From c340cd4409fb9acf14a913af940517e159a4105c Mon Sep 17 00:00:00 2001 From: bburns632 Date: Tue, 27 Jan 2026 15:41:17 +0000 Subject: [PATCH] Update website documentation to v0.6.0 --- docs/404.html | 29 +- docs/CLAUDE.html | 255 + docs/CODE_OF_CONDUCT.html | 20 +- docs/CONTRIBUTING.html | 24 +- docs/LICENSE-text.html | 20 +- docs/articles/index.html | 20 +- docs/articles/pkgnet-intro.html | 57 +- .../htmltools-fill-0.5.9/fill.css | 21 + .../visNetwork-binding-2.1.4/visNetwork.js | 4371 +++++++++++++++++ docs/articles/publishing-reports.html | 39 +- docs/authors.html | 38 +- docs/index.html | 35 +- docs/news/index.html | 50 +- docs/pkgdown.yml | 7 +- docs/reference/AbstractGraph.html | 38 +- docs/reference/AbstractGraphReporter.html | 32 +- docs/reference/AbstractPackageReporter.html | 34 +- docs/reference/CreatePackageReport.html | 36 +- docs/reference/CreatePackageVignette.html | 34 +- docs/reference/DefaultReporters.html | 28 +- docs/reference/DependencyReporter.html | 30 +- docs/reference/DirectedGraph.html | 32 +- docs/reference/DirectedGraphMeasures.html | 30 +- docs/reference/FunctionReporter.html | 34 +- docs/reference/InheritanceReporter.html | 28 +- docs/reference/PackageReport.html | 34 +- docs/reference/SimpleLogger.html | 268 + docs/reference/SummaryReporter.html | 28 +- docs/reference/index.html | 20 +- docs/reference/pkgnet-package.html | 28 +- docs/reference/pkgnet.html | 8 + docs/sitemap.xml | 118 +- 32 files changed, 5364 insertions(+), 482 deletions(-) create mode 100644 docs/CLAUDE.html create mode 100644 docs/articles/pkgnet-intro_files/htmltools-fill-0.5.9/fill.css create mode 100644 docs/articles/pkgnet-intro_files/visNetwork-binding-2.1.4/visNetwork.js create mode 100644 docs/reference/SimpleLogger.html create mode 100644 docs/reference/pkgnet.html diff --git a/docs/404.html b/docs/404.html index 156ab50f..4cbf1f1e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,12 +6,11 @@ Page not found (404) • pkgnet - - - - - - + + + + + @@ -33,7 +32,7 @@ - +
@@ -73,7 +72,7 @@
  • - +
    • @@ -82,7 +81,7 @@
    - + @@ -90,7 +89,7 @@ - +
    @@ -118,17 +117,17 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + + + +
    +
    + + + +
    +
    +
    +

    CLAUDE.md

    +
    + +
    + +

    This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

    +
    +

    Project Overview

    +

    pkgnet is an R package for analyzing R packages using graph theory. It builds network representations of packages to: - Analyze function interdependencies within a package - Map recursive package dependencies - Trace class inheritance structures (S4, R5/Reference Classes, R6) - Prioritize functions for unit testing based on centrality metrics

    +

    The core functionality is CreatePackageReport() which generates HTML reports analyzing package structure.

    +
    +
    +

    Architecture

    +
    +

    Reporter System (R6-based)

    +

    The package uses an object-oriented architecture built on R6 classes with a hierarchical reporter system:

    +

    Base Classes: - AbstractPackageReporter (R/AbstractPackageReporter.R): Base class for all reporters. Handles package setup via set_package() method. - AbstractGraphReporter (R/AbstractGraphReporter.R): Extends AbstractPackageReporter for network-based reporters. Provides nodes, edges, network_measures, and pkg_graph active bindings.

