Package: RISmed 2.3.2

RISmed: Download Content from NCBI Databases

A set of tools to extract bibliographic content from the National Center for Biotechnology Information (NCBI) databases, including PubMed. The name RISmed is a portmanteau of RIS (for Research Information Systems, a common tag format for bibliographic data) and PubMed.

Authors:Stephanie Kovalchik [aut, cre]

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RISmed/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/skoval/rismed/issues

Datasets:
  • myeloma - Example of results from 'EUtilsGet'

On CRAN:

6.94 score 39 stars 3 packages 248 scripts 676 downloads 24 mentions 94 exports 11 dependencies

Last updated 3 years agofrom:f61c84dc29. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winERRORNov 05 2024
R-4.5-linuxERRORNov 05 2024
R-4.4-winERRORNov 05 2024
R-4.4-macERRORNov 05 2024
R-4.3-winERRORNov 05 2024
R-4.3-macERRORNov 05 2024

Exports:AbstractTextAffiliationArticleIdArticleTitleAuthorBookBeginningDateBookEditorsBookEndingDateBookMediumBookPublisherBookPublisherLocationBookTitleCitationsCOIStatementCopyrightInformationCountryDayAcceptedDayArticleDateDayEntrezDayEpublishDayMedlineDayPmcDayPpublishDayPubDateDayPubmedDayReceivedDayRevisedDOIELocationIDEUtilsGetEUtilsQueryEUtilsSummaryGrantIDHourAcceptedHourEntrezHourEpublishHourMedlineHourPmcHourPpublishHourPubmedHourReceivedISOAbbreviationISSNISSNLinkingIssueKeywordsLanguageMedlineMedlinePgnMedlineTAMeshMinuteAcceptedMinuteEntrezMinuteEpublishMinuteMedlineMinutePmcMinutePpublishMinutePubmedMinuteReceivedMonthAcceptedMonthArticleDateMonthEntrezMonthEpublishMonthMedlineMonthPmcMonthPpublishMonthPubDateMonthPubmedMonthReceivedMonthRevisedNlmUniqueIDPMIDprintPublicationStatusPublicationTypeQueryQueryCountQueryIdQueryTranslationshowsummaryTitleVolumeYearAcceptedYearArticleDateYearEntrezYearEpublishYearMedlineYearPmcYearPpublishYearPubDateYearPubmedYearReceivedYearRevised

