commonmeta-ruby 3.5.4 → 3.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (275) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile.lock +16 -5
  3. data/bin/commonmeta +1 -1
  4. data/lib/commonmeta/readers/crossref_xml_reader.rb +1 -1
  5. data/lib/commonmeta/utils.rb +6 -6
  6. data/lib/commonmeta/version.rb +1 -1
  7. data/spec/cli_spec.rb +13 -8
  8. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/default.yml +13 -13
  9. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_bibtex.yml +13 -13
  10. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_crossref_xml.yml +25 -25
  11. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_datacite.yml +13 -13
  12. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref/to_schema_org.yml +13 -13
  13. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/default.yml +7 -7
  14. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_bibtex.yml +7 -7
  15. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_crossref_xml.yml +7 -59
  16. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_datacite.yml +7 -7
  17. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_file/crossref_xml/to_schema_org.yml +7 -7
  18. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/default.yml +24 -24
  19. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_bibtex.yml +24 -24
  20. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_citation.yml +24 -24
  21. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_crossref_xml.yml +24 -24
  22. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_datacite.yml +24 -24
  23. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_jats.yml +24 -24
  24. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/crossref/to_schema_org.yml +24 -24
  25. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/default.yml +16 -16
  26. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_bibtex.yml +16 -16
  27. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_citation.yml +16 -16
  28. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_datacite.yml +16 -16
  29. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_jats.yml +16 -16
  30. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/datacite/to_schema_org.yml +16 -16
  31. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/default.yml +479 -946
  32. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/to_crossref_xml.yml +957 -1891
  33. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/to_datacite.yml +479 -946
  34. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/convert_from_id/schema_org/to_schema_org.yml +481 -950
  35. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_blog.yml +5540 -968
  36. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_blog_unknown_blog_id.yml +22 -29
  37. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_id.yml +25 -39
  38. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/encode/by_id_unknown_uuid.yml +18 -28
  39. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/crossref.yml +7 -7
  40. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/datacite.yml +7 -7
  41. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/jalc.yml +7 -7
  42. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/kisti.yml +7 -7
  43. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/medra.yml +7 -7
  44. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/find_from_format_by_id/op.yml +7 -7
  45. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_blog_id.yml +46 -0
  46. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_by_blog.yml +5578 -246
  47. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_not_indexed.yml +13 -2201
  48. data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_unregistered.yml +176 -72
  49. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/change_metadata_as_datacite_xml/with_data_citation.yml +16 -16
  50. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/crossref.yml +6 -6
  51. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/datacite.yml +6 -6
  52. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/jalc.yml +6 -6
  53. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/kisti.yml +6 -6
  54. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/medra.yml +6 -6
  55. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/not_found.yml +6 -6
  56. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/doi_registration_agency/op.yml +6 -6
  57. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref.yml +6 -6
  58. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/crossref_doi_not_url.yml +6 -6
  59. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite.yml +6 -6
  60. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/datacite_doi_http.yml +6 -6
  61. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml +6 -6
  62. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_blog_id_for_json_feed_item_id/by_blog_post_id.yml +27 -105
  63. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_blog_id_for_json_feed_item_id/not_found.yml +20 -27
  64. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/cff-converter-python.yml +51 -25
  65. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff.yml +12 -12
  66. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_cff_metadata/ruby-cff_repository_url.yml +9 -9
  67. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/maremma.yml +10 -10
  68. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_codemeta_metadata/metadata_reports.yml +11 -11
  69. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml +78 -78
  70. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml +76 -76
  71. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/DOI_with_data_citation.yml +35 -35
  72. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/JaLC.yml +162 -162
  73. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/KISTI.yml +131 -131
  74. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/OP.yml +75 -75
  75. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/affiliation_is_space.yml +76 -76
  76. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book.yml +113 -113
  77. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/another_book_chapter.yml +74 -74
  78. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/article_id_as_page_number.yml +77 -77
  79. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/author_literal.yml +84 -84
  80. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book.yml +77 -77
  81. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter.yml +75 -75
  82. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_chapter_with_RDF_for_container.yml +73 -73
  83. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/book_oup.yml +72 -72
  84. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/component.yml +94 -94
  85. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset.yml +104 -104
  86. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dataset_usda.yml +136 -136
  87. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/date_in_future.yml +80 -80
  88. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/dissertation.yml +103 -103
  89. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/empty_given_name.yml +75 -75
  90. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/invalid_date.yml +77 -77
  91. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article.yml +76 -76
  92. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_original_language_title.yml +73 -73
  93. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with.yml +128 -210
  94. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_RDF_for_container.yml +74 -74
  95. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_article_with_funding.yml +76 -76
  96. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/journal_issue.yml +72 -72
  97. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/mEDRA.yml +72 -72
  98. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/markup.yml +81 -81
  99. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/missing_contributor.yml +71 -71
  100. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_issn.yml +75 -75
  101. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles.yml +71 -71
  102. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/multiple_titles_with_missing.yml +573 -573
  103. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/not_found_error.yml +65 -65
  104. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/peer_review.yml +77 -77
  105. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content.yml +74 -74
  106. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/posted_content_copernicus.yml +76 -76
  107. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/report_osti.yml +120 -120
  108. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/vor_with_url.yml +78 -78
  109. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book.yml +74 -74
  110. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_metadata/yet_another_book_chapter.yml +73 -73
  111. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_crossref_raw/journal_article.yml +59 -59
  112. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/SoftwareSourceCode.yml +4 -4
  113. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/dissertation.yml +13 -13
  114. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/funding_references.yml +15 -15
  115. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_datacite_metadata/subject_scheme.yml +120 -120
  116. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_id.yml +5540 -555
  117. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_id.yml +31 -42
  118. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_post_id_specific_prefix.yml +25 -39
  119. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/by_blog_id.yml +5540 -247
  120. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/not_indexed_posts.yml +14 -26
  121. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/unregistered_posts.yml +176 -72
  122. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/archived_wordpress_post.yml +27 -95
  123. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blog_post_with_non-url_id.yml +28 -106
  124. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml +21 -65
  125. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_author_name_suffix.yml +20 -208
  126. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_doi.yml +26 -97
  127. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_institutional_author.yml +24 -55
  128. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_organizational_author.yml +27 -70
  129. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers.yml +41 -143
  130. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers_and_funding.yml +54 -132
  131. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers_and_link_to_peer-reviewed_article.yml +304 -818
  132. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_without_doi.yml +24 -169
  133. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post.yml +24 -63
  134. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post_with_anonymous_author.yml +25 -40
  135. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/substack_post_with_broken_reference.yml +278 -591
  136. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/syldavia_gazette_post_with_references.yml +59 -101
  137. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/upstream_post_with_references.yml +135 -331
  138. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post.yml +24 -134
  139. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_many_references.yml +578 -2967
  140. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_references.yml +44 -205
  141. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_tracking_code_on_url.yml +26 -160
  142. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/affiliation_is_space.yml +21 -21
  143. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_familyName.yml +15 -15
  144. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/has_name_in_display-order_with_ORCID.yml +13 -13
  145. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/name_with_affiliation_crossref.yml +16 -16
  146. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_one_author/only_familyName_and_givenName.yml +66 -61
  147. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting.yml +145 -146
  148. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/BlogPosting_with_new_DOI.yml +149 -150
  149. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/get_schema_org_metadata_front_matter/BlogPosting.yml +114 -115
  150. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/harvard_dataverse.yml +300 -289
  151. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/pangaea.yml +66 -61
  152. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/upstream_blog.yml +64 -57
  153. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_schema_org_metadata/zenodo.yml +27 -24
  154. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/DOI_RA_not_Crossref_or_DataCite.yml +6 -6
  155. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/handle_input/unknown_DOI_prefix.yml +6 -6
  156. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/json_schema_errors/is_valid.yml +16 -16
  157. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/BlogPosting.yml +10 -10
  158. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/Dataset.yml +10 -10
  159. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/authors_with_affiliations.yml +16 -16
  160. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/climate_data.yml +10 -10
  161. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/from_schema_org.yml +145 -146
  162. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/keywords_subject_scheme.yml +8 -8
  163. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/maremma.yml +12 -12
  164. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/text.yml +8 -8
  165. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_data_citation.yml +16 -16
  166. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_bibtex/with_pages.yml +16 -16
  167. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/Collection_of_Jupyter_notebooks.yml +13 -13
  168. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_Zenodo.yml +13 -13
  169. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/SoftwareSourceCode_also_Zenodo.yml +8 -8
  170. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_cff/ruby-cff.yml +10 -10
  171. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Dataset.yml +10 -10
  172. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article.yml +16 -16
  173. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Journal_article_vancouver_style.yml +21 -21
  174. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/Missing_author.yml +15 -15
  175. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/interactive_resource_without_dates.yml +8 -8
  176. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/software_w/version.yml +8 -8
  177. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite.yml +8 -8
  178. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml +8 -8
  179. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_commonmeta/with_data_citation.yml +12 -12
  180. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/another_schema_org_from_front-matter.yml +32 -32
  181. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article.yml +5 -5
  182. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article_from_datacite.yml +5 -5
  183. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article_plos.yml +16 -16
  184. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_anonymous_author.yml +25 -40
  185. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_doi.yml +24 -134
  186. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_organizational_author.yml +27 -70
  187. data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_from_rogue_scholar_with_relations.yml +41 -143
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64
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65
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66
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67
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71
- so helps to contextualise research efforts as being highly tentative and fallible.</p><h4>Introduction</h4><p>The
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- videos of the presentations at the Metascience2023 conference were recently
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74
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75
- making: Navigating ambiguity in research practice”: </p><div id=\"youtube2-5omWDTPcsNo\"
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- I summarise Van Drimmelen’s excellent work and share my thoughts on his ideas.</p><h4>What
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- is Researcher Discretion?</h4><p>Van Drimmelen (2023) explained that, during
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- the research process, researchers have discretion over numerous decisions
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- that they make about their methodology and analyses. During the data analysis
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- stage, this <em>researcher discretion</em> may be perceived negatively as
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- <em>researcher degrees of freedom</em> that is susceptible to <em>researcher
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- bias</em> and <em>questionable research practices</em> (John et al., 2012;
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- Simmons et al., 2011).</p><div class=\"captioned-image-container\"><figure><a
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- type=\"image/webp\" srcset=\"https://substackcdn.com/image/fetch/w_424,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2Fd6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png
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- 424w, https://substackcdn.com/image/fetch/w_848,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2Fd6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png
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- 848w, https://substackcdn.com/image/fetch/w_1272,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2Fd6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png
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- 1272w, https://substackcdn.com/image/fetch/w_1456,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2Fd6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png
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- 1456w\" sizes=\"100vw\"><img src=\"https://substackcdn.com/image/fetch/w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2Fd6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png\"
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- width=\"1430\" height=\"759\" data-attrs=\"{&quot;src&quot;:&quot;https://substack-post-media.s3.amazonaws.com/public/images/d6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png&quot;,&quot;srcNoWatermark&quot;:null,&quot;fullscreen&quot;:null,&quot;imageSize&quot;:null,&quot;height&quot;:759,&quot;width&quot;:1430,&quot;resizeWidth&quot;:null,&quot;bytes&quot;:511459,&quot;alt&quot;:null,&quot;title&quot;:null,&quot;type&quot;:&quot;image/png&quot;,&quot;href&quot;:null,&quot;belowTheFold&quot;:false,&quot;topImage&quot;:true,&quot;internalRedirect&quot;:null}\"
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- class=\"sizing-normal\" alt=\"\" srcset=\"https://substackcdn.com/image/fetch/w_424,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2Fd6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png
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- 424w, https://substackcdn.com/image/fetch/w_848,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2Fd6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png
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- 848w, https://substackcdn.com/image/fetch/w_1272,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2Fd6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png
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- 1272w, https://substackcdn.com/image/fetch/w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2Fd6f03976-0133-406f-8572-cdbcbbdc3aef_1430x759.png
101
- 1456w\" sizes=\"100vw\" fetchpriority=\"high\"></picture><div class=\"image-link-expand\"><svg
102
- xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" viewBox=\"0
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- 0 24 24\" fill=\"none\" stroke=\"#FFFFFF\" stroke-width=\"2\" stroke-linecap=\"round\"
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- stroke-linejoin=\"round\" class=\"lucide lucide-maximize2\"><polyline points=\"15
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- 3 21 3 21 9\"></polyline><polyline points=\"9 21 3 21 3 15\"></polyline><line
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- x1=\"21\" x2=\"14\" y1=\"3\" y2=\"10\"></line><line x1=\"3\" x2=\"10\" y1=\"21\"
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- y2=\"14\"></line></svg></div></div></a><figcaption class=\"image-caption\"><em>Figure
108
- 1. </em>Tom van Drimmelen illustrates the numerous decisions that researchers
109
- make during the research process.</figcaption></figure></div><h4>Researcher
110
- Discretion Emerges in Both Over- and Under-Determined Research Plans</h4><p>In
111
- theory, it is possible to reduce and/or reveal researcher discretion during
112
- data analyses by preregistering one or more methodological and analytical
113
- research paths. However, Van Drimmelen (2023) and colleagues were interested
114
- in how researcher discretion operates <em>in practice</em>. To investigate,
115
- they conducted an ethnographic study in which they observed researcher discretion
116
- in two different research groups. They found that researcher discretion emerged
117
- when researchers used two categories of research plan.</p><p>1.&nbsp;&nbsp;&nbsp;&nbsp;
118
- <em>Underdetermined plans</em>: Researcher discretion emerged when research
119
- plans were not precise enough to determine specific actions for the researchers.
120
- In this case, researchers needed to use their own discretion to fill in the
121
- gaps of the research plan and figure out how to proceed. Researchers often
122
- find themselves in this situation because preregistered research plans are
123
- often vague (e.g., Bakker et al., 2020; Heirene et al., 2021; Van den Akker
124
- et al., 2023).</p><p>2.&nbsp;&nbsp;&nbsp;&nbsp; <em>Overdetermined plans</em>:
125
- Researcher discretion also emerged when there were unforeseen changes in the
126
- research situation that made the original research plan undesirable or impossible,
127
- necessitating an alternative research approach. Again, this situation is common,
128
- because most researchers do not possess “godlike planning abilities” (Navarro,
129
- 2020). To attempt to address this issue, researchers can preregister “if…then”
130
- contingencies (i.e., decision trees) that accommodate <em>anticipated</em>
131
- changes in the research situation (Nosek et al., 2018, p. 2602). In addition,
132
- it may be possible to update a preregistered analysis plan prior to the data
133
- analysis in order to take account of <em>unanticipated</em> events (Nosek
134
- et al., 2019, p. 817). However, it is often the case that <em>unanticipated</em>
135
- events arise <em>during data analyses</em>. As Reinhart (2015, p. 95) explained
136
- (paraphrasing Helmuth von Moltke), “no analysis plan survives contact with
137
- the data.” In these cases, researchers either need to stick to an inadequate
138
- preregistered analysis plan or deviate and adapt their approach to address
139
- the current situation. The evidence shows that researchers often deviate from
140
- their preregistered plans (e.g., Abrams et al., 2020; Claesen et al., 2021;
141
- Heirene et al., 2021).</p><h4>A Prescriptiveness Trade-Off in Preregistered
142
- Plans</h4><p>Van Drimmelen’s (2023) work shows us that researchers are forced
143
- to either deviate from overdetermined plans to overcome unforeseen events
144
- or fill in the gaps of vague, underdetermined plans. Hence, researcher discretion
145
- emerges in the case of both over- and under-determined plans. As Van Drimmelen
146
- (2023) put it, “researcher discretion is an integral and unavoidable part
147
- of the research practice.”</p><p>I think Van Drimmelen’s (2023) evidence also
148
- points to a trade-off between the prescriptiveness of preregistered research
149
- plans and the feasibility of their implementation in an unpredictable world.
150
- As preregistered plans become more precise and prescriptive, there is a greater
151
- chance that researchers will need to deviate from them in order to accommodate
152
- unforeseen and/or uncontrolled events that occur during the implementation
153
- of the plan. For example, researchers are more likely to deviate from a plan
154
- to test “300 participants” than they are to deviate from a less prescriptive
155
- plan to test “<em>around</em> 300 participants,” because uncontrolled events
156
- (e.g., the number of participant exclusions during data analysis) may result
157
- in a final sample size that is only close to 300 participants and not exactly
158
- 300 participants (e.g., Claesen et al., 2021, pp. 6-7). Consequently, as preregistered
159
- plans become more prescriptive, they are more likely to result in deviations
160
- that turn their planned confirmatory tests into unplanned exploratory tests.<sup>1</sup>
161
- Of course, preregistration continues to distinguish between confirmatory and
162
- exploratory tests in this situation, and it prevents exploratory tests from
163
- being falsely portrayed as confirmatory tests. Nonetheless, it remains the
164
- case that, as plans for confirmatory tests become more prescriptive, the actual
165
- implementation of these confirmatory tests in the real world becomes less
166
- likely.</p><p>On the other hand, as preregistered plans become vaguer and
167
- less prescriptive, confirmatory hypothesis tests will become not only more
168
- feasible to achieve without deviation, but also more susceptible to researcher
169
- degrees of freedom and questionable research practices. For example, it is
170
- more feasible to test “<em>around</em> 300 participants” than to test exactly
171
- “300 participants.” However, the first sampling plan does not prevent the
172
- questionable research practice of optional stopping (John et al., 2021; Simmons
173
- et al., 2011), whereas the second, more prescriptive plan does.</p><p>In summary,
174
- researchers need to consider a <em>prescriptiveness trade-off </em>when writing
175
- their preregistered plans: All other things being equal, plans that are more
176
- prescriptive are more likely to result in deviations that turn their confirmatory
177
- tests into exploratory tests, and plans that are less prescriptive are more
178
- likely to result in confirmatory tests that are susceptible to questionable
179
- research practices. Hence, researchers face a difficult choice between prescriptive
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- confirmatory tests that they are less likely to carry out in practice and
181
- vague confirmatory tests that are more prone to questionable research practices.</p><div
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- class=\"captioned-image-container\"><figure><a class=\"image-link is-viewable-img
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- image2\" target=\"_blank\" href=\"https://substackcdn.com/image/fetch/f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg\"
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- data-component-name=\"Image2ToDOM\"><div class=\"image2-inset\"><picture><source
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- type=\"image/webp\" srcset=\"https://substackcdn.com/image/fetch/w_424,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg
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- 424w, https://substackcdn.com/image/fetch/w_848,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg
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- 848w, https://substackcdn.com/image/fetch/w_1272,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg
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- 1272w, https://substackcdn.com/image/fetch/w_1456,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg
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- 1456w\" sizes=\"100vw\"><img src=\"https://substackcdn.com/image/fetch/w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg\"
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- width=\"284\" height=\"429.408\" data-attrs=\"{&quot;src&quot;:&quot;https://substack-post-media.s3.amazonaws.com/public/images/26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg&quot;,&quot;srcNoWatermark&quot;:null,&quot;fullscreen&quot;:null,&quot;imageSize&quot;:null,&quot;height&quot;:756,&quot;width&quot;:500,&quot;resizeWidth&quot;:284,&quot;bytes&quot;:93786,&quot;alt&quot;:null,&quot;title&quot;:null,&quot;type&quot;:&quot;image/jpeg&quot;,&quot;href&quot;:null,&quot;belowTheFold&quot;:true,&quot;topImage&quot;:false,&quot;internalRedirect&quot;:null}\"
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- class=\"sizing-normal\" alt=\"\" srcset=\"https://substackcdn.com/image/fetch/w_424,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg
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- 424w, https://substackcdn.com/image/fetch/w_848,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg
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- 848w, https://substackcdn.com/image/fetch/w_1272,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg
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- 1272w, https://substackcdn.com/image/fetch/w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F26ad757c-146e-4d8f-88a5-f34cf5c71c58_500x756.jpeg
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- 1456w\" sizes=\"100vw\" loading=\"lazy\"></picture><div class=\"image-link-expand\"><svg
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- xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" viewBox=\"0
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- 0 24 24\" fill=\"none\" stroke=\"#FFFFFF\" stroke-width=\"2\" stroke-linecap=\"round\"
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- stroke-linejoin=\"round\" class=\"lucide lucide-maximize2\"><polyline points=\"15
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- 3 21 3 21 9\"></polyline><polyline points=\"9 21 3 21 3 15\"></polyline><line
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- x1=\"21\" x2=\"14\" y1=\"3\" y2=\"10\"></line><line x1=\"3\" x2=\"10\" y1=\"21\"
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- y2=\"14\"></line></svg></div></div></a></figure></div><h4>Researchers Sometimes
202
- Make Implicit Decisions</h4><p>Van Drimmelen and colleagues (2023) also identified
203
- another interesting issue in their work. At times, they found it difficult
204
- to identify researcher discretion because there were multiple potential methodological
205
- or analytical approaches available that researchers did not consider. In other
206
- words, sometimes <em>researchers</em> <em>were not aware that they were making
207
- decisions</em>!</p><p>This idea of unconscious and implicit research decisions
208
- reminds me of something that Donald Rumsfeld, the United States Secretary
209
- of Defence, said at a press briefing in 2002:</p><blockquote><p>There are
210
- known knowns; there are things we know we know. We also know there are known
211
- unknowns; that is to say we know there are some things we do not know. But
212
- there are also unknown unknowns—the ones we don’t know we don’t know. (Wikipedia,
213
- 2023)</p></blockquote><p>In the context of Figure 1, our <em>known knowns</em>
214
- are the path or paths that we reported following in our research (e.g., the
215
- green paths). In these cases, we know what we did, and we know what we found
216
- as a result. In contrast, our <em>known unknowns</em> are the paths that we
217
- actively decided not to follow (e.g., all the other paths in Figure 1). We
218
- know these paths exist, but we don’t yet know what results lie at the end
219
- of them.</p><p>But what about our <em>unknown unknowns</em>? These paths don’t
220
- appear in Figure 1! They relate to decisions that we didn’t even consider,
221
- at least not at a conscious level. For example, we may not have considered
222
- the time of day of testing, the ambient temperature, or a host of other unspecified
223
- variables that may be influential on our results. Instead, we unconsciously
224
- relegated these unknown unknowns to a <em>ceteris paribus</em> clause (i.e.,
225
- “all other things being equal”), which assumes that no other influential factors
226
- are at play (Meehl, 1990). The problem is that our unconscious and implicit
227
- decision to assume the irrelevance of these factors may be wrong! Indeed,
228
- the history of science is full of cases in which factors that were not initially
229
- considered to be important subsequently turned out to be crucial moderators
230
- or boundary conditions of effects (for some examples, see Firestein, 2016).</p><div
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- class=\"captioned-image-container\"><figure><a class=\"image-link is-viewable-img
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- image2\" target=\"_blank\" href=\"https://substackcdn.com/image/fetch/f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg\"
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- data-component-name=\"Image2ToDOM\"><div class=\"image2-inset\"><picture><source
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- type=\"image/webp\" srcset=\"https://substackcdn.com/image/fetch/w_424,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg
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- 424w, https://substackcdn.com/image/fetch/w_848,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg
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- 848w, https://substackcdn.com/image/fetch/w_1272,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg
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- 1272w, https://substackcdn.com/image/fetch/w_1456,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg
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- 1456w\" sizes=\"100vw\"><img src=\"https://substackcdn.com/image/fetch/w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg\"
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- width=\"296\" height=\"444\" data-attrs=\"{&quot;src&quot;:&quot;https://substack-post-media.s3.amazonaws.com/public/images/96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg&quot;,&quot;srcNoWatermark&quot;:null,&quot;fullscreen&quot;:null,&quot;imageSize&quot;:null,&quot;height&quot;:750,&quot;width&quot;:500,&quot;resizeWidth&quot;:296,&quot;bytes&quot;:89822,&quot;alt&quot;:null,&quot;title&quot;:null,&quot;type&quot;:&quot;image/jpeg&quot;,&quot;href&quot;:null,&quot;belowTheFold&quot;:true,&quot;topImage&quot;:false,&quot;internalRedirect&quot;:null}\"
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- class=\"sizing-normal\" alt=\"\" srcset=\"https://substackcdn.com/image/fetch/w_424,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg
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- 424w, https://substackcdn.com/image/fetch/w_848,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg
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- 848w, https://substackcdn.com/image/fetch/w_1272,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg
243
- 1272w, https://substackcdn.com/image/fetch/w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F96e8d69a-f2c1-4c22-b375-8c5c4fd72689_500x750.jpeg
244
- 1456w\" sizes=\"100vw\" loading=\"lazy\"></picture><div class=\"image-link-expand\"><svg
245
- xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" viewBox=\"0
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- 0 24 24\" fill=\"none\" stroke=\"#FFFFFF\" stroke-width=\"2\" stroke-linecap=\"round\"
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- stroke-linejoin=\"round\" class=\"lucide lucide-maximize2\"><polyline points=\"15
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- 3 21 3 21 9\"></polyline><polyline points=\"9 21 3 21 3 15\"></polyline><line
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- x1=\"21\" x2=\"14\" y1=\"3\" y2=\"10\"></line><line x1=\"3\" x2=\"10\" y1=\"21\"
250
- y2=\"14\"></line></svg></div></div></a></figure></div><h4>We Can’t Be Transparent
251
- About Unknown Unknowns, But We Should Acknowledge They Exist!</h4><p>Van Drimmelen
252
- (2023) concluded that “we might not be able to be effectively transparent
253
- because <em>we don’t know which decisions we’ve actually made</em>” (my emphasis).
254
- In other words, our lack of awareness about our potentially important implicit
255
- decisions means that we can’t be transparent about them: We can report our
256
- known knowns, and we can be transparent and speculative about our known unknowns,
257
- but we can’t say much about our unknown unknowns because we don’t know what
258
- they are! By definition, as soon as we start to speculate on a potentially
259
- influential factor in our research, it becomes a <em>known</em> unknown about
260
- which we need to make conscious decisions!</p><p>Despite our inability to
261
- specify our unknown unknowns, Van Drimmelen’s (2023) work reminds us that
262
- it’s important to acknowledge this type of ignorance in science because it
263
- helps to contextualise our research efforts as being highly tentative and
264
- fallible steps in a collective process of discovery and theory development.
265
- Acknowledging our unknown unknowns also helps to address recent calls for
266
- greater intellectual humility and modesty in science (Hoekstra &amp; Vazire,
267
- 2021; Ramsey, 2021).</p><p>I’ll end with a nice example of scientists acknowledging
268
- unknown unknowns. Here’s Errington et al. (2021, p. 12) discussing the challenges
269
- of assessing replicability in preclinical cancer biology:</p><blockquote><p>It
270
- might also be that, in some cases, a failure to replicate was caused by the
271
- replication team deviating from the protocol in some way that was not recognized,
272
- or that a key part of the procedure was left out of the protocol inadvertently.
273
- It is also possible that the effect reported in the original paper depended
274
- on methodological factors that were not identified by original authors, the
275
- replication team, or any other experts involved in the peer review of the
276
- original paper or the Registered Report.</p></blockquote><h4>References</h4><p>Abrams,
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- E., Libgober, J., &amp; List, J. A. (2020). Research registries: Facts, myths,
278
- and possible improvements (No. w27250). <em>National Bureau of Economic Research.
279
- </em><a href=\"https://doi.org/10.3386/w27250\">https://doi.org/10.3386/w27250</a></p><p>Bakker,
280
- M., Veldkamp, C. L., van Assen, M. A., Crompvoets, E. A., Ong, H. H., Nosek,
281
- B. A.,…&amp; Wicherts, J. M. (2020). Ensuring the quality and specificity
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- of preregistrations. <em>PLoS Biology, 18</em>(12), e3000937. <a href=\"https://doi.org/10.1371/journal.pbio.3000937\">https://doi.org/10.1371/journal.pbio.3000937</a></p><p>Claesen,
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- practice.</em> Metascience2023, Washington, DC. Abstract: <a href=\"https://metascience.info/events/researchers-decision-making-navigating-ambiguity-in-research-practice/\">https://metascience.info/events/researchers-decision-making-navigating-ambiguity-in-research-practice/</a>
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327
- (2023, March 16). There are unknown unknowns. <em>Wikipedia</em>. https://en.wikipedia.org/wiki/There_are_unknown_unknowns</p><h4>Endnotes</h4><p>1.&nbsp;Here,
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- I define confirmatory tests as planned tests, and exploratory tests as unplanned
329
- tests. This conceptualization is consistent with the frequentist rationale
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- for preregistration, according to which unplanned tests undermine assumptions
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- regarding Type I error rates (Nosek et al., 2019, p. 816). I acknowledge that
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- there are other definitions for “confirmatory” and “exploratory”, including
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- definitions that view them as existing at opposite ends of a continuum rather
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- than as discrete categories (e.g., Fife &amp; Rodgers, 2019). According to
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- this continuum perspective, larger deviations from preregistered plans result
336
- in “more exploratory” tests than smaller deviations. I don’t subscribe to
337
- this continuum perspective, because it is unclear how to formally assess some
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- deviations as being “larger” or “smaller” than others. I agree that research
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- studies can be described as being more confirmatory or exploratory, because
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- they can contain a greater proportion of planned or unplanned tests. However,
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- in my view, the tests themselves can only be either confirmatory or exploratory,
342
- because they can only be either planned or unplanned.</p><h4>Acknowledgements</h4><p>I’m
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- grateful to Tom van Drimmelen for his comments on an earlier version of this
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- article.</p><h4>PDF Download</h4><p>You can download a PDF version of this
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- article <a href=\"https://doi.org/10.31222/osf.io/3t7pc\">here</a>.</p><h4>Reference</h4><p>The
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- reference for this article is:</p><p>Rubin, M. (2023, June 7). The preregistration
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- prescriptiveness trade-off and unknown unknowns in science: Comments on Van
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- Drimmelen (2023). <em>Critical Metascience: MetaArXiv</em>. <a href=\"https://doi.org/10.31222/osf.io/3t7pc\">https://doi.org/10.31222/osf.io/3t7pc</a></p><h4>Please
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