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removed redundant colons from docs (#284) (#285)
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Co-authored-by: Kasia <katarzyna.kulma@gmail.com>
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@jameslamb @KKulma
jameslamb and KKulma committed Nov 8, 2020
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Showing 16 changed files with 134 additions and 134 deletions.
12 changes: 6 additions & 6 deletions R/AbstractGraphReporter.R
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Expand Up @@ -28,26 +28,26 @@
#' }
#' @section Public Fields:
#' \describe{
#' \item{\bold{\code{nodes}}}{: a data.table, containing information about
#' \item{\bold{\code{nodes}}}{a data.table, containing information about
#' the nodes of the network the reporter is analyzing. The \code{node}
#' column acts the identifier. Read-only.
#' }
#' \item{\bold{\code{edges}}}{: a data.table, containing information about
#' \item{\bold{\code{edges}}}{a data.table, containing information about
#' the edge connections of the network the reporter is analyzing. Each
#' row is one edge, and the columns \code{SOURCE} and \code{TARGET}
#' specify the node identifiers. Read-only.
#' }
#' \item{\bold{\code{network_measures}}}{: a list, containing any measures
#' \item{\bold{\code{network_measures}}}{a list, containing any measures
#' of the network calculated by the reporter. Read-only.
#' }
#' \item{\bold{\code{pkg_graph}}}{: a graph model object. See \link{DirectedGraph}
#' \item{\bold{\code{pkg_graph}}}{a graph model object. See \link{DirectedGraph}
#' for additional documentation. Read-only.
#' }
#' \item{\bold{\code{graph_viz}}}{: a graph visualization object. A
#' \item{\bold{\code{graph_viz}}}{a graph visualization object. A
#' \code{\link[visNetwork:visNetwork]{visNetwork::visNetwork}} object.
#' Read-only.
#' }
#' \item{\bold{\code{layout_type}}}{: a character string, the current layout
#' \item{\bold{\code{layout_type}}}{a character string, the current layout
#' type for the graph visualization. Can be assigned a new valid layout
#' type value. Use use
#' \code{grep("^layout_\\\\S", getNamespaceExports("igraph"), value = TRUE)}
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4 changes: 2 additions & 2 deletions R/AbstractPackageReporter.R
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Expand Up @@ -70,10 +70,10 @@
#'
#' @section Public Fields:
#' \describe{
#' \item{\bold{\code{pkg_name}}}{: character string, name of set package.
#' \item{\bold{\code{pkg_name}}}{character string, name of set package.
#' Read-only.
#' }
#' \item{\bold{\code{report_markdown_path}}}{: character string, path to
#' \item{\bold{\code{report_markdown_path}}}{character string, path to
#' R Markdown template for this reporter. Read-only.
#' }
#' }
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18 changes: 9 additions & 9 deletions R/CreatePackageReport.R
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Expand Up @@ -16,7 +16,7 @@
#' \itemize{
#' \item{Initialize an instance of a package report object.}
#' \item{\bold{Args:}}{\itemize{
#' \item{\bold{\code{pkg_name}}: (character string) name of
#' \item{\bold{\code{pkg_name}} (character string) name of
#' package
#' }
#' \item{\bold{\code{pkg_path}}: (character string) optional
Expand Down Expand Up @@ -66,22 +66,22 @@
#'
#' @section Public Fields:
#' \describe{
#' \item{\bold{\code{pkg_name}}}{: (character string) name of package.
#' \item{\bold{\code{pkg_name}}}{(character string) name of package.
#' Read-only.
#' }
#' \item{\bold{\code{pkg_path}}}{: (character string) path to source code of
#' \item{\bold{\code{pkg_path}}}{(character string) path to source code of
#' the package. Read-only.
#' }
#' \item{\bold{\code{report_path}}}{: (character string) path and filename
#' \item{\bold{\code{report_path}}}{(character string) path and filename
#' of output report.
#' }
#' \item{\bold{\code{SummaryReporter}}}{: instantiated pkgnet
#' \item{\bold{\code{SummaryReporter}}}{instantiated pkgnet
#' \code{\link{SummaryReporter}} object}
#' \item{\bold{\code{DependencyReporter}}}{: instantiated pkgnet
#' \item{\bold{\code{DependencyReporter}}}{instantiated pkgnet
#' \code{\link{DependencyReporter}} object}
#' \item{\bold{\code{FunctionReporter}}}{: instantiated pkgnet
#' \item{\bold{\code{FunctionReporter}}}{instantiated pkgnet
#' \code{\link{FunctionReporter}} object}
#' \item{\bold{\code{InheritanceReporter}}}{: instantiated pkgnet
#' \item{\bold{\code{InheritanceReporter}}}{instantiated pkgnet
#' \code{\link{InheritanceReporter}} object}
#' }
#'
Expand All @@ -95,7 +95,7 @@
#' }
#' \item{\bold{Args:}}{
#' \itemize{
#' \item{\bold{\code{deep}}: (logical) Whether to recursively
#' \item{\bold{\code{deep}}(logical) Whether to recursively
#' clone nested R6 objects.