Dependencies:askpassclicurlhttrjsonlitemimeopensslR6rlangsysxml2

Readme and manuals

Help Manual

Help pageTopics
Download content from NCBI databases.RISmed-package RISmed
Extracts 'AbstractText' from 'Medline' object.AbstractText
~~ Methods for Function 'AbstractText' in Package 'RISmed' ~~AbstractText,Medline-method AbstractText-methods
Extracts 'Affiliation' from 'Medline' object.Affiliation
~~ Methods for Function 'Affiliation' in Package 'RISmed' ~~Affiliation,Medline-method Affiliation-methods
Extracts 'ArticleId' from 'Medline' object.ArticleId
~~ Methods for Function 'ArticleId' in Package 'RISmed' ~~ArticleId,Medline-method ArticleId-methods
Extracts 'ArticleTitle' from 'Medline' object.ArticleTitle
~~ Methods for Function 'ArticleTitle' in Package 'RISmed' ~~ArticleTitle,Medline-method ArticleTitle-methods
Extracts 'Author' from 'Medline' object.Author
~~ Methods for Function 'Author' in Package 'RISmed' ~~Author,Medline-method Author-methods
Extracts 'BookBeginningDate' from 'Medline' object.BookBeginningDate
~~ Methods for Function 'BookBeginningDate' in Package 'RISmed' ~~BookBeginningDate,Medline-method BookBeginningDate-methods
Extracts 'BookEditors' from 'Medline' object.BookEditors
~~ Methods for Function 'BookEditors' in Package 'RISmed' ~~BookEditors,Medline-method BookEditors-methods
Extracts 'BookEndingDate' from 'Medline' object.BookEndingDate
~~ Methods for Function 'BookEndingDate' in Package 'RISmed' ~~BookEndingDate,Medline-method BookEndingDate-methods
Extracts 'BookMedium' from 'Medline' object.BookMedium
~~ Methods for Function 'BookMedium' in Package 'RISmed' ~~BookMedium,Medline-method BookMedium-methods
Extracts 'BookPublisher' from 'Medline' object.BookPublisher
~~ Methods for Function 'BookPublisher' in Package 'RISmed' ~~BookPublisher,Medline-method BookPublisher-methods
Extracts 'BookPublisherLocation' from 'Medline' object.BookPublisherLocation
~~ Methods for Function 'BookPublisherLocation' in Package 'RISmed' ~~BookPublisherLocation,Medline-method BookPublisherLocation-methods
Extracts 'BookTitle' from 'Medline' object.BookTitle
~~ Methods for Function 'BookTitle' in Package 'RISmed' ~~BookTitle,Medline-method BookTitle-methods
Concatenate Medlinec,ANY,ANY-method c,Medline-method
List of citing article titles where listed in PubMed.Citations
~~ Methods for Function 'Citations' in Package 'RISmed' ~~Citations,EUtilsSummary-method Citations,Medline-method Citations-methods
Extracts 'COIStatement' from 'Medline' object.COIStatement
~~ Methods for Function 'COIStatement' in Package 'RISmed' ~~COIStatement,Medline-method COIStatement-methods
Extracts 'CopyrightInformation' from 'Medline' object.CopyrightInformation
~~ Methods for Function 'CopyrightInformation' in Package 'RISmed' ~~CopyrightInformation,Medline-method CopyrightInformation-methods
Extracts 'Country' from 'Medline' object.Country
~~ Methods for Function 'Country' in Package 'RISmed' ~~Country,Medline-method Country-methods
Extracts 'DayAccepted' from 'Medline' object.DayAccepted
~~ Methods for Function 'DayAccepted' in Package 'RISmed' ~~DayAccepted,Medline-method DayAccepted-methods
Extracts 'DayArticleDate' from 'Medline' object.DayArticleDate
~~ Methods for Function 'DayArticleDate' in Package 'RISmed' ~~DayArticleDate,Medline-method DayArticleDate-methods
Extracts 'DayEntrez' from 'Medline' object.DayEntrez
~~ Methods for Function 'DayEntrez' in Package 'RISmed' ~~DayEntrez,Medline-method DayEntrez-methods
Extracts 'DayEpublish' from 'Medline' object.DayEpublish
~~ Methods for Function 'DayEpublish' in Package 'RISmed' ~~DayEpublish,Medline-method DayEpublish-methods
Extracts 'DayMedline' from 'Medline' object.DayMedline
