/
util-networks-covariates.R
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util-networks-covariates.R
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## This file is part of coronet, which is free software: you
## can redistribute it and/or modify it under the terms of the GNU General
## Public License as published by the Free Software Foundation, version 2.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License along
## with this program; if not, write to the Free Software Foundation, Inc.,
## 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
##
## Copyright 2017 by Felix Prasse <prassefe@fim.uni-passau.de>
## Copyright 2018-2019 by Claus Hunsen <hunsen@fim.uni-passau.de>
## Copyright 2018-2019 by Thomas Bock <bockthom@fim.uni-passau.de>
## Copyright 2021, 2023-2024 by Thomas Bock <bockthom@cs.uni-saarland.de>
## Copyright 2018-2019 by Klara Schlüter <schluete@fim.uni-passau.de>
## Copyright 2018 by Jakob Kronawitter <kronawij@fim.uni-passau.de>
## Copyright 2020 by Christian Hechtl <hechtl@cs.uni-saarland.de>
## Copyright 2021 by Johannes Hostert <s8johost@stud.uni-saarland.de>
## Copyright 2022 by Niklas Schneider <s8nlschn@stud.uni-saarland.de>
## Copyright 2022 by Jonathan Baumann <joba00002@stud.uni-saarland.de>
## All Rights Reserved.
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Libraries ---------------------------------------------------------------
requireNamespace("logging") # for logging
requireNamespace("parallel") # for parallel computation
requireNamespace("plyr") # for ldply function
requireNamespace("igraph") # networks
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Utility functions -------------------------------------------------------
#' Utility function to compute vertex attributes for a list of network
#'
#' Important: This function only works for lists of networks which have timestamps used in their range names.
#'
#' This method is a wrapper combining the steps of splitting the project data and calculating the attribute.
#'
#' Important: If a vertex attribute can have multiple values per vertex, the \code{compute.attr} function
#' has to wrap all attribute vectors of a single vertex into a list. In that case, also the
#' \code{default.value} needs to be put into a list. By that, this function can differentiate between
#' attributes having multiple values and attributes having, at most, one value.
#'
#' @param list.of.networks The list of networks to add vertex attributes to
#' @param project.data The entire project data
#' @param attr.name The name of the attribute to add
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value
#' @param compute.attr The function to compute the attribute to add. Must return a named list
#' with the names being the name of the vertex.
#'
#' @return A list of networks with the added attribute
split.and.add.vertex.attribute = function(list.of.networks, project.data, attr.name,
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value, compute.attr, list.attributes = FALSE) {
aggregation.level = match.arg.or.default(aggregation.level, default = "range")
net.to.range.list = split.data.by.networks(list.of.networks, project.data, aggregation.level)
nets.with.attr = add.vertex.attribute(net.to.range.list, attr.name, default.value, compute.attr, list.attributes)
return(nets.with.attr)
}
#' Utility function to compute vertex attributes for a list of network-to-range tuples.
#'
#' Important: If a vertex attribute can have multiple values per vertex, the \code{compute.attr} function
#' has to wrap all attribute vectors of a single vertex into a list. In that case, also the
#' \code{default.value} needs to be put into a list. By that, this function can differentiate between
#' attributes having multiple values and attributes having, at most, one value.
#'
#' @param net.to.range.list A list containing tuples with networks and corresponding range data.
#' @param attr.name The name of the attribute to add
#' @param default.value The default value to add if a vertex has no matching value
#' @param compute.attr The function to compute the attribute to add. Must return a named list
#' with the names being the name of the vertex.
