├── data └── myeloma.RData ├── man ├── id.Rd ├── count.Rd ├── COIStatement.Rd ├── DOI-methods.Rd ├── ISSN-methods.Rd ├── PMID-methods.Rd ├── ISSN.Rd ├── PMID.Rd ├── Issue-methods.Rd ├── Query-methods.Rd ├── Title-methods.Rd ├── Cited.Rd ├── DayPmc-methods.Rd ├── Issue.Rd ├── Title.Rd ├── Volume-methods.Rd ├── translation.Rd ├── Country-methods.Rd ├── GrantID-methods.Rd ├── HourPmc-methods.Rd ├── Volume.Rd ├── YearPmc-methods.Rd ├── Country.Rd ├── Keywords-methods.Rd ├── Language-methods.Rd ├── MonthPmc-methods.Rd ├── ArticleId-methods.Rd ├── BookTitle-methods.Rd ├── DayEntrez-methods.Rd ├── DayPubmed-methods.Rd ├── MedlineTA-methods.Rd ├── MinutePmc-methods.Rd ├── Query.Rd ├── print-method.Rd ├── print.Rd ├── show-Medline-methods.Rd ├── show-methods.Rd ├── Language.Rd ├── ArticleId.Rd ├── BookMedium-methods.Rd ├── BookTitle.Rd ├── DayMedline-methods.Rd ├── DayPubDate-methods.Rd ├── DayRevised-methods.Rd ├── HourEntrez-methods.Rd ├── HourPubmed-methods.Rd ├── MedlinePgn-methods.Rd ├── MedlineTA.Rd ├── YearEntrez-methods.Rd ├── YearPubmed-methods.Rd ├── Affiliation-methods.Rd ├── BookEditors-methods.Rd ├── DayAccepted-methods.Rd ├── DayEpublish-methods.Rd ├── DayPpublish-methods.Rd ├── DayReceived-methods.Rd ├── ELocationID-methods.Rd ├── HourMedline-methods.Rd ├── ISSNLinking-methods.Rd ├── Keywords.Rd ├── MonthEntrez-methods.Rd ├── MonthPubmed-methods.Rd ├── NlmUniqueID-methods.Rd ├── YearMedline-methods.Rd ├── YearPubDate-methods.Rd ├── YearRevised-methods.Rd ├── summary-methods.Rd ├── AbstractText-methods.Rd ├── ArticleTitle-methods.Rd ├── BookMedium.Rd ├── COIStatement-methods.Rd ├── HourAccepted-methods.Rd ├── HourEpublish-methods.Rd ├── HourPpublish-methods.Rd ├── HourReceived-methods.Rd ├── MedlinePgn.Rd ├── MinuteEntrez-methods.Rd ├── MinutePubmed-methods.Rd ├── MonthMedline-methods.Rd ├── MonthPubDate-methods.Rd ├── MonthRevised-methods.Rd ├── YearAccepted-methods.Rd ├── YearEpublish-methods.Rd ├── YearPpublish-methods.Rd ├── YearReceived-methods.Rd ├── Affiliation.Rd ├── BookEditors.Rd ├── BookPublisher-methods.Rd ├── ELocationID.Rd ├── ISSNLinking.Rd ├── MinuteMedline-methods.Rd ├── MonthAccepted-methods.Rd ├── MonthEpublish-methods.Rd ├── MonthPpublish-methods.Rd ├── MonthReceived-methods.Rd ├── NlmUniqueID.Rd ├── AbstractText.Rd ├── ArticleTitle.Rd ├── BookEndingDate-methods.Rd ├── DayArticleDate-methods.Rd ├── MinuteAccepted-methods.Rd ├── MinuteEpublish-methods.Rd ├── MinutePpublish-methods.Rd ├── MinuteReceived-methods.Rd ├── BookPublisher.Rd ├── ISOAbbreviation-methods.Rd ├── PublicationType-methods.Rd ├── YearArticleDate-methods.Rd ├── c-methods.Rd ├── BookEndingDate.Rd ├── MonthArticleDate-methods.Rd ├── BookBeginningDate-methods.Rd ├── Cited-methods.Rd ├── PublicationStatus-methods.Rd ├── PublicationType.Rd ├── ISOAbbreviation.Rd ├── DOI.Rd ├── BookBeginningDate.Rd ├── PublicationStatus.Rd ├── CopyrightInformation-methods.Rd ├── BookPublisherLocation-methods.Rd ├── GrantID.Rd ├── CopyrightInformation.Rd ├── BookPublisherLocation.Rd ├── Author-methods.Rd ├── myeloma.Rd ├── Mesh-methods.Rd ├── Author.Rd ├── DayEntrez.Rd ├── DayPmc.Rd ├── DayPubDate.Rd ├── DayRevised.Rd ├── DayMedline.Rd ├── HourEntrez.Rd ├── YearEntrez.Rd ├── YearPubDate.Rd ├── YearRevised.Rd ├── DayAccepted.Rd ├── DayReceived.Rd ├── HourMedline.Rd ├── HourPmc.Rd ├── MonthEntrez.Rd ├── YearMedline.Rd ├── YearPmc.Rd ├── DayEpublish.Rd ├── HourAccepted.Rd ├── HourReceived.Rd ├── MonthPmc.Rd ├── MonthPubDate.Rd ├── MonthRevised.Rd ├── YearAccepted.Rd ├── YearReceived.Rd ├── DayPpublish.Rd ├── MinuteEntrez.Rd ├── MonthAccepted.Rd ├── MonthMedline.Rd ├── MonthReceived.Rd ├── DayPubmed.Rd ├── HourEpublish.Rd ├── HourPpublish.Rd ├── MinuteMedline.Rd ├── MinutePmc.Rd ├── YearEpublish.Rd ├── YearPpublish.Rd ├── DayArticleDate.Rd ├── HourPubmed.Rd ├── MinuteAccepted.Rd ├── MinuteReceived.Rd ├── MonthEpublish.Rd ├── MonthPpublish.Rd ├── YearPubmed.Rd ├── MinuteEpublish.Rd ├── MonthPubmed.Rd ├── MinutePpublish.Rd ├── YearArticleDate.Rd ├── MinutePubmed.Rd ├── MonthArticleDate.Rd ├── Mesh.Rd ├── RISmed-package.Rd ├── EUtilsSummary-class.Rd ├── EUtilsGet.Rd ├── EUtilsQuery.Rd ├── EUtilsSummary.Rd └── Medline.Rd ├── DESCRIPTION ├── NAMESPACE ├── R ├── EUtilsSummary.R ├── EUtils.R ├── MedlineC.R ├── AllGenerics.R ├── ParseMedline.R └── Medline.R └── NEWS /data/myeloma.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/skoval/RISmed/HEAD/data/myeloma.RData -------------------------------------------------------------------------------- /man/id.Rd: -------------------------------------------------------------------------------- 1 | \name{QueryId} 2 | \title{Get ids from EUtilsQuery} 3 | \usage{QueryId(object)} 4 | \description{Returns the vector Ids from a E-utility query} 5 | \value{character vector of ids} 6 | \seealso{\code{\link{EUtilsSummary}}} 7 | \alias{QueryId,EUtilsSummary-method} 8 | \alias{QueryId} 9 | \author{Stephanie Kovalchik} 10 | \arguments{\item{object}{object of the \code{EUtilsSummary} class.}} 11 | -------------------------------------------------------------------------------- /man/count.Rd: -------------------------------------------------------------------------------- 1 | \name{QueryCount} 2 | \title{Count of record results for EUtilsQuery} 3 | \usage{QueryCount(object)} 4 | \description{Returns the number of Ids from a E-utility query} 5 | \value{numeric count} 6 | \seealso{\code{\link{EUtilsSummary}}} 7 | \alias{QueryCount,EUtilsSummary-method} 8 | \alias{QueryCount} 9 | \author{Stephanie Kovalchik} 10 | \arguments{\item{object}{object of the \code{EUtilsSummary} class.}} 11 | -------------------------------------------------------------------------------- /man/COIStatement.Rd: -------------------------------------------------------------------------------- 1 | \name{COIStatement} 2 | \alias{COIStatement} 3 | 4 | \title{ 5 | Extracts \code{COIStatement} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{COIStatement} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | COIStatement(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | -------------------------------------------------------------------------------- /man/DOI-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DOI-methods} 2 | \docType{methods} 3 | \alias{DOI-methods} 4 | \alias{DOI,Medline-method} 5 | \title{ ~~ Methods for Function \code{DOI} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DOI} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/ISSN-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{ISSN-methods} 2 | \docType{methods} 3 | \alias{ISSN-methods} 4 | \alias{ISSN,Medline-method} 5 | \title{ ~~ Methods for Function \code{ISSN} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{ISSN} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/PMID-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{PMID-methods} 2 | \docType{methods} 3 | \alias{PMID-methods} 4 | \alias{PMID,Medline-method} 5 | \title{ ~~ Methods for Function \code{PMID} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{PMID} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/ISSN.Rd: -------------------------------------------------------------------------------- 1 | \name{ISSN} 2 | \alias{ISSN} 3 | 4 | \title{ 5 | Extracts \code{ISSN} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{ISSN} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | ISSN(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | ISSN(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/PMID.Rd: -------------------------------------------------------------------------------- 1 | \name{PMID} 2 | \alias{PMID} 3 | 4 | \title{ 5 | Extracts \code{PMID} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{PMID} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | PMID(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | PMID(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/Issue-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Issue-methods} 2 | \docType{methods} 3 | \alias{Issue-methods} 4 | \alias{Issue,Medline-method} 5 | \title{ ~~ Methods for Function \code{Issue} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Issue} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Query-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Query-methods} 2 | \docType{methods} 3 | \alias{Query-methods} 4 | \alias{Query,Medline-method} 5 | \title{ ~~ Methods for Function \code{Query} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Query} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Title-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Title-methods} 2 | \docType{methods} 3 | \alias{Title-methods} 4 | \alias{Title,Medline-method} 5 | \title{ ~~ Methods for Function \code{Title} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Title} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Cited.Rd: -------------------------------------------------------------------------------- 1 | \name{Citations} 2 | \alias{Citations} 3 | 4 | \title{ 5 | List of citing article titles where listed in PubMed. 6 | } 7 | 8 | \description{ 9 | Retrieves the number of citations in PubMed Central for the articles contained in the \code{Medline} object. 10 | } 11 | 12 | \usage{ 13 | Citations(object) 14 | } 15 | 16 | \arguments{ 17 | \item{object}{instance of class \code{Medline}} 18 | } 19 | 20 | \value{vector} 21 | 22 | \seealso{\code{\link{Medline}}} 23 | -------------------------------------------------------------------------------- /man/DayPmc-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayPmc-methods} 2 | \docType{methods} 3 | \alias{DayPmc-methods} 4 | \alias{DayPmc,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayPmc} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayPmc} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Issue.Rd: -------------------------------------------------------------------------------- 1 | \name{Issue} 2 | \alias{Issue} 3 | 4 | \title{ 5 | Extracts \code{Issue} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{Issue} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Issue(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | Issue(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/Title.Rd: -------------------------------------------------------------------------------- 1 | \name{Title} 2 | \alias{Title} 3 | 4 | \title{ 5 | Extracts \code{Title} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{Title} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Title(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | Title(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/Volume-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Volume-methods} 2 | \docType{methods} 3 | \alias{Volume-methods} 4 | \alias{Volume,Medline-method} 5 | \title{ ~~ Methods for Function \code{Volume} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Volume} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/translation.Rd: -------------------------------------------------------------------------------- 1 | \name{QueryTranslation} 2 | \title{Get the NCBI query translation from EUtilsQuery} 3 | \usage{QueryTranslation(object)} 4 | \description{Returns the string translation of a E-utility query} 5 | \value{character query translation} 6 | \seealso{\code{\link{EUtilsSummary}}} 7 | \alias{QueryTranslation,EUtilsSummary-method} 8 | \alias{QueryTranslation} 9 | \author{Stephanie Kovalchik} 10 | \arguments{\item{object}{object of the \code{EUtilsSummary} class.}} 11 | -------------------------------------------------------------------------------- /man/Country-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Country-methods} 2 | \docType{methods} 3 | \alias{Country-methods} 4 | \alias{Country,Medline-method} 5 | \title{ ~~ Methods for Function \code{Country} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Country} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/GrantID-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{GrantID-methods} 2 | \docType{methods} 3 | \alias{GrantID-methods} 4 | \alias{GrantID,Medline-method} 5 | \title{ ~~ Methods for Function \code{GrantID} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{GrantID} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/HourPmc-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{HourPmc-methods} 2 | \docType{methods} 3 | \alias{HourPmc-methods} 4 | \alias{HourPmc,Medline-method} 5 | \title{ ~~ Methods for Function \code{HourPmc} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{HourPmc} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Volume.Rd: -------------------------------------------------------------------------------- 1 | \name{Volume} 2 | \alias{Volume} 3 | 4 | \title{ 5 | Extracts \code{Volume} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{Volume} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Volume(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | Volume(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/YearPmc-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearPmc-methods} 2 | \docType{methods} 3 | \alias{YearPmc-methods} 4 | \alias{YearPmc,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearPmc} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearPmc} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Country.Rd: -------------------------------------------------------------------------------- 1 | \name{Country} 2 | \alias{Country} 3 | 4 | \title{ 5 | Extracts \code{Country} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{Country} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Country(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | Country(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/Keywords-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Keywords-methods} 2 | \docType{methods} 3 | \alias{Keywords-methods} 4 | \alias{Keywords,Medline-method} 5 | \title{ ~~ Methods for Function \code{Keywords} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Keywords} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Language-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Language-methods} 2 | \docType{methods} 3 | \alias{Language-methods} 4 | \alias{Language,Medline-method} 5 | \title{ ~~ Methods for Function \code{Language} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Language} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MonthPmc-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthPmc-methods} 2 | \docType{methods} 3 | \alias{MonthPmc-methods} 4 | \alias{MonthPmc,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthPmc} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthPmc} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/ArticleId-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{ArticleId-methods} 2 | \docType{methods} 3 | \alias{ArticleId-methods} 4 | \alias{ArticleId,Medline-method} 5 | \title{ ~~ Methods for Function \code{ArticleId} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{ArticleId} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/BookTitle-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{BookTitle-methods} 2 | \docType{methods} 3 | \alias{BookTitle-methods} 4 | \alias{BookTitle,Medline-method} 5 | \title{ ~~ Methods for Function \code{BookTitle} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{BookTitle} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/DayEntrez-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayEntrez-methods} 2 | \docType{methods} 3 | \alias{DayEntrez-methods} 4 | \alias{DayEntrez,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayEntrez} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayEntrez} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/DayPubmed-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayPubmed-methods} 2 | \docType{methods} 3 | \alias{DayPubmed-methods} 4 | \alias{DayPubmed,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayPubmed} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayPubmed} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MedlineTA-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MedlineTA-methods} 2 | \docType{methods} 3 | \alias{MedlineTA-methods} 4 | \alias{MedlineTA,Medline-method} 5 | \title{ ~~ Methods for Function \code{MedlineTA} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MedlineTA} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MinutePmc-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MinutePmc-methods} 2 | \docType{methods} 3 | \alias{MinutePmc-methods} 4 | \alias{MinutePmc,Medline-method} 5 | \title{ ~~ Methods for Function \code{MinutePmc} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MinutePmc} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Query.Rd: -------------------------------------------------------------------------------- 1 | \name{Query} 2 | \alias{Query} 3 | 4 | \title{ 5 | Extract \code{Query} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the translated \code{Query} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Query(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | 20 | \value{vector} 21 | 22 | \seealso{\code{\link{Medline}}} 23 | 24 | \examples{ 25 | data(myeloma) 26 | Query(myeloma) 27 | } 28 | -------------------------------------------------------------------------------- /man/print-method.Rd: -------------------------------------------------------------------------------- 1 | \name{print-Medline} 2 | \docType{methods} 3 | \alias{print,Medline-method} 4 | 5 | \title{ Print method for Medline object } 6 | 7 | \description{ 8 | 9 | Print object of class \code{Medline} 10 | 11 | } 12 | 13 | \section{Methods}{ 14 | 15 | \describe{ 16 | 17 | \item{\code{signature(object = "Medline")}}{ 18 | Query translation (if provided) and total fetched record count for \code{Medline} object. 19 | } 20 | 21 | } 22 | } 23 | 24 | \keyword{methods} 25 | 26 | -------------------------------------------------------------------------------- /man/print.Rd: -------------------------------------------------------------------------------- 1 | \name{print-methods} 2 | \docType{methods} 3 | \alias{print-methods} 4 | \alias{print,EUtilsSummary-method} 5 | 6 | \title{ Print method for EUtilsSummary object } 7 | 8 | \description{ 9 | 10 | Print object of class \code{EUtilsSummary} 11 | 12 | } 13 | 14 | \section{Methods}{ 15 | 16 | \describe{ 17 | 18 | \item{\code{signature(object = "EUtilsSummary")}}{ 19 | Query translation for \code{EUtilsSummary} object. 