~~ Methods for Function 'DayMedline' in Package 'RISmed' ~~DayMedline,Medline-method DayMedline-methods
Extracts 'DayPmc' from 'Medline' object.DayPmc
~~ Methods for Function 'DayPmc' in Package 'RISmed' ~~DayPmc,Medline-method DayPmc-methods
Extracts 'DayPpublish' from 'Medline' object.DayPpublish
~~ Methods for Function 'DayPpublish' in Package 'RISmed' ~~DayPpublish,Medline-method DayPpublish-methods
Extracts 'DayPubDate' from 'Medline' object.DayPubDate
~~ Methods for Function 'DayPubDate' in Package 'RISmed' ~~DayPubDate,Medline-method DayPubDate-methods
Extracts 'DayPubmed' from 'Medline' object.DayPubmed
~~ Methods for Function 'DayPubmed' in Package 'RISmed' ~~DayPubmed,Medline-method DayPubmed-methods
Extracts 'DayReceived' from 'Medline' object.DayReceived
~~ Methods for Function 'DayReceived' in Package 'RISmed' ~~DayReceived,Medline-method DayReceived-methods
Extracts 'DayRevised' from 'Medline' object.DayRevised
~~ Methods for Function 'DayRevised' in Package 'RISmed' ~~DayRevised,Medline-method DayRevised-methods
Extracts 'DOI' from 'Medline' object.DOI
~~ Methods for Function 'DOI' in Package 'RISmed' ~~DOI,Medline-method DOI-methods
Extracts 'ELocationID' from 'Medline' object.ELocationID
~~ Methods for Function 'ELocationID' in Package 'RISmed' ~~ELocationID,Medline-method ELocationID-methods
Results of an NCBI EUtils queryEUtilsGet
Construct URL to make NCBI EUtils queryEUtilsQuery EUtilsQuery-class
Get summary of NCBI EUtils queryEUtilsSummary
Class '"EUtilsSummary"'EUtilsSummary-class
Extracts list of 'GrantID' info 'Medline' object including 'GrantID' and 'GrantAgency' where listed in PubMed.GrantID
~~ Methods for Function 'GrantID' in Package 'RISmed' ~~GrantID,Medline-method GrantID-methods
Extracts 'HourAccepted' from 'Medline' object.HourAccepted
~~ Methods for Function 'HourAccepted' in Package 'RISmed' ~~HourAccepted,Medline-method HourAccepted-methods
Extracts 'HourEntrez' from 'Medline' object.HourEntrez
~~ Methods for Function 'HourEntrez' in Package 'RISmed' ~~HourEntrez,Medline-method HourEntrez-methods
Extracts 'HourEpublish' from 'Medline' object.HourEpublish
~~ Methods for Function 'HourEpublish' in Package 'RISmed' ~~HourEpublish,Medline-method HourEpublish-methods
Extracts 'HourMedline' from 'Medline' object.HourMedline
~~ Methods for Function 'HourMedline' in Package 'RISmed' ~~HourMedline,Medline-method HourMedline-methods
Extracts 'HourPmc' from 'Medline' object.HourPmc
~~ Methods for Function 'HourPmc' in Package 'RISmed' ~~HourPmc,Medline-method HourPmc-methods
Extracts 'HourPpublish' from 'Medline' object.HourPpublish
~~ Methods for Function 'HourPpublish' in Package 'RISmed' ~~HourPpublish,Medline-method HourPpublish-methods
Extracts 'HourPubmed' from 'Medline' object.HourPubmed
~~ Methods for Function 'HourPubmed' in Package 'RISmed' ~~HourPubmed,Medline-method HourPubmed-methods
Extracts 'HourReceived' from 'Medline' object.HourReceived
~~ Methods for Function 'HourReceived' in Package 'RISmed' ~~HourReceived,Medline-method HourReceived-methods
Extracts 'ISOAbbreviation' from 'Medline' object.ISOAbbreviation
~~ Methods for Function 'ISOAbbreviation' in Package 'RISmed' ~~ISOAbbreviation,Medline-method ISOAbbreviation-methods
Extracts 'ISSN' from 'Medline' object.ISSN
~~ Methods for Function 'ISSN' in Package 'RISmed' ~~ISSN,Medline-method ISSN-methods
Extracts 'ISSNLinking' from 'Medline' object.ISSNLinking
~~ Methods for Function 'ISSNLinking' in Package 'RISmed' ~~ISSNLinking,Medline-method ISSNLinking-methods
Extracts 'Issue' from 'Medline' object.Issue
~~ Methods for Function 'Issue' in Package 'RISmed' ~~Issue,Medline-method Issue-methods
Extracts list of 'Keywords' info from 'Medline' object.Keywords
