_pkgdown.yml

destination: docs
template:
  bootstrap: 5
reference:
- title: __IO__
  desc:  Functions to create and read temporary files in R.
- contents:
  - io_make_folder
  - io_delete_folder
  - io_make_file
  - io_make_file
  - io_make_folder
  - io_delete_folder
  - make_temporary_file
  - read_temporary_file
- title: __Source Code__
  desc: >
    Source Code File Parsers and Network Transformations. Git
    Log data is not required.
- subtitle: Static Dependencies
  desc: >
    Identification of static dependencies from source code. See the
    [File Networks](../articles/depends_showcase.html) or
    [Kaiaulu Architecture](../articles/kaiaulu_architecture.html)
    Notebooks for examples.
- contents:
  - parse_dependencies
  - parse_r_dependencies
  - transform_dependencies_to_network
  - transform_r_dependencies_to_network
- subtitle: __Gang of Four Patterns__
  desc: >
    Gang of Four pattern detection using sub-graphs.
    See the [Graph GoF](../articles/graph_gof_showcase.html)
    Notebook for examples.
- contents:
  - parse_gof_patterns
  - write_gof_patterns
  - subset_gof_class
- subtitle: __Syntax Extraction__
  desc: >
    Annotate and query source code elements, such as identifiers and docstrings.
    See the [Text GoF](../articles/text_gof_showcase.html) Notebook for examples.
- contents:
  - annotate_src_text
  - query_src_text
  - query_src_text_class_names
  - query_src_text_namespace
- title: __Git__
  desc:  Parsing, Network Transformers, and  Git Command Interface
- subtitle: __Git Log__
  desc: >
     Git Log Numstat and Git Blame Parsers. See the
     [Git Log](../articles/gitlog_showcase.html) Notebook for examples.
- contents:
  - parse_gitlog
  - parse_git_blame
  - parse_gitlog_entity
  - parse_commit_message_id
  - transform_gitlog_to_bipartite_network
  - transform_gitlog_to_temporal_network
  - transform_gitlog_to_entity_bipartite_network
  - transform_gitlog_to_entity_temporal_network
  - transform_commit_message_id_to_network
- subtitle: __Git Command__
  desc:  R Interface to Git Commands
- contents:
  - git_add
  - git_commit
  - git_init
  - git_mv
  - git_checkout
  - git_head
  - git_log
  - git_blame
  - git_create_sample_log
  - git_delete_sample_log
- title: __Filters__
  desc: >
     Filters for file extensions, and substrings, such as test files,
     and time intervals. See the
     [Git Log](../articles/gitlog_showcase.html) and
     [Line Metrics](../articles/line_metrics_showcase.html) Notebooks for
     examples.
- contents:
  - filter_by_file_extension
  - filter_by_filepath_substring
  - filter_by_commit_interval
  - filter_by_last_files_change
  - filter_by_commit_size
- title: __Mail__
  desc: >
      Download, parsing and data generation of mailing lists.
      See the [Download Mbox](../articles/download_mod_mbox.html)
      and [Reply](../articles/reply_communication_showcase.html)
      Notebooks for details.
- contents:
  - download_pipermail
  - convert_pipermail_to_mbox
  - download_mod_mbox
  - download_mod_mbox_per_month
  - parse_mbox
  - make_mbox_reply
  - make_mbox_mailing_list
- title: __JIRA__
  desc: >
       Downloading, parsing, data generation and
       network transformations of JIRA. See the
       [JIRA](../articles/download_jira_data.html)
       Notebook for details.
- contents:
  - parse_jira
  - parse_jira_latest_date
  - parse_jira_replies
  - parse_jira_rss_xml
  - make_jira_issue
  - make_jira_issue_tracker
  - download_jira_issues
  - download_jira_issues_by_date
  - download_jira_issues_by_issue_key
  - refresh_jira_issues
- title: __GitHub__
  desc: >
       Functions to interact and download data from GitHub API.