20 | } 21 | 22 | } 23 | } 24 | \keyword{methods} 25 | 26 | -------------------------------------------------------------------------------- /man/show-Medline-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{show-Medline} 2 | \docType{methods} 3 | \alias{show,Medline-method} 4 | 5 | \title{ Show method for Medline object } 6 | 7 | \description{ 8 | 9 | Show object of class \code{Medline} 10 | 11 | } 12 | 13 | \section{Methods}{ 14 | 15 | \describe{ 16 | 17 | \item{\code{signature(object = "Medline")}}{ 18 | Query translation (if provided) and total fetched record count for \code{Medline} object. 19 | } 20 | 21 | } 22 | } 23 | \keyword{methods} 24 | 25 | -------------------------------------------------------------------------------- /man/show-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{show-methods} 2 | \docType{methods} 3 | \alias{show-methods} 4 | \alias{show,EUtilsSummary-method} 5 | 6 | \title{ Show method for EUtilsSummary object } 7 | 8 | \description{ 9 | 10 | Show object of class \code{EUtilsSummary} 11 | 12 | } 13 | 14 | \section{Methods}{ 15 | 16 | \describe{ 17 | 18 | \item{\code{signature(object = "EUtilsSummary")}}{ 19 | Query translation for \code{EUtilsSummary} object. 20 | } 21 | 22 | } 23 | } 24 | \keyword{methods} 25 | 26 | -------------------------------------------------------------------------------- /man/Language.Rd: -------------------------------------------------------------------------------- 1 | \name{Language} 2 | \alias{Language} 3 | 4 | \title{ 5 | Extracts \code{Language} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{Language} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Language(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | Language(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/ArticleId.Rd: -------------------------------------------------------------------------------- 1 | \name{ArticleId} 2 | \alias{ArticleId} 3 | 4 | \title{ 5 | Extracts \code{ArticleId} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{ArticleId} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | ArticleId(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | ArticleId(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/BookMedium-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{BookMedium-methods} 2 | \docType{methods} 3 | \alias{BookMedium-methods} 4 | \alias{BookMedium,Medline-method} 5 | \title{ ~~ Methods for Function \code{BookMedium} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{BookMedium} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/BookTitle.Rd: -------------------------------------------------------------------------------- 1 | \name{BookTitle} 2 | \alias{BookTitle} 3 | 4 | \title{ 5 | Extracts \code{BookTitle} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{BookTitle} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | BookTitle(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | BookTitle(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/DayMedline-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayMedline-methods} 2 | \docType{methods} 3 | \alias{DayMedline-methods} 4 | \alias{DayMedline,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayMedline} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayMedline} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/DayPubDate-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayPubDate-methods} 2 | \docType{methods} 3 | \alias{DayPubDate-methods} 4 | \alias{DayPubDate,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayPubDate} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayPubDate} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/DayRevised-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayRevised-methods} 2 | \docType{methods} 3 | \alias{DayRevised-methods} 4 | \alias{DayRevised,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayRevised} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayRevised} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/HourEntrez-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{HourEntrez-methods} 2 | \docType{methods} 3 | \alias{HourEntrez-methods} 4 | \alias{HourEntrez,Medline-method} 5 | \title{ ~~ Methods for Function \code{HourEntrez} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{HourEntrez} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/HourPubmed-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{HourPubmed-methods} 2 | \docType{methods} 3 | \alias{HourPubmed-methods} 4 | \alias{HourPubmed,Medline-method} 5 | \title{ ~~ Methods for Function \code{HourPubmed} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{HourPubmed} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MedlinePgn-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MedlinePgn-methods} 2 | \docType{methods} 3 | \alias{MedlinePgn-methods} 4 | \alias{MedlinePgn,Medline-method} 5 | \title{ ~~ Methods for Function \code{MedlinePgn} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MedlinePgn} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MedlineTA.Rd: -------------------------------------------------------------------------------- 1 | \name{MedlineTA} 2 | \alias{MedlineTA} 3 | 4 | \title{ 5 | Extracts \code{MedlineTA} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MedlineTA} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | MedlineTA(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | MedlineTA(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/YearEntrez-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearEntrez-methods} 2 | \docType{methods} 3 | \alias{YearEntrez-methods} 4 | \alias{YearEntrez,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearEntrez} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearEntrez} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/YearPubmed-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearPubmed-methods} 2 | \docType{methods} 3 | \alias{YearPubmed-methods} 4 | \alias{YearPubmed,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearPubmed} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearPubmed} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Affiliation-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Affiliation-methods} 2 | \docType{methods} 3 | \alias{Affiliation-methods} 4 | \alias{Affiliation,Medline-method} 5 | \title{ ~~ Methods for Function \code{Affiliation} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Affiliation} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/BookEditors-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{BookEditors-methods} 2 | \docType{methods} 3 | \alias{BookEditors-methods} 4 | \alias{BookEditors,Medline-method} 5 | \title{ ~~ Methods for Function \code{BookEditors} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{BookEditors} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/DayAccepted-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayAccepted-methods} 2 | \docType{methods} 3 | \alias{DayAccepted-methods} 4 | \alias{DayAccepted,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayAccepted} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayAccepted} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/DayEpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayEpublish-methods} 2 | \docType{methods} 3 | \alias{DayEpublish-methods} 4 | \alias{DayEpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayEpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayEpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/DayPpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayPpublish-methods} 2 | \docType{methods} 3 | \alias{DayPpublish-methods} 4 | \alias{DayPpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayPpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayPpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/DayReceived-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayReceived-methods} 2 | \docType{methods} 3 | \alias{DayReceived-methods} 4 | \alias{DayReceived,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayReceived} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayReceived} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/ELocationID-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{ELocationID-methods} 2 | \docType{methods} 3 | \alias{ELocationID-methods} 4 | \alias{ELocationID,Medline-method} 5 | \title{ ~~ Methods for Function \code{ELocationID} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{ELocationID} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/HourMedline-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{HourMedline-methods} 2 | \docType{methods} 3 | \alias{HourMedline-methods} 4 | \alias{HourMedline,Medline-method} 5 | \title{ ~~ Methods for Function \code{HourMedline} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{HourMedline} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/ISSNLinking-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{ISSNLinking-methods} 2 | \docType{methods} 3 | \alias{ISSNLinking-methods} 4 | \alias{ISSNLinking,Medline-method} 5 | \title{ ~~ Methods for Function \code{ISSNLinking} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{ISSNLinking} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Keywords.Rd: -------------------------------------------------------------------------------- 1 | \name{Keywords} 2 | \alias{Keywords} 3 | 4 | \title{ 5 | Extracts list of \code{Keywords} info from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{Keywords} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Keywords(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | Keywords(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/MonthEntrez-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthEntrez-methods} 2 | \docType{methods} 3 | \alias{MonthEntrez-methods} 4 | \alias{MonthEntrez,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthEntrez} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthEntrez} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MonthPubmed-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthPubmed-methods} 2 | \docType{methods} 3 | \alias{MonthPubmed-methods} 4 | \alias{MonthPubmed,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthPubmed} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthPubmed} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/NlmUniqueID-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{NlmUniqueID-methods} 2 | \docType{methods} 3 | \alias{NlmUniqueID-methods} 4 | \alias{NlmUniqueID,Medline-method} 5 | \title{ ~~ Methods for Function \code{NlmUniqueID} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{NlmUniqueID} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/YearMedline-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearMedline-methods} 2 | \docType{methods} 3 | \alias{YearMedline-methods} 4 | \alias{YearMedline,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearMedline} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearMedline} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/YearPubDate-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearPubDate-methods} 2 | \docType{methods} 3 | \alias{YearPubDate-methods} 4 | \alias{YearPubDate,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearPubDate} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearPubDate} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/YearRevised-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearRevised-methods} 2 | \docType{methods} 3 | \alias{YearRevised-methods} 4 | \alias{YearRevised,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearRevised} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearRevised} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/summary-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{summary-methods} 2 | \docType{methods} 3 | \alias{summary-methods} 4 | \alias{summary,EUtilsSummary-method} 5 | 6 | \title{ Summary method for EUtilsSummary object} 7 | 8 | \description{ 9 | 10 | Summary of object of class \code{EUtilsSummary} 11 | 12 | } 13 | 14 | \section{Methods}{ 15 | \describe{ 16 | 17 | \item{\code{signature(object = "EUtilsSummary",...)}}{ 18 | Returns the number of records and id vector. 19 | } 20 | } 21 | } 22 | 23 | \keyword{methods} 24 | 25 | -------------------------------------------------------------------------------- /man/AbstractText-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{AbstractText-methods} 2 | \docType{methods} 3 | \alias{AbstractText-methods} 4 | \alias{AbstractText,Medline-method} 5 | \title{ ~~ Methods for Function \code{AbstractText} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{AbstractText} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/ArticleTitle-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{ArticleTitle-methods} 2 | \docType{methods} 3 | \alias{ArticleTitle-methods} 4 | \alias{ArticleTitle,Medline-method} 5 | \title{ ~~ Methods for Function \code{ArticleTitle} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{ArticleTitle} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/BookMedium.Rd: -------------------------------------------------------------------------------- 1 | \name{BookMedium} 2 | \alias{BookMedium} 3 | 4 | \title{ 5 | Extracts \code{BookMedium} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{BookMedium} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | BookMedium(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | BookMedium(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/COIStatement-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{COIStatement-methods} 2 | \docType{methods} 3 | \alias{COIStatement-methods} 4 | \alias{COIStatement,Medline-method} 5 | \title{ ~~ Methods for Function \code{COIStatement} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{COIStatement} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/HourAccepted-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{HourAccepted-methods} 2 | \docType{methods} 3 | \alias{HourAccepted-methods} 4 | \alias{HourAccepted,Medline-method} 5 | \title{ ~~ Methods for Function \code{HourAccepted} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{HourAccepted} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/HourEpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{HourEpublish-methods} 2 | \docType{methods} 3 | \alias{HourEpublish-methods} 4 | \alias{HourEpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{HourEpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{HourEpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/HourPpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{HourPpublish-methods} 2 | \docType{methods} 3 | \alias{HourPpublish-methods} 4 | \alias{HourPpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{HourPpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{HourPpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/HourReceived-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{HourReceived-methods} 2 | \docType{methods} 3 | \alias{HourReceived-methods} 4 | \alias{HourReceived,Medline-method} 5 | \title{ ~~ Methods for Function \code{HourReceived} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{HourReceived} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MedlinePgn.Rd: -------------------------------------------------------------------------------- 1 | \name{MedlinePgn} 2 | \alias{MedlinePgn} 3 | 4 | \title{ 5 | Extracts \code{MedlinePgn} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MedlinePgn} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | MedlinePgn(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | MedlinePgn(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/MinuteEntrez-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteEntrez-methods} 2 | \docType{methods} 3 | \alias{MinuteEntrez-methods} 4 | \alias{MinuteEntrez,Medline-method} 5 | \title{ ~~ Methods for Function \code{MinuteEntrez} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MinuteEntrez} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MinutePubmed-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MinutePubmed-methods} 2 | \docType{methods} 3 | \alias{MinutePubmed-methods} 4 | \alias{MinutePubmed,Medline-method} 5 | \title{ ~~ Methods for Function \code{MinutePubmed} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MinutePubmed} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MonthMedline-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthMedline-methods} 2 | \docType{methods} 3 | \alias{MonthMedline-methods} 4 | \alias{MonthMedline,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthMedline} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthMedline} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MonthPubDate-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthPubDate-methods} 2 | \docType{methods} 3 | \alias{MonthPubDate-methods} 4 | \alias{MonthPubDate,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthPubDate} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthPubDate} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MonthRevised-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthRevised-methods} 2 | \docType{methods} 3 | \alias{MonthRevised-methods} 4 | \alias{MonthRevised,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthRevised} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthRevised} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/YearAccepted-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearAccepted-methods} 2 | \docType{methods} 3 | \alias{YearAccepted-methods} 4 | \alias{YearAccepted,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearAccepted} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearAccepted} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/YearEpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearEpublish-methods} 2 | \docType{methods} 3 | \alias{YearEpublish-methods} 4 | \alias{YearEpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearEpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearEpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/YearPpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearPpublish-methods} 