 6, 2, 3, 4, 5, 7, 9, 0, 1, 2, 3, 6, 9, 2, 4, 9, 0, 1, 3, 4, 6, 7, 8), p = c(0, 5, 11, 17, 22, 28, 32, 38, 44, 47, 54), Dim = c(10, 10), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()))

Here is my R environment.

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] iGraphMatch_2.0.3

loaded via a namespace (and not attached):
 [1] compiler_4.3.2  magrittr_2.0.3  Matrix_1.6-5    cli_3.6.2       igraph_2.0.3   
 [6] glue_1.6.2      Rcpp_1.0.11     grid_4.3.2      lifecycle_1.0.4 pkgconfig_2.0.3
[11] rlang_1.1.2     lattice_0.22-5   

1. I tried to install the iGraphMatch package via master or dev branch but there's a following error:
   Error : (converted from warning) /private/var/folders/0f/g_bjrzdd2qv38bwffzml_03m0000gn/T/RtmpYlURc0/R.INSTALL3747bca4b7d/iGraphMatch/man/center_graph.Rd:22: unknown macro '\hat'.

I think there might be a typo in center_graph document: A-\hat{Q}, where \hat{Q}. In dev_splr branch, it is written as A - Q, where Q is an approximate. Installing iGraphMatch package via dev_splr branch works.

2. I think the development version of iGraphMatch package might require higher version of R. I can't install devtools package somehow under 3.3.2 version. After upgrading to the latest version, devtools package works. Do we need to mention it?

Give a useful error message if we see non-square matrices in our methods.

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I understand that it makes the adjmat in [-1,1].
But, this assumes that the original adjmat is in [0,1], right?

Then, what if the original adjmat is not in [0,1]?
For example, my "unnormalized" weighted graph is on [0,57], and the center_graph changes it to [-1, 113] !?
I wonder if the center_graph on this graph is simply "no-effect" for matching or is there something more to it?
That is, I wonder if I need to rerun the matching without center_graph in this case?

Also, if your original intention of this function is to make all the graph in [-1,1], then 2*A[]-1 should be modified?

Is this function going to be used for all seed checking? Check soft seeds seems to be the wrong name since the function is restricted to one-to-one seeds whereas for soft seeds we'll likely want many-to-many seeds as encoded in a doubly stochastic matrix or something.

Prepare for release:

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• rhub::check_with_sanitizers()
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• Accepted 🎉
• git push
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• usethis::use_dev_version()
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• I'm not sure that "adaptive seeds" is the right word our adding seeds procedure.
• Do we need separate functions such as graph_match_adpt_seeds and graph_match_soft_seeds. Again, I'm a bit sure about the naming for these. I think overall these might be too high level. I think these procedures would serve as great examples but they are in some ways too specific to be broadly useful.
• Will the other functions, swap_order, fix_hard_D, ... be exported? Either way they should have some basic commenting.

Matrix 1.5-5 will fix a number of bugs affecting subscripts of objects
inheriting from the virtual class 'Matrix'. Your package iGraphMatch
currently defines three methods

 [,matrix_list,ANY,missing,ANY
 [,matrix_list,missing,ANY,ANY
 [,matrix_list,missing,missing,ANY

that do

 xl[i, , drop]
 xl[, j, drop]
 xl[,  , drop]

where I can only assume that the author meant this

 xl[i, , drop = drop]
 xl[, j, drop = drop]
 xl[,  , drop = drop]

to ensure that the value of 'drop' is correctly matched to the formal
argument 'drop' and not the formal argument '...'. Matrix 1.5-5 will
make your current (incorrect) usage an error, so it must be changed.

Please correct and verify that your package passes its checks under the
development version of Matrix, which you can install with Subversion,
like so:

$ svn checkout svn://svn.r-forge.r-project.org/svnroot/matrix/pkg/Matrix
$ R CMD build Matrix
$ R CMD INSTALL Matrix_1.5-5.tar.gz

{
Note that installing in the usual way

 > install.packages("Matrix", repos = "http://r-forge.r-project.org/")

 seems to provide an outdated version of Matrix, due to a glitch
 in R-Forge, which I hope is just temporary ...

 If you do not have Subversion, then I can try to host a tarball on
 GitHub for you ...

}

We have not yet fixed a date for the release of Matrix 1.5-5 {as 1.5-4
was just released recently}. Still, we are trying to give maintainers
as much notice as possible about required changes.

I think.

Prepare for release:

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Error: Installation failed: Not Found (404)
Is this because dpmcsuss/iGraphMatch is a private repository?

Implement a gradient ascent approach that uses Sinkhorn projection rather than LAP.

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Wait for CRAN...

• Accepted 🎉
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• usethis::use_dev_version(push = TRUE)