#'
#' @return A list of networks with the added attribute
add.vertex.attribute = function(net.to.range.list, attr.name, default.value, compute.attr, list.attributes = FALSE) {
nets.with.attr = mapply(
names(net.to.range.list), net.to.range.list,
SIMPLIFY = FALSE, FUN = function(range, net.to.range) {
current.network = net.to.range[["network"]]
range.data = net.to.range[["data"]]
attrs.by.vertex.name = compute.attr(range, range.data, current.network)
## catch the primitive case that the list of given attributes is empty or not set
if (length(attrs.by.vertex.name) == 0 || is.null(attrs.by.vertex.name)) {
## construct list of attribute name and type
attributes = structure(class(default.value), names = attr.name)
## add the vertex attribute (default value = 'NA')
net.with.attr = add.attributes.to.network(current.network, "vertex", attributes)
## overwrite set vertex attribute with 'default.value', given the case that there are indeed vertices
## in the current network
net.with.attr = igraph::set.vertex.attribute(net.with.attr, attr.name, value = default.value)
## return immediately
return(net.with.attr)
}
get.or.default = function(name, data, default) {
if (name %in% names(data)) {
return(data[[name]])
} else {
return(default)
}
}
attributes = lapply(igraph::V(current.network)$name,
function(x) get.or.default(x, attrs.by.vertex.name, default.value))
## simplify the list of attributes to a vector if all its elements are just vectors (not lists)
if (length(attributes) > 0 && !any(sapply(attributes, is.list))) {
attributes = unlist(attributes)
}
## otherwise, the list of attributes contains lists, so we can only remove the outermost list
else if (!list.attributes) {
attributes = unlist(attributes, recursive = FALSE)
}
net.with.attr = igraph::set.vertex.attribute(current.network, attr.name, value = attributes)
return(net.with.attr)
}
)
return(nets.with.attr)
}
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Author network functions ------------------------------------------------
#' Add count-based attribute based on \code{count.method}
#'
#' Note: This is a helper function for all other functions adding a count-based
#' vertex attribute.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#' @param commit.count.method The method reference for counting the data
#' @param name.column The name of the column which contains the author information
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.count.helper = function(list.of.networks, project.data, name,
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value = 0L, count.method, name.column) {
aggregation.level = match.arg.or.default(aggregation.level, default = "range")
nets.with.attr = split.and.add.vertex.attribute(
list.of.networks, project.data, name, aggregation.level, default.value,
function(range, range.data, net) {
count.df = count.method(range.data)[c(name.column, "freq")]
if (!is.data.frame(count.df)) {
return(list())
}
count.list = structure(count.df[["freq"]], names = count.df[[name.column]])
return(count.list)
}
)
return(nets.with.attr)
}
## * Commit count ----------------------------------------------------------
#' Add commit-count attribute based on author name
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "commit.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.commit.count = function(list.of.networks, project.data, name = "commit.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value = 0L) {
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, get.author.commit.count, "author.name"
)
return(nets.with.attr)
}
#' Add commit-count attribute based on author name where author is not committer
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "commit.count.author.not.committer"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.commit.count.not.committer = function(list.of.networks, project.data,
name = "commit.count.author.not.committer",
aggregation.level = c("range", "cumulative",
"all.ranges",
"project.cumulative",
"project.all.ranges",
"complete"),
default.value = 0L) {
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, get.committer.not.author.commit.count, "author.name"
)
return(nets.with.attr)
}
#' Add commit-count attribute based on comitter name
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "commit.count.committer"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.commit.count.committer = function(list.of.networks, project.data,
name = "commit.count.committer",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative",
"project.all.ranges",
"complete"),
default.value = 0L) {
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, get.committer.commit.count, "committer.name"
)
return(nets.with.attr)
}
#' Add commit-count attribute based on comitter name where committer is not author
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "commit.count.committer.not.author"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.commit.count.committer.not.author = function(list.of.networks, project.data,
name = "commit.count.committer.not.author",
aggregation.level = c("range", "cumulative",
"all.ranges",
"project.cumulative",
"project.all.ranges",
"complete"),
default.value = 0L) {
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, get.committer.not.author.commit.count, "committer.name"
)
return(nets.with.attr)
}
#' Add commit-count attribute based on committer name where the committer equals the author.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "commit.count.committer.and.author"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.commit.count.committer.and.author = function(list.of.networks, project.data,