2 | \docType{methods} 3 | \alias{YearPpublish-methods} 4 | \alias{YearPpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearPpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearPpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/YearReceived-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearReceived-methods} 2 | \docType{methods} 3 | \alias{YearReceived-methods} 4 | \alias{YearReceived,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearReceived} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearReceived} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Affiliation.Rd: -------------------------------------------------------------------------------- 1 | \name{Affiliation} 2 | \alias{Affiliation} 3 | 4 | \title{ 5 | Extracts \code{Affiliation} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{Affiliation} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Affiliation(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | Affiliation(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/BookEditors.Rd: -------------------------------------------------------------------------------- 1 | \name{BookEditors} 2 | \alias{BookEditors} 3 | 4 | \title{ 5 | Extracts \code{BookEditors} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{BookEditors} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | BookEditors(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | BookEditors(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/BookPublisher-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{BookPublisher-methods} 2 | \docType{methods} 3 | \alias{BookPublisher-methods} 4 | \alias{BookPublisher,Medline-method} 5 | \title{ ~~ Methods for Function \code{BookPublisher} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{BookPublisher} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/ELocationID.Rd: -------------------------------------------------------------------------------- 1 | \name{ELocationID} 2 | \alias{ELocationID} 3 | 4 | \title{ 5 | Extracts \code{ELocationID} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{ELocationID} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | ELocationID(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | ELocationID(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/ISSNLinking.Rd: -------------------------------------------------------------------------------- 1 | \name{ISSNLinking} 2 | \alias{ISSNLinking} 3 | 4 | \title{ 5 | Extracts \code{ISSNLinking} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{ISSNLinking} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | ISSNLinking(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | ISSNLinking(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/MinuteMedline-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteMedline-methods} 2 | \docType{methods} 3 | \alias{MinuteMedline-methods} 4 | \alias{MinuteMedline,Medline-method} 5 | \title{ ~~ Methods for Function \code{MinuteMedline} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MinuteMedline} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MonthAccepted-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthAccepted-methods} 2 | \docType{methods} 3 | \alias{MonthAccepted-methods} 4 | \alias{MonthAccepted,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthAccepted} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthAccepted} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MonthEpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthEpublish-methods} 2 | \docType{methods} 3 | \alias{MonthEpublish-methods} 4 | \alias{MonthEpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthEpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthEpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MonthPpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthPpublish-methods} 2 | \docType{methods} 3 | \alias{MonthPpublish-methods} 4 | \alias{MonthPpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthPpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthPpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MonthReceived-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthReceived-methods} 2 | \docType{methods} 3 | \alias{MonthReceived-methods} 4 | \alias{MonthReceived,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthReceived} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthReceived} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/NlmUniqueID.Rd: -------------------------------------------------------------------------------- 1 | \name{NlmUniqueID} 2 | \alias{NlmUniqueID} 3 | 4 | \title{ 5 | Extracts \code{NlmUniqueID} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{NlmUniqueID} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | NlmUniqueID(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | NlmUniqueID(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/AbstractText.Rd: -------------------------------------------------------------------------------- 1 | \name{AbstractText} 2 | \alias{AbstractText} 3 | 4 | \title{ 5 | Extracts \code{AbstractText} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{AbstractText} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | AbstractText(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | AbstractText(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/ArticleTitle.Rd: -------------------------------------------------------------------------------- 1 | \name{ArticleTitle} 2 | \alias{ArticleTitle} 3 | 4 | \title{ 5 | Extracts \code{ArticleTitle} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{ArticleTitle} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | ArticleTitle(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | ArticleTitle(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/BookEndingDate-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{BookEndingDate-methods} 2 | \docType{methods} 3 | \alias{BookEndingDate-methods} 4 | \alias{BookEndingDate,Medline-method} 5 | \title{ ~~ Methods for Function \code{BookEndingDate} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{BookEndingDate} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/DayArticleDate-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{DayArticleDate-methods} 2 | \docType{methods} 3 | \alias{DayArticleDate-methods} 4 | \alias{DayArticleDate,Medline-method} 5 | \title{ ~~ Methods for Function \code{DayArticleDate} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{DayArticleDate} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MinuteAccepted-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteAccepted-methods} 2 | \docType{methods} 3 | \alias{MinuteAccepted-methods} 4 | \alias{MinuteAccepted,Medline-method} 5 | \title{ ~~ Methods for Function \code{MinuteAccepted} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MinuteAccepted} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MinuteEpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteEpublish-methods} 2 | \docType{methods} 3 | \alias{MinuteEpublish-methods} 4 | \alias{MinuteEpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{MinuteEpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MinuteEpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MinutePpublish-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MinutePpublish-methods} 2 | \docType{methods} 3 | \alias{MinutePpublish-methods} 4 | \alias{MinutePpublish,Medline-method} 5 | \title{ ~~ Methods for Function \code{MinutePpublish} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MinutePpublish} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/MinuteReceived-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteReceived-methods} 2 | \docType{methods} 3 | \alias{MinuteReceived-methods} 4 | \alias{MinuteReceived,Medline-method} 5 | \title{ ~~ Methods for Function \code{MinuteReceived} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MinuteReceived} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/BookPublisher.Rd: -------------------------------------------------------------------------------- 1 | \name{BookPublisher} 2 | \alias{BookPublisher} 3 | 4 | \title{ 5 | Extracts \code{BookPublisher} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{BookPublisher} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | BookPublisher(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | BookPublisher(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/ISOAbbreviation-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{ISOAbbreviation-methods} 2 | \docType{methods} 3 | \alias{ISOAbbreviation-methods} 4 | \alias{ISOAbbreviation,Medline-method} 5 | \title{ ~~ Methods for Function \code{ISOAbbreviation} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{ISOAbbreviation} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/PublicationType-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{PublicationType-methods} 2 | \docType{methods} 3 | \alias{PublicationType-methods} 4 | \alias{PublicationType,Medline-method} 5 | \title{ ~~ Methods for Function \code{PublicationType} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{PublicationType} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/YearArticleDate-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{YearArticleDate-methods} 2 | \docType{methods} 3 | \alias{YearArticleDate-methods} 4 | \alias{YearArticleDate,Medline-method} 5 | \title{ ~~ Methods for Function \code{YearArticleDate} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{YearArticleDate} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/c-methods.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/MedlineC.R 3 | \docType{methods} 4 | \name{c,Medline-method} 5 | \alias{c,Medline-method} 6 | \alias{c,ANY,ANY-method} 7 | \title{Concatenate Medline} 8 | \usage{ 9 | \S4method{c}{Medline}(x, ...) 10 | } 11 | \arguments{ 12 | \item{x}{a Medline object} 13 | 14 | \item{...}{Additional Medline objects to concatenate} 15 | } 16 | \value{ 17 | A Medline object 18 | } 19 | \description{ 20 | Concatenates multiple Medline objects 21 | } 22 | -------------------------------------------------------------------------------- /man/BookEndingDate.Rd: -------------------------------------------------------------------------------- 1 | \name{BookEndingDate} 2 | \alias{BookEndingDate} 3 | 4 | \title{ 5 | Extracts \code{BookEndingDate} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{BookEndingDate} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | BookEndingDate(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | BookEndingDate(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/MonthArticleDate-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthArticleDate-methods} 2 | \docType{methods} 3 | \alias{MonthArticleDate-methods} 4 | \alias{MonthArticleDate,Medline-method} 5 | \title{ ~~ Methods for Function \code{MonthArticleDate} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{MonthArticleDate} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/BookBeginningDate-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{BookBeginningDate-methods} 2 | \docType{methods} 3 | \alias{BookBeginningDate-methods} 4 | \alias{BookBeginningDate,Medline-method} 5 | \title{ ~~ Methods for Function \code{BookBeginningDate} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{BookBeginningDate} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/Cited-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Citations-methods} 2 | \docType{methods} 3 | \alias{Citations-methods} 4 | \alias{Citations,Medline-method} 5 | \alias{Citations,EUtilsSummary-method} 6 | \title{ ~~ Methods for Function \code{Citations} in Package \pkg{RISmed} ~~} 7 | \description{ 8 | ~~ Methods for function \code{Citations} in package \pkg{RISmed} ~~ 9 | } 10 | \section{Methods}{ 11 | \describe{ 12 | 13 | \item{\code{signature(object = "Medline")}}{ 14 | %% ~~describe this method here~~ 15 | } 16 | }} 17 | 18 | \keyword{methods} 19 | 20 | -------------------------------------------------------------------------------- /man/PublicationStatus-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{PublicationStatus-methods} 2 | \docType{methods} 3 | \alias{PublicationStatus-methods} 4 | \alias{PublicationStatus,Medline-method} 5 | \title{ ~~ Methods for Function \code{PublicationStatus} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{PublicationStatus} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/PublicationType.Rd: -------------------------------------------------------------------------------- 1 | \name{PublicationType} 2 | \alias{PublicationType} 3 | 4 | \title{ 5 | Extracts \code{PublicationType} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{PublicationType} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | PublicationType(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{list} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | PublicationType(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/ISOAbbreviation.Rd: -------------------------------------------------------------------------------- 1 | \name{ISOAbbreviation} 2 | \alias{ISOAbbreviation} 3 | 4 | \title{ 5 | Extracts \code{ISOAbbreviation} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{ISOAbbreviation} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | ISOAbbreviation(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | ISOAbbreviation(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/DOI.Rd: -------------------------------------------------------------------------------- 1 | \name{DOI} 2 | \alias{DOI} 3 | 4 | \title{ 5 | Extracts \code{DOI} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DOI} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | DOI(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DOI(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/BookBeginningDate.Rd: -------------------------------------------------------------------------------- 1 | \name{BookBeginningDate} 2 | \alias{BookBeginningDate} 3 | 4 | \title{ 5 | Extracts \code{BookBeginningDate} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{BookBeginningDate} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | BookBeginningDate(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | BookBeginningDate(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/PublicationStatus.Rd: -------------------------------------------------------------------------------- 1 | \name{PublicationStatus} 2 | \alias{PublicationStatus} 3 | 4 | \title{ 5 | Extracts \code{PublicationStatus} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{PublicationStatus} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | PublicationStatus(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | PublicationStatus(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/CopyrightInformation-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{CopyrightInformation-methods} 2 | \docType{methods} 3 | \alias{CopyrightInformation-methods} 4 | \alias{CopyrightInformation,Medline-method} 5 | \title{ ~~ Methods for Function \code{CopyrightInformation} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{CopyrightInformation} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/BookPublisherLocation-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{BookPublisherLocation-methods} 2 | \docType{methods} 3 | \alias{BookPublisherLocation-methods} 4 | \alias{BookPublisherLocation,Medline-method} 5 | \title{ ~~ Methods for Function \code{BookPublisherLocation} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{BookPublisherLocation} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | %% ~~describe this method here~~ 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/GrantID.Rd: -------------------------------------------------------------------------------- 1 | \name{GrantID} 2 | \alias{GrantID} 3 | 4 | \title{ 5 | Extracts list of \code{GrantID} info \code{Medline} object including \code{GrantID} and \code{GrantAgency} where listed in PubMed. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{GrantID} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | GrantID(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | GrantID(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/CopyrightInformation.Rd: -------------------------------------------------------------------------------- 1 | \name{CopyrightInformation} 2 | \alias{CopyrightInformation} 3 | 4 | \title{ 5 | Extracts \code{CopyrightInformation} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{CopyrightInformation} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | CopyrightInformation(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | CopyrightInformation(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/BookPublisherLocation.Rd: -------------------------------------------------------------------------------- 1 | \name{BookPublisherLocation} 2 | \alias{BookPublisherLocation} 3 | 4 | \title{ 5 | Extracts \code{BookPublisherLocation} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{BookPublisherLocation} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | BookPublisherLocation(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | BookPublisherLocation(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/Author-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Author-methods} 2 | \docType{methods} 3 | \alias{Author-methods} 4 | \alias{Author,Medline-method} 5 | \title{ ~~ Methods for Function \code{Author} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Author} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | 12 | \item{\code{signature(object = "Medline")}}{ 13 | List by Pubmed article. Each list contains a data frame with \code{LastName}, \code{ForeName}, \code{Initials}, and \code{order} of article authors. 14 | } 15 | }} 16 | \keyword{methods} 17 | 18 | -------------------------------------------------------------------------------- /man/myeloma.Rd: -------------------------------------------------------------------------------- 1 | \name{myeloma} 2 | \docType{data} 3 | \alias{myeloma} 4 | \title{Example of results from \code{EUtilsGet}} 5 | 6 | \description{ 7 | First five records of query of NCBI PubMed for "myeloma[MeSh]" in the past year (at the time of this writing) as a Medline object. 