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Work on the simplification of multi-relation edges in networks #255

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Mar 22, 2024
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Work on the simplification of multi-relation edges in networks #255

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a34b5bd
Disambiguate and sort the 'relation' edge-attribute, if specified
maxloeffler Feb 14, 2024
3451641
Correctly obtain the unique relation sources
maxloeffler Feb 28, 2024
78f4351
Make 'relation' edge-attribute lambda default
maxloeffler Mar 7, 2024
338b069
Add tests for network simplification using both algorithms
maxloeffler Mar 7, 2024
1f272e1
Bump CI pipeline to use v4 of 'checkout'
maxloeffler Mar 18, 2024
d310fdc
Move 'simplify.networks' to the end of public network-creation functions
maxloeffler Mar 18, 2024
8a6f47b
Simplify networks using config parameter and clean testing-code up
maxloeffler Mar 18, 2024
e01908c
Add basic 'simplify.networks' test, analogous to 'simplify.network' test
maxloeffler Mar 19, 2024
7b6848f
Explicitly test for length and names when using 'simplify.networks'
maxloeffler Mar 20, 2024
57e613f
Test 'get.data.sources.from.relations' with multi-relational edges
maxloeffler Mar 20, 2024
503ab2a
Update 'NEWS.md'
maxloeffler Mar 20, 2024
58d77b0
Allow networks with multi-relational edges to be plotted
maxloeffler Mar 22, 2024
dc32d44
Feature network simplification explicitly in 'showcase.R'
maxloeffler Mar 22, 2024
b017092
Update & fix 'NEWS.md'
maxloeffler Mar 22, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/pull_request.yml
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Expand Up @@ -11,7 +11,7 @@
## with this program; if not, write to the Free Software Foundation, Inc.,
## 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
##
## Copyright 2023 by Maximilian Löffler <[email protected]>
## Copyright 2023-2024 by Maximilian Löffler <[email protected]>
## Copyright 2024 by Thomas Bock <[email protected]>
## All Rights Reserved.

Expand Down Expand Up @@ -41,7 +41,7 @@ jobs:

steps:
- name: Checkout Repo
uses: actions/checkout@v3
uses: actions/checkout@v4
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- name: Update system
run: |
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187 changes: 187 additions & 0 deletions tests/test-networks.R
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,193 @@ test_that("Simplify network with more than one relation", {

})

test_that("Simplify basic multi-relational network", {

##
## Simplify networks with vertices connected by multi-relational edges
##

## create artifact network with vertices connected by "cochange" and "mail edges"
network =
igraph::make_empty_graph(n = 0, directed = FALSE) +
igraph::vertices("A", "B", type = TYPE.ARTIFACT, kind = "feature")
for (i in 1:3) {
network = igraph::add.edges(network, c("A", "B"), type = TYPE.EDGES.INTRA, relation = "mail")
network = igraph::add.edges(network, c("A", "B"), type = TYPE.EDGES.INTRA, relation = "cochange")
}

network.expected = igraph::make_empty_graph(n = 0, directed = FALSE) +
igraph::vertices("A", "B", type = TYPE.ARTIFACT, kind = "feature") +
igraph::edges("A", "B", type = TYPE.EDGES.INTRA, relation = "mail") +
igraph::edges("A", "B", type = TYPE.EDGES.INTRA, relation = "cochange")

## simplify network without simplifying multiple relations into single edges
network.simplified = simplify.network(network, simplify.multiple.relations = FALSE)
assert.networks.equal(network.simplified, network.expected)

## simplify network with simplifying multiple relations into single edges
network.simplified = simplify.network(network, simplify.multiple.relations = TRUE)
expect_identical(igraph::ecount(simplify.network(network.simplified)), 1)
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expect_identical(igraph::E(network.simplified)$type[[1]], "Unipartite")
expect_identical(igraph::E(network.simplified)$relation[[1]], c("cochange", "mail"))
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})

test_that("Simplify author-network with relation = c('cochange', 'mail') using both algorithms", {

## configurations
proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
proj.conf$update.value("commits.filter.base.artifact", FALSE)
net.conf = NetworkConf$new()
net.conf$update.values(updated.values = list(author.relation = c("cochange", "mail"), simplify = TRUE))