~~ Methods for Function 'Keywords' in Package 'RISmed' ~~Keywords,Medline-method Keywords-methods
Extracts 'Language' from 'Medline' object.Language
~~ Methods for Function 'Language' in Package 'RISmed' ~~Language,Medline-method Language-methods
Class '"Medline"'Medline Medline-class
Extracts 'MedlinePgn' from 'Medline' object.MedlinePgn
~~ Methods for Function 'MedlinePgn' in Package 'RISmed' ~~MedlinePgn,Medline-method MedlinePgn-methods
Extracts 'MedlineTA' from 'Medline' object.MedlineTA
~~ Methods for Function 'MedlineTA' in Package 'RISmed' ~~MedlineTA,Medline-method MedlineTA-methods
Extracts 'Mesh' headings from 'Medline' object.Mesh
~~ Methods for Function 'Mesh' in Package 'RISmed' ~~Mesh,Medline-method Mesh-methods
Extracts 'MinuteAccepted' from 'Medline' object.MinuteAccepted
~~ Methods for Function 'MinuteAccepted' in Package 'RISmed' ~~MinuteAccepted,Medline-method MinuteAccepted-methods
Extracts 'MinuteEntrez' from 'Medline' object.MinuteEntrez
~~ Methods for Function 'MinuteEntrez' in Package 'RISmed' ~~MinuteEntrez,Medline-method MinuteEntrez-methods
Extracts 'MinuteEpublish' from 'Medline' object.MinuteEpublish
~~ Methods for Function 'MinuteEpublish' in Package 'RISmed' ~~MinuteEpublish,Medline-method MinuteEpublish-methods
Extracts 'MinuteMedline' from 'Medline' object.MinuteMedline
~~ Methods for Function 'MinuteMedline' in Package 'RISmed' ~~MinuteMedline,Medline-method MinuteMedline-methods
Extracts 'MinutePmc' from 'Medline' object.MinutePmc
~~ Methods for Function 'MinutePmc' in Package 'RISmed' ~~MinutePmc,Medline-method MinutePmc-methods
Extracts 'MinutePpublish' from 'Medline' object.MinutePpublish
~~ Methods for Function 'MinutePpublish' in Package 'RISmed' ~~MinutePpublish,Medline-method MinutePpublish-methods
Extracts 'MinutePubmed' from 'Medline' object.MinutePubmed
~~ Methods for Function 'MinutePubmed' in Package 'RISmed' ~~MinutePubmed,Medline-method MinutePubmed-methods
Extracts 'MinuteReceived' from 'Medline' object.MinuteReceived
~~ Methods for Function 'MinuteReceived' in Package 'RISmed' ~~MinuteReceived,Medline-method MinuteReceived-methods
Extracts 'MonthAccepted' from 'Medline' object.MonthAccepted
~~ Methods for Function 'MonthAccepted' in Package 'RISmed' ~~MonthAccepted,Medline-method MonthAccepted-methods
Extracts 'MonthArticleDate' from 'Medline' object.MonthArticleDate
~~ Methods for Function 'MonthArticleDate' in Package 'RISmed' ~~MonthArticleDate,Medline-method MonthArticleDate-methods
Extracts 'MonthEntrez' from 'Medline' object.MonthEntrez
~~ Methods for Function 'MonthEntrez' in Package 'RISmed' ~~MonthEntrez,Medline-method MonthEntrez-methods
Extracts 'MonthEpublish' from 'Medline' object.MonthEpublish
~~ Methods for Function 'MonthEpublish' in Package 'RISmed' ~~MonthEpublish,Medline-method MonthEpublish-methods
Extracts 'MonthMedline' from 'Medline' object.MonthMedline
~~ Methods for Function 'MonthMedline' in Package 'RISmed' ~~MonthMedline,Medline-method MonthMedline-methods
Extracts 'MonthPmc' from 'Medline' object.MonthPmc
~~ Methods for Function 'MonthPmc' in Package 'RISmed' ~~MonthPmc,Medline-method MonthPmc-methods
Extracts 'MonthPpublish' from 'Medline' object.MonthPpublish
~~ Methods for Function 'MonthPpublish' in Package 'RISmed' ~~MonthPpublish,Medline-method MonthPpublish-methods
Extracts 'MonthPubDate' from 'Medline' object.MonthPubDate
~~ Methods for Function 'MonthPubDate' in Package 'RISmed' ~~MonthPubDate,Medline-method MonthPubDate-methods
Extracts 'MonthPubmed' from 'Medline' object.MonthPubmed
~~ Methods for Function 'MonthPubmed' in Package 'RISmed' ~~MonthPubmed,Medline-method MonthPubmed-methods
Extracts 'MonthReceived' from 'Medline' object.MonthReceived
~~ Methods for Function 'MonthReceived' in Package 'RISmed' ~~MonthReceived,Medline-method MonthReceived-methods