8 | } 9 | 10 | \usage{myeloma} 11 | 12 | \format{A list object with five PubMed article records.} 13 | 14 | \source{PubMed database of the US National Library of Medicine} 15 | 16 | \seealso{\code{\link{EUtilsGet}},\code{\link{Medline}}} 17 | 18 | \author{Stephanie Kovalchik \email{s.a.kovalchik@gmail.com}} 19 | -------------------------------------------------------------------------------- /man/Mesh-methods.Rd: -------------------------------------------------------------------------------- 1 | \name{Mesh-methods} 2 | \docType{methods} 3 | \alias{Mesh-methods} 4 | \alias{Mesh,Medline-method} 5 | \title{ ~~ Methods for Function \code{Mesh} in Package \pkg{RISmed} ~~} 6 | \description{ 7 | ~~ Methods for function \code{Mesh} in package \pkg{RISmed} ~~ 8 | } 9 | \section{Methods}{ 10 | \describe{ 11 | \item{\code{signature(object = "Medline")}}{ 12 | List by Pubmed article. Each list contains a data frame with \code{Heading} and \code{Type}. The \code{Heading} is a MeSH Term and \code{Type} is either a \code{Descriptor} or a \code{Qualifier} of a Descriptor term. 13 | } 14 | }} 15 | \keyword{methods} 16 | 17 | -------------------------------------------------------------------------------- /man/Author.Rd: -------------------------------------------------------------------------------- 1 | \name{Author} 2 | \alias{Author} 3 | 4 | \title{ 5 | Extracts \code{Author} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{Author} of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Author(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{List by Pubmed article. Each list contains a data frame with \code{CollectiveName}, \code{LastName}, \code{ForeName}, \code{Initials}, and \code{order} of article authors.} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \examples{ 24 | data(myeloma) 25 | Author(myeloma) 26 | } 27 | -------------------------------------------------------------------------------- /man/DayEntrez.Rd: -------------------------------------------------------------------------------- 1 | \name{DayEntrez} 2 | \alias{DayEntrez} 3 | 4 | \title{ 5 | Extracts \code{DayEntrez} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayEntrez} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | DayEntrez(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayEntrez(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayPmc.Rd: -------------------------------------------------------------------------------- 1 | \name{DayPmc} 2 | \alias{DayPmc} 3 | 4 | \title{ 5 | Extracts \code{DayPmc} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayPmc} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | DayPmc(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayPmc(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayPubDate.Rd: -------------------------------------------------------------------------------- 1 | \name{DayPubDate} 2 | \alias{DayPubDate} 3 | 4 | \title{ 5 | Extracts \code{DayPubDate} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayPubDate} of a \code{Medline} object. This date corresponds to the date the article was PubDate. 10 | } 11 | \usage{ 12 | DayPubDate(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayPubDate(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayRevised.Rd: -------------------------------------------------------------------------------- 1 | \name{DayRevised} 2 | \alias{DayRevised} 3 | 4 | \title{ 5 | Extracts \code{DayRevised} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayRevised} of a \code{Medline} object. This date corresponds to the date the article was Revised. 10 | } 11 | \usage{ 12 | DayRevised(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayRevised(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayMedline.Rd: -------------------------------------------------------------------------------- 1 | \name{DayMedline} 2 | \alias{DayMedline} 3 | 4 | \title{ 5 | Extracts \code{DayMedline} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayMedline} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | DayMedline(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayMedline(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/HourEntrez.Rd: -------------------------------------------------------------------------------- 1 | \name{HourEntrez} 2 | \alias{HourEntrez} 3 | 4 | \title{ 5 | Extracts \code{HourEntrez} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{HourEntrez} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | HourEntrez(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | HourEntrez(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearEntrez.Rd: -------------------------------------------------------------------------------- 1 | \name{YearEntrez} 2 | \alias{YearEntrez} 3 | 4 | \title{ 5 | Extracts \code{YearEntrez} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearEntrez} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | YearEntrez(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearEntrez(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearPubDate.Rd: -------------------------------------------------------------------------------- 1 | \name{YearPubDate} 2 | \alias{YearPubDate} 3 | 4 | \title{ 5 | Extracts \code{YearPubDate} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearPubDate} of a \code{Medline} object. This date corresponds to the date the article was PubDate. 10 | } 11 | \usage{ 12 | YearPubDate(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearPubDate(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearRevised.Rd: -------------------------------------------------------------------------------- 1 | \name{YearRevised} 2 | \alias{YearRevised} 3 | 4 | \title{ 5 | Extracts \code{YearRevised} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearRevised} of a \code{Medline} object. This date corresponds to the date the article was Revised. 10 | } 11 | \usage{ 12 | YearRevised(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearRevised(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayAccepted.Rd: -------------------------------------------------------------------------------- 1 | \name{DayAccepted} 2 | \alias{DayAccepted} 3 | 4 | \title{ 5 | Extracts \code{DayAccepted} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayAccepted} of a \code{Medline} object. This date corresponds to the date the article was accepted. 10 | } 11 | \usage{ 12 | DayAccepted(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayAccepted(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayReceived.Rd: -------------------------------------------------------------------------------- 1 | \name{DayReceived} 2 | \alias{DayReceived} 3 | 4 | \title{ 5 | Extracts \code{DayReceived} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayReceived} of a \code{Medline} object. This date corresponds to the date the article was received. 10 | } 11 | \usage{ 12 | DayReceived(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayReceived(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/HourMedline.Rd: -------------------------------------------------------------------------------- 1 | \name{HourMedline} 2 | \alias{HourMedline} 3 | 4 | \title{ 5 | Extracts \code{HourMedline} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{HourMedline} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | HourMedline(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | HourMedline(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/HourPmc.Rd: -------------------------------------------------------------------------------- 1 | \name{HourPmc} 2 | \alias{HourPmc} 3 | 4 | \title{ 5 | Extracts \code{HourPmc} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{HourPmc} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | HourPmc(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | HourPmc(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthEntrez.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthEntrez} 2 | \alias{MonthEntrez} 3 | 4 | \title{ 5 | Extracts \code{MonthEntrez} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthEntrez} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | MonthEntrez(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthEntrez(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearMedline.Rd: -------------------------------------------------------------------------------- 1 | \name{YearMedline} 2 | \alias{YearMedline} 3 | 4 | \title{ 5 | Extracts \code{YearMedline} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearMedline} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | YearMedline(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearMedline(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearPmc.Rd: -------------------------------------------------------------------------------- 1 | \name{YearPmc} 2 | \alias{YearPmc} 3 | 4 | \title{ 5 | Extracts \code{YearPmc} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearPmc} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | YearPmc(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearPmc(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayEpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{DayEpublish} 2 | \alias{DayEpublish} 3 | 4 | \title{ 5 | Extracts \code{DayEpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayEpublish} of a \code{Medline} object. This date corresponds to the date the article was published online. 10 | } 11 | \usage{ 12 | DayEpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayEpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/HourAccepted.Rd: -------------------------------------------------------------------------------- 1 | \name{HourAccepted} 2 | \alias{HourAccepted} 3 | 4 | \title{ 5 | Extracts \code{HourAccepted} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{HourAccepted} of a \code{Medline} object. This date corresponds to the date the article was accepted. 10 | } 11 | \usage{ 12 | HourAccepted(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | HourAccepted(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/HourReceived.Rd: -------------------------------------------------------------------------------- 1 | \name{HourReceived} 2 | \alias{HourReceived} 3 | 4 | \title{ 5 | Extracts \code{HourReceived} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{HourReceived} of a \code{Medline} object. This date corresponds to the date the article was received. 10 | } 11 | \usage{ 12 | HourReceived(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | HourReceived(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthPmc.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthPmc} 2 | \alias{MonthPmc} 3 | 4 | \title{ 5 | Extracts \code{MonthPmc} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthPmc} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | MonthPmc(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthPmc(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthPubDate.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthPubDate} 2 | \alias{MonthPubDate} 3 | 4 | \title{ 5 | Extracts \code{MonthPubDate} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthPubDate} of a \code{Medline} object. This date corresponds to the date the article was PubDate. 10 | } 11 | \usage{ 12 | MonthPubDate(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthPubDate(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthRevised.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthRevised} 2 | \alias{MonthRevised} 3 | 4 | \title{ 5 | Extracts \code{MonthRevised} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthRevised} of a \code{Medline} object. This date corresponds to the date the article was Revised. 10 | } 11 | \usage{ 12 | MonthRevised(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthRevised(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearAccepted.Rd: -------------------------------------------------------------------------------- 1 | \name{YearAccepted} 2 | \alias{YearAccepted} 3 | 4 | \title{ 5 | Extracts \code{YearAccepted} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearAccepted} of a \code{Medline} object. This date corresponds to the date the article was accepted. 10 | } 11 | \usage{ 12 | YearAccepted(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearAccepted(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearReceived.Rd: -------------------------------------------------------------------------------- 1 | \name{YearReceived} 2 | \alias{YearReceived} 3 | 4 | \title{ 5 | Extracts \code{YearReceived} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearReceived} of a \code{Medline} object. This date corresponds to the date the article was received. 10 | } 11 | \usage{ 12 | YearReceived(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearReceived(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayPpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{DayPpublish} 2 | \alias{DayPpublish} 3 | 4 | \title{ 5 | Extracts \code{DayPpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayPpublish} of a \code{Medline} object. This date corresponds to the date the article was published in print. 10 | } 11 | \usage{ 12 | DayPpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayPpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MinuteEntrez.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteEntrez} 2 | \alias{MinuteEntrez} 3 | 4 | \title{ 5 | Extracts \code{MinuteEntrez} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MinuteEntrez} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | MinuteEntrez(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MinuteEntrez(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthAccepted.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthAccepted} 2 | \alias{MonthAccepted} 3 | 4 | \title{ 5 | Extracts \code{MonthAccepted} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthAccepted} of a \code{Medline} object. This date corresponds to the date the article was accepted. 10 | } 11 | \usage{ 12 | MonthAccepted(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthAccepted(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthMedline.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthMedline} 2 | \alias{MonthMedline} 3 | 4 | \title{ 5 | Extracts \code{MonthMedline} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthMedline} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | MonthMedline(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthMedline(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthReceived.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthReceived} 2 | \alias{MonthReceived} 3 | 4 | \title{ 5 | Extracts \code{MonthReceived} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthReceived} of a \code{Medline} object. This date corresponds to the date the article was received. 10 | } 11 | \usage{ 12 | MonthReceived(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthReceived(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayPubmed.Rd: -------------------------------------------------------------------------------- 1 | \name{DayPubmed} 2 | \alias{DayPubmed} 3 | 4 | \title{ 5 | Extracts \code{DayPubmed} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayPubmed} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | DayPubmed(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayPubmed(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/HourEpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{HourEpublish} 2 | \alias{HourEpublish} 3 | 4 | \title{ 5 | Extracts \code{HourEpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{HourEpublish} of a \code{Medline} object. This date corresponds to the date the article was published online. 10 | } 11 | \usage{ 12 | HourEpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | HourEpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/HourPpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{HourPpublish} 2 | \alias{HourPpublish} 3 | 4 | \title{ 5 | Extracts \code{HourPpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{HourPpublish} of a \code{Medline} object. This date corresponds to the date the article was published in print. 10 | } 11 | \usage{ 12 | HourPpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | HourPpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MinuteMedline.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteMedline} 2 | \alias{MinuteMedline} 3 | 4 | \title{ 5 | Extracts \code{MinuteMedline} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MinuteMedline} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | MinuteMedline(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MinuteMedline(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MinutePmc.Rd: -------------------------------------------------------------------------------- 1 | \name{MinutePmc} 2 | \alias{MinutePmc} 3 | 4 | \title{ 5 | Extracts \code{MinutePmc} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MinutePmc} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | MinutePmc(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MinutePmc(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearEpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{YearEpublish} 2 | \alias{YearEpublish} 3 | 4 | \title{ 5 | Extracts \code{YearEpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearEpublish} of a \code{Medline} object. This date corresponds to the date the article was published online. 10 | } 11 | \usage{ 12 | YearEpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearEpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearPpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{YearPpublish} 2 | \alias{YearPpublish} 3 | 4 | \title{ 5 | Extracts \code{YearPpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearPpublish} of a \code{Medline} object. This date corresponds to the date the article was published in print. 