       See the [GitHub API](../articles/github_api_showcase.html)
       Notebook to learn how to set an API Key, and how to use
       it to download issues and comments on the
       [GitHub Downloader and Parser](../articles/download_github_comments.html)
       Notebook.
- subtitle: Issues
  desc: Download and parsing GitHub's Issues, Pull Requests and Events
- contents:
  - github_api_rate_limit
  - parse_github_replies
  - github_api_project_issue_events
  - github_parse_project_issue_events
  - github_api_project_issue
  - github_api_project_issue_refresh
  - github_parse_project_issue
  - github_api_project_issue_search
  - github_api_project_issue_by_date
  - github_api_project_issue_refresh
  - github_parse_search_issues_refresh
  - github_api_project_issue_or_pr_comments_by_date
  - github_api_project_issue_or_pr_comment_refresh

- subtitle: Pull Request
  desc: GitHub's Pull Request
- contents:
  - github_api_project_pull_request
  - github_parse_project_pull_request
- subtitle: Issue and Pull Request Comments
  desc: >
    GitHub's assumes Issues and Pull Requests to be
    the same in regards to comments.
- contents:
  - github_api_project_issue_or_pr_comments
  - github_parse_project_issue_or_pr_comments
- subtitle: Commits
  desc: GitHub's Commits
- contents:
  - github_api_project_commits
  - github_parse_project_commits
  - github_api_project_contributors
- title: __Bugzilla__
  desc: >
    Downloading and parsing of Bugzilla. See the
    _bugzilla_showcase.Rmd Notebook source code for examples.
- contents:
  - download_bugzilla_perceval_traditional_issue_comments
  - download_bugzilla_perceval_rest_issue_comments
  - download_bugzilla_rest_issues
  - download_bugzilla_rest_comments
  - download_bugzilla_rest_issues_comments
  - parse_bugzilla_perceval_traditional_issue_comments
  - parse_bugzilla_perceval_rest_issue_comments
  - parse_bugzilla_rest_issues
  - parse_bugzilla_rest_comments
  - parse_bugzilla_rest_issues_comments
- title: __Reply__
  desc:  Functions used to parse communication data from mail and issue trackers.
- contents:
  - transform_reply_to_bipartite_network
- title: __Software Vulnerabilities__
  desc: >
    Software Vulnerabilities feed parsers. See the
    [Software Vulnerability](../articles/gitlog_vulnerabilities_showcase.html)
    Notebook for examples.
- contents:
  - parse_nvdfeed
  - transform_cve_cwe_file_to_network
- title: __Identity__
  desc: >
      Provide the same id to authors who use variations of names or emails.
      See the [Social Smells](../articles/social_smell_showcase.html)
      Notebook for examples.
- contents:
  - format_name_email
  - split_name_email
  - is_same_identity
  - assign_exact_identity
  - identity_match
- title: __Interval__
  desc:  Provides different types of interval windows (e.g. release) for metric functions.
- contents:
  - interval_commit_metric
  - get_date_from_commit_hash
- title: __Metrics__
  desc: >
      Various metrics used to estimate code quality,
      complexity and effort. For example usage,
      see [File Line Metrics](../articles/line_metrics_showcase.html),
      [Causal Flaws](../articles/causal_flaws.html), or
      [Bug Count](../articles/bug_count.html) Notebooks.
- contents:
  - parse_line_metrics
  - metric_file_bug_frequency
  - metric_file_non_bug_frequency
  - metric_file_bug_churn
  - metric_file_non_bug_churn
  - metric_file_churn
  - metric_churn_per_commit_interval
  - metric_churn_per_commit_per_file
  - commit_message_id_coverage
  - metric_churn
- title: __Graph__
  desc:  Provide graph models to construct networks and algorithms for graph analysis.
- contents:
  - model_directed_graph
  - bipartite_graph_projection
  - temporal_graph_projection
  - weight_scheme_sum_edges
  - weight_scheme_count_deleted_nodes
  - weight_scheme_cum_temporal
  - weight_scheme_pairwise_cum_temporal
  - community_oslom
  - recolor_network_by_community
  - graph_to_dsmj
- title: __Social-Technical Congruence and Social Smells__
  desc: >
      Sub-graph patterns that identify bad social practices.
