Package: metacheck 0.4.1.2

Lisa DeBruine

metacheck: Check Research Outputs for Best Practices

A modular, extendable system for checking research outputs for best practices using text search, R code, and/or (optional) LLM queries.

Authors:Lisa DeBruine [aut, cre], Cristian Mesquida [aut], Jakub Werner [aut], Raphael Merz [ctb], Lukas Wallrich [ctb], Daniel Lakens [aut]

metacheck_0.4.1.2.tar.gz
metacheck_0.4.1.2.zip(r-4.7-any)metacheck_0.4.1.2.zip(r-4.6-any)metacheck_0.4.1.2.zip(r-4.5-any)
metacheck_0.4.1.2.tgz(r-4.6-any)metacheck_0.4.1.2.tgz(r-4.5-any)
metacheck_0.4.1.2.tar.gz(r-4.7-any)metacheck_0.4.1.2.tar.gz(r-4.6-any)
metacheck_0.4.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
metacheck/json (API)

# Install 'metacheck' in R:
install.packages('metacheck', repos = c('https://scienceverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/scienceverse/metacheck/issues

Pkgdown/docs site:https://scienceverse.github.io

Datasets:

On CRAN:

Conda:

metasciencequarto

7.10 score 50 stars 297 scripts 312 exports 103 dependencies

Last updated from:7b6cd21c3d. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develWARNING237
source / vignettesOK413
linux-releaseWARNING201
macos-releaseWARNING210
macos-oldrelWARNING257
windows-develWARNING218
windows-releaseWARNING207
windows-oldrelWARNING220
wasm-releaseOK160

Exports:.aspredicted_info.bibtype_convert.detect_header_row.fsd_info.github_config.gitlab_config.grobid_to_bibr.is_paper.is_paper_list.llm_model_list_groq.llm_ollama_native.osf_file_data.osf_headers.osf_info.osf_node_data.osf_parent_project.osf_pat_validate.osf_preprint_data.osf_reg_data.osf_user_data.paper_coerce.paper_schema.psycharchives_info.rbox_info.read_bibr.tabular_usable.xml_find_text.xml_find1_text.xml_read_grobid.xml2bib.zenodo_info%||%%empty_or%accuracyadd_bib_matchaspredicted_infoaspredicted_linkscap_gate_countcausal_relationscheck_file_namingcheck_orcidcode_abs_pathcode_extract_pycode_extract_qmd_pycode_extract_rcode_file_refscode_install_packagescode_langcode_library_linescode_library_namescode_line_statscode_packagescode_parse_rcode_readcode_remove_commentscode_setwdcollapse_sectionconvertconvert_bibrconvert_grobidcredit_rolescrossref_doicrossref_querydata_check_case_issuesdata_check_colnamedata_check_colname_collisionsdata_check_constantdata_check_demographicdata_check_design_namedata_check_emptydata_check_is_behaversedata_check_is_inquisitdata_check_is_jspsychdata_check_is_psychopydata_check_is_qualtricsdata_check_numeric_in_textdata_check_outliersdata_check_pii_freetextdata_check_pii_geodata_check_pii_namedata_check_pii_valuesdata_check_scale_valuesdata_check_spss_filterdata_check_whitespacedata_classify_filesdata_col_conceptdata_col_facetsdata_col_statsdata_col_typedata_formatdata_group_llmdata_is_manifestdata_promote_header_rowdata_read_headdata_strip_qualtrics_headerdata_study_rosterdatacite_doidataone_infodataone_linksdataverse_file_downloaddataverse_infodataverse_linksdataverse_patdemofiledemopaperdoi_cleandoi_lookupdoi_resolvesdoi_valid_formatdownload_repo_filesdryad_authdryad_file_downloaddryad_infodryad_linksdryad_patdspace_linksdspace7_file_downloaddspace7_linksemailexpand_textexport_jasp_htmlexport_mplus_htmlexport_omv_htmlexport_spv_htmlexport_stata_smcl_htmlextract_eqextract_p_valuesextract_testsextract_urlsfig_image_viewfigshare_file_downloadfigshare_infofigshare_linksfigshare_patfile_categoryfiletypeFLoRAFLoRA_dateFLoRA_updateformat_bib_authorsformat_reffsd_infofsd_linksget_orcidget_prev_outputsgithub_filesgithub_infogithub_languagesgithub_linksgithub_readmegithub_repogithub_tree_filesgitlab_linksgitlab_patgitlab_repogitlab_tree_filesgrobid_to_bibrimport_jaspimport_mplus_outputimport_omvimport_spvimport_stata_smcljson_expandlastlogldbase_infoldbase_linkslinkllmllm_cachellm_cache_clearllm_max_callsllm_max_tokensllm_modelllm_model_listllm_reasoningllm_timeoutllm_uselocal_filesloggerlogpathmanifest_mergematch_column_labelsmatch_reported_outputmendeley_infomendeley_linksmessagemetacheck_cache_infomodule_helpmodule_infomodule_installmodule_installedmodule_listmodule_removemodule_reportmodule_runmodule_templatemodule_updateonlineopenalex_doiopenalex_queryorcid_personosf_api_checkosf_apposf_cache_clearosf_check_idosf_delayosf_file_downloadosf_get_all_pagesosf_infoosf_linksosf_patosf_preprint_listosf_typeosf_user_projectspaperpaper_idpaper_tablepaper_validatepaper_writepaperlistpapers_availablepapers_loadpapers_metadatapapers_removeparse_codebookparse_qsfpath_sanitizepbpluralpsycharchives_file_downloadpsycharchives_infopsycharchives_linkspsychds_file_planpubpeer_commentsrbox_file_downloadrbox_inforbox_linksreadread_r_outputread_stat_tablesref_tableregcheck_base_urlregcheck_compareregcheck_setup_localregcheck_start_localregcheck_stop_localregcheck_tidyrep_ifrepo_cache_clearrepo_cache_dirrepo_cache_sizerepo_info_cacherepo_info_cache_clearreportreport_appreport_module_runreport_qmdreport_repositoryreport_tablereport_typerepro_defined_varsrepro_dependenciesrepro_dependencies_pyrepro_docker_availablerepro_file_iorepro_install_depsrepro_install_deps_dockerrepro_install_deps_pyrepro_install_deps_py_dockerrepro_materialize_layoutrepro_missing_inputsrepro_rewrite_pathsrepro_run_orderrepro_run_scriptsrepro_run_scripts_dockerrepro_run_scripts_pyrepro_run_scripts_py_dockerrepro_write_scriptsresearchdata4tu_file_downloadresearchdata4tu_inforesearchdata4tu_linksresearchdata4tu_patreshare_file_downloadreshare_inforeshare_linksretractionwatchrwrw_daterw_updatescroll_tablesearch_textstat_output_jsonstat_output_validatestat_output_writestat_results_longstato_type_columnstatstest_papertext_expandtext_peektext_searchtxt_classify_contentvalidateverbosezenodo_file_downloadzenodo_infozenodo_linkszenodo_patzenodo_uploadzip_decisionzip_peekzip_peek_cache_clear