Extracts 'MonthRevised' from 'Medline' object.MonthRevised
~~ Methods for Function 'MonthRevised' in Package 'RISmed' ~~MonthRevised,Medline-method MonthRevised-methods
Example of results from 'EUtilsGet'myeloma
Extracts 'NlmUniqueID' from 'Medline' object.NlmUniqueID
~~ Methods for Function 'NlmUniqueID' in Package 'RISmed' ~~NlmUniqueID,Medline-method NlmUniqueID-methods
Extracts 'PMID' from 'Medline' object.PMID
~~ Methods for Function 'PMID' in Package 'RISmed' ~~PMID,Medline-method PMID-methods
Print method for Medline objectprint,Medline-method
Print method for EUtilsSummary objectprint,EUtilsSummary-method print-methods
Extracts 'PublicationStatus' from 'Medline' object.PublicationStatus
~~ Methods for Function 'PublicationStatus' in Package 'RISmed' ~~PublicationStatus,Medline-method PublicationStatus-methods
Extracts 'PublicationType' from 'Medline' object.PublicationType
~~ Methods for Function 'PublicationType' in Package 'RISmed' ~~PublicationType,Medline-method PublicationType-methods
Extract 'Query' from 'Medline' object.Query
~~ Methods for Function 'Query' in Package 'RISmed' ~~Query,Medline-method Query-methods
Count of record results for EUtilsQueryQueryCount QueryCount,EUtilsSummary-method
Get ids from EUtilsQueryQueryId QueryId,EUtilsSummary-method
Get the NCBI query translation from EUtilsQueryQueryTranslation QueryTranslation,EUtilsSummary-method
Show method for Medline objectshow,Medline-method
Show method for EUtilsSummary objectshow,EUtilsSummary-method show-methods
Summary method for EUtilsSummary objectsummary,EUtilsSummary-method summary-methods
Extracts 'Title' from 'Medline' object.Title
~~ Methods for Function 'Title' in Package 'RISmed' ~~Title,Medline-method Title-methods
Extracts 'Volume' from 'Medline' object.Volume
~~ Methods for Function 'Volume' in Package 'RISmed' ~~Volume,Medline-method Volume-methods
Extracts 'YearAccepted' from 'Medline' object.YearAccepted
~~ Methods for Function 'YearAccepted' in Package 'RISmed' ~~YearAccepted,Medline-method YearAccepted-methods
Extracts 'YearArticleDate' from 'Medline' object.YearArticleDate
~~ Methods for Function 'YearArticleDate' in Package 'RISmed' ~~YearArticleDate,Medline-method YearArticleDate-methods
Extracts 'YearEntrez' from 'Medline' object.YearEntrez
~~ Methods for Function 'YearEntrez' in Package 'RISmed' ~~YearEntrez,Medline-method YearEntrez-methods
Extracts 'YearEpublish' from 'Medline' object.YearEpublish
~~ Methods for Function 'YearEpublish' in Package 'RISmed' ~~YearEpublish,Medline-method YearEpublish-methods
Extracts 'YearMedline' from 'Medline' object.YearMedline
~~ Methods for Function 'YearMedline' in Package 'RISmed' ~~YearMedline,Medline-method YearMedline-methods
Extracts 'YearPmc' from 'Medline' object.YearPmc
~~ Methods for Function 'YearPmc' in Package 'RISmed' ~~YearPmc,Medline-method YearPmc-methods
Extracts 'YearPpublish' from 'Medline' object.YearPpublish
~~ Methods for Function 'YearPpublish' in Package 'RISmed' ~~YearPpublish,Medline-method YearPpublish-methods
Extracts 'YearPubDate' from 'Medline' object.YearPubDate
~~ Methods for Function 'YearPubDate' in Package 'RISmed' ~~YearPubDate,Medline-method YearPubDate-methods
Extracts 'YearPubmed' from 'Medline' object.YearPubmed
~~ Methods for Function 'YearPubmed' in Package 'RISmed' ~~YearPubmed,Medline-method YearPubmed-methods
Extracts 'YearReceived' from 'Medline' object.YearReceived
~~ Methods for Function 'YearReceived' in Package 'RISmed' ~~YearReceived,Medline-method YearReceived-methods
Extracts 'YearRevised' from 'Medline' object.YearRevised
~~ Methods for Function 'YearRevised' in Package 'RISmed' ~~YearRevised,Medline-method YearRevised-methods