Add multi-edges to the author and artifact networks

NEWS.md

@@ -1,5 +1,47 @@
 # codeface-extraction-r – Changelog
 
+## unversioned
+
+### Add relations to authors and artifacts (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+- add for new relation types for each edge
+- accept vector with more than one relation for `author.relation` and `artifact.relation` in util-conf.R
+
+### Changes in util-networks (#98, 2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+
+#### Build Networks (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+- edit function `get.author.network` to handle more than one relation
+- edit function `get.artifact.network` to handle more than one artifact relation
+- handle more than one relation type and merge the resulting vertex lists and edge lists in `get.bipartite.network`
+- enable for different relations for `authors.to.artifacts` in `get.multi.network`, add information about the relation
+  and merge vertex sets
+- add new vertex attribute `kind`
+(7c628fb93eb21f280c7d9da66680f817e107fa24, 7ad49c4ad937c9a6c7398a45179e25d5d5c03faa)
+- remove vertex attribute `id` in artifact vertices (7ad49c4ad937c9a6c7398a45179e25d5d5c03faa)
+
+#### Network and Edge Construction (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+- function `construct.network.from.list` split in two functions  `construct.edge.list.from.key.value.list` and `construct.network.from.edge.list`
+- add function `merge.network.data` und `merge.networks`
+- handle more than one relation in function `add.edges.for.bipartite.relation` and set the edge attribute `relation`
+- add function `create.empty.edge.list`
+- enable for different relations in `get.bipartite.relation` and save the type of the relation in an attribute `relation`
+
+#### Simplify (021ac8b88e9a181364a51e89807df55cb741ed44)
+- iterate over the different types of relations and simplfy the subnetworks relating to the `relation` attribute
+- the `EDGE.ATTR.HANDLING` of the attribute `relation` is "first"
+
+### Changes in test suite (784c417c50eb1de5d0143908a390ead6ba22dbbf, 7ad49c4ad937c9a6c7398a45179e25d5d5c03faa, be6ee8cd48dc7692e02b7f1c512870591300fa8a)
+- add relation attribute `relation` to result data frames
+- remove vertex attribute `id`
+- write new tests for networks with more than one relation type
+
+### Changes in util-plot (b55d3e84a5f9b122dacd0ee52784d930f22d1f4b, f190ca130a15a82e5eed836e9ffc53b8a34aac20)
+- colors of the edges depending on the relation type
+- line shape depend on the edge type (inter or intra)
+- change colors of edges
+- remove colors from `plot.fix.type.attributes`
+- use palette 'viridis'
+- different colors for artifacts
+
 
 ## unversioned
 

README.md

@@ -43,6 +43,7 @@ When selecting a version to work with, you should consider the following points:
 - `ggraph`: For plotting of networks (needs `udunits2` system library, e.g., `libudunits2-dev` on Ubuntu!)
 - `markovchain`: For core/peripheral transition probabilities
 - `lubridate`: For convenient date conversion and parsing
+- `viridis`: For plotting of networks with nice colours
 
 
 ## How-To
@@ -214,7 +215,7 @@ Updates to the parameters can be done by calling `NetworkConf$update.variables(.
 **Note**: Default values are shown in *italics*.
 
 - `author.relation`
-  * The relation among authors, encoded as edges in an author network
+  * The relation(s) among authors, encoded as edges in an author network
   * **Note**: The  author--artifact relation in bipartite and multi networks is configured by `artifact.relation`!
   * possible values: [*`"mail"`*, `"cochange"`, `"issue"`]
 - `author.directed`
@@ -228,7 +229,7 @@ Updates to the parameters can be done by calling `NetworkConf$update.variables(.
   * Remove all authors from an author network (including bipartite and multi networks) who are not present in an author network constructed with `artifact.relation` as relation, i.e., all authors that have no biparite relations in a bipartite/multi network are removed.
   * [`TRUE`, *`FALSE`*]
 - `artifact.relation`
-  * The relation among artifacts, encoded as edges in an artifact network
+  * The relation(s) among artifacts, encoded as edges in an artifact network
   * **Note**: This relation configures also the author--artifact relation in bipartite and multi networks!
   * possible values: [*`"cochange"`*, `"callgraph"`, `"mail"`, `"issue"`]
 - `artifact.directed`
@@ -239,13 +240,14 @@ Updates to the parameters can be done by calling `NetworkConf$update.variables(.
   * The list of edge-attribute names and information
   * a subset of the following as a single vector:
        - timestamp information: *`"date"`*, `"date.offset"`
+       - general information: *`"artifact.type"`*
        - author information: `"author.name"`, `"author.email"`
        - committer information: `"committer.date"`, `"committer.name"`, `"committer.email"`
        - e-mail information: *`"message.id"`*, *`"thread"`*, `"subject"`
-       - commit information: *`"hash"`*, *`"file"`*, *`"artifact.type"`*, *`"artifact"`*, `"changed.files"`, `"added.lines"`, `"deleted.lines"`, `"diff.size"`, `"artifact.diff.size"`, `"synchronicity"`
+       - commit information: *`"hash"`*, *`"file"`*, *`"artifact"`*, `"changed.files"`, `"added.lines"`, `"deleted.lines"`, `"diff.size"`, `"artifact.diff.size"`, `"synchronicity"`
        - PaStA information: `"pasta"`,
        - issue information: *`"issue.id"`*, *`"event.name"`*, `"issue.state"`, `"creation.date"`, `"closing.date"`, `"is.pull.request"`
-  * **Note**: `"date"` is always included as this information is needed for several parts of the library, e.g., time-based splitting.
+  * **Note**: `"date"` and `"artifact.type"` are always included as this information is needed for several parts of the library, e.g., time-based splitting.
   * **Note**: For each type of network that can be built, only the applicable part of the given vector of names is respected.
   * **Note**: For the edge attributes `"pasta"` and `"synchronicity"`, the project configuration's parameters `pasta` and `synchronicity` need to be set to `TRUE`, respectively (see below).
 - `simplify`
@@ -267,6 +269,20 @@ You can also update the `NetworkConf` object at any time by calling `NetworkBuil
 For more examples, please look in the file `showcase.R`.
 