Dependencies:askpassbase64encbibtexbitbit64brewbslibcachemcallrclicliprcommonmarkcorocpp11crayoncrosstalkcurldescdigestdplyrDTellmerevaluatefarverfastmapfontawesomefsgenericsggplot2gitcredsgluegtablehighrhmshtmltoolshtmlwidgetshttrhttr2isobandjaneaustenrjpegjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixmemoisemimeopensslotelpillarpkgbuildpkgconfigpkgloadplyrprettyunitsprocessxprogresspromisespspurrrquartoR6rappdirsRColorBrewerRcpprdtoolsreadrrlangrmarkdownroxygen2rprojrootrstudioapirvestS7sassscalesselectrSnowballCstatcheckstringistringrsystibbletidyrtidyselecttidytexttinytextokenizerstzdbutf8vctrsviridisLitevroomwithrxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Accuracyaccuracy
Match table from bib tableadd_bib_match
Retrieve info from AsPredicted by URLaspredicted_info
Find AsPredicted Links in Papersaspredicted_links
Extract causal relations from sentence(s) via a Hugging Face Spacecausal_relations
Return Absolute Pathscode_abs_path
Convert a Jupyter notebook to code onlycode_extract_py
Extract Python chunks from a Quarto documentcode_extract_qmd_py
Convert Rmd/qmd files to R code onlycode_extract_r
Get files referenced in codecode_file_refs
Find install.packages() calls in codecode_install_packages
Detect Code Languagecode_lang
Get Code Library Linescode_library_lines
Get package names loaded in codecode_library_names
Get Code Composition Statscode_line_stats
Distinct packages from a code_check tablecode_packages
Parse code to check for errorscode_parse_r
Read code from filescode_read
Remove comments from code textcode_remove_comments
Find setwd() calls in codecode_setwd
Make Collapsible Sectioncollapse_section
Convert documentsconvert
Convert documents using bibrconvert_bibr
Convert a PDF to Grobid XMLconvert_grobid
CrossRef Info from DOIcrossref_doi
Look up Reference in CrossRefcrossref_query
Doi.org Info from DataCitedatacite_doi
Retrieve info from DataONE by URLdataone_info
Find DataONE Links in Papersdataone_links
Download all files from a Dataverse datasetdataverse_file_download
Retrieve info from Dataverse by URLdataverse_info
Find Dataverse Links in Papersdataverse_links
Set or get a Dataverse API tokendataverse_pat
Get a demo filedemofile
Get demo paperdemopaper
Clean DOIsdoi_clean
Doi.org Info from DOIdoi_lookup
Check whether a DOI resolvesdoi_resolves
Validate DOI formatdoi_valid_format
Set or get Dryad OAuth2 client credentialsdryad_auth
Download all files from a Dryad datasetdryad_file_download
Retrieve info from Dryad by URLdryad_info
Find Dryad Links in Papersdryad_links
Set or get a Dryad API tokendryad_pat
Find DSpace (legacy REST API) Links in Papersdspace_links
Retrieve public file list from a DSpace 7+ installation by URLdspace7_file_download
Find DSpace 7+ Links in Papersdspace7_links
Set or get emailemail
Emojisemojis
Export a JASP (.jasp) file's own rendered output as standalone HTMLexport_jasp_html
Export an Mplus (.out) output file as standalone HTMLexport_mplus_html
Export a jamovi (.omv) file's own rendered output as standalone HTMLexport_omv_html
Export an SPSS Viewer (.spv) file's tables and charts as standalone HTMLexport_spv_html
Export a Stata (.smcl) output log as standalone HTMLexport_stata_smcl_html
Extract Equationsextract_eq
Extract P-Valuesextract_p_values
Extract the statistical tests a paper reportsextract_tests
Extract URLsextract_urls
View a figure imagefig_image_view
Download all files from a Figshare articlefigshare_file_download
Retrieve info from Figshare by URLfigshare_info
Find Figshare Links in Papersfigshare_links
Set or get a Figshare API tokenfigshare_pat
Categorise filesfile_category
Get file Type from Extensionfiletype
FORRT Replication Database (FLoRA)FLoRA
Get date FLoRA was updatedFLoRA_date
Update FLoRAFLoRA_update