name = "commit.count.committer.and.author",
aggregation.level = c("range", "cumulative",
"all.ranges",
"project.cumulative",
"project.all.ranges",
"complete"),
default.value = 0L) {
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, get.committer.and.author.commit.count, "committer.name"
)
return(nets.with.attr)
}
#' Add commit-count attribute based on commits where the person represented by the vertex is the committer
#' or the author.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "commit.count.committer.or.author"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.commit.count.committer.or.author = function(list.of.networks, project.data,
name = "commit.count.committer.or.author",
aggregation.level = c("range", "cumulative",
"all.ranges",
"project.cumulative",
"project.all.ranges",
"complete"),
default.value = 0L) {
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, get.committer.or.author.commit.count, "name"
)
return(nets.with.attr)
}
#' Add unique artifact count attribute
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "artifact.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.artifact.count = function(list.of.networks, project.data, name = "artifact.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value = 0L) {
aggregation.level = match.arg.or.default(aggregation.level, default = "range")
nets.with.attr = split.and.add.vertex.attribute(
list.of.networks, project.data, name, aggregation.level, default.value,
function(range, range.data, net) {
lapply(range.data$group.artifacts.by.data.column("commits", "author.name"),
function(x) {
length(unique(x[["artifact"]]))
}
)
}
)
return(nets.with.attr)
}
## * Mail count ----------------------------------------------------------
#' Add mail-count attribute based on the total number of mails sent,
#' where the person represented by the vertex is the author.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "mail.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.mail.count = function(list.of.networks, project.data,
name = "mail.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value = 0L) {
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, get.author.mail.count, "author.name"
)
return(nets.with.attr)
}
#' Add mail-thread-count attribute based on the number of mail threads participated in,
#' where the person represented by the vertex is the author.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "mail.thread.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.mail.thread.count = function(list.of.networks, project.data,
name = "mail.thread.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value = 0L) {
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, get.author.mail.thread.count, "author.name"
)
return(nets.with.attr)
}
## * Issue / PR count --------------------------------------------------------------
#' Add issue-count attribute based on the number of issues participated in,
#' where the person represented by the vertex is the author.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add. You might want to change this [default: "issue.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#' @param issue.type The issue kind,see \code{preprocess.issue.data} [default: "all"]
#' @param use.unfiltered.data whether to use unfiltered issue data (see \code{preprocess.issue.data}) [default: FALSE]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.issue.count = function(list.of.networks, project.data,
name = "issue.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value = 0L, issue.type = c("all", "pull.requests", "issues"),
use.unfiltered.data = FALSE) {
issue.type = match.arg(issue.type)
if (missing(name) && identical(issue.type, "pull.requests")) {
name = "pull.request.count"
}
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level, default.value,
function(data) {
return(get.author.issue.count(data, type = issue.type,use.unfiltered.data = use.unfiltered.data))
},
"author.name"
)
return(nets.with.attr)
}
#' Add issue-count attribute based on the number of issues participated in by commenting,
#' where the person represented by the vertex is the author.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "issues.commented.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#' @param issue.type The issue kind,see \code{preprocess.issue.data} [default: "all"]
#' @param use.unfiltered.data whether to use unfiltered issue data (see \code{preprocess.issue.data}) [default: FALSE]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.issues.commented.count = function(list.of.networks, project.data,
name = "issues.commented.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative",
"project.all.ranges",
"complete"),
default.value = 0L, issue.type = c("all", "pull.requests",
"issues"),
use.unfiltered.data = FALSE) {
issue.type = match.arg(issue.type)
if (missing(name) && identical(issue.type, "pull.requests")) {
name = "pull.requests.commented.count"
}
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, function(data) {
return(get.author.issues.commented.in.count(data, type = issue.type,
use.unfiltered.data = use.unfiltered.data))
},
"author.name"
)
return(nets.with.attr)
}
#' Add issue-count attribute based on the number of issues created,
#' where the person represented by the vertex is the author.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "issue.creation.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#' @param issue.type The issue kind,see \code{preprocess.issue.data} [default: "all"]
#' @param use.unfiltered.data whether to use unfiltered issue data (see \code{preprocess.issue.data}).
#' Note that filtered data may not contain issue creation events.