    +

    Concrete Reporters: - DependencyReporter (R/DependencyReporter.R): Analyzes recursive package dependencies - FunctionReporter (R/FunctionReporter.R): Maps function call networks and test coverage - InheritanceReporter (R/InheritanceReporter.R): Traces S4/R5/R6 class inheritance

    +

    Report Generation: - PackageReport (R/CreatePackageReport.R): Aggregates multiple reporters and renders HTML via rmarkdown - CreatePackageReport(): Convenience function that instantiates PackageReport with default reporters

    +
    +
    +

    Graph Models

    +

    DirectedGraph class (R/GraphClasses.R) wraps igraph functionality and provides: - Node and graph measure calculations - Network visualization via visNetwork - Integration with reporter system

    +
    +
    +

    Key Patterns

    +
    1. +Reporter Lifecycle: Instantiate → set_package() → extract nodes/edges → calculate measures → render
      2. +
    2. +Active Bindings: Reporters use R6 active bindings for lazy evaluation of nodes, edges, and network_measures +
      3. +
    3. +Namespacing: All non-base function calls must use :: namespace operator (e.g., data.table::data.table())
      4. +
    4. +data.table convention: data.table objects named with DT suffix (e.g., nodesDT)
      5. +
    +
    +
    +

    Commands

    +
    +

    Testing

    +

    Run full test suite (builds tarball and runs R CMD check):

    +
    ./test.sh
    +

    This script: - Builds package tarball with R CMD build - Runs R CMD check --as-cran in isolated directory - Fails if any WARNINGs found - Fails if NOTEs exceed allowed count (currently 0)

    +

    Run tests interactively in R:

    +
    +# Set to run NOT_CRAN tests
+Sys.setenv(NOT_CRAN = "true")
+
+# Run all tests
+devtools::test()
+
+# Run specific test file
+devtools::test(filter = "FunctionReporter")
    +
    +
    +

    Test Environment

    +

    Tests use a temporary package library (PKGNET_TEST_LIB) with fake test packages (baseballstats, sartre, milne). Setup/teardown in: - tests/testthat/setup-setTestEnv.R - tests/testthat/teardown-setTestEnv.R

    +

    On CRAN, only test-cran-true.R runs due to complications with temporary package handling.

    +
    +
    +

    Building

    +
    # Build tarball
+R CMD build .
+
+# Install locally
+R CMD INSTALL pkgnet_*.tar.gz
+
+# Build documentation
+Rscript -e "devtools::document()"
    +
    +
    +

    Coverage

    + +
    +
    +
    +

    Code Style

    +
    +

    Naming Conventions

    +
    • +R6 classes: UpperCamelCase (e.g., FunctionReporter)
      • +
    • +Exported functions: UpperCamelCase (e.g., CreatePackageReport)
      • +
    • +Methods/fields: snake_case (e.g., set_package, pkg_name)
      • +
    • +data.table objects: camelCase ending in DT (e.g., nodesDT)
      • +
    +
    +

    Dependencies

    +
    • Always use :: namespacing for non-base calls
      • +
    • Add #' @importFrom package function in roxygen docs
      • +
    • Exceptions: operators like %>% and := don’t need namespacing
      • +
    • New package dependencies must be added to DESCRIPTION Imports +
      • +
    +
    +

    Indentation

    +
    • Use 4 spaces (never tabs)
      • +
    • Comma-first style for multi-line lists:
      • +
    +sample_list <- list(
+    norm_sample = rnorm(100)
+    , unif_sample = runif(100)
+    , t_sample = rt(100, df = 100)
+)
    +
    +
    +

    Comments

    +
    • All comments above code, never beside
      • +
    • Avoid comments where code is self-evident
      • +
    +
    +

    Roxygen Documentation

    +

    Functions require: - #' @title - #' @name - #' @description - #' @param (for each parameter) - #' @export (if public API)

    +

    R6 Classes require sections: - #' @section Class Constructor: - #' @section Public Methods: - #' @section Public Members: - Document all public methods and active bindings

    +
    +
    +
    +

    R6 Method Support

    +

    FunctionReporter treats R6 methods as functions with naming convention: - Format: <classname>$<methodtype>$<methodname> - Example: FunctionReporter$private$extract_nodes - Uses generator object name from namespace, not classname attribute

    +

    InheritanceReporter naming: - Reference Classes: Uses Class arg from setRefClass() - R6 Classes: Uses generator object name in namespace (not classname arg)

    +
    +
    +

    Known Limitations

    +
    1. +FunctionReporter: +
      • Non-standard evaluation can cause false positives when column names match function names
        • +
      • Functions stored in lists (not namespace) are invisible
        • +
      • Instantiated R6/reference object method calls not recognized
        • +
      • Reference class methods not yet supported
        • +
      2. +
    2. +InheritanceReporter: +
      • S3 classes not supported (no formal class definitions)
        • +
      3. +
    +
    +