Format Bib Authorsformat_bib_authors
Format Referenceformat_ref
Retrieve info from FSD by URLfsd_info
Find FSD Links in Papersfsd_links
Get Previous Outputsget_prev_outputs
Get File List from GitHubgithub_files
Get GitHub Repo Infogithub_info
Get Languages from GitHub Repogithub_languages
Find GitHub Links in Papersgithub_links
Get README from GitHubgithub_readme
Get Short GitHub Repo Namegithub_repo
Find GitLab Links in Papersgitlab_links
Set or get a GitLab API tokengitlab_pat
Get Short GitLab Project Pathgitlab_repo
Convert Grobid TEI XML file to bibr formatgrobid_to_bibr
Read a JASP (.jasp) fileimport_jasp
Read an Mplus (.out) output fileimport_mplus_output
Read a jamovi (.omv) fileimport_omv
Read the statistical result tables from an SPSS Viewer (.spv) fileimport_spv
Read a Stata Markup and Control Language (.smcl) output logimport_stata_smcl
Expand a JSON columnjson_expand
Get the last loglastlog
Get the files of LDbase projects, datasets, code and documentsldbase_info
Find LDbase links in a paperldbase_links
Make an html linklink
Query an LLMllm
Enable, disable, or query the LLM response cachellm_cache
Clear the on-disk LLM response cachellm_cache_clear
Set the maximum number of calls to the LLMllm_max_calls
Set the default max_tokens for LLM callsllm_max_tokens
Set the default LLM modelllm_model
List LLM Modelsllm_model_list
Set the default reasoning effort for LLM callsllm_reasoning
Set the per-call timeout for LLM requestsllm_timeout
Set or get metacheck LLM usellm_use
List Local Fileslocal_files
Log messageslogger
Merge fields into a metacheck manifest, preserving other sectionsmanifest_merge
Match reported statistical tests against the extracted analysis outputmatch_reported_output
Retrieve info from Mendeley Data by URLmendeley_info
Find Mendeley Data Links in Papersmendeley_links
Show where metacheck's caches live and how big they aremetacheck_cache_info
Get Module Helpmodule_help
Get module informationmodule_info
Install modules from GitHubmodule_install
List installed module repositoriesmodule_installed
List modulesmodule_list
Remove installed modulesmodule_remove
Report from module outputmodule_report
Run a modulemodule_run
Create a Module from a Templatemodule_template
Update installed modulesmodule_update
OpenAlex info from DOIopenalex_doi
Look up a reference in OpenAlexopenalex_query
Check OSF API Server Statusosf_api_check
Launch OSF Download Apposf_app
Clear the session cache of OSF listingsosf_cache_clear
Check OSF IDsosf_check_id
Set the OSF delayosf_delay
Download all OSF Project Filesosf_file_download
Get All OSF API Query Pagesosf_get_all_pages
Retrieve info from the OSF by IDosf_info
Find OSF Links in Papersosf_links
Set or get the OSF personal access tokenosf_pat
Get A list of preprints from the OSFosf_preprint_list
Get OSF GUID Typeosf_type
List the Projects Belonging to an OSF Userosf_user_projects
Get Paper IDspaper_id
Paper tablespaper_table
Validate a Paper Objectpaper_validate
Write paperpaper_write
List available paper corporapapers_available
Load a paper corpuspapers_load
Get a paper corpus's Dublin Core metadatapapers_metadata
Remove a cached paper corpuspapers_remove
Sanitize File Pathpath_sanitize
Pluraliseplural
Retrieve public file list from PsychArchives by URLpsycharchives_file_download
Retrieve info from PsychArchives by URLpsycharchives_info
Find PsychArchives Links in Paperspsycharchives_links
Get Pubpeer Commentspubpeer_comments
Retrieve files from ResearchBox by URLrbox_file_download
Retrieve info from ResearchBox by URLrbox_info
Find ResearchBox Links in Papersrbox_links
Read in grobid XML or bibr JSONread
Extract statistical results from captured R console outputread_r_output
Read the statistical result tables from a JASP, jamovi or notebook fileread_stat_tables