#' [default: TRUE]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.issue.creation.count = function(list.of.networks, project.data,
name = "issue.creation.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative",
"project.all.ranges",
"complete"),
default.value = 0L, issue.type = c("all", "pull.requests",
"issues"),
use.unfiltered.data = TRUE) {
issue.type = match.arg(issue.type)
if (missing(name) && identical(issue.type, "pull.requests")) {
name = "pull.request.creation.count"
}
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, function(data) {
return(get.author.issues.created.count(data, type = issue.type, use.unfiltered.data = use.unfiltered.data))
}, "author.name"
)
return(nets.with.attr)
}
#' Add issue-comments-count attribute based on the number of comments in issues, where the person represented by the
#' vertex is the author.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "issue.comment.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#' @param issue.type The issue kind,see \code{preprocess.issue.data} [default: "all"]
#' @param use.unfiltered.data whether to use unfiltered issue data (see \code{preprocess.issue.data}) [default: FALSE]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.issue.comment.count = function(list.of.networks, project.data,
name = "issue.comment.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative",
"project.all.ranges",
"complete"),
default.value = 0L, issue.type = c("all", "pull.requests",
"issues"),
use.unfiltered.data = FALSE) {
issue.type = match.arg(issue.type)
if (missing(name) && identical(issue.type, "pull.requests")) {
name = "pull.request.comment.count"
}
nets.with.attr = add.vertex.attribute.count.helper(
list.of.networks, project.data, name, aggregation.level,
default.value, function(data) {
return(get.author.issue.comment.count(data, type = issue.type, use.unfiltered.data = use.unfiltered.data))
}, "author.name"
)
return(nets.with.attr)
}
## * Meta-data -------------------------------------------------------------
#' Add author email attribute
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "author.email"]
#' @param default.value The default value to add if a vertex has no matching value [default: NA]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.email = function(list.of.networks, project.data, name = "author.email",
default.value = NA) {
nets.with.attr = split.and.add.vertex.attribute(
list.of.networks, project.data, name, "complete", default.value,
function(range, range.data, net) {
authors = range.data$get.authors()
author.to.mail = structure(names = authors[["author.name"]],
authors[["author.email"]])
return(author.to.mail)
}
)
return(nets.with.attr)
}
## * Activity --------------------------------------------------------------
#' Add first activity attribute.
#'
#' @param list.of.networks The network list.
#' @param project.data The project data.
#' @param activity.types The kinds of activity to use as basis: One or more of \code{mails}, \code{commits} and
#' \code{issues}. [default: c("mails", "commits", "issues")]
#' @param name The attribute name to add. [default: "first.activity"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "complete"]
#' @param default.value The default value to add if a vertex has no matching value. [default: NA].
#' @param combine.all.activity.types Flag indicating that one value, computed over all given
#' \code{activity.types} is of interest (instead of one value per type).
#' [default: FALSE]
#'
#' @return A list of networks with the added attribute.
add.vertex.attribute.author.first.activity = function(list.of.networks, project.data,
activity.types = c("mails", "commits", "issues"),
name = "first.activity",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value = NA,
combine.activity.types = FALSE) {
aggregation.level = match.arg.or.default(aggregation.level, default = "complete")
parsed.activity.types = match.arg.or.default(activity.types, several.ok = TRUE)
## make sure that the default value contains a tzone attribute (even if the default value is NA)
default.value = get.date.from.string(default.value)
## the given default.value is interpreted as default per author and type.
type.default = default.value
## the default value appended to vertices where no data is available is structured
## and named analogously to the vertex attributes containing available data.
vertex.default = default.value
if (!combine.activity.types) {
vertex.default = rep(list(vertex.default), length(parsed.activity.types))
names(vertex.default) = parsed.activity.types
}
compute.attr = function(range, range.data, net) {
data = get.first.activity.data(range.data, parsed.activity.types, type.default)
## If configured, find minimum over all activity types per author, for example:
## data
## list(authorA = list(mails = 1, commits = 2), authorB = list(mails = 3, commits = 3))
## yields
## list(authorA = list(all.activities = 1), authorB = list(all.activities = 3))
if (combine.activity.types) {
data = parallel::mclapply(data, function(item.list) {
min.value = min(do.call(base::c, item.list), na.rm = TRUE)
return(list(all.activities = min.value))
})
}
return(data)
}
nets.with.attr = split.and.add.vertex.attribute(list.of.networks, project.data, name, aggregation.level,
vertex.default, compute.attr, list.attributes = TRUE)
return(nets.with.attr)
}
#' Add active-ranges attribute
#'
#' Notice: One vertex can be active in multiple ranges, therefore there may be a vector of ranges as
#' active-ranges attribute.