    Package Versioning

    +

    Follows semantic versioning (MAJOR.MINOR.PATCH): - Development versions append .9999 (e.g., 0.5.0.9999) - Release versions remove .9999 for CRAN submission

    +
    +
    +

    CI/CD

    +

    GitHub Actions workflows: - .github/workflows/ci.yml: Tests on Ubuntu/macOS with R release - .github/workflows/release.yml: Tests on R-devel for CRAN submission - .github/workflows/smoke-tests.yaml: Runs CreatePackageReport() on many packages - .github/workflows/website.yaml: Builds pkgdown site

    +
    +
    +

    Rendering Reports

    +

    Reports use rmarkdown templates from inst/package_report/: - Work done in temp directory to avoid writing to package repo - See PackageReport$render_report() in R/CreatePackageReport.R:67-98

    +
    +
    + +
    + + + +
    + + + +
    +

    Developed by Brian Burns, James Lamb, Jay Qi.

    +
    + +
    +

    Site built with pkgdown 2.2.0.

    +
    + +
    + + + + diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html index 027352a2..6bd6ed18 100644 --- a/docs/CODE_OF_CONDUCT.html +++ b/docs/CODE_OF_CONDUCT.html @@ -1,5 +1,5 @@ -Contributor Covenant Code of Conduct • pkgnetContributor Covenant Code of Conduct • pkgnet - +
    @@ -46,19 +46,19 @@ - +
    - +
    @@ -122,16 +122,16 @@

    Attribution -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Table of contents • pkgnet - +
    @@ -46,19 +46,19 @@ - +
    - +
    @@ -273,13 +273,13 @@

    Once CRAN Accepts, Merge the PR

    Create a Release on GitHub

    -

    We use the releases section in the repo to categorize certain important commits as release checkpoints. This makes it easier for developers to associate changes in the source code with the release history on CRAN, and enables features like remotes::install_github() for old versions.

    +

    We use the releases section in the repo to categorize certain important commits as release checkpoints. This makes it easier for developers to associate changes in the source code with the release history on CRAN, and enables features like remotes::install_github() for old versions.

    Navigate to https://github.com/uptake/pkgnet/releases/new. Click the drop down in the “target” section, then click “recent commits”. Choose the latest commit for the release PR you just merged. This will automatically create a git tag on that commit and tell Github which revision to build when people ask for a given release.

    Add some notes explaining what has changed since the previous release (usually a copy-paste from NEWS.md)

    Update the Website

    -

    Adding the new version tag in the previous step should have triggered a Github Action to build the website docs and create a PR. If not, manually trigger the workflow and create a PR to update the docs. Merge that in!

    +

    Adding the new version tag in the previous step should have triggered a Github Action to build the website docs and create a branch named website_docs_update. Review and merge.

    Open a new PR to begin development on the next version

    @@ -310,16 +310,16 @@
    - + License • pkgnet - +
    @@ -46,19 +46,19 @@ - +

    - +
    @@ -86,16 +86,16 @@

    License

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Articles • pkgnet - +
    @@ -46,19 +46,19 @@ - +
    - +
    @@ -84,16 +84,16 @@

    All vignettes

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + @@ -20,8 +19,6 @@ - - @@ -91,10 +88,10 @@ - + - +
    @@ -102,7 +99,7 @@

    Exploring the Structure and Dependencies of an R Package

    - Source: vignettes/pkgnet-intro.Rmd + Source: vignettes/pkgnet-intro.Rmd
    @@ -336,18 +333,18 @@

    Network Graph Model Object
     report2$FunctionReporter$pkg_graph$node_measures(c('hubScore', 'authorityScore'))

    #> Key: <node>
-#>            node hubScore authorityScore
-#>          <char>    <num>          <num>
-#> 1:          OPS        1            0.0
-#> 2:      at_bats        0            1.0
-#> 3:  batting_avg        1            0.5
-#> 4:  on_base_pct        0            0.0
-#> 5: slugging_avg        1            0.5
    +#> node hubScore authorityScore +#> <char> <num> <num> +#> 1: OPS 1.0000000 0 +#> 2: at_bats 0.0000000 0 +#> 3: batting_avg 0.5000339 1 +#> 4: on_base_pct 0.0000000 0 +#> 5: slugging_avg 0.5000339 1 
     report2$FunctionReporter$pkg_graph$igraph
    -
    #> IGRAPH b97bc79 DN-- 5 4 -- 
+
    #> IGRAPH f6674de DN-- 5 4 -- 
 #> + attr: name (v/c)
-#> + edges from b97bc79 (vertex names):
+#> + edges from f6674de (vertex names):
 #> [1] slugging_avg->at_bats      batting_avg ->at_bats     
 #> [3] OPS         ->slugging_avg OPS         ->batting_avg
    