      See [Social Motifs](../articles/motif_analysis.html), or
      [Social Smells](../articles/social_smell_showcase.html) Notebooks.
- contents:
  - motif_factory
  - motif_factory_triangle
  - motif_factory_square
  - motif_factory_anti_triangle
  - motif_factory_anti_square
  - smell_missing_links
  - smell_organizational_silo
  - smell_sociotechnical_congruence
  - smell_radio_silence
- title: __Architectural Flaws__
  desc: >
   Sub-graph patterns that identify bad architectural practices.
   Requires a DV8 Archdia license (https://archdia.com). See the
   [Architectural Flaws](../articles/dv8_showcase.html) Notebook
   for examples.
- subtitle: Design Structure Matrix (DSM)
  desc: >
    Parsing DSMs from raw data, convert between
    JSON DSMs and DV8's binary DSMs, combine DSMs,
    and DSM export to Excel.
- contents:
  - gitlog_to_hdsmj
  - dv8_gitlog_to_gitnumstat
  - dv8_gitnumstat_to_hdsmb
  - dependencies_to_sdsmj
  - dv8_depends_to_sdsmj
  - dv8_dsmj_to_dsmb
  - dv8_dsmb_to_dsmj
  - dv8_hdsmb_sdsmb_to_mdsmb
  - dv8_mdsmb_drhier_to_excel
  - transform_dependencies_to_sdsmj
  - transform_gitlog_to_hdsmj
  - transform_temporal_gitlog_to_adsmj
- subtitle: Metrics
  desc: >
    Various DV8 metrics, Parsing into R Memory,
    and File to Flaw mapping.
- contents:
  - dv8_mdsmb_to_flaws
  - parse_dv8_architectural_flaws
  - dv8_mdsmb_to_decoupling_level
  - parse_dv8_metrics_decoupling_level
  - dv8_mdsmb_to_hierclsxb
- subtitle: Clustering
  desc: >
    Hierarchical Clustering, Parsing into R Memory, and Clustering
    conversion between JSON and DV8's binary.
- contents:
  - dv8_clsxb_to_clsxj
  - dv8_clsxj_to_clsxb
  - parse_dv8_clusters
- title: __Config__
  desc: >
   Get functions to access config fields.
   The use of get() in Notebooks and executable
   scripts is encouraged fornotebook compatibility
   in future versions of the config.
- contents:
  - parse_config
  - get_tool_project
  - gitlog_to_hdsmj
  - get_bugzilla_issue_comment_path
  - get_bugzilla_issue_path
  - get_bugzilla_project_key
  - get_cveid_regex
  - get_depends_code_language
  - get_depends_keep_dependencies_type
  - get_dv8_flaws_params
  - get_dv8_folder_path
  - get_enumeration_commits
  - get_file_extensions
  - get_filter_commit_size
  - get_git_branches
  - get_git_repo_path
  - get_github_commit_path
  - get_github_issue_event_path
  - get_github_issue_or_pr_comment_path
  - get_github_issue_path
  - get_github_issue_search_path
  - get_github_keys
  - get_github_owner
  - get_github_pull_request_path
  - get_github_repo
  - get_issue_id_regex
  - get_jira_domain
  - get_jira_issues_comments_path
  - get_jira_issues_path
  - get_jira_keys
  - get_jira_project_key_name
  - get_mbox_domain
  - get_mbox_input_file
  - get_mbox_key_indexes
  - get_mbox_path
  - get_nvdfeed_folder_path
  - get_pattern4_filepath
  - get_pattern4_folder_path
  - get_pipermail_domain
  - get_pipermail_input_file
  - get_pipermail_path
  - get_srcml_filepath
  - get_substring_filepath
  - get_topics
  - get_uctags_line_types
  - get_understand_code_language
  - get_understand_keep_dependencies_type
  - get_understand_output_path
  - get_understand_project_path
  - get_window_end_commit
  - get_window_size
  - get_window_start_commit