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "active.ranges"]
#' @param activity.types The kinds of activity to use as basis: One or more of \code{mails}, \code{commits} and
#' \code{issues}. [default: c("mails", "commits", "issues")]
#' @param default.value The default value to add if a vertex has no matching value [default: list()]
#' @param combine.activity.types Flag indicating that one value, computed over all given
#' \code{activity.types} is of interest (instead of one value per type).
#' [default: FALSE]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.active.ranges = function(list.of.networks, project.data, name = "active.ranges",
activity.types = c("mails", "commits", "issues"),
default.value = list(),
combine.activity.types = FALSE) {
net.to.range.list = split.data.by.networks(list.of.networks, project.data, "range")
parsed.activity.types = match.arg.or.default(activity.types, several.ok = TRUE)
## the given default.value is interpreted as default per author and type.
type.default = default.value
compute.attr = function(range, range.data, net) {
data = get.active.ranges.data(parsed.activity.types, net.to.range.list, type.default)
## combine the active ranges of all attributes to one list if desired
if (combine.activity.types) {
data = lapply(data, function(person) {
flattened.person = (list("all.activity.types" = as.list(unique(unlist(person)))))
return(list(flattened.person))
})
}
return(data)
}
## the default value appended to vertices where no data is available is structured
## and named analogously to the vertex attributes containing available data.
vertex.default = default.value
if (combine.activity.types) {
vertex.default = list(default.value)
names(vertex.default) = c("all.activity.types")
} else {
vertex.default = rep(list(default.value), length(parsed.activity.types))
names(vertex.default) = parsed.activity.types
}
vertex.default = list(vertex.default)
nets.with.attr = add.vertex.attribute(net.to.range.list, name, vertex.default, compute.attr)
return(nets.with.attr)
}
## * Role ------------------------------------------------------------------
#' Add author role attribute, while using the classification method
#' \code{get.author.class.by.type} to provide the attributes
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "author.role"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param type The type of author classification. One of \code{"network.degree"},
#' \code{"network.eigen"}, \code{"commit.count"}, and \code{"loc.count"}.
#' @param default.value The default value to add if a vertex has no matching value [default: NA]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.role.simple = function(list.of.networks, project.data, name = "author.role",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
type = c("network.degree", "network.eigen",
"commit.count", "loc.count"),
default.value = NA) {
classification.function = function(network, range.data) {
classification = get.author.class.by.type(network, range.data, type)
return(classification)
}
nets.with.attr = add.vertex.attribute.author.role.function(
list.of.networks, project.data, classification.function, name,
aggregation.level, default.value
)
return(nets.with.attr)
}
#' Add author role attribute using a specified classification function
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param classification.result A name of an author-classification function. Must return a tuple
#' of two lists containing the authors named "core" and "peripheral".
#' See the functions \code{get.author.class.*}.
#' @param name The attribute name to add [default: "author.role"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: NA]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.role.function = function(list.of.networks, project.data, classification.function,
name = "author.role",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value = NA) {
aggregation.level = match.arg.or.default(aggregation.level, default = "range")
net.to.range.list = split.data.by.networks(list.of.networks, project.data, aggregation.level)
classification.results = lapply(
net.to.range.list,
function(net.to.range) {
author.class = classification.function(net.to.range[["network"]], net.to.range[["data"]])
return(author.class)
}
)
nets.with.attr = add.vertex.attribute.author.role(
list.of.networks, classification.results, name, default.value
)
return(nets.with.attr)
}
#' Add author role attribute by classification results
#'
#' Important: The lists \code{list.of.networks} and \code{classification.results} needs to be of the same
#' length for this to work properly.