 
    
@@ -516,9 +513,7 @@ 
    More Information
 
-        
-
    + @@ -531,17 +526,17 @@

    More Information

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + @@ -20,8 +19,6 @@ - - @@ -91,7 +88,7 @@ - +
    @@ -99,7 +96,7 @@

    Publishing Your pkgnet Package Report

    - Source: vignettes/publishing-reports.Rmd + Source: vignettes/publishing-reports.Rmd
    @@ -151,7 +148,7 @@

    Publish as a vignette in your pac anyone installing your package will have it available, and it will also be available through CRAN if you choose to publish your package. You can preview what it will look like with -devtools::build_vignettes(). If you use pkgdown, it will +devtools::build_vignettes(). If you use pkgdown, it will also be built into an article when you use pkgdown::build_site().

    You can check out our example @@ -171,9 +168,7 @@

    @@ -186,17 +181,17 @@

    Citation

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + @@ -34,7 +33,7 @@ - +
    @@ -74,7 +73,7 @@
  • - +
    • @@ -83,7 +82,7 @@
    - + @@ -91,7 +90,7 @@ - +
    @@ -190,9 +189,9 @@

    Citation

    Developers

      -
    • Brian Burns
      Author, maintainer
      • -
    • James Lamb
      Author
      • -
    • Jay Qi
      Author
      • +
    • Brian Burns
      Author, maintainer
      • +
    • James Lamb
      Author
      • +
    • Jay Qi
      Author
    @@ -209,17 +208,17 @@

    Developers

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Changelog • pkgnet - +
    @@ -46,27 +46,55 @@ - +
    - +

    Changelog

    - Source: NEWS.md + Source: NEWS.md
    +
    +

    pkgnet 0.6.02026-01-27

    +
    +

    NEW FEATURES

    +
    +
    +

    CHANGES

    +
    • Replaced futile.logger with custom SimpleLogger R6 class implementation using only base R. This reduces external dependencies and improves maintainability. (#338)
      • +
    • Updated minimum igraph version requirement from >= 1.3 to >= 2.1 to align with modern igraph APIs. (#338)
      • +
    • Updated deprecated igraph function calls to current API: (#338) +
      • +graph.edgelist() → graph_from_edgelist() +
        • +
      • +neighborhood.size() → ego_size() +
        • +
      • +hub_score() / authority_score() → hits_scores() (unified API)
        • +
      • +
    • Test suite improvements: removed static CSV fixtures for graph measures in favor of structure/behavior validation. Tests are now more maintainable across igraph versions. (#338)
      • +
    • Added CLAUDE.md project documentation file for AI-assisted development tools.
      • +
    +
    +

    BUGFIXES

    +
    • Moved rmarkdown::render interium files to occur within a temp directory, not the installed package directory (#329 Thanks @jcarbaut!)
      • +
    • Removed futile.logger dependency to eliminate potential compatibility issues and reduce maintenance burden. (#338)
      • +
    +

    pkgnet 0.5.02024-05-03

    @@ -238,16 +266,16 @@

    BUG FIXES -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Base class for Graphs — AbstractGraph • pkgnet - +
    @@ -51,25 +51,25 @@ - +
    - +

    Base class for Graphs

    - Source: R/GraphClasses.R + Source: R/GraphClasses.R
    @@ -98,22 +98,22 @@

    Active bindings

    available_node_measures
    -

    character vector of all supported node measures. +

    character vector of all supported node measures. See Node Measures section in DirectedGraphMeasures for details about each measure.

    available_graph_measures
    -

    character vector of all supported graph measures. +

    character vector of all supported graph measures. See Graph Measures section in DirectedGraphMeasures for details about each measure. Read-only.

    default_node_measures
    -

    character vector of default node measures. +

    character vector of default node measures. See Node Measures section in DirectedGraphMeasures for details about each measure.

    default_graph_measures
    -

    character vector of default graph measures. +

    character vector of default graph measures. See Graph Measures section in DirectedGraphMeasures for details about each measure. Read-only.

