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"dspace7_file_download" ] }, { "page": "dspace7_links", "title": "Find DSpace 7+ Links in Papers", "topics": [ "dspace7_links" ] }, { "page": "email", "title": "Set or get email", "topics": [ "email" ] }, { "page": "emojis", "title": "Emojis", "topics": [ "emojis" ] }, { "page": "export_jasp_html", "title": "Export a JASP (.jasp) file's own rendered output as standalone HTML", "topics": [ "export_jasp_html" ] }, { "page": "export_mplus_html", "title": "Export an Mplus (.out) output file as standalone HTML", "topics": [ "export_mplus_html" ] }, { "page": "export_omv_html", "title": "Export a jamovi (.omv) file's own rendered output as standalone HTML", "topics": [ "export_omv_html" ] }, { "page": "export_spv_html", "title": "Export an SPSS Viewer (.spv) file's tables and charts as standalone HTML", "topics": [ "export_spv_html" ] }, { "page": "export_stata_smcl_html", "title": "Export a Stata (.smcl) output log as standalone HTML", "topics": [ "export_stata_smcl_html" ] }, { "page": "extract_eq", "title": "Extract Equations", "topics": [ "extract_eq" ] }, { "page": "extract_p_values", "title": "Extract P-Values", "topics": [ "extract_p_values" ] }, { "page": "extract_tests", "title": "Extract the statistical tests a paper reports", "topics": [ "extract_tests" ] }, { "page": "extract_urls", "title": "Extract URLs", "topics": [ "extract_urls" ] }, { "page": "fig_image_view", "title": "View a figure image", "topics": [ "fig_image_view" ] }, { "page": "figshare_file_download", "title": "Download all files from a Figshare article", "topics": [ "figshare_file_download" ] }, { "page": "figshare_info", "title": "Retrieve info from Figshare by URL", "topics": [ "figshare_info" ] }, { "page": "figshare_links", "title": "Find Figshare Links in Papers", "topics": [ "figshare_links" ] }, { "page": "figshare_pat", "title": "Set or get a Figshare API token", "topics": [ "figshare_pat" ] }, { "page": "file_category", "title": "Categorise files", "topics": [ "file_category" ] }, { "page": "filetype", "title": "Get file Type from Extension", "topics": [ "filetype" ] }, { "page": "FLoRA", "title": "FORRT Replication Database (FLoRA)", "topics": [ "FLoRA" ] }, { "page": "FLoRA_date", "title": "Get date FLoRA was updated", "topics": [ "FLoRA_date" ] }, { "page": "FLoRA_update", "title": "Update FLoRA", "topics": [ "FLoRA_update" ] }, { "page": "format_bib_authors", "title": "Format Bib Authors", "topics": [ "format_bib_authors" ] }, { "page": "format_ref", "title": "Format Reference", "topics": [ "format_ref" ] }, { "page": "fsd_info", "title": "Retrieve info from FSD by URL", "topics": [ "fsd_info" ] }, { "page": "fsd_links", "title": "Find FSD Links in Papers", "topics": [ "fsd_links" ] }, { "page": "get_prev_outputs", "title": "Get Previous Outputs", "topics": [ "get_prev_outputs" ] }, { "page": "github_files", "title": "Get File List from GitHub", "topics": [ "github_files" ] }, { "page": "github_info", "title": "Get GitHub Repo Info", "topics": [ "github_info" ] }, { "page": "github_languages", "title": "Get Languages from GitHub Repo", "topics": [ "github_languages" ] }, { "page": "github_links", "title": "Find GitHub Links in Papers", "topics": [ "github_links" ] }, { "page": "github_readme", "title": "Get README from GitHub", "topics": [ "github_readme" ] }, { "page": "github_repo", "title": "Get Short GitHub Repo Name", "topics": [ "github_repo" ] }, { "page": "gitlab_links", "title": "Find GitLab Links in Papers", "topics": [ "gitlab_links" ] }, { "page": "gitlab_pat", "title": "Set or get a GitLab API token", "topics": [ "gitlab_pat" ] }, { "page": "gitlab_repo", "title": "Get Short GitLab Project Path", "topics": [ "gitlab_repo" ] }, { "page": "grobid_to_bibr", "title": "Convert Grobid TEI XML file to bibr format", "topics": [ "grobid_to_bibr" ] }, { "page": "import_jasp", "title": "Read a JASP (.jasp) file", "topics": [ "import_jasp" ] }, { "page": "import_mplus_output", "title": "Read an Mplus (.out) output