diff --git a/R/AbstractGraphReporter.R b/R/AbstractGraphReporter.R index 742449be..d6a22d39 100644 --- a/R/AbstractGraphReporter.R +++ b/R/AbstractGraphReporter.R @@ -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)} diff --git a/R/AbstractPackageReporter.R b/R/AbstractPackageReporter.R index 5add1661..51c1b142 100644 --- a/R/AbstractPackageReporter.R +++ b/R/AbstractPackageReporter.R @@ -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. #' } #' } diff --git a/R/CreatePackageReport.R b/R/CreatePackageReport.R index 62c50929..b25aeec8 100644 --- a/R/CreatePackageReport.R +++ b/R/CreatePackageReport.R @@ -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 @@ -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} #' } #' @@ -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. #' } #' } diff --git a/R/GraphClasses.R b/R/GraphClasses.R index 47d0dc06..52ecd4f8 100644 --- a/R/GraphClasses.R +++ b/R/GraphClasses.R @@ -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.} #' } @@ -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}}. diff --git a/R/pkgnet.R b/R/pkgnet.R index c859463f..9df0dc18 100644 --- a/R/pkgnet.R +++ b/R/pkgnet.R @@ -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. #' } #' } diff --git a/man/DependencyReporter.Rd b/man/DependencyReporter.Rd index 4f068186..40d72dba 100644 --- a/man/DependencyReporter.Rd +++ b/man/DependencyReporter.Rd @@ -97,36 +97,36 @@ This reporter looks at the recursive network of its dependencies \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. } } \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)} diff --git a/man/DirectedGraph.Rd b/man/DirectedGraph.Rd index 853c1705..43dd2f9a 100644 --- a/man/DirectedGraph.Rd +++ b/man/DirectedGraph.Rd @@ -62,19 +62,19 @@ R6 class defining a directed graph model for representing a \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.} } @@ -83,40 +83,40 @@ R6 class defining a directed graph model for representing a \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}]} @@ -126,27 +126,27 @@ R6 class defining a directed graph model for representing a \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}}. diff --git a/man/DirectedGraphMeasures.Rd b/man/DirectedGraphMeasures.Rd index 485519da..e7b1173e 100644 --- a/man/DirectedGraphMeasures.Rd +++ b/man/DirectedGraphMeasures.Rd @@ -10,40 +10,40 @@ Descriptions for all available node and graph measures for \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}]} @@ -53,27 +53,27 @@ Descriptions for all available node and graph measures for \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}}. diff --git a/man/FunctionReporter.Rd b/man/FunctionReporter.Rd index 9696bf6f..1d82fe4e 100644 --- a/man/FunctionReporter.Rd +++ b/man/FunctionReporter.Rd @@ -139,36 +139,36 @@ This reporter looks at the network of interdependencies of its \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. } } \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)} diff --git a/man/GraphClasses.Rd b/man/GraphClasses.Rd index 8b1e9e26..139c8184 100644 --- a/man/GraphClasses.Rd +++ b/man/GraphClasses.Rd @@ -79,19 +79,19 @@ pkgnet uses R6 classes to define and encapsulate the graph \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.} } diff --git a/man/InheritanceReporter.Rd b/man/InheritanceReporter.Rd index d4eb655e..32644270 100644 --- a/man/InheritanceReporter.Rd +++ b/man/InheritanceReporter.Rd @@ -125,36 +125,36 @@ Note the following details about class naming: \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. } } \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)} diff --git a/man/NetworkReporters.Rd b/man/NetworkReporters.Rd index 3f372f20..41d87263 100644 --- a/man/NetworkReporters.Rd +++ b/man/NetworkReporters.Rd @@ -34,26 +34,26 @@ \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)} diff --git a/man/PackageReport.Rd b/man/PackageReport.Rd index bec64585..80452162 100644 --- a/man/PackageReport.Rd +++ b/man/PackageReport.Rd @@ -21,7 +21,7 @@ pkgnet compiles one or more package reporters into a package \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 @@ -75,22 +75,22 @@ pkgnet compiles one or more package reporters into a package \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} } } @@ -106,7 +106,7 @@ pkgnet compiles one or more package reporters into a package } \item{\bold{Args:}}{ \itemize{ - \item{\bold{\code{deep}}: (logical) Whether to recursively + \item{\bold{\code{deep}}(logical) Whether to recursively clone nested R6 objects. } } diff --git a/man/PackageReporters.Rd b/man/PackageReporters.Rd index 8c492f00..18064c7b 100644 --- a/man/PackageReporters.Rd +++ b/man/PackageReporters.Rd @@ -78,10 +78,10 @@ pkgnet defines several package reporter R6 classes that analyze \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. } } diff --git a/man/SummaryReporter.Rd b/man/SummaryReporter.Rd index a88ec1c3..d042ac4c 100644 --- a/man/SummaryReporter.Rd +++ b/man/SummaryReporter.Rd @@ -79,10 +79,10 @@ This reporter provides a high-level overview of a package via \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. } } diff --git a/man/pkgnet-package.Rd b/man/pkgnet-package.Rd index e43145cb..b9412c05 100644 --- a/man/pkgnet-package.Rd +++ b/man/pkgnet-package.Rd @@ -33,17 +33,17 @@ R packages can be complex bodies of code and functionality with 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. } }