    @@ -121,7 +121,7 @@

    Active bindings

    Methods

    - +

    Public methods

    @@ -165,7 +165,7 @@

    Usage

    Arguments

    measures
    -

    character vector of measure names. +

    character vector of measure names. Default NULL will return those that are already calculated.

    @@ -178,7 +178,7 @@

    Returns

    Method graph_measures()

    -

    Return specified graph-level measures, calculating if necessary. +

    Return specified graph-level measures, calculating if necessary. See Graph Measures section in DirectedGraphMeasures for details about each measure.

    Usage

    AbstractGraph$graph_measures(measures = NULL)

    @@ -187,7 +187,7 @@

    Usage

    Arguments

    measures
    -

    character vector of measure names. +

    character vector of measure names. Default NULL will return those that are already calculated.

    @@ -242,16 +242,16 @@

    Arguments -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Abstract Network Reporter Class — AbstractGraphReporter • pkgnet - +
    @@ -51,25 +51,25 @@ - +

    - +

    Abstract Network Reporter Class

    - Source: R/AbstractGraphReporter.R + Source: R/AbstractGraphReporter.R
    @@ -91,7 +91,7 @@

    Super class

    Active bindings

    nodes

    A data.table, containing information about -the nodes of the network the reporter is analyzing. The node +the nodes of the network the reporter is analyzing. The node column acts the identifier. Read-only.

    @@ -103,7 +103,7 @@

    Active bindings

    network_measures
    -

    A list, containing any measures +

    A list, containing any measures of the network calculated by the reporter. Read-only.

    @@ -113,13 +113,13 @@

    Active bindings

    graph_viz
    -

    a graph visualization object. A +

    a graph visualization object. A visNetwork::visNetwork object. Read-only.

    layout_type
    -

    a character string, the current layout type for the graph visualization. +

    a character string, the current layout type for the graph visualization. Can be assigned a new valid layout type value. Use use grep("^layout_\\S", getNamespaceExports("igraph"), value = TRUE) to see valid options.

    @@ -127,7 +127,7 @@

    Active bindings

    Methods

    - +

    Public methods

    @@ -191,16 +191,16 @@

    Arguments -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Abstract Package Reporter — AbstractPackageReporter • pkgnet
    - +

    Abstract Package Reporter

    - Source: R/AbstractPackageReporter.R + Source: R/AbstractPackageReporter.R
    -

    pkgnet defines several package reporter R6 classes that analyze +

    pkgnet defines several package reporter R6 classes that analyze some particular aspect of a package. These reporters share common functionality and interfaces defined by a base reporter class AbstractPackageReporter.

    @@ -93,7 +93,7 @@

    Active bindings

    Methods

    - +

    Public methods

    @@ -102,8 +102,8 @@

    Public methods

    AbstractPackageReporter$clone()

    Method set_package()

    -

    Set the package that the reporter will analyze. This can -only be done once for a given instance of a reporter. +

    Set the package that the reporter will analyze. This can +only be done once for a given instance of a reporter. Instantiate a new copy of the reporter if you need to analyze a different package.

    Usage

    AbstractPackageReporter$set_package(pkg_name, pkg_path = NULL)

    @@ -116,7 +116,7 @@

    ArgumentsReturns

    Method get_summary_view()

    -

    Returns an htmlwidget object that summarizes the analysis of the reporter. +

    Returns an htmlwidget object that summarizes the analysis of the reporter. Used when creating a package report.

    Usage

    AbstractPackageReporter$get_summary_view()

    @@ -172,16 +172,16 @@

    Arguments -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + pkgnet Analysis Report for an R package — CreatePackageReport • pkgnet - +
    @@ -46,25 +46,25 @@ - +

    - +

    pkgnet Analysis Report for an R package

    - Source: R/CreatePackageReport.R + Source: R/CreatePackageReport.R
    @@ -83,30 +83,30 @@

    pkgnet Analysis Report for an R package

    Arguments

    -
    pkg_name
    + + +
    pkg_name

    (string) name of a package

    -
    pkg_reporters
    +
    pkg_reporters

    (list) a list of package reporters

    -
    pkg_path
    +
    pkg_path

    (string) The path to the package repository. If given, coverage will be calculated for each function. pkg_path can be an absolute or relative path.