## construct objects
proj.data = ProjectData$new(project.conf = proj.conf)
network.builder = NetworkBuilder$new(project.data = proj.data, network.conf = net.conf)

## vertex attributes
authors = data.frame(name = c("Björn", "Olaf", "Karl", "Thomas", "udo", "Fritz [email protected]", "georg", "Hans"),
kind = TYPE.AUTHOR,
type = TYPE.AUTHOR)


## ---------------------- simplify.multiple.relations == FALSE -------------------------- ##

## edge attributes
data = data.frame(comb.1. = c("Björn", "Olaf", "Olaf", "Karl", # cochange
"Björn", "Olaf"), # mail
comb.2. = c("Olaf", "Karl", "Thomas", "Thomas", # cochange
"Olaf", "Thomas")) # mail
data$date = list(get.date.from.string(c("2016-07-12 15:58:59", "2016-07-12 16:00:45")),
get.date.from.string(c("2016-07-12 16:05:41", "2016-07-12 16:06:10")),
get.date.from.string(c("2016-07-12 16:05:41", "2016-07-12 16:06:32")),
get.date.from.string(c("2016-07-12 16:06:10", "2016-07-12 16:06:32")), # cochange
get.date.from.string(c("2016-07-12 15:58:40", "2016-07-12 15:58:50")),
get.date.from.string(c("2016-07-12 16:04:40", "2016-07-12 16:05:37"))) # mail
data$artifact.type = list(c("Feature", "Feature"), c("Feature", "Feature"),
c("Feature", "Feature"), c("Feature", "Feature"), # cochange
c("Mail", "Mail"), c("Mail", "Mail")) # mail
data$hash = list(c("72c8dd25d3dd6d18f46e2b26a5f5b1e2e8dc28d0", "5a5ec9675e98187e1e92561e1888aa6f04faa338"),
c("3a0ed78458b3976243db6829f63eba3eead26774", "1143db502761379c2bfcecc2007fc34282e7ee61"),
c("3a0ed78458b3976243db6829f63eba3eead26774", "0a1a5c523d835459c42f33e863623138555e2526"),
c("1143db502761379c2bfcecc2007fc34282e7ee61", "0a1a5c523d835459c42f33e863623138555e2526"),
as.character(c(NA, NA)), as.character(c(NA, NA)))
data$file = list(c("test.c", "test.c"), c("test2.c", "test3.c"), c("test2.c", "test2.c"), c("test3.c", "test2.c"),
as.character(c(NA, NA)), as.character(c(NA, NA)))
data$artifact = list(c("A", "A"), c("Base_Feature", "Base_Feature"), c("Base_Feature", "Base_Feature"),
c("Base_Feature", "Base_Feature"), as.character(c(NA, NA)), as.character(c(NA, NA)))
data$weight = rep(2, 6)
data$type = rep(TYPE.EDGES.INTRA, 6)
data$relation = c(rep("cochange", 4), rep("mail", 2))
data$message.id = list(as.character(c(NA, NA)), as.character(c(NA, NA)), as.character(c(NA, NA)), as.character(c(NA, NA)),
c("<[email protected]>",
"<[email protected]>"),
c("<[email protected]>",
"<[email protected]>"))
data$thread = list(as.character(c(NA, NA)), as.character(c(NA, NA)), as.character(c(NA, NA)), as.character(c(NA, NA)),
c("<thread-13#8>", "<thread-13#8>"), c("<thread-13#9>", "<thread-13#9>"))

## build expected network
network.expected = igraph::graph.data.frame(data, vertices = authors,
directed = net.conf$get.value("author.directed"))

## build simplified network
network.built = network.builder$get.author.network()

assert.networks.equal(network.built, network.expected)