10 | } 11 | \usage{ 12 | YearPpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearPpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/DayArticleDate.Rd: -------------------------------------------------------------------------------- 1 | \name{DayArticleDate} 2 | \alias{DayArticleDate} 3 | 4 | \title{ 5 | Extracts \code{DayArticleDate} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{DayArticleDate} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | DayArticleDate(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | DayArticleDate(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/HourPubmed.Rd: -------------------------------------------------------------------------------- 1 | \name{HourPubmed} 2 | \alias{HourPubmed} 3 | 4 | \title{ 5 | Extracts \code{HourPubmed} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{HourPubmed} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | HourPubmed(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | HourPubmed(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MinuteAccepted.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteAccepted} 2 | \alias{MinuteAccepted} 3 | 4 | \title{ 5 | Extracts \code{MinuteAccepted} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MinuteAccepted} of a \code{Medline} object. This date corresponds to the date the article was accepted. 10 | } 11 | \usage{ 12 | MinuteAccepted(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MinuteAccepted(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MinuteReceived.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteReceived} 2 | \alias{MinuteReceived} 3 | 4 | \title{ 5 | Extracts \code{MinuteReceived} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MinuteReceived} of a \code{Medline} object. This date corresponds to the date the article was received. 10 | } 11 | \usage{ 12 | MinuteReceived(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MinuteReceived(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthEpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthEpublish} 2 | \alias{MonthEpublish} 3 | 4 | \title{ 5 | Extracts \code{MonthEpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthEpublish} of a \code{Medline} object. This date corresponds to the date the article was published online. 10 | } 11 | \usage{ 12 | MonthEpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthEpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthPpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthPpublish} 2 | \alias{MonthPpublish} 3 | 4 | \title{ 5 | Extracts \code{MonthPpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthPpublish} of a \code{Medline} object. This date corresponds to the date the article was published in print. 10 | } 11 | \usage{ 12 | MonthPpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthPpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearPubmed.Rd: -------------------------------------------------------------------------------- 1 | \name{YearPubmed} 2 | \alias{YearPubmed} 3 | 4 | \title{ 5 | Extracts \code{YearPubmed} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearPubmed} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | YearPubmed(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearPubmed(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MinuteEpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{MinuteEpublish} 2 | \alias{MinuteEpublish} 3 | 4 | \title{ 5 | Extracts \code{MinuteEpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MinuteEpublish} of a \code{Medline} object. This date corresponds to the date the article was published online. 10 | } 11 | \usage{ 12 | MinuteEpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MinuteEpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthPubmed.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthPubmed} 2 | \alias{MonthPubmed} 3 | 4 | \title{ 5 | Extracts \code{MonthPubmed} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthPubmed} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | MonthPubmed(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthPubmed(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MinutePpublish.Rd: -------------------------------------------------------------------------------- 1 | \name{MinutePpublish} 2 | \alias{MinutePpublish} 3 | 4 | \title{ 5 | Extracts \code{MinutePpublish} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MinutePpublish} of a \code{Medline} object. This date corresponds to the date the article was published in print. 10 | } 11 | \usage{ 12 | MinutePpublish(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MinutePpublish(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/YearArticleDate.Rd: -------------------------------------------------------------------------------- 1 | \name{YearArticleDate} 2 | \alias{YearArticleDate} 3 | 4 | \title{ 5 | Extracts \code{YearArticleDate} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{YearArticleDate} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | YearArticleDate(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | YearArticleDate(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MinutePubmed.Rd: -------------------------------------------------------------------------------- 1 | \name{MinutePubmed} 2 | \alias{MinutePubmed} 3 | 4 | \title{ 5 | Extracts \code{MinutePubmed} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MinutePubmed} of a \code{Medline} object. This date corresponds to the date the article was made available through Pubmed Central. 10 | } 11 | \usage{ 12 | MinutePubmed(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MinutePubmed(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /man/MonthArticleDate.Rd: -------------------------------------------------------------------------------- 1 | \name{MonthArticleDate} 2 | \alias{MonthArticleDate} 3 | 4 | \title{ 5 | Extracts \code{MonthArticleDate} from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{MonthArticleDate} of a \code{Medline} object. This date corresponds to the date the article was ArticleDate. 10 | } 11 | \usage{ 12 | MonthArticleDate(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{vector} 20 | 21 | \seealso{\code{\link{Medline}}} 22 | 23 | \references{\url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html#phst}} 24 | 25 | \examples{ 26 | data(myeloma) 27 | MonthArticleDate(myeloma) 28 | } 29 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: RISmed 2 | Version: 2.3.2 3 | Type: Package 4 | Title: Download Content from NCBI Databases 5 | Date: 2021-07-02 6 | Authors@R: person("Stephanie", "Kovalchik", email = "s.a.kovalchik@gmail.com", 7 | role = c("aut", "cre")) 8 | Depends: R (>= 3.6.0), methods 9 | Imports: httr, xml2 10 | Description: A set of tools to extract bibliographic content from the National 11 | Center for Biotechnology Information (NCBI) databases, including PubMed. The 12 | name RISmed is a portmanteau of RIS (for Research Information Systems, a common 13 | tag format for bibliographic data) and PubMed. 14 | License: GPL (>= 2) 15 | LazyData: true 16 | NeedsCompilation: no 17 | Packaged: 2016-11-02 00:05:19 UTC; skovalchik 18 | Author: Stephanie Kovalchik [aut, cre] 19 | Maintainer: Stephanie Kovalchik 20 | RoxygenNote: 7.1.1 21 | -------------------------------------------------------------------------------- /man/Mesh.Rd: -------------------------------------------------------------------------------- 1 | \name{Mesh} 2 | \alias{Mesh} 3 | 4 | \title{ 5 | Extracts \code{Mesh} headings from \code{Medline} object. 6 | } 7 | 8 | \description{ 9 | Extractor for the \code{Mesh} headings of a \code{Medline} object. 10 | } 11 | \usage{ 12 | Mesh(object) 13 | } 14 | 15 | \arguments{ 16 | \item{object}{instance of class \code{Medline}} 17 | } 18 | 19 | \value{List by Pubmed article. Each list contains a data frame with \code{Heading} and \code{Type}. The \code{Heading} is a MeSH Term and \code{Type} is either a \code{Descriptor} or a \code{Qualifier} of a Descriptor term. Qualifiers of a Descriptor immediately follow the Descriptor term in the data frame. When MeSH headings have not been included with a MEDLINE record, the list will contain \code{NAs} (see details). 20 | } 21 | 22 | \seealso{\code{\link{Medline}}} 23 | 24 | \details{In Process and publisher-supplied records lack MeSH terms. See the MeSH home page 25 | \url{https://www.nlm.nih.gov/mesh/meshhome.html} for additional information about MeSH. 26 | Note that more recent records may lack MeSH headings. 27 | } 28 | -------------------------------------------------------------------------------- /man/RISmed-package.Rd: -------------------------------------------------------------------------------- 1 | \name{RISmed-package} 2 | \alias{RISmed-package} 3 | \alias{RISmed} 4 | 5 | \docType{package} 6 | 7 | \title{ 8 | 9 | Download content from NCBI databases. 10 | 11 | 12 | } 13 | 14 | \description{ 15 | Download content from NCBI databases. This package is intended to facilitate analyses of NCBI database content. This package is not intended for reference management. 16 | } 17 | 18 | \details{ 19 | \tabular{ll}{ 20 | Package: \tab RISmed\cr 21 | Type: \tab Package\cr 22 | Version: \tab 2.1.3\cr 23 | Date: \tab 2014-7-20\cr 24 | License: \tab GPL (>=2)\cr 25 | LazyLoad: \tab yes\cr 26 | } 27 | 28 | Note on usage: 29 | 30 | In order not to overload the E-utility servers, NCBI recommends that users post no more than three URL requests per second and limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time during weekdays. Failure to comply with this policy may result in an IP address being blocked from accessing NCBI. 31 | 32 | } 33 | \author{ 34 | 35 | Maintainer: Stephanie Kovalchik 36 | 37 | } 38 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | import(methods) 2 | exportClasses(EUtilsSummary,Medline) 3 | export(Medline,EUtilsSummary,EUtilsQuery,EUtilsGet,QueryTranslation,QueryId,QueryCount) 4 | exportMethods(AbstractText,Affiliation,ArticleId,ArticleTitle,Author,COIStatement,CopyrightInformation,Country,DayAccepted,DayArticleDate,DayEntrez,DayEpublish,DayMedline,DayPmc,DayPpublish,DayPubDate,DayPubmed,DayReceived,DayRevised,DOI,ELocationID,GrantID,HourAccepted,HourEntrez,HourEpublish,HourMedline,HourPmc,HourPpublish,HourPubmed,HourReceived,ISOAbbreviation,ISSN,ISSNLinking,Issue,Language,MedlinePgn,MedlineTA,Mesh,MinuteAccepted,MinuteEntrez,MinuteEpublish,MinuteMedline,MinutePmc,MinutePpublish,MinutePubmed,MinuteReceived,MonthAccepted,MonthArticleDate,MonthEntrez,MonthEpublish,MonthMedline,MonthPmc,MonthPpublish,MonthPubDate,MonthPubmed,MonthReceived,MonthRevised,NlmUniqueID,PMID,PublicationStatus,PublicationType,Query,Title,Volume,YearAccepted,YearArticleDate,YearEntrez,YearEpublish,YearMedline,YearPmc,YearPpublish,YearPubDate,YearPubmed,YearReceived,YearRevised,Keywords,Citations,BookPublisher,BookPublisherLocation,BookTitle,BookBeginningDate,BookEndingDate,BookEditors,BookMedium) 5 | exportMethods(print,show,summary,c) 6 | -------------------------------------------------------------------------------- /man/EUtilsSummary-class.Rd: -------------------------------------------------------------------------------- 1 | \name{EUtilsSummary-class} 2 | \docType{class} 3 | \alias{EUtilsSummary-class} 4 | 5 | \title{Class \code{"EUtilsSummary"}} 6 | 7 | \description{ 8 | Summary of query of an NCBI E-utility 9 | } 10 | 11 | \section{Objects from the Class}{ 12 | Objects can be created by calls of the form \code{new("EUtilsSummary", ...)}. 13 | } 14 | \section{Slots}{ 15 | \describe{ 16 | \item{\code{db}:}{Name of database} 17 | \item{\code{count}:}{total ids} 18 | \item{\code{retmax}:}{limit on number of records to return} 19 | \item{\code{retstart}:}{numeric indicating where return records start} 20 | \item{\code{PMID}:}{character vector of matching ids} 21 | \item{\code{querytranslation}:}{character of NCBI translation of query} 22 | } 23 | } 24 | \section{Methods}{ 25 | \describe{ 26 | \item{QueryCount}{\code{signature(object = "EUtilsSummary")}: ... } 27 | \item{QueryId}{\code{signature(object = "EUtilsSummary")}: ... } 28 | \item{print}{\code{signature(x = "EUtilsSummary")}: ... } 29 | \item{show}{\code{signature(object = "EUtilsSummary")}: ... } 30 | \item{summary}{\code{signature(object = "EUtilsSummary")}: ... } 31 | \item{QueryTranslation}{\code{signature(object = "EUtilsSummary")}: ... } 32 | } 33 | } 34 | 35 | 36 | \author{ 37 | Stephanie Kovalchik 38 | } 39 | 40 | \keyword{classes} 41 | -------------------------------------------------------------------------------- /R/EUtilsSummary.R: -------------------------------------------------------------------------------- 1 | setClass("EUtilsSummary", 2 | representation( 3 | db = "character", 4 | count = "numeric", 5 | retmax = "numeric", 6 | retstart = "numeric", 7 | PMID = "character", 8 | querytranslation = "character" 9 | ) 10 | ) 11 | 12 | EUtilsSummary <- function(query,type="esearch",db="pubmed",url=NULL,encoding="unknown",...){ 13 | 14 | if(is.null(url)){ 15 | url <- EUtilsQuery(query,type,db,...) 16 | } 17 | 18 | lines <- readLines(url,warn=FALSE,encoding=encoding) 19 | res <- ParseTags(lines) 20 | 21 | EMPTYCHECK <- length(grep("^(?:)?0<\\/Count>", lines))!=0 22 | 23 | if(EMPTYCHECK){ 24 | res$Id <- character(0) 25 | res$Count <- 0 26 | } 27 | 28 | new("EUtilsSummary", 29 | db = db, 30 | count = res$Count, 31 | retstart = res$RetStart, 32 | retmax = res$RetMax, 33 | PMID = res$Id, 34 | querytranslation = res$QueryTranslation 35 | ) 36 | } 37 | 38 | setMethod("print","EUtilsSummary",function(x,...) print(x@querytranslation)) 39 | setMethod("show","EUtilsSummary",function(object) print(object@querytranslation)) 40 | setMethod("summary","EUtilsSummary",function(object,...){ 41 | 42 | cat("Query:\n") 43 | cat(object@querytranslation,"\n\n") 44 | cat("Result count: ",object@count) 45 | 46 | invisible(object@PMID) 47 | 48 | }) 49 | 50 | # GENERICS 51 | setMethod("QueryCount","EUtilsSummary",function(object) object@count) 52 | setMethod("QueryId","EUtilsSummary",function(object) object@PMID) 53 | setMethod("QueryTranslation","EUtilsSummary",function(object) object@querytranslation) 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | -------------------------------------------------------------------------------- /man/EUtilsGet.Rd: -------------------------------------------------------------------------------- 1 | \name{EUtilsGet} 2 | \alias{EUtilsGet} 3 | 4 | \title{Results of an NCBI EUtils query} 5 | 6 | \description{ 7 | Download results of a query for any database of the National Center for Biotechnology Information (NCBI). 8 | } 9 | 10 | \usage{ 11 | EUtilsGet(x,type="efetch",db="pubmed") 12 | } 13 | 14 | \arguments{ 15 | 16 | \item{x}{Either vector of NCBI records ids, i.e. returned ids from \code{EUtilsSummary}, or the \code{EUtilsSummary} object itself} 17 | \item{type}{string indicating type of NCBI Eutility, \code{efetch}, \code{esummary}, etc.} 18 | \item{db}{string indicating the NCBI database used in query} 19 | } 20 | 21 | 22 | 23 | \details{ 24 | 25 | Possible E-utilities to supply to \code{type} are \code{efetch}, \code{esummary}, and \code{elink}. 26 | 27 | The database name supplied to \code{db} can be any valid Entrez database, such as \code{pubmed}, \code{protein}, \code{nlm}, etc. 28 | 29 | For further details on available E-utilities and databases visit \url{https://www.ncbi.nlm.nih.gov/books/NBK25499/}. 30 | 31 | Note on usage: 32 | 33 | In order not to overload the E-utility servers, NCBI recommends that users post no more than three URL requests per second and limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time during weekdays. Failure to comply with this policy may result in an IP address being blocked from accessing NCBI. 34 | 35 | } 36 | 37 | \value{ 38 | For queries to PubMed, a list by article, with named vectors for each field of the article result. 39 | 40 | For all other database, a list of the \code{XML} tree strucure used where XML output is available in E-Utils. 41 | } 42 | 43 | \seealso{\code{\link{EUtilsSummary}}} 44 | 45 | \references{ 46 | Summary help: 47 | 48 | \url{https://www.ncbi.nlm.nih.gov/books/NBK3827/} 49 | 50 | MEDLINE/PubMed Field Descriptions 51 | 52 | \url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html} 53 | 54 | } 55 | 56 | \author{Stephanie Kovalchik \email{s.a.kovalchik@gmail.com}} 57 | -------------------------------------------------------------------------------- /man/EUtilsQuery.Rd: -------------------------------------------------------------------------------- 1 | \name{EUtilsQuery} 2 | \alias{EUtilsQuery} 3 | \alias{EUtilsQuery-class} 4 | 5 | \title{Construct URL to make NCBI EUtils query} 6 | 7 | \description{ 8 | 9 | Construct a URL query for any database of the National Center for Biotechnology Information (NCBI). 10 | } 11 | 12 | \usage{ 13 | EUtilsQuery(query,type="esearch",db="pubmed",...) 14 | } 15 | 16 | \arguments{ 17 | 18 | \item{query}{string query as given in NCBI search box} 19 | \item{type}{string indicating type of NCBI Eutility} 20 | \item{db}{string indicating the NCBI database used in query} 21 | \item{...}{additional limits added to query} 22 | } 23 | 24 | 25 | 26 | \details{ 27 | 28 | Possible E-utilities to supply to \code{type} are \code{einfo}, \code{esearch}, \code{epost}, \code{esummary}, \code{elink}, \code{egquery}, \code{espell}. 29 | 30 | The database name supplied to \code{db} can be any valid Entrez database, such as \code{pubmed}, \code{protein}, \code{nlm}, etc. 31 | 32 | For further details on available E-utilities and databases visit \url{https://www.ncbi.nlm.nih.gov/books/NBK25499/}. 33 | 34 | Limits that can be supplied to \code{...} to refine the \code{query} include: 35 | 36 | \tabular{ll}{ 37 | \code{reldate} \tab Limits search results to be within the specified number of days from current date. \cr 38 | \code{mindate} \tab Minimum of date range for search results (examples: 2002; 2002/01/01); must be supplied with \code{maxdate}.\cr 39 | \code{maxdate} \tab Maximum of date range for search results; must be supplied with \code{mindate}.\cr 40 | \code{datetype} \tab Which date field to use in setting date limits. Possible choices are \code{edat}, Entrez date, which is the date article was added to Entez, or \code{ppdt}, the article publication date. Default is \code{edat}.\cr 41 | \code{retstart} \tab Where in the sequence of returned results to begin retrieving, default is 0.\cr 42 | \code{retmax} \tab Maximum number of records to retrieve, default is 1000. 43 | } 44 | 45 | } 46 | 47 | \value{ 48 | String URL to access NCBI E-utility. 