Reference and DOI tableref_table
Compare a Preregistration with a Paper via RegCheckregcheck_compare
Set up the local RegCheck server (manual Python path)regcheck_setup_local
Start the local RegCheck serverregcheck_start_local
Stop the local RegCheck serverregcheck_stop_local
Delete the downloaded-repository file cacherepo_cache_clear
Locate the downloaded-repository file cacherepo_cache_dir
Size of the downloaded-repository file cacherepo_cache_size
Enable, disable, or query the repository-listing cacherepo_info_cache
Clear the on-disk repository-listing cacherepo_info_cache_clear
Create a Reportreport
Launch Report Appreport_app
Run modules for a reportreport_module_run
Create Report from Module Outputreport_qmd
Create a Report for a Local Repositoryreport_repository
Display a Table in a Reportreport_table
Set or get the report typereport_type
Find the variables each script defines at top levelrepro_defined_vars
Collect the package dependencies a set of code files declarerepro_dependencies
Collect the package dependencies a set of Python files declarerepro_dependencies_py
Is Docker available and running?repro_docker_available
Extract the files a script reads, writes, and sourcesrepro_file_io
Install a paper's declared dependencies into a throwaway libraryrepro_install_deps
Install R dependencies inside a throwaway Docker containerrepro_install_deps_docker
Install a paper's declared Python dependencies into a throwaway environmentrepro_install_deps_py
Install Python dependencies inside a throwaway Docker containerrepro_install_deps_py_docker
Materialise the Psych-DS layout for a paper into a throwaway directoryrepro_materialize_layout
Diagnose why a referenced input file is unavailablerepro_missing_inputs
Rewrite a code file's data-file paths to the Psych-DS layoutrepro_rewrite_paths
Determine the order code files must run inrepro_run_order
Run the paper's scripts, in order, in isolated subprocessesrepro_run_scripts
Run the paper's scripts, in order, each in an isolated Docker containerrepro_run_scripts_docker
Run Python scripts, in order, each in an isolated subprocessrepro_run_scripts_py
Run Python scripts, in order, each in an isolated Docker containerrepro_run_scripts_py_docker
Write path-rewritten scripts into the materialised layoutrepro_write_scripts
Download all files from a 4TU.ResearchData articleresearchdata4tu_file_download
Retrieve info from 4TU.ResearchData by URLresearchdata4tu_info
Find 4TU.ResearchData Links in Papersresearchdata4tu_links
Set or get a 4TU.ResearchData API tokenresearchdata4tu_pat
Download all files from a ReShare depositreshare_file_download
Retrieve info from ReShare by URLreshare_info
Find ReShare Links in Papersreshare_links
RetractionWatch dataretractionwatch rw
Get date retractionwatch was updatedrw_date
Update retractionwatchrw_update
Make Scroll Tablescroll_table
Serialise extracted result tables as a structured statistical-output documentstat_output_json
Validate a statistical-output document's native shapestat_output_validate
Write extracted statistical output to a dedicated folderstat_output_write
Flatten extracted result tables into one queryable long data framestat_results_long
Type a result-table column by its header, with a guaranteed fallbackstato_type_column
Check Statsstats
Test papertest_paper
Expand textexpand_text text_expand
Search textsearch_text text_search
Validate a module's output against coded ground truthvalidate
Download all Zenodo Project Fileszenodo_file_download
Retrieve info from Zenodo by URLzenodo_info
Find Zenodo Links in Paperszenodo_links
Set or get the Zenodo personal access tokenzenodo_pat
Upload Folders to Zenodozenodo_upload
Clear the on-disk zip-peek cachezip_peek_cache_clear