## ---------------------- simplify.multiple.relations == TRUE --------------------------- ##

data = data.frame(comb.1. = c("Björn", "Olaf", "Olaf", "Karl"),
comb.2. = c("Olaf", "Karl", "Thomas", "Thomas"))

data$date = list(get.date.from.string(c("2016-07-12 15:58:59", "2016-07-12 16:00:45", # cochange
"2016-07-12 15:58:40", "2016-07-12 15:58:50")), # mail
get.date.from.string(c("2016-07-12 16:05:41", "2016-07-12 16:06:10")), # cochange
get.date.from.string(c("2016-07-12 16:05:41", "2016-07-12 16:06:32", # cochange
"2016-07-12 16:04:40", "2016-07-12 16:05:37")), # mail
get.date.from.string(c("2016-07-12 16:06:10", "2016-07-12 16:06:32"))) # cochange
data$artifact.type = list(c("Feature", "Feature", "Mail", "Mail"),
c("Feature", "Feature"),
c("Feature", "Feature", "Mail", "Mail"),
c("Feature", "Feature"))
data$hash = list(as.character(c("72c8dd25d3dd6d18f46e2b26a5f5b1e2e8dc28d0", "5a5ec9675e98187e1e92561e1888aa6f04faa338", NA, NA)),
c("3a0ed78458b3976243db6829f63eba3eead26774", "1143db502761379c2bfcecc2007fc34282e7ee61"),
as.character(c("3a0ed78458b3976243db6829f63eba3eead26774", "0a1a5c523d835459c42f33e863623138555e2526", NA, NA)),
c("1143db502761379c2bfcecc2007fc34282e7ee61", "0a1a5c523d835459c42f33e863623138555e2526"))
data$file = list(as.character(c("test.c", "test.c", NA, NA)), c("test2.c", "test3.c"),
as.character(c("test2.c", "test2.c", NA, NA)), c("test3.c", "test2.c"))
data$artifact = list(as.character(c("A", "A", NA, NA)), c("Base_Feature", "Base_Feature"),
as.character(c("Base_Feature", "Base_Feature", NA, NA)), c("Base_Feature", "Base_Feature"))
data$weight = c(4, 2, 4, 2)
data$type = rep(TYPE.EDGES.INTRA, 4)
data$relation = list(c("cochange", "mail"), c("cochange"), c("cochange", "mail"), c("cochange"))
data$message.id = list(as.character(c(NA, NA, "<[email protected]>",
"<[email protected]>")),
as.character(c(NA, NA)),
as.character(c(NA, NA, "<[email protected]>",
"<[email protected]>")),
as.character(c(NA, NA)))
data$thread = list(as.character(c(NA, NA, "<thread-13#8>", "<thread-13#8>")),
as.character(c(NA, NA)),
as.character(c(NA, NA, "<thread-13#9>", "<thread-13#9>")),
as.character(c(NA, NA)))

## build expected network
network.expected = igraph::graph.data.frame(data, vertices = authors,
directed = net.conf$get.value("author.directed"))

## build simplified network
network.builder$update.network.conf(updated.values = list(simplify.multiple.relations = TRUE))
network.built = network.builder$get.author.network()

assert.networks.equal(network.built, network.expected)

})

test_that("Simplify multiple basic multi-relational networks", {

##
## Simplify networks with vertices connected by multi-relational edges
##

## create artifact network with vertices connected by "cochange" and "mail edges"
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network.A =
igraph::make_empty_graph(n = 0, directed = FALSE) +
igraph::vertices("A", "B", type = TYPE.ARTIFACT, kind = "feature")
network.B =
igraph::make_empty_graph(n = 0, directed = FALSE) +
igraph::vertices("C", "D", type = TYPE.AUTHOR, kind = TYPE.AUTHOR)
for (i in 1:3) {
network.A = igraph::add.edges(network.A, c("A", "B"), type = TYPE.EDGES.INTRA, relation = "mail")
network.A = igraph::add.edges(network.A, c("A", "B"), type = TYPE.EDGES.INTRA, relation = "cochange")
network.B = igraph::add.edges(network.B, c("C", "D"), type = TYPE.EDGES.INTRA, relation = "mail")
network.B = igraph::add.edges(network.B, c("C", "D"), type = TYPE.EDGES.INTRA, relation = "cochange")
}

network.A.expected = igraph::make_empty_graph(n = 0, directed = FALSE) +
igraph::vertices("A", "B", type = TYPE.ARTIFACT, kind = "feature") +
igraph::edges("A", "B", type = TYPE.EDGES.INTRA, relation = "mail") +
igraph::edges("A", "B", type = TYPE.EDGES.INTRA, relation = "cochange")
network.B.expected = igraph::make_empty_graph(n = 0, directed = FALSE) +
igraph::vertices("C", "D", type = TYPE.AUTHOR, kind = TYPE.AUTHOR) +
igraph::edges("C", "D", type = TYPE.EDGES.INTRA, relation = "mail") +
igraph::edges("C", "D", type = TYPE.EDGES.INTRA, relation = "cochange")