49 | } 50 | 51 | \references{ 52 | Query help: 53 | 54 | \url{https://www.ncbi.nlm.nih.gov/books/NBK3827/} 55 | 56 | MEDLINE/PubMed Field Descriptions 57 | 58 | \url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html} 59 | } 60 | 61 | \examples{ 62 | 63 | # PUBMED QUERY 64 | EUtilsQuery("myeloma[ti] jones[au]") 65 | 66 | # RESTRICT TO RECORDS WITHIN LAST 30 days 67 | EUtilsQuery("myeloma[ti] jones[au]",reldat=30) 68 | 69 | 70 | } 71 | 72 | \author{Stephanie Kovalchik \email{s.a.kovalchik@gmail.com}} 73 | -------------------------------------------------------------------------------- /man/EUtilsSummary.Rd: -------------------------------------------------------------------------------- 1 | \name{EUtilsSummary} 2 | \alias{EUtilsSummary} 3 | 4 | \title{Get summary of NCBI EUtils query} 5 | 6 | \description{ 7 | Get summary information on the results of a query for any database of the National Center for Biotechnology Information (NCBI). 8 | } 9 | 10 | \usage{ 11 | EUtilsSummary(query,type="esearch",db="pubmed",url=NULL,encoding="unknown",...) 12 | } 13 | 14 | \arguments{ 15 | 16 | \item{query}{string query as given in NCBI search box} 17 | \item{type}{string indicating type of NCBI Eutility} 18 | \item{db}{string indicating the NCBI database used in query} 19 | \item{url}{string of url to bypass query construction} 20 | \item{encoding}{encoding to be assumed for input strings, see \code{\link{readLines}}} 21 | \item{...}{additional limits added to query} 22 | } 23 | 24 | 25 | 26 | \details{ 27 | 28 | Possible E-utilities to supply to \code{type} are \code{einfo}, \code{esearch}, \code{epost}, \code{esummary}, \code{elink}, \code{egquery}, \code{espell}. 29 | 30 | The database name supplied to \code{db} can be any valid Entrez database, such as \code{pubmed}, \code{protein}, \code{nlm}, etc. 31 | 32 | For further details on available E-utilities and databases visit \url{https://www.ncbi.nlm.nih.gov/books/NBK25499/}. 33 | 34 | Limits that can be supplied to \code{...} to refine the \code{query} include: 35 | 36 | \tabular{ll}{ 37 | \code{reldate} \tab Limits search results to be within the specified number of days from current date. \cr 38 | \code{mindate} \tab Minimum of date range for search results (examples: 2002; 2002/01/01); must be supplied with \code{maxdate}.\cr 39 | \code{maxdate} \tab Maximum of date range for search results; must be supplied with \code{mindate}.\cr 40 | \code{datetype} \tab Which date field to use in setting date limits. Possible choices are \code{edat}, Entrez date, which is the date article was added to Entez, or \code{ppdt}, the article publication date. Default is \code{edat}.\cr 41 | \code{retstart} \tab Where in the sequence of returned results to begin retrieving, default is 0.\cr 42 | \code{retmax} \tab Maximum number of records to retrieve, default is 1000. 43 | } 44 | 45 | } 46 | 47 | \value{ 48 | Returns an \code{EUtilsSummary} object. 49 | } 50 | 51 | \seealso{\code{\link{EUtilsQuery}}} 52 | 53 | \references{ 54 | Summary help: 55 | 56 | \url{https://www.ncbi.nlm.nih.gov/books/NBK3827/} 57 | 58 | MEDLINE/PubMed Field Descriptions 59 | 60 | \url{https://www.nlm.nih.gov/bsd/mms/medlineelements.html} 61 | } 62 | 63 | \author{Stephanie Kovalchik \email{s.a.kovalchik@gmail.com}} 64 | -------------------------------------------------------------------------------- /R/EUtils.R: -------------------------------------------------------------------------------- 1 | # MAKING RNCBI PACKAGE 2 | collapse <- function(...){paste(...,sep="",collapse="")} 3 | 4 | EUtilsURL <- function(type="esearch",db="pubmed"){ 5 | 6 | # CONSTRUCT ANY SERVICE TYPE AND DATABASE 7 | url <- "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/type.fcgi?db=DB&" 8 | 9 | sub("(.*)(type)(.*)(DB)(.*)",collapse("\\1",type,"\\3",db,"\\5"),url) 10 | } 11 | 12 | 13 | EUtilsQuery <- function(query,type="esearch",db="pubmed",...){ 14 | 15 | # CREATE URL WITH REQUEST 16 | PubMedURL <- EUtilsURL(type,db) 17 | Query <- gsub(" ","+",query) 18 | 19 | # PARTIAL MATCH OF POSSIBLE LIMITS 20 | OPTIONS <- c( 21 | "retstart", 22 | "retmax", 23 | "rettype", 24 | "field", 25 | "datetype", 26 | "reldate", 27 | "mindate", 28 | "maxdate" 29 | ) 30 | 31 | ArgList <- list(...) # NEED FUNCTION PARTIAL MATCH HERE 32 | 33 | if(length(ArgList)==0){ 34 | ArgList$retmax <- 1000 # DEFAULT 1000 RECORDS RETURNED 35 | } 36 | else{ 37 | WhichArgs <- pmatch(names(ArgList),OPTIONS) 38 | if(any(is.na(WhichArgs))||sapply(WhichArgs,length)>1) 39 | stop("Error in specified limits.") 40 | names(ArgList) <- OPTIONS[WhichArgs] 41 | if(all(names(ArgList)!="retmax")) 42 | ArgList$retmax <- 1000 # DEFAULT 1000 RECORDS RETURNED 43 | } 44 | 45 | ArgList$tool <- "RISmed" 46 | ArgList$email <- "s.a.kovalchik@gmail.com" 47 | 48 | # REPLACE RETMAX IF NOT USED 49 | ArgStr <- paste(names(ArgList),unlist(ArgList),sep="=") 50 | ArgStr <- paste(ArgStr,collapse="&") 51 | 52 | paste(PubMedURL,"term=",Query,"&",ArgStr,sep="",collapse="") 53 | } 54 | 55 | ParseTags <- function(lines){ 56 | 57 | StripLines <- sapply(lines, function(x)gsub("> +",">",x)) # REPLACE WHITE SPACE 58 | 59 | Fields <- c("Count", 60 | "RetMax", 61 | "RetStart", 62 | "Id", 63 | "QueryTranslation") 64 | 65 | Patterns <- paste("(.*<",Fields,">)(.*)(<\\/",Fields,">).*",sep="") 66 | 67 | FieldIndex <- lapply(Patterns, function(pattern) grep(pattern, StripLines)) 68 | FieldIndex[[1]] <- FieldIndex[[1]][1] # TAKE COUNT OF COMBINED QUERY 69 | 70 | Values <- lapply(1:length(Fields), 71 | function(i){ 72 | result <- sapply(StripLines[FieldIndex[[i]]], 73 | function(x) sub(Patterns[i],"\\2",x),USE.NAMES=FALSE) 74 | as.vector(result) 75 | }) 76 | 77 | 78 | names(Values) <- Fields 79 | Values$Count <- as.numeric(Values$Count) 80 | Values$RetMax <- as.numeric(Values$RetMax) 81 | Values$RetStart <- as.numeric(Values$RetStart) 82 | 83 | Values 84 | } 85 | 86 | 87 | SplitIDs <- function(ids){ 88 | 89 | if(length(ids)>200){ 90 | group <- rep(1:ceiling(length(ids)/200),each=200) 91 | group <- group[1:length(ids)] 92 | split(ids,group) 93 | } 94 | else{ 95 | list(ids) 96 | } 97 | 98 | } 99 | 100 | 101 | EUtilsGet <- function(x, type="efetch", db="pubmed"){ 102 | 103 | if(class(x)[1]=="EUtilsSummary"){ 104 | query <- x@querytranslation 105 | x <- x@PMID 106 | } 107 | else{ 108 | query <- "" 109 | } 110 | 111 | IDList <- SplitIDs(x) 112 | Result <- lapply(IDList, EUtilsSubGet, type = type, db = db) 113 | Result <- unlist(Result, recursive=FALSE) 114 | 115 | if(type=="efetch"&db=="pubmed"){ 116 | 117 | Result <- Medline(Result, query) 118 | } 119 | 120 | Result 121 | } 122 | 123 | 124 | EUtilsSubGet <- function(ids, type="efetch", db="pubmed"){ 125 | 126 | FetchURL <- EUtilsURL(type,db=db) 127 | IDStr <- collapse("id=",paste(ids,collapse=",")) 128 | EUtilsFetch <- collapse(FetchURL,IDStr) 129 | 130 | res <- readLines(collapse(EUtilsFetch,"&retmode=xml"), warn = FALSE, encoding = "UTF-8") 131 | res <- readLines(collapse(EUtilsFetch,"&retmode=xml"), warn = FALSE, encoding = "UTF-8") 132 | res <- xml2::read_xml(collapse(EUtilsFetch,"&retmode=xml"), encoding = "UTF-8") 133 | res <- xml2::as_list(res)[[1]] 134 | 135 | if(db == "pubmed"){ 136 | res <- lapply(res, ParseMedline) # Return list for each artcile, missing elements are NULL 137 | } 138 | 139 | res 140 | } 141 | 142 | 143 | 144 | 145 | -------------------------------------------------------------------------------- /NEWS: -------------------------------------------------------------------------------- 1 | Version 2.0 2 | ------------------------------------------------------------------------------ 3 | 4 | Because of the limitations of calling through hubmed.org, RISmed now downloads 5 | content directly from NCBI. This has required major revisions to the package including the 6 | dropping of the Reference class and export functions. 7 | 8 | The name of the package will be retained but its design will focus on getting NCBI content for analysis not for reference management. 9 | 10 | The current version has the main advantages of no longer having a reference limit to downloaded records. It also can access any valid Entrez database. It still sucks because there is not much processing of content so 2.0 should be considered an alpha version. 11 | 12 | ------------------------------------------------------------------------------ 13 | 14 | Version 2.0.1 15 | 16 | Changed id, count, translation to QueryID, QueryCount, and QueryTranslation so that there would be no naming conflict with the plyr package. 17 | 18 | Created Medline class to process output for E-fetch from PubMed database. 19 | 20 | Usage disclaimer added. 21 | 22 | ------------------------------------------------------------------------------- 23 | 24 | Version 2.1.0 25 | 26 | Corrected web link; Added MeSH Terms for MEDLINE object 27 | 28 | ------------------------------------------------------------------------------- 29 | 30 | Version 2.1.1 31 | 32 | Revised fields to accept bracketed (foreign-language) titles. 33 | 34 | ------------------------------------------------------------------------------- 35 | 36 | Version 2.1.2 37 | 38 | Fixed bug with author field for cases with missing forename/middle name; Fixed error message for queries with no result and instead return EUtilsSummary object with "0" record count. 39 | 40 | ------------------------------------------------------------------------------- 41 | 42 | Version 2.1.3 43 | 44 | Corrected problem with extraction of publication date. 45 | 46 | ------------------------------------------------------------------------------- 47 | 48 | Version 2.1.4 49 | 50 | Changed Publication Type to list to allow for multiple types to be extracted from Pubmed records. 51 | 52 | ------------------------------------------------------------------------------- 53 | 54 | Version 2.1.5 55 | 56 | Add method Cited for Medline and EUtilsSummary classes. Fixed bug with Day extractor. Expanded date extractors for Medline object (Year, Month, Day, Hour, Minute) to allow dates for the following events in article publication history: accepted, received, epublish, ppublish, pmc, and pubmed. Corrected issue with structured abstracts. 57 | 58 | ------------------------------------------------------------------------------- 59 | 60 | Version 2.1.6 61 | 62 | Added concatenate method for Medline class. 63 | 64 | ------------------------------------------------------------------------------- 65 | 66 | Version 2.1.7 67 | 68 | Added additional Affiliations to Affiliation method, now returns a list of all affiliations in the same order as the authors. 69 | 70 | ------------------------------------------------------------------------------- 71 | 72 | Version 2.1.8 73 | 74 | Added COIStatement to Medline methods. 75 | 76 | -------------------------------------------------------------------------------- 77 | 78 | Version 2.1.9 79 | 80 | Added names to Affiliations to link to authors 81 | 82 | -------------------------------------------------------------------------------- 83 | 84 | Version 2.1.10 85 | 86 | Changes value identification to take anything between <> in the event special characters are present. 87 | 88 | -------------------------------------------------------------------------------- 89 | 90 | Version 2.1.11 91 | 92 | Fixed doi vs pii, added additional date variables, and fixed bug with structured abstracts. 93 | 94 | ------------------------------------------------------------------------------- 95 | 96 | Version 2.2 97 | 98 | Rebuild for R version 3.6.2 and put dependency on R >= 3.6.0. 99 | 100 | 101 | ------------------------------------------------------------------------------- 102 | 103 | Version 2.3.0 104 | 105 | Adds xml2 to read in xml records and ensure a reliable structure. Parses XML as a list. Add Keywords and Citations to Medline object. 106 | 107 | ------------------------------------------------------------------------------- 108 | 109 | Version 2.3.1 110 | 111 | Adds methods for books. Corrects some bugs in a few Medline object output (DOI, ISSN, etc.) -------------------------------------------------------------------------------- /R/MedlineC.R: -------------------------------------------------------------------------------- 1 | ############################################################## 2 | #' Concatenate Medline 3 | #' 4 | #' Concatenates multiple Medline objects 5 | #' 6 | #' @param x a Medline object 7 | #' @param ... Additional Medline objects to concatenate 8 | #' 9 | #' @return A Medline object 10 | #' @export 11 | #' @docType methods 12 | #' @rdname c-methods 13 | #' @aliases c,ANY,ANY-method 14 | setMethod("c","Medline", function(x, ...){ 15 | 16 | slots <- slotNames(x) 17 | 18 | addx <- list(...) 19 | addx <- c(list(x), addx) 20 | 21 | # Make a list of all the components 22 | GetComponents <- lapply(addx, function(y){ 23 | result <- lapply(slots, function(z) slot(y, z)) 24 | names(result) <- slots 25 | result 26 | }) 27 | 28 | MeshTerms <- list() 29 | for(x in GetComponents) 30 | MeshTerms <- c(MeshTerms, x[["Mesh"]]) 31 | 32 | Authors <- list() 33 | for(x in GetComponents) 34 | Authors <- c(Authors, x[["Author"]]) 35 | 36 | Editors <- list() 37 | for(x in GetComponents) 38 | Editors <- c(Editors, x[["BookEditors"]]) 39 | 40 | Affilitations <- list() 41 | for(x in GetComponents) 42 | Affilitations <- c(Affilitations, x[["Affiliation"]]) 43 | 44 | Keywords <- list() 45 | for(x in GetComponents) 46 | Keywords<- c(Keywords, x[["Keywords"]]) 47 | 48 | Citations <- list() 49 | for(x in GetComponents) 50 | Citations <- c(Citations, x[["Citations"]]) 51 | 52 | GrantID <- list() 53 | for(x in GetComponents) 54 | GrantID <- c(GrantID, x[["GrantID"]]) 55 | 56 | PublicationType <- list() 57 | for(x in PublicationType) 58 | PublicationType <- c(PublicationType, x[["PublicationType"]]) 59 | 60 | 61 | new("Medline", 62 | Query = sapply(GetComponents, function(x) x[["Query"]]), 63 | PMID = unlist(lapply(GetComponents, function(x) x[["PMID"]])), 64 | YearRevised = unlist(lapply(GetComponents, function(x) x[["YearRevised"]])), 65 | MonthRevised = unlist(lapply(GetComponents, function(x) x[["MonthRevised"]])), 66 | DayRevised = unlist(lapply(GetComponents, function(x) x[["DayRevised"]])), 67 | YearPubDate = unlist(lapply(GetComponents, function(x) x[["YearPubDate"]])), 68 | MonthPubDate = unlist(lapply(GetComponents, function(x) x[["MonthPubDate"]])), 69 | DayPubDate = unlist(lapply(GetComponents, function(x) x[["DayPubDate"]])), 70 | YearArticleDate = unlist(lapply(GetComponents, function(x) x[["YearArticleDate"]])), 71 | MonthArticleDate = unlist(lapply(GetComponents, function(x) x[["MonthArticleDate"]])), 72 | DayArticleDate = unlist(lapply(GetComponents, function(x) x[["DayArticleDate"]])), 73 | YearEntrez = unlist(lapply(GetComponents, function(x) x[["YearEntrez"]])), 74 | MonthEntrez = unlist(lapply(GetComponents, function(x) x[["MonthEntrez"]])), 75 | DayEntrez = unlist(lapply(GetComponents, function(x) x[["DayEntrez"]])), 76 | HourEntrez = unlist(lapply(GetComponents, function(x) x[["HourEntrez"]])), 77 | MinuteEntrez = unlist(lapply(GetComponents, function(x) x[["MinuteEntrez"]])), 78 | YearMedline = unlist(lapply(GetComponents, function(x) x[["YearMedline"]])), 79 | MonthMedline = unlist(lapply(GetComponents, function(x) x[["MonthMedline"]])), 80 | DayMedline = unlist(lapply(GetComponents, function(x) x[["DayMedline"]])), 81 | HourMedline = unlist(lapply(GetComponents, function(x) x[["HourMedline"]])), 82 | MinuteMedline = unlist(lapply(GetComponents, function(x) x[["MinuteMedline"]])), 83 | YearAccepted = unlist(lapply(GetComponents, function(x) x[["YearAccepted"]])), 84 | MonthAccepted = unlist(lapply(GetComponents, function(x) x[["MonthAccepted"]])), 85 | DayAccepted = unlist(lapply(GetComponents, function(x) x[["DayAccepted"]])), 86 | HourAccepted = unlist(lapply(GetComponents, function(x) x[["HourAccepted"]])), 87 | MinuteAccepted = unlist(lapply(GetComponents, function(x) x[["MinuteAccepted"]])), 88 | YearReceived = unlist(lapply(GetComponents, function(x) x[["YearReceived"]])), 89 | MonthReceived = unlist(lapply(GetComponents, function(x) x[["MonthReceived"]])), 90 | DayReceived = unlist(lapply(GetComponents, function(x) x[["DayReceived"]])), 91 | HourReceived = unlist(lapply(GetComponents, function(x) x[["HourReceived"]])), 92 | MinuteReceived = unlist(lapply(GetComponents, function(x) x[["MinuteReceived"]])), 93 | YearEpublish = unlist(lapply(GetComponents, function(x) x[["YearEpublish"]])), 94 | MonthEpublish = unlist(lapply(GetComponents, function(x) x[["MonthEpublish"]])), 95 | DayEpublish = unlist(lapply(GetComponents, function(x) x[["DayEpublish"]])), 96 | HourEpublish = unlist(lapply(GetComponents, function(x) x[["HourEpublish"]])), 97 | MinuteEpublish = unlist(lapply(GetComponents, function(x) x[["MinuteEpublish"]])), 98 | YearPpublish = unlist(lapply(GetComponents, function(x) x[["YearPpublish"]])), 99 | MonthPpublish = unlist(lapply(GetComponents, function(x) x[["MonthPpublish"]])), 100 | DayPpublish = unlist(lapply(GetComponents, function(x) x[["DayPpublish"]])), 101 | HourPpublish = unlist(lapply(GetComponents, function(x) x[["HourPpublish"]])), 102 | MinutePpublish = unlist(lapply(GetComponents, function(x) x[["MinutePpublish"]])), 103 | YearPmc = unlist(lapply(GetComponents, function(x) x[["YearPmc"]])), 104 | MonthPmc = unlist(lapply(GetComponents, function(x) x[["MonthPmc"]])), 105 | DayPmc = unlist(lapply(GetComponents, function(x) x[["DayPmc"]])), 106 | HourPmc = unlist(lapply(GetComponents, function(x) x[["HourPmc"]])), 107 | MinutePmc = unlist(lapply(GetComponents, function(x) x[["MinutePmc"]])), 108 | YearPubmed = unlist(lapply(GetComponents, function(x) x[["YearPubmed"]])), 109 | MonthPubmed = unlist(lapply(GetComponents, function(x) x[["MonthPubmed"]])), 110 | DayPubmed = unlist(lapply(GetComponents, function(x) x[["DayPubmed"]])), 111 | HourPubmed = unlist(lapply(GetComponents, function(x) x[["HourPubmed"]])), 112 | MinutePubmed = unlist(lapply(GetComponents, function(x) x[["MinutePubmed"]])), 113 | ISSN = unlist(lapply(GetComponents, function(x) x[["ISSN"]])), 114 | Title = unlist(lapply(GetComponents, function(x) x[["Title"]])), 115 | Author = Authors, 116 | ArticleTitle = unlist(lapply(GetComponents, function(x) x[["ArticleTitle"]])), 117 | ELocationID = unlist(lapply(GetComponents, function(x) x[["ELocationID"]])), 118 | AbstractText = unlist(lapply(GetComponents, function(x) x[["AbstractText"]])), 119 | Affiliation = Affilitations, 120 | Language = unlist(lapply(GetComponents, function(x) x[["Language"]])), 121 | PublicationType = PublicationType, 122 | MedlineTA = unlist(lapply(GetComponents, function(x) x[["MedlineTA"]])), 123 | NlmUniqueID = unlist(lapply(GetComponents, function(x) x[["NlmUniqueID"]])), 124 | ISSNLinking = unlist(lapply(GetComponents, function(x) x[["ISSNLinking"]])), 125 | PublicationStatus = unlist(lapply(GetComponents, function(x) x[["PublicationStatus"]])), 126 | ArticleId = unlist(lapply(GetComponents, function(x) x[["ArticleId"]])), 127 | DOI = unlist(lapply(GetComponents, function(x) x[["DOI"]])), 128 | Volume = unlist(lapply(GetComponents, function(x) x[["Volume"]])), 129 | Issue = unlist(lapply(GetComponents, function(x) x[["Issue"]])), 130 | ISOAbbreviation = unlist(lapply(GetComponents, function(x) x[["ISOAbbreviation"]])), 131 | MedlinePgn = unlist(lapply(GetComponents, function(x) x[["MedlinePgn"]])), 132 | CopyrightInformation = unlist(lapply(GetComponents, function(x) x[["CopyrightInformation"]])), 133 | Country = unlist(lapply(GetComponents, function(x) x[["Country"]])), 134 | GrantID = GrantID, 135 | COIStatement = unlist(lapply(GetComponents, function(x) x[["COIStatement"]])), 136 | Mesh = MeshTerms, 137 | Keywords = Keywords, 138 | Citations = Citations, 139 | BookPublisher = unlist(lapply(GetComponents, function(x) x[["BookPublisher"]])), 140 | BookPublisherLocation = unlist(lapply(GetComponents, function(x) x[["BookPublisherLocation"]])), 141 | BookTitle = unlist(lapply(GetComponents, function(x) x[["BookTitle"]])), 142 | BookBeginningDate = unlist(lapply(GetComponents, function(x) x[["BookBeginningDate"]])), 143 | BookEndingDate = unlist(lapply(GetComponents, function(x) x[["BookEndingDate"]])), 144 | BookMedium = unlist(lapply(GetComponents, function(x) x[["BookMedium"]])), 145 | BookEditors = Editors 146 | ) 147 | 148 | }) -------------------------------------------------------------------------------- /R/AllGenerics.R: -------------------------------------------------------------------------------- 1 | # RISmed GENERICS 2 | setGeneric("QueryCount",function(object) standardGeneric("QueryCount")) 3 | setGeneric("QueryId",function(object) standardGeneric("QueryId")) 4 | setGeneric("QueryTranslation",function(object) standardGeneric("QueryTranslation")) 5 | setGeneric("Query",function(object) standardGeneric("Query")) 6 | setGeneric("PMID",function(object) standardGeneric("PMID")) 7 | setGeneric("YearRevised",function(object) standardGeneric("YearRevised")) 8 | setGeneric("MonthRevised",function(object) standardGeneric("MonthRevised")) 9 | setGeneric("DayRevised",function(object) standardGeneric("DayRevised")) 10 | setGeneric("YearPubDate",function(object) standardGeneric("YearPubDate")) 11 | setGeneric("MonthPubDate",function(object) standardGeneric("MonthPubDate")) 12 | setGeneric("DayPubDate",function(object) standardGeneric("DayPubDate")) 13 | setGeneric("YearArticleDate",function(object) standardGeneric("YearArticleDate")) 14 | setGeneric("MonthArticleDate",function(object) standardGeneric("MonthArticleDate")) 15 | setGeneric("DayArticleDate",function(object) standardGeneric("DayArticleDate")) 16 | setGeneric("YearEntrez",function(object) standardGeneric("YearEntrez")) 17 | setGeneric("MonthEntrez",function(object) standardGeneric("MonthEntrez")) 18 | setGeneric("DayEntrez",function(object) standardGeneric("DayEntrez")) 19 | setGeneric("HourEntrez",function(object) standardGeneric("HourEntrez")) 20 | setGeneric("MinuteEntrez",function(object) standardGeneric("MinuteEntrez")) 21 | setGeneric("YearMedline",function(object) standardGeneric("YearMedline")) 22 | setGeneric("MonthMedline",function(object) standardGeneric("MonthMedline")) 23 | setGeneric("DayMedline",function(object) standardGeneric("DayMedline")) 24 | setGeneric("HourMedline",function(object) standardGeneric("HourMedline")) 25 | setGeneric("MinuteMedline",function(object) standardGeneric("MinuteMedline")) 26 | 27 | setGeneric("YearAccepted",function(object) standardGeneric("YearAccepted")) 28 | setGeneric("MonthAccepted",function(object) standardGeneric("MonthAccepted")) 29 | setGeneric("DayAccepted",function(object) standardGeneric("DayAccepted")) 30 | setGeneric("HourAccepted",function(object) standardGeneric("HourAccepted")) 31 | setGeneric("MinuteAccepted",function(object) standardGeneric("MinuteAccepted")) 32 | setGeneric("YearReceived",function(object) standardGeneric("YearReceived")) 33 | setGeneric("MonthReceived",function(object) standardGeneric("MonthReceived")) 34 | setGeneric("DayReceived",function(object) standardGeneric("DayReceived")) 35 | setGeneric("HourReceived",function(object) standardGeneric("HourReceived")) 36 | setGeneric("MinuteReceived",function(object) standardGeneric("MinuteReceived")) 37 | setGeneric("YearEpublish",function(object) standardGeneric("YearEpublish")) 38 | setGeneric("MonthEpublish",function(object) standardGeneric("MonthEpublish")) 39 | setGeneric("DayEpublish",function(object) standardGeneric("DayEpublish")) 40 | setGeneric("HourEpublish",function(object) standardGeneric("HourEpublish")) 41 | setGeneric("MinuteEpublish",function(object) standardGeneric("MinuteEpublish")) 42 | setGeneric("YearPpublish",function(object) standardGeneric("YearPpublish")) 43 | setGeneric("MonthPpublish",function(object) standardGeneric("MonthPpublish")) 44 | setGeneric("DayPpublish",function(object) standardGeneric("DayPpublish")) 45 | setGeneric("HourPpublish",function(object) standardGeneric("HourPpublish")) 46 | setGeneric("MinutePpublish",function(object) standardGeneric("MinutePpublish")) 47 | setGeneric("YearPmc",function(object) standardGeneric("YearPmc")) 48 | setGeneric("MonthPmc",function(object) standardGeneric("MonthPmc")) 49 | setGeneric("DayPmc",function(object) standardGeneric("DayPmc")) 50 | setGeneric("HourPmc",function(object) standardGeneric("HourPmc")) 51 | setGeneric("MinutePmc",function(object) standardGeneric("MinutePmc")) 52 | setGeneric("YearPubmed",function(object) standardGeneric("YearPubmed")) 53 | setGeneric("MonthPubmed",function(object) standardGeneric("MonthPubmed")) 54 | setGeneric("DayPubmed",function(object) standardGeneric("DayPubmed")) 55 | setGeneric("HourPubmed",function(object) standardGeneric("HourPubmed")) 56 | setGeneric("MinutePubmed",function(object) standardGeneric("MinutePubmed")) 57 | setGeneric("Author", function(object) standardGeneric("Author")) 58 | setGeneric("ISSN",function(object) standardGeneric("ISSN")) 59 | setGeneric("Title",function(object) standardGeneric("Title")) 60 | setGeneric("ArticleTitle",function(object) standardGeneric("ArticleTitle")) 61 | setGeneric("ELocationID",function(object) standardGeneric("ELocationID")) 62 | setGeneric("AbstractText",function(object) standardGeneric("AbstractText")) 63 | setGeneric("Affiliation", function(object) standardGeneric("Affiliation")) 64 | setGeneric("Language",function(object) standardGeneric("Language")) 65 | setGeneric("PublicationType",function(object) standardGeneric("PublicationType")) 66 | setGeneric("MedlineTA",function(object) standardGeneric("MedlineTA")) 67 | setGeneric("NlmUniqueID",function(object) standardGeneric("NlmUniqueID")) 68 | setGeneric("ISSNLinking",function(object) standardGeneric("ISSNLinking")) 69 | setGeneric("PublicationStatus",function(object) standardGeneric("PublicationStatus")) 70 | setGeneric("ArticleId",function(object) standardGeneric("ArticleId")) 71 | setGeneric("DOI",function(object) standardGeneric("DOI")) 72 | setGeneric("Volume",function(object) standardGeneric("Volume")) 73 | setGeneric("Issue",function(object) standardGeneric("Issue")) 74 | setGeneric("ISOAbbreviation",function(object) standardGeneric("ISOAbbreviation")) 75 | setGeneric("MedlinePgn",function(object) standardGeneric("MedlinePgn")) 76 | setGeneric("CopyrightInformation",function(object) standardGeneric("CopyrightInformation")) 77 | setGeneric("Country",function(object) standardGeneric("Country")) 78 | setGeneric("GrantID", function(object) standardGeneric("GrantID")) 79 | setGeneric("COIStatement",function(object) standardGeneric("COIStatement")) 80 | setGeneric("Mesh", function(object) standardGeneric("Mesh")) 81 | setGeneric("Keywords", function(object) standardGeneric("Keywords")) 82 | setGeneric("Citations", function(object) standardGeneric("Citations")) 83 | 84 | setGeneric("BookPublisher",function(object) standardGeneric("BookPublisher")) 85 | setGeneric("BookPublisherLocation",function(object) standardGeneric("BookPublisherLocation")) 86 | setGeneric("BookTitle",function(object) standardGeneric("BookTitle")) 87 | setGeneric("BookBeginningDate",function(object) standardGeneric("BookBeginningDate")) 88 | setGeneric("BookEndingDate",function(object) standardGeneric("BookEndingDate")) 89 | setGeneric("BookEditors",function(object) standardGeneric("BookEditors")) 90 | setGeneric("BookMedium",function(object) standardGeneric("BookMedium")) 91 | 92 | -------------------------------------------------------------------------------- /man/Medline.Rd: -------------------------------------------------------------------------------- 1 | \name{Medline-class} 2 | \docType{class} 3 | \alias{Medline} 4 | \alias{Medline-class} 5 | 6 | \title{Class \code{"Medline"}} 7 | 8 | \description{ 9 | Class for Medline citation of query to PubMed. 10 | } 11 | 12 | \section{Objects from the Class}{ 13 | Objects can be created by calls of the form \code{new("Medline", ...)}. 14 | } 15 | \section{Slots}{ 16 | Unless stated otherwise, each of the components is a vector of the given field where each element corresponds to a PubMed article. 17 | \describe{ 18 | \item{\code{Query}:}{} 19 | \item{\code{PMID}:}{} 20 | \item{\code{YearPubDate}:}{} 21 | \item{\code{MonthPubDate}:}{} 22 | \item{\code{DayPubDate}:}{} 23 | \item{\code{YearRevised}:}{} 24 | \item{\code{MonthRevised}:}{} 25 | \item{\code{DayRevised}:}{} 26 | \item{\code{YearEntrez}:}{} 27 | \item{\code{MonthEntrez}:}{} 28 | \item{\code{DayEntrez}:}{} 29 | \item{\code{HourEntrez}:}{} 30 | \item{\code{MinuteEntrez}:}{} 31 | \item{\code{YearArticleDate}:}{} 32 | \item{\code{MonthArticleDate}:}{} 33 | \item{\code{DayArticleDate}:}{} 34 | \item{\code{YearMedline}:}{} 35 | \item{\code{MonthMedline}:}{} 36 | \item{\code{DayMedline}:}{} 37 | \item{\code{HourMedline}:}{} 38 | \item{\code{MinuteMedline}:}{} 39 | \item{\code{YearAccepted}:}{} 40 | \item{\code{MonthAccepted}:}{} 41 | \item{\code{DayAccepted}:}{} 42 | \item{\code{HourAccepted}:}{} 43 | \item{\code{MinuteAccepted}:}{} 44 | \item{\code{YearReceived}:}{} 45 | \item{\code{MonthReceived}:}{} 46 | \item{\code{DayReceived}:}{} 47 | \item{\code{HourReceived}:}{} 48 | \item{\code{MinuteReceived}:}{} 49 | \item{\code{YearEpublish}:}{} 50 | \item{\code{MonthEpublish}:}{} 51 | \item{\code{DayEpublish}:}{} 52 | \item{\code{HourEpublish}:}{} 53 | \item{\code{MinuteEpublish}:}{} 54 | \item{\code{YearPpublish}:}{} 55 | \item{\code{MonthPpublish}:}{} 56 | \item{\code{DayPpublish}:}{} 57 | \item{\code{HourPpublish}:}{} 58 | \item{\code{MinutePpublish}:}{} 59 | \item{\code{YearPmc}:}{} 60 | \item{\code{MonthPmc}:}{} 61 | \item{\code{DayPmc}:}{} 62 | \item{\code{HourPmc}:}{} 63 | \item{\code{MinutePmc}:}{} 64 | \item{\code{YearPubmed}:}{} 65 | \item{\code{MonthPubmed}:}{} 66 | \item{\code{DayPubmed}:}{} 67 | \item{\code{HourPubmed}:}{} 68 | \item{\code{MinutePubmed}:}{} 69 | \item{\code{Author}:}{ list of data frames giving \code{LastName}, \code{ForeName}, \code{Initials}, and \code{order} of authors by PubMed article.} 70 | \item{\code{ISSN}:}{} 71 | \item{\code{Title}:}{} 72 | \item{\code{ArticleTitle}:}{} 73 | \item{\code{ELocationID}:}{} 74 | \item{\code{AbstractText}:}{} 75 | \item{\code{Affiliation}:}{} 76 | \item{\code{Language}:}{} 77 | \item{\code{PublicationType}:}{} 78 | \item{\code{MedlineTA}:}{} 79 | \item{\code{NlmUniqueID}:}{} 80 | \item{\code{ISSNLinking}:}{} 81 | \item{\code{PublicationStatus}:}{} 82 | \item{\code{ArticleId}:}{} 83 | \item{\code{DOI}:}{} 84 | \item{\code{Volume}:}{} 85 | \item{\code{Issue}:}{} 86 | \item{\code{ISOAbbreviation}:}{} 87 | \item{\code{MedlinePgn}:}{} 88 | \item{\code{CopyrightInformation}:}{} 89 | \item{\code{Country}:}{} 90 | \item{\code{GrantID}:}{} 91 | \item{\code{COIStatement}:}{} 92 | \item{\code{Mesh}:}{ list of data frames giving \code{Heading} and \code{Type} of MeSH term or \code{NA} if no terms are in MEDLINE record} 93 | \item{\code{Keywords}:}{} 94 | \item{\code{Citations}:}{} 95 | } 96 | } 97 | \section{Methods}{ 98 | In addition to \code{print} and \code{show} methods, each slot of the \code{Medline} class has a corresponding extractor of the same name. 99 | \describe{ 100 | \item{print}{\code{signature(x = "Medline", ...)}: ...} 101 | \item{show}{\code{signature(object = "Medline")}: ...} 102 | \item{c}{\code{signature(x = "Medline", ...)}: ...} 103 | \item{Query}{\code{signature(object = "Medline")}: ...} 104 | \item{PMID}{\code{signature(object = "Medline")}: ...} 105 | \item{YearPubDate}{\code{signature(object = "Medline")}: ...} 106 | \item{MonthPubDate}{\code{signature(object = "Medline")}: ...} 107 | \item{DayPubDate}{\code{signature(object = "Medline")}: ...} 108 | \item{YearRevised}{\code{signature(object = "Medline")}: ...} 109 | \item{MonthRevised}{\code{signature(object = "Medline")}: ...} 110 | \item{DayRevised}{\code{signature(object = "Medline")}: ...} 111 | \item{YearEntrez}{\code{signature(object = "Medline")}: ...} 112 | \item{MonthEntrez}{\code{signature(object = "Medline")}: ...} 113 | \item{DayEntrez}{\code{signature(object = "Medline")}: ...} 114 | \item{HourEntrez}{\code{signature(object = "Medline")}: ...} 115 | \item{MinuteEntrez}{\code{signature(object = "Medline")}: ...} 116 | \item{YearArticleDate}{\code{signature(object = "Medline")}: ...} 117 | \item{MonthArticleDate}{\code{signature(object = "Medline")}: ...} 118 | \item{DayArticleDate}{\code{signature(object = "Medline")}: ...} 119 | \item{YearMedline}{\code{signature(object = "Medline")}: ...} 120 | \item{MonthMedline}{\code{signature(object = "Medline")}: ...} 121 | \item{DayMedline}{\code{signature(object = "Medline")}: ...} 122 | \item{HourMedline}{\code{signature(object = "Medline")}: ...} 123 | \item{MinuteMedline}{\code{signature(object = "Medline")}: ...} 124 | \item{YearAccepted}{\code{signature(object = "Medline")}: ...} 125 | \item{MonthAccepted}{\code{signature(object = "Medline")}: ...} 126 | \item{DayAccepted}{\code{signature(object = "Medline")}: ...} 127 | \item{HourAccepted}{\code{signature(object = "Medline")}: ...} 128 | \item{MinuteAccepted}{\code{signature(object = "Medline")}: ...} 129 | \item{YearReceived}{\code{signature(object = "Medline")}: ...} 130 | \item{MonthReceived}{\code{signature(object = "Medline")}: ...} 131 | \item{DayReceived}{\code{signature(object = "Medline")}: ...} 132 | \item{HourReceived}{\code{signature(object = "Medline")}: ...} 133 | \item{MinuteReceived}{\code{signature(object = "Medline")}: ...} 134 | \item{YearEpublish}{\code{signature(object = "Medline")}: ...} 135 | \item{MonthEpublish}{\code{signature(object = "Medline")}: ...} 136 | \item{DayEpublish}{\code{signature(object = "Medline")}: ...} 137 | \item{HourEpublish}{\code{signature(object = "Medline")}: ...} 138 | \item{MinuteEpublish}{\code{signature(object = "Medline")}: ...} 139 | \item{YearPpublish}{\code{signature(object = "Medline")}: ...} 140 | \item{MonthPpublish}{\code{signature(object = "Medline")}: ...} 141 | \item{DayPpublish}{\code{signature(object = "Medline")}: ...} 142 | \item{HourPpublish}{\code{signature(object = "Medline")}: ...} 143 | \item{MinutePpublish}{\code{signature(object = "Medline")}: ...} 144 | \item{YearPmc}{\code{signature(object = "Medline")}: ...} 145 | \item{MonthPmc}{\code{signature(object = "Medline")}: ...} 146 | \item{DayPmc}{\code{signature(object = "Medline")}: ...} 147 | \item{HourPmc}{\code{signature(object = "Medline")}: ...} 148 | \item{MinutePmc}{\code{signature(object = "Medline")}: ...} 149 | \item{YearPubmed}{\code{signature(object = "Medline")}: ...} 150 | \item{MonthPubmed}{\code{signature(object = "Medline")}: ...} 151 | \item{DayPubmed}{\code{signature(object = "Medline")}: ...} 152 | \item{HourPubmed}{\code{signature(object = "Medline")}: ...} 153 | \item{MinutePubmed}{\code{signature(object = "Medline")}: ...} 154 | \item{Author}{\code{signature(object = "Medline")}: ...} 155 | \item{ISSN}{\code{signature(object = "Medline")}: ...} 156 | \item{Title}{\code{signature(object = "Medline")}: ...} 157 | \item{ArticleTitle}{\code{signature(object = "Medline")}: ...} 158 | \item{ELocationID}{\code{signature(object = "Medline")}: ...} 159 | \item{AbstractText}{\code{signature(object = "Medline")}: ...} 160 | \item{Affiliation}{\code{signature(object = "Medline")}: ...} 161 | \item{Language}{\code{signature(object = "Medline")}: ...} 162 | \item{PublicationType}{\code{signature(object = "Medline")}: ...} 163 | \item{MedlineTA}{\code{signature(object = "Medline")}: ...} 164 | \item{NlmUniqueID}{\code{signature(object = "Medline")}: ...} 165 | \item{ISSNLinking}{\code{signature(object = "Medline")}: ...} 166 | \item{PublicationStatus}{\code{signature(object = "Medline")}: ...} 167 | \item{ArticleId}{\code{signature(object = "Medline")}: ...} 168 | \item{DOI}{\code{signature(object = "Medline")}: ...} 169 | \item{Volume}{\code{signature(object = "Medline")}: ...} 170 | \item{Issue}{\code{signature(object = "Medline")}: ...} 171 | \item{ISOAbbreviation}{\code{signature(object = "Medline")}: ...} 172 | \item{MedlinePgn}{\code{signature(object = "Medline")}: ...} 173 | \item{CopyrightInformation}{\code{signature(object = "Medline")}: ...} 174 | \item{Country}{\code{signature(object = "Medline")}: ...} 175 | \item{GrantID}{\code{signature(object = "Medline")}: ...} 176 | \item{COIStatement}{\code{signature(object = "Medline")}: ...} 177 | \item{Mesh}{\code{signature(object = "Medline")}: ...} 178 | \item{Keywords}{\code{signature(object = "Medline")}: ...} 179 | \item{Affiliations}{\code{signature(object = "Medline")}: ...} 180 | \item{BookPublisher}{\code{signature(object = "Medline")}: ...