file", "topics": [ "import_mplus_output" ] }, { "page": "import_omv", "title": "Read a jamovi (.omv) file", "topics": [ "import_omv" ] }, { "page": "import_spv", "title": "Read the statistical result tables from an SPSS Viewer (.spv) file", "topics": [ "import_spv" ] }, { "page": "import_stata_smcl", "title": "Read a Stata Markup and Control Language (.smcl) output log", "topics": [ "import_stata_smcl" ] }, { "page": "json_expand", "title": "Expand a JSON column", "topics": [ "json_expand" ] }, { "page": "lastlog", "title": "Get the last log", "topics": [ "lastlog" ] }, { "page": "ldbase_info", "title": "Get the files of LDbase projects, datasets, code and documents", "topics": [ "ldbase_info" ] }, { "page": "ldbase_links", "title": "Find LDbase links in a paper", "topics": [ "ldbase_links" ] }, { "page": "link", "title": "Make an html link", "topics": [ "link" ] }, { "page": "llm", "title": "Query an LLM", "topics": [ "llm" ] }, { "page": "llm_cache", "title": "Enable, disable, or query the LLM response cache", "topics": [ "llm_cache" ] }, { "page": "llm_cache_clear", "title": "Clear the on-disk LLM response cache", "topics": [ "llm_cache_clear" ] }, { "page": "llm_max_calls", "title": "Set the maximum number of calls to the LLM", "topics": [ "llm_max_calls" ] }, { "page": "llm_max_tokens", "title": "Set the default max_tokens for LLM calls", "topics": [ "llm_max_tokens" ] }, { "page": "llm_model", "title": "Set the default LLM model", "topics": [ "llm_model" ] }, { "page": "llm_model_list", "title": "List LLM Models", "topics": [ "llm_model_list" ] }, { "page": "llm_reasoning", "title": "Set the default reasoning effort for LLM calls", "topics": [ "llm_reasoning" ] }, { "page": "llm_timeout", "title": "Set the per-call timeout for LLM requests", "topics": [ "llm_timeout" ] }, { "page": "llm_use", "title": "Set or get metacheck LLM use", "topics": [ "llm_use" ] }, { "page": "local_files", "title": "List Local Files", "topics": [ "local_files" ] }, { "page": "logger", "title": "Log messages", "topics": [ "logger" ] }, { "page": "manifest_merge", "title": "Merge fields into a metacheck manifest, preserving other sections", "topics": [ "manifest_merge" ] }, { "page": "match_reported_output", "title": "Match reported statistical tests against the extracted analysis output", "topics": [ "match_reported_output" ] }, { "page": "mendeley_info", "title": "Retrieve info from Mendeley Data by URL", "topics": [ "mendeley_info" ] }, { "page": "mendeley_links", "title": "Find Mendeley Data Links in Papers", "topics": [ "mendeley_links" ] }, { "page": "metacheck_cache_info", "title": "Show where metacheck's caches live and how big they are", "topics": [ "metacheck_cache_info" ] }, { "page": "module_help", "title": "Get Module Help", "topics": [ "module_help" ] }, { "page": "module_info", "title": "Get module information", "topics": [ "module_info" ] }, { "page": "module_install", "title": "Install modules from GitHub", "topics": [ "module_install" ] }, { "page": "module_installed", "title": "List installed module repositories", "topics": [ "module_installed" ] }, { "page": "module_list", "title": "List modules", "topics": [ "module_list" ] }, { "page": "module_remove", "title": "Remove installed modules", "topics": [ "module_remove" ] }, { "page": "module_report", "title": "Report from module output", "topics": [ "module_report" ] }, { "page": "module_run", "title": "Run a module", "topics": [ "module_run" ] }, { "page": "module_template", "title": "Create a Module from a Template", "topics": [ "module_template" ] }, { "page": "module_update", "title": "Update installed modules", "topics": [ "module_update" ] }, { "page": "openalex_doi", "title": "OpenAlex info from DOI", "topics": [ "openalex_doi" ] }, { "page": "openalex_query", "title": "Look up a reference in OpenAlex", "topics": [ "openalex_query" ] }, { "page": "osf_api_check", "title": "Check OSF API Server Status", "topics": [ "osf_api_check" ] }, { "page": "osf_app", "title": "Launch OSF Download App", "topics": [ "osf_app" ] }, { "page": "osf_cache_clear", "title": "Clear the session cache of OSF listings", "topics": [ "osf_cache_clear" ] }, { "page": "osf_check_id", "title": "Check OSF IDs", "topics": [ "osf_check_id" ] }, { "page": "osf_delay", "title": "Set the OSF delay", "topics": [ "osf_delay" ] }, { "page": "osf_file_download", "title": "Download all OSF Project Files", "topics": [ "osf_file_download" ] }, { "page": "osf_get_all_pages", "title": "Get All OSF API Query Pages", "topics": [ "osf_get_all_pages" ] }, { "page": "osf_info", "title": "Retrieve info from the OSF by ID", "topics": [ "osf_info" ] }, { "page": "osf_links", "title": "Find OSF Links in Papers", "topics": [ "osf_links" ] }, { "page": "osf_pat", "title": "Set or get the OSF personal access token", "topics": [ "osf_pat" ] }, { "page": "osf_preprint_list", "title": "Get A list of preprints from the OSF", "topics": [ "osf_preprint_list" ] }, { "page": "osf_type", "title": "Get OSF GUID Type", "topics": [ "osf_type" ] }, { "page": "osf_user_projects", "title": "List the Projects Belonging to an OSF User", "topics": [ "osf_user_projects" ] }, { "page": "paper_id", "title": "Get Paper IDs", "topics": [ "paper_id" ] }, { "page": "paper_table", "title": "Paper tables", "topics": [ "paper_table" ] }, { "page": "paper_validate", "title": "Validate a Paper Object", "topics": [ "paper_validate" ] }, { "page": "paper_write", "title": "Write paper", "topics": [ "paper_write" ] }, { "page": "papers_available", "title": "List available paper corpora", "topics": [ "papers_available" ] }, { "page": "papers_load", "title": "Load a paper corpus", "topics": [ "papers_load" ] }, { "page": "papers_metadata", "title": "Get a paper corpus's Dublin Core metadata", "topics": [ "papers_metadata" ] }, { "page": "papers_remove", "title": "Remove a cached paper corpus", "topics": [ "papers_remove" ] }, { "page": "path_sanitize", "title": "Sanitize File Path", "topics": [ "path_sanitize" ] }, { "page": "plural", "title": "Pluralise", "topics": [ "plural" ] }, { "page": "psycharchives_file_download", "title": "Retrieve public file list from PsychArchives by URL", "topics": [ "psycharchives_file_download" ] }, { "page": "psycharchives_info", "title": "Retrieve info from PsychArchives by URL", "topics": [ "psycharchives_info" ] }, { "page": "psycharchives_links", "title": "Find PsychArchives Links in Papers", "topics": [ "psycharchives_links" ] }, { "page": "pubpeer_comments", "title": "Get Pubpeer Comments", "topics": [ "pubpeer_comments" ] }, { "page": "rbox_file_download", "title": "Retrieve files from ResearchBox by URL", "topics": [ "rbox_file_download" ] }, { "page": "rbox_info", "title": "Retrieve info from ResearchBox by URL", "topics": [ "rbox_info" ] }, { "page": "rbox_links", "title": "Find ResearchBox Links in Papers", "topics": [ "rbox_links" ] }, { "page": "read", "title": "Read in grobid XML or bibr JSON", "topics": [ "read" ] }, { "page": "read_r_output", "title": 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"report_type" ] }, { "page": "repro_defined_vars", "title": "Find the variables each script defines at top level", "topics": [ "repro_defined_vars" ] }, { "page": "repro_dependencies", "title": "Collect the package dependencies a set of code files declare", "topics": [ "repro_dependencies" ] }, { "page": "repro_dependencies_py", "title": "Collect the package dependencies a set of Python files declare", "topics": [ "repro_dependencies_py" ] }, { "page": "repro_docker_available", "title": "Is Docker available and running?", "topics": [ "repro_docker_available" ] }, { "page": "repro_file_io", "title": "Extract the files a script reads, writes, and sources", "topics": [ "repro_file_io" ] }, { "page": "repro_install_deps", "title": "Install a paper's declared dependencies into a throwaway library", "topics": [ "repro_install_deps" ] }, { "page": "repro_install_deps_docker", "title": "Install R dependencies inside a throwaway Docker container", "topics": [ "repro_install_deps_docker" ] }, { "page": "repro_install_deps_py", "title": "Install