#' }
#' }
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44 changes: 22 additions & 22 deletions R/GraphClasses.R
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Expand Up @@ -72,19 +72,19 @@
#'
#' @section Public Fields:
#' \describe{
#' \item{\bold{\code{nodes}}}{: node data.table, read-only}
#' \item{\bold{\code{edges}}}{: edge data.table, read-only}
#' \item{\bold{\code{igraph}}}{: igraph object, read-only}
#' \item{\bold{\code{available_node_measures}}}{: character vector of all
#' \item{\bold{\code{nodes}}}{node data.table, read-only}
#' \item{\bold{\code{edges}}}{edge data.table, read-only}
#' \item{\bold{\code{igraph}}}{igraph object, read-only}
#' \item{\bold{\code{available_node_measures}}}{character vector of all
#' supported node measures. See Node Measures section below for detailed
#' descriptions. Read-only.}
#' \item{\bold{\code{available_graph_measures}}}{: character vector of all
#' \item{\bold{\code{available_graph_measures}}}{character vector of all
#' supported graph measures. See Graph Measures section below for detailed
#' descriptions. Read-only.}
#' \item{\bold{\code{default_node_measures}}}{: character vector of default
#' \item{\bold{\code{default_node_measures}}}{character vector of default
#' node measures. See Node Measures section below for detailed descriptions.
#' Read-only.}
#' \item{\bold{\code{default_graph_measures}}}{: character vector of default
#' \item{\bold{\code{default_graph_measures}}}{character vector of default
#' graph measures. See Graph Measures section below for detailed descriptions.
#' Read-only.}
#' }
Expand Down Expand Up @@ -544,67 +544,67 @@ DirectedGraph <- R6::R6Class(
#' networks modeled by \link{DirectedGraph}.
#' @section Node Measures:
#' \describe{
#' \item{\bold{\code{outDegree}}}{: outdegree, the number of outward edges (tail ends).
#' \item{\bold{\code{outDegree}}}{outdegree, the number of outward edges (tail ends).
#' Calculated by \code{\link[igraph:degree]{igraph::degree}}.
#' [\href{https://en.wikipedia.org/wiki/Directed_graph#Indegree_and_outdegree}{Wikipedia}]}
#' \item{\bold{\code{inDegree}}}{: indegree, number of inward edges (head ends).
#' \item{\bold{\code{inDegree}}}{indegree, number of inward edges (head ends).
#' Calculated by \code{\link[igraph:degree]{igraph::degree}}.
#' [\href{https://en.wikipedia.org/wiki/Directed_graph#Indegree_and_outdegree}{Wikipedia}]}
#' \item{\bold{\code{outCloseness}}}{: closeness centrality (out), a measure of
#' \item{\bold{\code{outCloseness}}}{closeness centrality (out), a measure of
#' path lengths to other nodes along edge directions.
#' Calculated by \code{\link[igraph:closeness]{igraph::closeness}}.
#' [\href{https://en.wikipedia.org/wiki/Closeness_centrality}{Wikipedia}]}
#' \item{\bold{\code{inCloseness}}}{: closeness centrality (in), a measure of
#' \item{\bold{\code{inCloseness}}}{closeness centrality (in), a measure of
#' path lengths to other nodes in reverse of edge directions.
#' Calculated by \code{\link[igraph:closeness]{igraph::closeness}}.
#' [\href{https://en.wikipedia.org/wiki/Closeness_centrality}{Wikipedia}]}
#' \item{\bold{\code{numRecursiveDeps}}}{: number recursive dependencies, i.e., count of all nodes reachable by following edges
#' \item{\bold{\code{numRecursiveDeps}}}{number recursive dependencies, i.e., count of all nodes reachable by following edges
#' out from this node.
#' Calculated by \code{\link[igraph:neighborhood.size]{igraph::neighborhood.size}}.
#' [\href{https://en.wikipedia.org/wiki/Rooted_graph}{Wikipedia}]}
#' \item{\bold{\code{numRecursiveRevDeps}}}{: number of recursive reverse dependencies (dependents), i.e., count all nodes reachable by following edges
#' \item{\bold{\code{numRecursiveRevDeps}}}{number of recursive reverse dependencies (dependents), i.e., count all nodes reachable by following edges
#' into this node in reverse direction.
#' Calculated by \code{\link[igraph:neighborhood.size]{igraph::neighborhood.size}}.
#' [\href{https://en.wikipedia.org/wiki/Rooted_graph}{Wikipedia}]}
#' \item{\bold{\code{betweenness}}}{: betweenness centrality, a measure of
#' \item{\bold{\code{betweenness}}}{betweenness centrality, a measure of
#' the number of shortest paths in graph passing through this node
#' Calculated by \code{\link[igraph:betweenness]{igraph::betweenness}}.