    -
    report_path
    +
    report_path

    (string) The path and filename of the output report. Default report will be produced in the temporary directory.

    Value

    - - -

    an instantiated PackageReport object

    +

    an instantiated PackageReport object

    @@ -121,16 +121,16 @@

    Value

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + pkgnet Report as Vignette — CreatePackageVignette • pkgnet
    - +

    pkgnet Report as Vignette

    - Source: R/CreatePackageVignette.R + Source: R/CreatePackageVignette.R
    @@ -100,15 +100,17 @@

    pkgnet Report as Vignette

    Arguments

    -
    pkg
    + + +
    pkg

    (string) path to root directory of package of interest

    -
    pkg_reporters
    +
    pkg_reporters

    (list) a list of initialized package reporters

    -
    vignette_path
    +
    vignette_path

    (string) The location of a file to store the output vignette file at. Must be an .Rmd file. By default, this will be '<pkg>/vignettes/pkgnet-report.Rmd' relative to the input to pkg

    @@ -127,16 +129,16 @@

    Arguments

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Default Reporters — DefaultReporters • pkgnet

    - +

    Default Reporters

    - Source: R/DefaultReporters.R + Source: R/DefaultReporters.R
    @@ -80,9 +80,7 @@

    Default Reporters

    Value

    - - -

    list of instantiated reporter objects

    +

    list of instantiated reporter objects

    Details

    @@ -91,7 +89,7 @@

    Details

  • FunctionReporter

    • Note, InheritanceReporter is not included in the default list.

    If desired, append a new instance of InheritanceReporter to the DefaultReporters list.

    -

    ex: +

    ex: c(DefaultReporters(), InheritanceReporter$new())

    @@ -107,16 +105,16 @@

    Details

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Recursive Package Dependency Reporter — DependencyReporter • pkgnet

    - +

    Recursive Package Dependency Reporter

    - Source: R/DependencyReporter.R + Source: R/DependencyReporter.R
    @@ -81,10 +81,10 @@

    Recursive Package Dependency Reporter

    See also

    -

    Other Network Reporters: +

    Other Network Reporters: FunctionReporter, InheritanceReporter

    -

    Other Package Reporters: +

    Other Package Reporters: FunctionReporter, InheritanceReporter, SummaryReporter

    @@ -103,7 +103,7 @@

    Active bindings

    Methods

    - +

    Public methods

    @@ -125,7 +125,7 @@

    Usage

    Arguments

    dep_types
    -

    (character vector) The sections within the DESCRIPTION file to be counted as dependencies. +

    (character vector) The sections within the DESCRIPTION file to be counted as dependencies. By default, c("Imports", "Depends", "LinkingTo") is chosen.

    @@ -204,16 +204,16 @@

    Examples

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Directed Graph Network Model — DirectedGraph • pkgnet
    - +

    Directed Graph Network Model

    - Source: R/GraphClasses.R + Source: R/GraphClasses.R
    @@ -87,7 +87,7 @@

    Directed Graph Network Model

    network reporter objects will initialize it as its pkg_graph field. If you have a network reporter named reporter, then you access this object's public -interface through pkg_graph---for example,

    +interface through pkg_graph—for example,

    reporter$pkg_graph$node_measures('hubScore')
    @@ -104,12 +104,12 @@

    Super class

    Active bindings

    default_node_measures
    -

    character vector of default node measures. +

    character vector of default node measures. See Node Measures section in DirectedGraphMeasures for details about each measure. Read-only.

    default_graph_measures
    -

    character vector of default graph measures. +

    character vector of default graph measures. See Graph Measures section in DirectedGraphMeasures for details about each measure. Read-only.

    @@ -117,7 +117,7 @@

    Active bindings

    Methods

    - +

    Public methods

    @@ -158,16 +158,16 @@

    Arguments -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Measures for Directed Graph Class — DirectedGraphMeasures • pkgnet
    - +