#'
#' @param list.of.networks The network list
#' @param classification.results A list of author-classification results. Each item needs to contain
#' a tuple of two lists containing the authors named "core" and "peripheral"
#' (see the functions \code{get.author.class.*}).
#' The list needs to be of the same length as \code{list.of.networks} and use
#' the same names.
#' @param name The attribute name to add [default: "author.role"]
#' @param default.value The default value to add if a vertex has no matching value [default: NA]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.author.role = function(list.of.networks, classification.results,
name = "author.role", default.value = NA) {
if (length(list.of.networks) != length(classification.results) ||
!identical(names(list.of.networks), names(classification.results))) {
logging::logwarn(paste("Adding author-classification vertex attribute: The classification",
"results do not match with the list of networks. Please see the",
"documentation of the function 'add.vertex.attribute.author.role'."))
}
## provide a list whose elements only contain the network as no data is needed here
net.list = lapply(list.of.networks, function(net) {
n = list()
n[["network"]] = net
return(n)
})
nets.with.attr = add.vertex.attribute(
net.list, name, default.value,
function(range, range.data, net) {
classification = classification.results[[range]]
author.class = plyr::ldply(classification, .id = NA)
author.to.role = structure(author.class[[".id"]], names = author.class[["author.name"]])
return(author.to.role)
}
)
return(nets.with.attr)
}
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Artifact network functions ----------------------------------------------
## * Commit-based metrics --------------------------------------------------
#' Add the count of unique editors (i.e., authors) that worked on an artifact
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "editor.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param editor.definition Determines, who is counted as editor of an artifact (one ore more of
#' \code{c("author", "committer")}). [default: "author"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.artifact.editor.count = function(list.of.networks, project.data, name = "editor.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
editor.definition = c("author", "committer"),
default.value = 0L) {
aggregation.level = match.arg.or.default(aggregation.level, default = "range")
## match editor definitions to column name in commit dataframe
if (missing(editor.definition)) {
editor.definition = "author"
} else {
editor.definition = match.arg.or.default(editor.definition, choices = c("author", "committer"),
several.ok = TRUE)
}
editor.definition = paste0(editor.definition, ".name")
nets.with.attr = split.and.add.vertex.attribute(
list.of.networks, project.data, name, aggregation.level, default.value,
function(range, range.data, net) {
vertex.attributes = lapply(range.data$group.authors.by.data.column("commits", "artifact"),
function(artifact.commits) {
editor.count = length(unique(unlist(artifact.commits[editor.definition])))
return(editor.count)
}
)
return(vertex.attributes)
}
)
return(nets.with.attr)
}
#' Add the amount of times the artifact was changed
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "change.count"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "range"]
#' @param default.value The default value to add if a vertex has no matching value [default: 0L]
#'
#' @return A list of networks with the added attribute
add.vertex.attribute.artifact.change.count = function(list.of.networks, project.data, name = "change.count",
aggregation.level = c("range", "cumulative", "all.ranges",
"project.cumulative", "project.all.ranges",
"complete"),
default.value = 0L) {
aggregation.level = match.arg.or.default(aggregation.level, default = "range")
nets.with.attr = split.and.add.vertex.attribute(
list.of.networks, project.data, name, aggregation.level, default.value,
function(range, range.data, net) {
artifact.to.commit = get.key.to.value.from.df(range.data$get.commits(), "artifact", "hash")
artifact.change.count = lapply(artifact.to.commit, function(x) {
length(unique(x[["hash"]]))
})
return(artifact.change.count)
}
)
return(nets.with.attr)
}
#' Add the first occurrence of the artifact
#'
#' @param list.of.networks The network list
#' @param project.data The project data
#' @param name The attribute name to add [default: "first.occurrence"]
#' @param aggregation.level Determines the data to use for the attribute calculation.
#' One of \code{"range"}, \code{"cumulative"}, \code{"all.ranges"},
#' \code{"project.cumulative"}, \code{"project.all.ranges"}, and
#' \code{"complete"}. See \code{split.data.by.networks} for
#' more details. [default: "complete"]
#' @param default.value The default value to add if a vertex has no matching value [default: NA]
#'
#' @return A list of networks with the added attribute