#' [\href{https://en.wikipedia.org/wiki/Betweenness_centrality}{Wikipedia}]}
#' \item{\bold{\code{pageRank}}}{: Google PageRank.
#' \item{\bold{\code{pageRank}}}{Google PageRank.
#' Calculated by \code{\link[igraph:page_rank]{igraph::page_rank}}.
#' [\href{https://en.wikipedia.org/wiki/PageRank}{Wikipedia}]}
#' \item{\bold{\code{hubScore}}}{: hub score from Hyperlink-Induced Topic
#' \item{\bold{\code{hubScore}}}{hub score from Hyperlink-Induced Topic
#' Search (HITS) algorithm.
#' Calculated by \code{\link[igraph:hub_score]{igraph::hub_score}}.
#' [\href{https://en.wikipedia.org/wiki/HITS_algorithm}{Wikipedia}]}
#' \item{\bold{\code{authorityScore}}}{: authority score from
#' \item{\bold{\code{authorityScore}}}{authority score from
#' Hyperlink-Induced Topic Search (HITS) algorithm.
#' Calculated by \code{\link[igraph:authority_score]{igraph::authority_score}}.
#' [\href{https://en.wikipedia.org/wiki/HITS_algorithm}{Wikipedia}]}
#' }
#' @section Graph Measures:
#' \describe{
#' \item{\bold{\code{graphOutDegree}}}{: graph freeman centralization for
#' \item{\bold{\code{graphOutDegree}}}{graph freeman centralization for
#' outdegree. A measure of the most central node by outdegree in relation to
#' all other nodes.
#' Calculated by \code{\link[igraph:centralize]{igraph::centralize}}.
#' [\href{https://en.wikipedia.org/wiki/Centrality#Freeman_centralization}{Wikipedia}]}
#' \item{\bold{\code{graphInDegree}}}{: graph Freeman centralization for
#' \item{\bold{\code{graphInDegree}}}{graph Freeman centralization for
#' indegree. A measure of the most central node by indegree in relation to
#' all other nodes.
#' Calculated by \code{\link[igraph:centralize]{igraph::centralize}}.
#' [\href{https://en.wikipedia.org/wiki/Centrality#Freeman_centralization}{Wikipedia}]}
#' \item{\bold{\code{graphOutClosness}}}{: graph Freeman centralization for
#' \item{\bold{\code{graphOutClosness}}}{graph Freeman centralization for
#' out-closeness. A measure of the most central node by out-closeness in relation to
#' all other nodes.
#' Calculated by \code{\link[igraph:centralize]{igraph::centralize}}.
#' [\href{https://en.wikipedia.org/wiki/Centrality#Freeman_centralization}{Wikipedia}]}
#' \item{\bold{\code{graphInCloseness}}}{: graph Freeman centralization for
#' \item{\bold{\code{graphInCloseness}}}{graph Freeman centralization for
#' outdegree. A measure of the most central node by outdegree in relation to
#' all other nodes.
#' Calculated by \code{\link[igraph:centralize]{igraph::centralize}}.
#' [\href{https://en.wikipedia.org/wiki/Centrality#Freeman_centralization}{Wikipedia}]}
#' \item{\bold{\code{graphBetweennness}}}{: graph Freeman centralization for
#' \item{\bold{\code{graphBetweennness}}}{graph Freeman centralization for
#' betweenness A measure of the most central node by betweenness in relation to
#' all other nodes.
#' Calculated by \code{\link[igraph:centralize]{igraph::centralize}}.
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8 changes: 4 additions & 4 deletions R/pkgnet.R
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Expand Up @@ -60,17 +60,17 @@ globalVariables(c('.'
#' package. The currently available reporters are:
#'
#' \describe{
#' \item{\bold{\code{\link{DependencyReporter}}}}{: analyze the recursive
#' \item{\bold{\code{\link{DependencyReporter}}}}{analyze the recursive
#' network of packages that the subject package depends on.
#' }
#' \item{\bold{\code{\link{FunctionReporter}}}}{: analyze the network of
#' \item{\bold{\code{\link{FunctionReporter}}}}{analyze the network of
#' interdependencies of the functions defined in the subject package
#' }
#' \item{\bold{\code{\link{InheritanceReporter}}}}{: analyze the class
#' \item{\bold{\code{\link{InheritanceReporter}}}}{analyze the class
#' inheritance trees for subject packages that use object-oriented
#' programming.
#' }
#' \item{\bold{\code{\link{SummaryReporter}}}}{: get an overview of the
#' \item{\bold{\code{\link{SummaryReporter}}}}{get an overview of the
#' subject package through its DESCRIPTION file.
#' }
#' }
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16 changes: 8 additions & 8 deletions man/DependencyReporter.Rd
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