    Measures for Directed Graph Class

    - Source: R/GraphClasses.R + Source: R/GraphClasses.R
    @@ -77,7 +77,7 @@

    Measures for Directed Graph Class

    Node Measures

    - +
    outDegree

    outdegree, the number of outward edges (tail ends). @@ -104,13 +104,13 @@

    Node Measures

    numRecursiveDeps

    number recursive dependencies, i.e., count of all nodes reachable by following edges out from this node. - Calculated by igraph::neighborhood.size. + Calculated by igraph::ego_size. [Wikipedia]

    numRecursiveRevDeps

    number of recursive reverse dependencies (dependents), i.e., count all nodes reachable by following edges into this node in reverse direction. - Calculated by igraph::neighborhood.size. + Calculated by igraph::ego_size. [Wikipedia]

    betweenness
    @@ -140,7 +140,7 @@

    Node Measures

    Graph Measures

    - +
    graphOutDegree

    graph freeman centralization for @@ -192,16 +192,16 @@

    Graph Measures

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Function Interdependency Reporter — FunctionReporter • pkgnet
    - +

    Function Interdependency Reporter

    - Source: R/FunctionReporter.R + Source: R/FunctionReporter.R
    @@ -76,14 +76,14 @@

    Function Interdependency Reporter

    This reporter looks at the network of interdependencies of its defined functions. Measures of centrality from graph theory can indicate which function is most important to a package. Combined with unit test -coverage information---also provided by this reporter--- it can be used +coverage information—also provided by this reporter— it can be used as a powerful tool to prioritize test writing.

    Details

    - +

    R6 Method Support:

    R6 classes are supported, with their methods treated as functions by the @@ -117,10 +117,10 @@

    Known Limitations:

    See also

    -

    Other Network Reporters: +

    Other Network Reporters: DependencyReporter, InheritanceReporter

    -

    Other Package Reporters: +

    Other Package Reporters: DependencyReporter, InheritanceReporter, SummaryReporter

    @@ -139,7 +139,7 @@

    Active bindings

    Methods

    - +

    Public methods

    @@ -191,16 +191,16 @@

    Arguments -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + - +
    @@ -52,25 +52,25 @@ - +

    - +

    Class Inheritance Reporter

    - Source: R/InheritanceReporter.R + Source: R/InheritanceReporter.R
    @@ -106,10 +106,10 @@

    Details

    See also

    -

    Other Network Reporters: +

    Other Network Reporters: DependencyReporter, FunctionReporter

    -

    Other Package Reporters: +

    Other Package Reporters: DependencyReporter, FunctionReporter, SummaryReporter

    @@ -128,7 +128,7 @@

    Active bindings

    Methods

    - +

    Public methods

    @@ -168,16 +168,16 @@

    Arguments -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + R6 Class Representing an R Package Report — PackageReport • pkgnet - +
    @@ -53,25 +53,25 @@ - +
    - +

    R6 Class Representing an R Package Report

    - Source: R/CreatePackageReport.R + Source: R/CreatePackageReport.R
    @@ -81,7 +81,7 @@

    R6 Class Representing an R Package Report

    holds all of those reporters and has a method render_report() to generate an HTML report file. You can access each individual reporter and modify it using its methods if you wish.

    -

    The function CreatePackageReport() is a shortcut for both +

    The function CreatePackageReport() is a shortcut for both generating a PackageReport object with instantiated reporters and creating the HTML report in one call.

    @@ -89,9 +89,7 @@

    R6 Class Representing an R Package Report

    Value

    - - -

    Self, invisibly.

    +

    Self, invisibly.

    Active bindings

    @@ -127,7 +125,7 @@

    Active bindings

    Methods

    - +

    Public methods

    @@ -153,12 +151,12 @@

    ArgumentsArguments -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + + + +
    +
    + + + +
    +
    +
    +

    Simple Logger Class

    + Source: R/logging.R + +
    + +
    +

    A minimal logging class using only base R functions. +Provides threshold-based logging with INFO, WARN, and FATAL levels.

    +
    + + +
    +

    Methods

    + +
    +

    Public methods

    + +

    +

    Method new()

    +

    Initialize a new SimpleLogger

    +

    Usage

    +

    SimpleLogger$new(threshold = 0)

    +
    + +
    +

    Arguments

    +

    threshold
    +

    Initial threshold level (default: 0 for silent)

    + + +

    +
    +
    +

    Returns

    +

    A new SimpleLogger instance

    +
    + +

    +

    Method info()

    +

    Log an informational message

    +

    Usage

    +

    SimpleLogger$info(msg, ...)

    +
    + +
    +

    Arguments

    +

    msg
    +

    Message to log

    + + +
    ...
    +

    Additional arguments (currently ignored)

    + + +

    +
    +
    +

    Returns

    +

    NULL invisibly

    +
    + +

    +

    Method warn()

    +

    Log a warning message

    +

    Usage

    +

    SimpleLogger$warn(msg, ...)