a paper's declared Python dependencies into a throwaway environment", "topics": [ "repro_install_deps_py" ] }, { "page": "repro_install_deps_py_docker", "title": "Install Python dependencies inside a throwaway Docker container", "topics": [ "repro_install_deps_py_docker" ] }, { "page": "repro_materialize_layout", "title": "Materialise the Psych-DS layout for a paper into a throwaway directory", "topics": [ "repro_materialize_layout" ] }, { "page": "repro_missing_inputs", "title": "Diagnose why a referenced input file is unavailable", "topics": [ "repro_missing_inputs" ] }, { "page": "repro_rewrite_paths", "title": "Rewrite a code file's data-file paths to the Psych-DS layout", "topics": [ "repro_rewrite_paths" ] }, { "page": "repro_run_order", "title": "Determine the order code files must run in", "topics": [ "repro_run_order" ] }, { "page": "repro_run_scripts", "title": "Run the paper's scripts, in order, in isolated subprocesses", "topics": [ "repro_run_scripts" ] }, { "page": "repro_run_scripts_docker", "title": "Run the paper's scripts, in order, each in an isolated Docker container", "topics": [ "repro_run_scripts_docker" ] }, { "page": "repro_run_scripts_py", "title": "Run Python scripts, in order, each in an isolated subprocess", "topics": [ "repro_run_scripts_py" ] }, { "page": "repro_run_scripts_py_docker", "title": "Run Python scripts, in order, each in an isolated Docker container", "topics": [ "repro_run_scripts_py_docker" ] }, { "page": "repro_write_scripts", "title": "Write path-rewritten scripts into the materialised layout", "topics": [ "repro_write_scripts" ] }, { "page": "researchdata4tu_file_download", "title": "Download all files from a 4TU.ResearchData article", "topics": [ "researchdata4tu_file_download" ] }, { "page": "researchdata4tu_info", "title": "Retrieve info from 4TU.ResearchData by URL", "topics": [ "researchdata4tu_info" ] }, { "page": "researchdata4tu_links", "title": "Find 4TU.ResearchData Links in Papers", "topics": [ "researchdata4tu_links" ] }, { "page": "researchdata4tu_pat", "title": "Set or get a 4TU.ResearchData API token", "topics": [ "researchdata4tu_pat" ] }, { "page": "reshare_file_download", "title": "Download all files from a ReShare deposit", "topics": [ "reshare_file_download" ] }, { "page": "reshare_info", "title": "Retrieve info from ReShare by URL", "topics": [ "reshare_info" ] }, { "page": "reshare_links", "title": "Find ReShare Links in Papers", "topics": [ "reshare_links" ] }, { "page": "retractionwatch", "title": "RetractionWatch data", "topics": [ "retractionwatch", "rw" ] }, { "page": "rw_date", "title": "Get date retractionwatch was updated", "topics": [ "rw_date" ] }, { "page": "rw_update", "title": "Update retractionwatch", "topics": [ "rw_update" ] }, { "page": "scroll_table", "title": "Make Scroll Table", "topics": [ "scroll_table" ] }, { "page": "stat_output_json", "title": "Serialise extracted result tables as a structured statistical-output document", "topics": [ "stat_output_json" ] }, { "page": "stat_output_validate", "title": "Validate a statistical-output document's native shape", "topics": [ "stat_output_validate" ] }, { "page": "stat_output_write", "title": "Write extracted statistical output to a dedicated folder", "topics": [ "stat_output_write" ] }, { "page": "stat_results_long", "title": "Flatten extracted result tables into one queryable long data frame", "topics": [ "stat_results_long" ] }, { "page": "stato_type_column", "title": "Type a result-table column by its header, with a guaranteed fallback", "topics": [ "stato_type_column" ] }, { "page": "stats", "title": "Check Stats", "topics": [ "stats" ] }, { "page": "test_paper", "title": "Test paper", "topics": [ "test_paper" ] }, { "page": "text_expand", "title": "Expand text", "topics": [ "expand_text", "text_expand" ] }, { "page": "text_search", "title": "Search text", "topics": [ "search_text", "text_search" ] }, { "page": "validate", 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