## simplify networks without simplifying multiple relations into single edges
networks.simplified = simplify.networks(list(network.A, network.B), simplify.multiple.relations = FALSE)
assert.networks.equal(networks.simplified[[1]], network.A.expected)
assert.networks.equal(networks.simplified[[2]], network.B.expected)
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## simplify network with simplifying multiple relations into single edges
networks.simplified = simplify.networks(list(network.A, network.B), simplify.multiple.relations = TRUE)
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for (i in 1:2) {
expect_identical(igraph::ecount(simplify.network(networks.simplified[[i]])), 1)
expect_identical(igraph::E(networks.simplified[[i]])$type[[1]], "Unipartite")
expect_identical(igraph::E(networks.simplified[[i]])$relation[[1]], c("cochange", "mail"))
}
})


## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Merge -------------------------------------------------------------------
Expand Down
28 changes: 20 additions & 8 deletions util-networks.R
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Expand Up @@ -56,7 +56,7 @@ EDGE.ATTR.HANDLING = list(
## network-analytic data
weight = "sum",
type = "first",
relation = "first",
relation = function(relation) sort(unique(relation)),

## commit data
changed.files = "sum",
Expand Down Expand Up @@ -781,6 +781,12 @@ NetworkBuilder = R6::R6Class("NetworkBuilder",
igraph::V(net)$kind = TYPE.AUTHOR
igraph::V(net)$type = TYPE.AUTHOR

## simplify network if wanted
if (private$network.conf$get.value("simplify")) {
net = simplify.network(net, simplify.multiple.relations =
private$network.conf$get.value("simplify.multiple.relations"))
}

## add range attribute for later analysis (if available)
if ("RangeData" %in% class(private$proj.data)) {
attr(net, "range") = private$proj.data$get.range()
Expand Down Expand Up @@ -822,6 +828,12 @@ NetworkBuilder = R6::R6Class("NetworkBuilder",
## set vertex and edge attributes for identifaction
igraph::V(net)$type = TYPE.ARTIFACT

## simplify network if wanted
if (private$network.conf$get.value("simplify")) {
net = simplify.network(net, simplify.multiple.relations =
private$network.conf$get.value("simplify.multiple.relations"))
}

## add range attribute for later analysis (if available)
if ("RangeData" %in% class(private$proj.data)) {
attr(net, "range") = private$proj.data$get.range()
Expand Down Expand Up @@ -922,6 +934,12 @@ NetworkBuilder = R6::R6Class("NetworkBuilder",
network = igraph::delete.vertices(network, authors.to.remove)
}

## simplify network if wanted
if (private$network.conf$get.value("simplify")) {
network = simplify.network(network, simplify.multiple.relations =
private$network.conf$get.value("simplify.multiple.relations"))
}

## add range attribute for later analysis (if available)
if ("RangeData" %in% class(private$proj.data)) {
attr(network, "range") = private$proj.data$get.range()
Expand Down Expand Up @@ -1306,12 +1324,6 @@ construct.network.from.edge.list = function(vertices, edge.list, network.conf, d
## initialize edge weights
net = igraph::set.edge.attribute(net, "weight", value = 1)

## transform multiple edges to edge weights
if (network.conf$get.value("simplify")) {
net = simplify.network(net,
simplify.multiple.relations = network.conf$get.value("simplify.multiple.relations"))
}

logging::logdebug("construct.network.from.edge.list: finished.")

return(net)
Expand Down Expand Up @@ -1786,7 +1798,7 @@ delete.authors.without.specific.edges = function(network, specific.edge.types =
#' empty relation, i.e. \code{character(0)}
get.data.sources.from.relations = function(network) {
## get all relations in the network
data.sources = unique(igraph::E(network)$relation)
data.sources = unique(unlist(igraph::E(network)$relation))
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## map them to data sources respectively using the defined translation constant
data.sources = sapply(data.sources, function(relation) {
Expand Down