    +
    + +
    +

    Arguments

    +

    msg
    +

    Message to log

    + + +
    ...
    +

    Additional arguments (currently ignored)

    + + +

    +
    +
    +

    Returns

    +

    NULL invisibly

    +
    + +

    +

    Method fatal()

    +

    Log a fatal error message

    +

    Usage

    +

    SimpleLogger$fatal(msg, ...)

    +
    + +
    +

    Arguments

    +

    msg
    +

    Message to log

    + + +
    ...
    +

    Additional arguments (currently ignored)

    + + +

    +
    +
    +

    Returns

    +

    NULL invisibly

    +
    + +

    +

    Method get_threshold()

    +

    Get current threshold

    +

    Usage

    +

    SimpleLogger$get_threshold()

    +
    + +
    +

    Returns

    +

    Current threshold value

    +
    + +

    +

    Method set_threshold()

    +

    Set threshold level

    +

    Usage

    +

    SimpleLogger$set_threshold(level)

    +
    + +
    +

    Arguments

    +

    level
    +

    Threshold level (0 = silent, 4 = INFO, 5 = WARN, 6 = FATAL)

    + + +

    +
    +
    +

    Returns

    +

    NULL invisibly

    +
    + +

    +

    Method clone()

    +

    The objects of this class are cloneable with this method.

    +

    Usage

    +

    SimpleLogger$clone(deep = FALSE)

    +
    + +
    +

    Arguments

    +

    deep
    +

    Whether to make a deep clone.

    + + +

    +
    + +
    + +
    + +
    + +
    + + +
    +

    Developed by Brian Burns, James Lamb, Jay Qi.

    +
    + +
    +

    Site built with pkgdown 2.2.0.

    +
    + +
    + + + + diff --git a/docs/reference/SummaryReporter.html b/docs/reference/SummaryReporter.html index 543e8d3a..ebffc62f 100644 --- a/docs/reference/SummaryReporter.html +++ b/docs/reference/SummaryReporter.html @@ -1,5 +1,5 @@ -Package Summary Reporter — SummaryReporter • pkgnetPackage Summary Reporter — SummaryReporter • pkgnet - +
    @@ -46,25 +46,25 @@ - +
    - +

    Package Summary Reporter

    - Source: R/SummaryReporter.R + Source: R/SummaryReporter.R
    @@ -75,7 +75,7 @@

    Package Summary Reporter

    See also

    -

    Other Package Reporters: +

    Other Package Reporters: DependencyReporter, FunctionReporter, InheritanceReporter

    @@ -94,7 +94,7 @@

    Active bindings

    Methods

    - +

    Public methods

    @@ -103,7 +103,7 @@

    Public methods

    Inherited methods

    Method get_summary_view()

    -

    Returns an htmlwidget object that summarizes the analysis of the reporter. +

    Returns an htmlwidget object that summarizes the analysis of the reporter. Used when creating a package report.

    Usage

    SummaryReporter$get_summary_view()

    @@ -146,16 +146,16 @@

    Arguments -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + Package index • pkgnet - +
    @@ -46,19 +46,19 @@ - +
    - +
    @@ -127,16 +127,16 @@

    Graph Classes
    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - + pkgnet : Network Analysis of R Packages — pkgnet-package • pkgnet
    - +

    pkgnet : Network Analysis of R Packages

    - Source: R/pkgnet.R + Source: R/pkgnet.R
    @@ -81,7 +81,7 @@

    pkgnet : Network Analysis of R Packages

    Package Report

    - +

    The simplest way of using pkgnet is through the function CreatePackageReport, e.g.,

    @@ -95,7 +95,7 @@

    Package Report

    Individual Reporters

    - +

    Reporters are the basic modules of functionality within pkgnet. Each type of reporter is used to analyze a particular aspect of the subject @@ -117,7 +117,7 @@

    Individual Reporters

    get an overview of the subject package through its DESCRIPTION file.

    - +

    CreatePackageReport uses a standard set of reporters by default. You can customize the reporters you want by passing in your own list of instantiated reporters, e.g.

    @@ -163,16 +163,16 @@

    Author

    -

    Site built with pkgdown 2.0.8.

    +

    Site built with pkgdown 2.2.0.

    - +