 
+###  Network properties
+
+- Mandatory vertex attributes
+  * *`"type"`*: [`"Author"`, `"Artifact"`]
+  * *`"kind"`*: [`"Author"`,`"File"`, `"Feature"`, `"Function"`, `"Mail"`, `"Issue"`,`"FeatureExpression"`]
+  * *`"name"`*
+
+- Mandatory edge attributes
+  * *`"type"`*: [`Unipartite`, `Bipartite`]
+  * *`"artifact.type"`*: [`"Author"`,`"File"`, `"Feature"`, `"Function"`, `"Mail"`, `"Issue"`,`"FeatureExpression"`]
+  * *`"relation"`*: [`mail`, `cochange`, `issue`, `callgraph`] (from `artifact.relation` and `author.relation` attributes in the `NetworkConf` class)
+  * *`"date"`*
+
+
 ## File/Module overview
 
 - `util-init.R`

tests/test-data-cut.R

@@ -14,6 +14,7 @@
 ## Copyright 2017 by Christian Hechtl <[email protected]>
 ## Copyright 2017 by Felix Prasse <[email protected]>
 ## Copyright 2018 by Claus Hunsen <[email protected]>
+## Copyright 2018 by Barbara Eckl <[email protected]>
 ## All Rights Reserved.
 
 
@@ -68,7 +69,8 @@ test_that("Cut commit and mail data to same date range.", {
                                     date = get.date.from.string("2016-07-12 16:04:40"),
                                     date.offset = as.integer(c(100)),
                                     subject = c("Re: Fw: busybox 2 tab"),
-                                    thread = sprintf("<thread-%s>", c(9)))
+                                    thread = sprintf("<thread-%s>", c(9)),
+                                    artifact.type = "Mail")
 
     commit.data = x.data$get.data.cut.to.same.date(data.sources = data.sources)$get.commits()
     rownames(commit.data) = 1:nrow(commit.data)

tests/test-networks-artifact.R

@@ -13,6 +13,7 @@
 ##
 ## Copyright 2017-2018 by Christian Hechtl <[email protected]>
 ## Copyright 2017 by Claus Hunsen <[email protected]>
+## Copyright 2018 by Barbara Eckl <[email protected]>
 ## All Rights Reserved.
 
 
@@ -47,22 +48,25 @@ test_that("Network construction of the undirected artifact-cochange network", {
     network.built = network.builder$get.artifact.network()
 
     ## vertex attributes
-    vertices = c("Base_Feature", "foo", "A")
+    vertices = data.frame(name = c("Base_Feature", "foo", "A"),
+                          kind = "Feature",
+                          type = TYPE.ARTIFACT)
 
-    data = data.frame(from = c("Base_Feature", "Base_Feature"),
-                      to = c("foo", "foo"),
-                      date = get.date.from.string(c("2016-07-12 16:06:32", "2016-07-12 16:06:32")),
-                      hash = c("0a1a5c523d835459c42f33e863623138555e2526", "0a1a5c523d835459c42f33e863623138555e2526"),
-                      file = c("test2.c", "test2.c"),
-                      artifact.type = c("Feature", "Feature"),
-                      artifact = c("Base_Feature", "foo"),
-                      weight = c(1, 1),
-                      type = TYPE.EDGES.INTRA)
+    data = data.frame(
+        from = c("Base_Feature", "Base_Feature"),
+        to = c("foo", "foo"),
+        date = get.date.from.string(c("2016-07-12 16:06:32", "2016-07-12 16:06:32")),
+        artifact.type = c("Feature", "Feature"),
+        hash = c("0a1a5c523d835459c42f33e863623138555e2526", "0a1a5c523d835459c42f33e863623138555e2526"),
+        file = c("test2.c", "test2.c"),
+        artifact = c("Base_Feature", "foo"),
+        weight = 1,
+        type = TYPE.EDGES.INTRA,
+        relation = "cochange"
+    )
 
     ## build expected network
     network.expected = igraph::graph.data.frame(data, directed = FALSE, vertices = vertices)
-    network.expected = igraph::set.vertex.attribute(network.expected, "id", value = igraph::get.vertex.attribute(network.expected, "name"))
-    igraph::V(network.expected)$type = TYPE.ARTIFACT
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })