Man pages for serghiou/rtransparent
Identifies indicators of transparency
| dot-bound | Place boundaries around words |
| dot-create_register_pmc_title | Identify registration titles - specific with no negation |
| dot-create_synonyms | A list of word synonyms |
| dot-encase | Encace words within parentheses and OR statements |
| dot-first_capital | Create a regular expression where the first letter is capital |
| dot-get_coi_pmc_fn | Identify elements with COI attributes |
| dot-get_coi_pmc_title | Identify COI titles using XML labels |
| dot-get_fund_pmc_group | Identify funding group elements in NLM XML files |
| dot-get_fund_pmc_source | Identify funding source elements in NLM XML files |
| dot-get_fund_pmc_title | Identify funding titles using XML labels |
| dot-get_ids | Extract PMIDs and DOIs |
| dot-get_text | Get the desired text from the xml_document |
| dot-get_xml | Read an XML file into an xml_document |
| dot-max_words | Place boundaries around words |
| dot-negate_coi_1 | Negate statements that mention conflict but are not COI |
| dot-negate_disclosure_1 | Negate disclosures that are funding statements |
| dot-negate_disclosure_2 | Negate disclosures that are neither COI nor funding... |
| dot-negate_registry_1 | Negate unwanted mentions of registry |
| dot-negate_reg_title_1 | Negate unwanted mentions of title |
| dot-negate_reg_title_2 | Negate titles that mention that there was no registration |
| dot-obliterate_apostrophe_1 | Remove apostrophe |
| dot-obliterate_comma_1 | Remove commas |
| dot-obliterate_contribs | Remove author contribution statements |
| dot-obliterate_fullstop_1 | Returns the list of paragraphs without potentially misleading... |
| dot-obliterate_hash_1 | Remove hash |
| dot-obliterate_honoraria_1 | Remove irrelevat mentions of honoraria |
| dot-obliterate_line_break_1 | Remove break of line tags. |
| dot-obliterate_punct_1 | Remove uninformative punctuation |
| dot-obliterate_references_1 | Remove references |
| dot-obliterate_refs_1 | Remove references |
| dot-obliterate_refs_2 | Remove mentions of previously reported registered studies |
| dot-obliterate_semicolon_1 | Remove semicolons when within parentheses |
| dot-reroot_xml | Reconfigure the PMC XML so that the top node is "article". |
| dot-rt_coi_pmc | Identify and extract Conflicts of Interest (COI) statements... |
| dot-rt_fund_pmc | Identify and extract Funding statements in PMC XML files. |
| dot-rt_register_pmc | Identify and extract Registration statements in PMC XML... |
| dot-title | Create a regex for titles |
| dot-title_strict | Create a regex for titles |
| dot-tokenize | Tokenize NLM XML files |
| dot-where_acknows_txt | Restrict to text after the body of the article and references |
| dot-where_methods_txt | Find the Methods section |
| dot-where_refs_txt | Find the index of the references |
| dot-which_advisor_1 | Identify advisors |
| dot-which_benefit_1 | Identify mentions of receiving benefits |
| dot-which_board_1 | Identify board membership |
| dot-which_brief | Identify mentions of brief explanation |
| dot-which_coi_1 | Identify standard mentions of COI statements |
| dot-which_coi_2 | Identify less explicit mentions of COI statements. |
| dot-which_commercial_1 | Identify less explicit mentions of commercial interest |
| dot-which_commercial_ack_1 | Identify mentions of commercial funding |
| dot-which_connections_1 | Identify mentions of financial connections |
| dot-which_connections_2 | Identify declarations of connections |
| dot-which_consultant_1 | Identify consultants |
| dot-which_consults_1 | Identify mentions of consulting |
| dot-which_ct_1 | Identify mentions of registration on ClinicalTrials.gov |
| dot-which_ct_2 | Identify mentions of registration on ClinicalTrials.gov |
| dot-which_ct_3 | Identify mentions of registration on ClinicalTrials.gov |
| dot-which_disclosure_1 | Identify mentions of financial disclosures |
| dot-which_fees_1 | Identify mentions of paid fees |
| dot-which_founder_1 | Identify founders |
| dot-which_funded_ct_1 | Identify mentions of funding followed by NCT |
| dot-which_grants_1 | Identify receipt of grants |
| dot-which_no_coi_1 | Identify statements of no COI |
| dot-which_no_funder_role_1 | Identify statements that the funders were not involved |
| dot-which_not_registered_1 | Identify mentions of lack of registration |
| dot-which_paid_1 | Identify payments |
| dot-which_prospero_1 | Identify mentions of registration on PROSPERO |
| dot-which_protocol_1 | Identify mentions of protocol |
| dot-which_protocol_2 | Identify mentions of protocol |
| dot-which_registered_1 | Identify generic mentions of registration |
| dot-which_registered_2 | Identify generic mentions of registration |
| dot-which_registered_3 | Identify generic mentions of registration |
| dot-which_registered_4 | Identify generic mentions of registration |
| dot-which_registered_5 | Identify generic mentions of registration |
| dot-which_registration_1 | Identify generic mentions of registration |
| dot-which_registration_2 | Identify generic mentions of registration |
| dot-which_registration_3 | Identify generic mentions of registration |
| dot-which_registration_4 | Identify generic mentions of registration |
| dot-which_registry_1 | Identify mentions of registry |
| dot-which_reg_title_1 | Identify registration titles - sensitive with negation |
| dot-which_reg_title_2 | Identify registration titles - specific with no negation |
| dot-which_reg_title_3 | Identify registration titles - specific |
| dot-which_reg_title_4 | Identify registration titles - specific |
| dot-which_rights_1 | Identify mentions of proprietary material |
| find_methods | Find the Methods section |
| get_acknow_1 | Identify mentions of "Acknowledgement and" |
| get_acknow_2 | Identify acknowledgements |
| get_authors_1 | Identify mentions of "the authors ... financial support |
| get_authors_2 | Identify mentions of "the authors have no funding ..." |
| get_common_1 | Get common phrases |
| get_common_2 | Get common phrases |
| get_common_3 | Get common phrases |
| get_common_4 | Get common phrases |
| get_common_5 | Get common phrases |
| get_ct_1 | Identify mentions of registration on ClinicalTrials.gov |
| get_ct_2 | Identify mentions of registration on ClinicalTrials.gov |
| get_developed_1 | Identify mentions of developed |
| get_disclosure_1 | Identify mentions of Disclosure statements |
| get_disclosure_2 | Identify mentions of Disclosure statements |
| get_financial_1 | Identify mentions of Financial support titles |
| get_financial_2 | Identify mentions of Financial support titles followed by... |
| get_financial_3 | Identify mentions of Financial support titles followed by... |
| get_french_1 | Identify mentions of Grant numbers in the... |
| get_fund_1 | Identify mentions of "funding for this study was..." |
| get_fund_2 | Identify mentions of Funding titles |
| get_fund_3 | Identify mentions of Funding titles |
| get_fund_acknow | Identify mentions of funds in acknowledgements |
| get_fund_acknow_new | Identify mentions of funds in acknowledgements |
| get_funded_ct_1 | Identify mentions of funding followed by NCT |
| get_grant_1 | Identify mentions of Financial support titles |
| get_not_registered_1 | Identify mentions of lack of registration |
| get_project_acknow | Identify mentions of project numbers. |
| get_prospero_1 | Identify mentions of registration on PROSPERO |
| get_protocol_1 | Identify mentions of protocol |
| get_protocol_2 | Identify mentions of protocol |
| get_received_1 | Identify mentions of received |
| get_received_2 | Identify mentions of received |
| get_recipient_1 | Identify mentions of recepient |
| get_registered_1 | Identify generic mentions of registration |
| get_registered_2 | Identify generic mentions of registration |
| get_registered_3 | Identify generic mentions of registration |
| get_registered_4 | Identify generic mentions of registration |
| get_registered_5 | Identify generic mentions of registration |
| get_registration_1 | Identify generic mentions of registration |
| get_registration_2 | Identify generic mentions of registration |
| get_registration_3 | Identify generic mentions of registration |
| get_registration_4 | Identify generic mentions of registration |
| get_registry_1 | Identify mentions of registry |
| get_reg_title_1 | Identify registration titles - sensitive with negation |
| get_reg_title_2 | Identify registration titles - specific with no negation |
| get_reg_title_3 | Identify registration titles - specific |
| get_reg_title_4 | Identify registration titles - specific |
| get_support_1 | Identify mentions of support |
| get_support_10 | Identify mentions of support |
| get_support_2 | Identify mentions of support |
| get_support_3 | Identify mentions of support |
| get_support_4 | Identify mentions of support |
| get_support_6 | Identify mentions of support |
| get_support_7 | Identify mentions of support |
| get_support_8 | Identify mentions of support |
| get_support_9 | Identify mentions of support |
| get_supported_1 | Identify mentions of "Supported by ..." |
| get_thank_1 | Identify mentions of "thank ... financial support |
| get_thank_2 | Identify mentions of thank you statements |
| negate_absence_1 | Avoid mentions that no funding information was provided |
| negate_conflict_1 | Avoid financial that is part of COI statements |
| negate_disclosure_1 | Avoid disclosures that are in fact COI statements |
| negate_disclosure_2 | Identify "Funding disclosure. Nothing to declare" statements |
| negate_registry_1 | Negate unwanted mentions of registry |
| negate_reg_title_1 | Negate unwanted mentions of title |
| obliterate_apostrophe_1 | Remove apostrophe |
| obliterate_comma_1 | Remove commas |
| obliterate_conflict_1 | Remove mentions of COIs that may cause FPs |
| obliterate_conflict_2 | Remove COI statements with language relevant to funding... |
| obliterate_disclosure_1 | Remove disclosures with inappropriate sentences |
| obliterate_fullstop_1 | Remove fullstops that are unlikely to represent end of... |
| obliterate_hash_1 | Remove hash |
| obliterate_misleading_fund_1 | Remove mentions of commonly misleading funding statements |
| obliterate_references_1 | Remove references |
| obliterate_refs_1 | Remove references |
| obliterate_semicolon_1 | Remove semicolons when within parentheses |
| rt_all | Identify and extract statements of COI, Funding and... |
| rt_all_pmc | Identify and extract statements of COI, Funding and... |
| rt_coi | Identify and extract Conflicts of Interest (COI) statements... |
| rt_coi_pmc | Identify and extract Conflicts of Interest (COI) statements... |
| rt_data_code | Identify and extract Data and Code statements in TXT files. |
| rt_data_code_pmc | Identify and extract Data and Code sharing from PMC XML... |
| rt_data_code_pmc_list | Identify and extract Data and Code sharing from PMC XML... |
| rt_fund | Identify and extract Funding statements in TXT files. |
| rt_fund_pmc | Identify and extract Funding statements in PMC XML files. |
| rtransparent-package | rtransparent: Identify indicators of transparency in the... |
| rt_read_pdf | Covert PDF files into TXT files. |
| rt_register | Identify and extract Registration statements in TXT files. |
| rt_register_pmc | Identify and extract Conflicts of Interest statements in PMC... |