} 181 | \item{BookPublisherLocation}{\code{signature(object = "Medline")}: ...} 182 | \item{BookTitle}{\code{signature(object = "Medline")}: ...} 183 | \item{BookBeginningDate}{\code{signature(object = "Medline")}: ...} 184 | \item{BookEndingDate}{\code{signature(object = "Medline")}: ...} 185 | \item{BookEditors}{\code{signature(object = "Medline")}: ...} 186 | \item{BookMedium}{\code{signature(object = "Medline")}: ...} 187 | } 188 | } 189 | 190 | 191 | \author{ 192 | Stephanie Kovalchik 193 | } 194 | 195 | \keyword{classes} 196 | -------------------------------------------------------------------------------- /R/ParseMedline.R: -------------------------------------------------------------------------------- 1 | ParseMedline <- function(x){ 2 | if(names(x)[[1]] == "BookDocument") 3 | ParseMedlineBook(x) 4 | else 5 | ParseMedlineArticle(x) 6 | } 7 | 8 | ParseMedlineArticle <- function(x){ 9 | 10 | Tags <- c("PMID", 11 | "YearRevised", 12 | "MonthRevised", 13 | "DayRevised", 14 | "YearPubDate", 15 | "MonthPubDate", 16 | "DayPubDate", 17 | "YearArticleDate", 18 | "MonthArticleDate", 19 | "DayArticleDate", 20 | "YearEntrez", 21 | "MonthEntrez", 22 | "DayEntrez", 23 | "HourEntrez", 24 | "MinuteEntrez", 25 | "YearMedline", 26 | "MonthMedline", 27 | "DayMedline", 28 | "HourMedline", 29 | "MinuteMedline", 30 | "YearAccepted", 31 | "MonthAccepted", 32 | "DayAccepted", 33 | "HourAccepted", 34 | "MinuteAccepted", 35 | "YearReceived", 36 | "MonthReceived", 37 | "DayReceived", 38 | "HourReceived", 39 | "MinuteReceived", 40 | "YearEpublish", 41 | "MonthEpublish", 42 | "DayEpublish", 43 | "HourEpublish", 44 | "MinuteEpublish", 45 | "YearPpublish", 46 | "MonthPpublish", 47 | "DayPpublish", 48 | "HourPpublish", 49 | "MinutePpublish", 50 | "YearPmc", 51 | "MonthPmc", 52 | "DayPmc", 53 | "HourPmc", 54 | "MinutePmc", 55 | "YearPubmed", 56 | "MonthPubmed", 57 | "DayPubmed", 58 | "HourPubmed", 59 | "MinutePubmed", 60 | "ISSN", 61 | "Title", 62 | "Author", 63 | "ArticleTitle", 64 | "ELocationID", 65 | "AbstractText", 66 | "Affiliation", 67 | "Language", 68 | "PublicationType", 69 | "MedlineTA", 70 | "NlmUniqueID", 71 | "ISSNLinking", 72 | "PublicationStatus", 73 | "ArticleId", 74 | "DOI", 75 | "Volume", 76 | "Issue", 77 | "ISOAbbreviation", 78 | "MedlinePgn", 79 | "CopyrightInformation", 80 | "Country", 81 | "GrantID", 82 | "COIStatement", 83 | "Mesh", 84 | "Keywords", 85 | "Citations", 86 | "BookPublisher", 87 | "BookPublisherLocation", 88 | "BookTitle", 89 | "BookBeginningDate", 90 | "BookEndingDate", 91 | "BookEditors", 92 | "BookMedium" 93 | ) 94 | 95 | Fields <- vector(mode = "list", length = length(Tags)) 96 | names(Fields) <- Tags 97 | 98 | 99 | Fields[["PMID"]] <- x$MedlineCitation$PMID[[1]] 100 | 101 | Fields[["YearRevised"]] <- x$MedlineCitation$DateRevised$Year[[1]] 102 | Fields[["MonthRevised"]] <- x$MedlineCitation$DateRevised$Month[[1]] 103 | Fields[["DayRevised"]] <- x$MedlineCitation$DateRevised$Day[[1]] 104 | Fields[["YearPubDate"]] <- x$MedlineCitation$Article$Journal$JournalIssue$PubDate$Year[[1]] 105 | Fields[["MonthPubDate"]] <- x$MedlineCitation$Article$Journal$JournalIssue$PubDate$Month[[1]] 106 | Fields[["DayPubDate"]] <- x$MedlineCitation$Article$Journal$JournalIssue$PubDate$Day[[1]] 107 | Fields[["YearArticleDate"]] <- x$MedlineCitation$Article$ArticleDate$Year[[1]] 108 | Fields[["MonthArticleDate"]] <- x$MedlineCitation$Article$ArticleDate$Month[[1]] 109 | Fields[["DayArticleDate"]] <- x$MedlineCitation$Article$ArticleDate$Day[[1]] 110 | 111 | pubmed_states <- sapply(x$PubmedData$History, function(z) attr(z, "PubStatus")) 112 | 113 | 114 | if(length(pubmed_states) > 0){ 115 | if(any(pubmed_states == "entrez")){ 116 | i <- which(pubmed_states == "entrez")[1] 117 | Fields[["YearEntrez"]] <- x$PubmedData$History[[i]]$Year[[1]] 118 | Fields[["MonthEntrez"]] <- x$PubmedData$History[[i]]$Month[[1]] 119 | Fields[["DayEntrez"]] <- x$PubmedData$History[[i]]$Day[[1]] 120 | Fields[["MinuteEntrez"]] <- x$PubmedData$History[[i]]$Minute[[1]] 121 | Fields[["HourEntrez"]] <- x$PubmedData$History[[i]]$Hour[[1]] 122 | } 123 | 124 | if(any(pubmed_states == "medline")){ 125 | i <- which(pubmed_states == "medline")[1] 126 | Fields[["YearMedline"]] <- x$PubmedData$History[[i]]$Year[[1]] 127 | Fields[["MonthMedline"]] <- x$PubmedData$History[[i]]$Month[[1]] 128 | Fields[["DayMedline"]] <- x$PubmedData$History[[i]]$Day[[1]] 129 | Fields[["MinuteMedline"]] <- x$PubmedData$History[[i]]$Minute[[1]] 130 | Fields[["HourMedline"]] <- x$PubmedData$History[[i]]$Hour[[1]] 131 | } 132 | 133 | if(any(pubmed_states == "accepted")){ 134 | i <- which(pubmed_states == "accepted")[1] 135 | Fields[["YearAccepted"]] <- x$PubmedData$History[[i]]$Year[[1]] 136 | Fields[["MonthAccepted"]] <- x$PubmedData$History[[i]]$Month[[1]] 137 | Fields[["DayAccepted"]] <- x$PubmedData$History[[i]]$Day[[1]] 138 | Fields[["MinuteAccepted"]] <- x$PubmedData$History[[i]]$Minute[[1]] 139 | Fields[["HourAccepted"]] <- x$PubmedData$History[[i]]$Hour[[1]] 140 | } 141 | 142 | if(any(pubmed_states == "received")){ 143 | i <- which(pubmed_states == "received")[1] 144 | Fields[["YearReceived"]] <- x$PubmedData$History[[i]]$Year[[1]] 145 | Fields[["MonthReceived"]] <- x$PubmedData$History[[i]]$Month[[1]] 146 | Fields[["DayReceived"]] <- x$PubmedData$History[[i]]$Day[[1]] 147 | Fields[["MinuteReceived"]] <- x$PubmedData$History[[i]]$Minute[[1]] 148 | Fields[["HourReceived"]] <- x$PubmedData$History[[i]]$Hour[[1]] 149 | } 150 | 151 | if(any(pubmed_states == "epublish")){ 152 | i <- which(pubmed_states == "epublish")[1] 153 | Fields[["YearEpublish"]] <- x$PubmedData$History[[i]]$Year[[1]] 154 | Fields[["MonthEpublish"]] <- x$PubmedData$History[[i]]$Month[[1]] 155 | Fields[["DayEpublish"]] <- x$PubmedData$History[[i]]$Day[[1]] 156 | Fields[["MinuteEpublish"]] <- x$PubmedData$History[[i]]$Minute[[1]] 157 | Fields[["HourEpublish"]] <- x$PubmedData$History[[i]]$Hour[[1]] 158 | } 159 | 160 | if(any(pubmed_states == "ppublish")){ 161 | i <- which(pubmed_states == "ppublish")[1] 162 | Fields[["YearPpublish"]] <- x$PubmedData$History[[i]]$Year[[1]] 163 | Fields[["MonthPpublish"]] <- x$PubmedData$History[[i]]$Month[[1]] 164 | Fields[["DayPpublish"]] <- x$PubmedData$History[[i]]$Day[[1]] 165 | Fields[["MinutePpublish"]] <- x$PubmedData$History[[i]]$Minute[[1]] 166 | Fields[["HourPpublish"]] <- x$PubmedData$History[[i]]$Hour[[1]] 167 | } 168 | 169 | if(any(pubmed_states == "pmc")){ 170 | i <- which(pubmed_states == "pmc") 171 | Fields[["YearPmc"]] <- x$PubmedData$History[[i]]$Year[[1]] 172 | Fields[["MonthPmc"]] <- x$PubmedData$History[[i]]$Month[[1]] 173 | Fields[["DayPmc"]] <- x$PubmedData$History[[i]]$Day[[1]] 174 | Fields[["MinutePmc"]] <- x$PubmedData$History[[i]]$Minute[[1]] 175 | Fields[["HourPmc"]] <- x$PubmedData$History[[i]]$Hour[[1]] 176 | } 177 | 178 | if(any(pubmed_states == "pubmed")){ 179 | i <- which(pubmed_states == "pubmed")[1] 180 | Fields[["YearPubmed"]] <- x$PubmedData$History[[i]]$Year[[1]] 181 | Fields[["MonthPubmed"]] <- x$PubmedData$History[[i]]$Month[[1]] 182 | Fields[["DayPubmed"]] <- x$PubmedData$History[[i]]$Day[[1]] 183 | Fields[["MinutePubmed"]] <- x$PubmedData$History[[i]]$Minute[[1]] 184 | Fields[["HourPubmed"]] <- x$PubmedData$History[[i]]$Hour[[1]] 185 | } 186 | } 187 | 188 | Fields[["ISSN"]] <- x$MedlineCitation$Article$Journal$ISSN[[1]] 189 | Fields[["Volume"]] <- x$MedlineCitation$Article$Journal$JournalIssue$Volume[[1]] 190 | Fields[["Issue"]] <- x$MedlineCitation$Article$Journal$JournalIssue$Issue[[1]] 191 | Fields[["Title"]] <- x$MedlineCitation$Article$Journal$Title[[1]] 192 | 193 | if(!is.null(x$MedlineCitation$Article$ArticleTitle)) 194 | Fields[["ArticleTitle"]] <- paste(unlist(x$MedlineCitation$Article[names(x$MedlineCitation$Article) == "ArticleTitle"]), collapse = "") 195 | 196 | if(!is.null(x$MedlineCitation$Article$AuthorList)){ 197 | 198 | Authors <- do.call("rbind", lapply(x$MedlineCitation$Article$AuthorList, function(z){ 199 | 200 | if(any(names(z) == "CollectiveName") | (is.null(z$ForeName) & is.null(z$Initials))){ 201 | data.frame( 202 | CollectiveName = ifelse(is.null(z$CollectiveName), as.character(z$LastName[[1]]), as.character(z$CollectiveName[[1]])), 203 | LastName = NA, 204 | ForeName = NA, 205 | Initials = NA, 206 | stringsAsFactors=FALSE 207 | ) 208 | } 209 | else{ 210 | data.frame( 211 | CollectiveName = NA, 212 | LastName = ifelse(is.null(z$LastName[[1]]), NA, as.character(z$LastName[[1]])), 213 | ForeName = ifelse(is.null(z$ForeName[[1]]), NA, as.character(z$ForeName[[1]])), 214 | Initials = ifelse(is.null(z$Initials[[1]]), NA, as.character(z$Initials[[1]])), 215 | stringsAsFactors=FALSE 216 | ) 217 | } 218 | })) 219 | 220 | Authors$order <- 1:nrow(Authors) 221 | 222 | Fields[["Author"]] <- Authors 223 | 224 | Affiliations <- lapply(x$MedlineCitation$Article$AuthorList, function(z){ 225 | z$AffiliationInfo$Affiliation[[1]] 226 | }) 227 | 228 | names(Affiliations) <- 1:length(Affiliations) 229 | 230 | Fields[["Affiliation"]] <- unlist(Affiliations) 231 | } 232 | 233 | elocations <- names(x$MedlineCitation$Article) 234 | 235 | if(any(elocations == "ELocationID")){ 236 | 237 | elocations <- x$MedlineCitation$Article[which(elocations == "ELocationID")] 238 | 239 | for(e in elocations){ 240 | if(attr(e, "EIdType") == "pii") 241 | Fields[["ELocationID"]] <- e[[1]] 242 | 243 | if(attr(e, "EIdType") == "doi") 244 | Fields[["DOI"]] <- e[[1]] 245 | } 246 | } 247 | 248 | if(!is.null(x$MedlineCitation$Article$Abstract)){ 249 | AbstractText <- paste(unlist(x$MedlineCitation$Article$Abstract[names(x$MedlineCitation$Article$Abstract) == "AbstractText"]), collapse = " ") 250 | 251 | Fields[["AbstractText"]] <- AbstractText 252 | } 253 | 254 | Fields[["Language"]] <- x$MedlineCitation$Article$Language[[1]] 255 | if(!is.null(x$MedlineCitation$Article$PublicationTypeList)) 256 | Fields[["PublicationType"]] <- unlist(x$MedlineCitation$Article$PublicationTypeList[names(x$MedlineCitation$Article$PublicationTypeList) == "PublicationType"]) 257 | Fields[["Country"]] <- x$MedlineCitation$MedlineJournalInfo$Country[[1]] 258 | Fields[["MedlineTA"]] <- x$MedlineCitation$MedlineJournalInfo$MedlineTA[[1]] 259 | Fields[["NlmUniqueID"]] <- x$MedlineCitation$MedlineJournalInfo$NlmUniqueID[[1]] 260 | Fields[["ISSNLinking"]] <- x$MedlineCitation$MedlineJournalInfo$ISSNLinking[[1]] 261 | Fields[["PublicationStatus"]] <- x$PubmedData$PublicationStatus[[1]] 262 | Fields[["ArticleId"]] <- x$PubmedData$ArticleIdList$ArticleId[[1]] 263 | Fields[["ISOAbbreviation"]] <- x$MedlineCitation$Article$Journal$ISOAbbreviation[[1]] 264 | Fields[["MedlinePgn"]] <- x$MedlineCitation$Article$Pagination$MedlinePgn[[1]] 265 | Fields[["CopyrightInformation"]] <- x$MedlineCitation$Article$Abstract$CopyrightInformation[[1]] 266 | 267 | 268 | if(!is.null(x$MedlineCitation$Article$GrantList)){ 269 | 270 | Grants <- do.call("rbind", lapply(x$MedlineCitation$Article$GrantList, function(z){ 271 | data.frame( 272 | GrantID = ifelse(is.null(z$GrantID[[1]]), NA, z$GrantID[[1]]), 273 | Agency = ifelse(is.null(z$Agency[[1]]), NA, z$Agency[[1]]), 274 | stringsAsFactors = F 275 | ) 276 | })) 277 | 278 | Fields[["GrantID"]] <- Grants 279 | } 280 | 281 | Fields[["COIStatement"]] <- x$MedlineCitation$CoiStatement[[1]] 282 | 283 | if(!is.null(x$MedlineCitation$KeywordList)){ 284 | keywords <- x$MedlineCitation$KeywordList[names(x$MedlineCitation$KeywordList) == "Keyword"] 285 | Fields[["Keywords"]] <- unlist(keywords) 286 | } 287 | 288 | 289 | if(!is.null(x$MedlineCitation$MeshHeadingList$MeshHeading)){ 290 | Mesh <- data.frame( 291 | Heading = unlist(x$MedlineCitation$MeshHeadingList), 292 | Type = ifelse(grepl("DescriptorName", names(unlist(x$MedlineCitation$MeshHeadingList))),"Descriptor","Qualifier"), 293 | stringsAsFactors = F 294 | ) 295 | 296 | Fields[["Mesh"]] <- Mesh 297 | } 298 | 299 | 300 | if(!is.null(x$PubmedData$ReferenceList)){ 301 | References <- lapply(x$PubmedData$ReferenceList, function(z){ 302 | paste(unlist(z), collapse = "") 303 | }) 304 | 305 | Fields[["Citations"]] <- References 306 | } 307 | 308 | Fields 309 | } 310 | 311 | 312 | 313 | 314 | ParseMedlineBook <- function(x){ 315 | 316 | Tags <- c("PMID", 317 | "YearRevised", 318 | "MonthRevised", 319 | "DayRevised", 320 | "YearPubDate", 321 | "MonthPubDate", 322 | "DayPubDate", 323 | "YearArticleDate", 324 | "MonthArticleDate", 325 | "DayArticleDate", 326 | "YearEntrez", 327 | "MonthEntrez", 328 | "DayEntrez", 329 | "HourEntrez", 330 | "MinuteEntrez", 331 | "YearMedline", 332 | "MonthMedline", 333 | "DayMedline", 334 | "HourMedline", 335 | "MinuteMedline", 336 | "YearAccepted", 337 | "MonthAccepted", 338 | "DayAccepted", 339 | "HourAccepted", 340 | "MinuteAccepted", 341 | "YearReceived", 342 | "MonthReceived", 343 | "DayReceived", 344 | "HourReceived", 345 | "MinuteReceived", 346 | "YearEpublish", 347 | "MonthEpublish", 348 | "DayEpublish", 349 | "HourEpublish", 350 | "MinuteEpublish", 351 | "YearPpublish", 352 | "MonthPpublish", 353 | "DayPpublish", 354 | "HourPpublish", 355 | "MinutePpublish", 356 | "YearPmc", 357 | "MonthPmc", 358 | "DayPmc", 359 | "HourPmc", 360 | "MinutePmc", 361 | "YearPubmed", 362 | "MonthPubmed", 363 | "DayPubmed", 364 | "HourPubmed", 365 | "MinutePubmed", 366 | "ISSN", 367 | "Title", 368 | "Author", 369 | "ArticleTitle", 370 | "ELocationID", 371 | "AbstractText", 372 | "Affiliation", 373 | "Language", 374 | "PublicationType", 375 | "MedlineTA", 376 | "NlmUniqueID", 377 | "ISSNLinking", 378 | "PublicationStatus", 379 | "ArticleId", 380 | "DOI", 381 | "Volume", 382 | "Issue", 383 | "ISOAbbreviation", 384 | "MedlinePgn", 385 | "CopyrightInformation", 386 | "Country", 387 | "GrantID", 388 | "COIStatement", 389 | "Mesh", 390 | "Keywords", 391 | "Citations", 392 | "BookPublisher", 393 | "BookPublisherLocation", 394 | "BookTitle", 395 | "BookBeginningDate", 396 | "BookEndingDate", 397 | "BookEditors", 398 | "BookMedium" 399 | ) 400 | 401 | Fields <- vector(mode = "list", length = length(Tags)) 402 | names(Fields) <- Tags 403 | 404 | 405 | Fields[["PMID"]] <- x$BookDocument$PMID[[1]] 406 | 407 | Fields[["YearRevised"]] <- x$BookDocument$DateRevised$Year[[1]] 408 | Fields[["MonthRevised"]] <- x$BookDocument$DateRevised$Month[[1]] 409 | Fields[["DayRevised"]] <- x$BookDocument$DateRevised$Day[[1]] 410 | Fields[["YearPubDate"]] <- x$BookDocument$Book$ContributionDate$Year[[1]] 411 | Fields[["MonthPubDate"]] <- x$BookDocument$Book$ContributionDate$Month[[1]] 412 | Fields[["DayPubDate"]] <- x$BookDocument$Book$ContributionDate$Day[[1]] 413 | Fields[["YearArticleDate"]] <- x$BookDocument$ArticleDate$Year[[1]] 414 | Fields[["MonthArticleDate"]] <- x$BookDocument$ArticleDate$Month[[1]] 415 | Fields[["DayArticleDate"]] <- x$BookDocument$ArticleDate$Day[[1]] 416 | 417 | pubmed_states <- sapply(x$PubmedBookData$History, function(z) attr(z, "PubStatus")) 418 | 419 | 420 | if(length(pubmed_states) > 0){ 421 | if(any(pubmed_states == "entrez")){ 422 | i <- which(pubmed_states == "entrez")[1] 423 | Fields[["YearEntrez"]] <- x$PubmedBookData$History[[i]]$Year[[1]] 424 | Fields[["MonthEntrez"]] <- x$PubmedBookData$History[[i]]$Month[[1]] 425 | Fields[["DayEntrez"]] <- x$PubmedBookData$History[[i]]$Day[[1]] 426 | Fields[["MinuteEntrez"]] <- x$PubmedBookData$History[[i]]$Minute[[1]] 427 | Fields[["HourEntrez"]] <- x$PubmedBookData$History[[i]]$Hour[[1]] 428 | } 429 | 430 | if(any(pubmed_states == "medline")){ 431 | i <- which(pubmed_states == "medline")[1] 432 | Fields[["YearMedline"]] <- x$PubmedBookData$History[[i]]$Year[[1]] 433 | Fields[["MonthMedline"]] <- x$PubmedBookData$History[[i]]$Month[[1]] 434 | Fields[["DayMedline"]] <- x$PubmedBookData$History[[i]]$Day[[1]] 435 | Fields[["MinuteMedline"]] <- x$PubmedBookData$History[[i]]$Minute[[1]] 436 | Fields[["HourMedline"]] <- x$PubmedBookData$History[[i]]$Hour[[1]] 437 | } 438 | 439 | if(any(pubmed_states == "accepted")){ 440 | i <- which(pubmed_states == "accepted")[1] 441 | Fields[["YearAccepted"]] <- x$PubmedBookData$History[[i]]$Year[[1]] 442 | Fields[["MonthAccepted"]] <- x$PubmedBookData$History[[i]]$Month[[1]] 443 | Fields[["DayAccepted"]] <- x$PubmedBookData$History[[i]]$Day[[1]] 444 | Fields[["MinuteAccepted"]] <- x$PubmedBookData$History[[i]]$Minute[[1]] 445 | Fields[["HourAccepted"]] <- x$PubmedBookData$History[[i]]$Hour[[1]] 446 | } 447 | 448 | if(any(pubmed_states == "received")){ 449 | i <- which(pubmed_states == "received")[1] 450 | Fields[["YearReceived"]] <- x$PubmedBookData$History[[i]]$Year[[1]] 451 | Fields[["MonthReceived"]] <- x$PubmedBookData$History[[i]]$Month[[1]] 452 | Fields[["DayReceived"]] <- x$PubmedBookData$History[[i]]$Day[[1]] 453 | Fields[["MinuteReceived"]] <- x$PubmedBookData$History[[i]]$Minute[[1]] 454 | Fields[["HourReceived"]] <- x$PubmedBookData$History[[i]]$Hour[[1]] 455 | } 456 | 457 | if(any(pubmed_states == "epublish")){ 458 | i <- which(pubmed_states == "epublish")[1] 459 | Fields[["YearEpublish"]] <- x$PubmedBookData$History[[i]]$Year[[1]] 460 | Fields[["MonthEpublish"]] <- x$PubmedBookData$History[[i]]$Month[[1]] 461 | Fields[["DayEpublish"]] <- x$PubmedBookData$History[[i]]$Day[[1]] 462 | Fields[["MinuteEpublish"]] <- x$PubmedBookData$History[[i]]$Minute[[1]] 463 | Fields[["HourEpublish"]] <- x$PubmedBookData$History[[i]]$Hour[[1]] 464 | } 465 | 466 | if(any(pubmed_states == "ppublish")){ 467 | i <- which(pubmed_states == "ppublish")[1] 468 | Fields[["YearPpublish"]] <- x$PubmedBookData$History[[i]]$Year[[1]] 469 | Fields[["MonthPpublish"]] <- x$PubmedBookData$History[[i]]$Month[[1]] 470 | Fields[["DayPpublish"]] <- x$PubmedBookData$History[[i]]$Day[[1]] 471 | Fields[["MinutePpublish"]] <- x$PubmedBookData$History[[i]]$Minute[[1]] 472 | Fields[["HourPpublish"]] <- x$PubmedBookData$History[[i]]$Hour[[1]] 473 | } 474 | 475 | if(any(pubmed_states == "pmc")){ 476 | i <- which(pubmed_states == "pmc") 477 | Fields[["YearPmc"]] <- x$PubmedBookData$History[[i]]$Year[[1]] 478 | Fields[["MonthPmc"]] <- x$PubmedBookData$History[[i]]$Month[[1]] 479 | Fields[["DayPmc"]] <- x$PubmedBookData$History[[i]]$Day[[1]] 480 | Fields[["MinutePmc"]] <- x$PubmedBookData$History[[i]]$Minute[[1]] 481 | Fields[["HourPmc"]] <- x$PubmedBookData$History[[i]]$Hour[[1]] 482 | } 483 | 484 | if(any(pubmed_states == "pubmed")){ 485 | i <- which(pubmed_states == "pubmed")[1] 486 | Fields[["YearPubmed"]] <- x$PubmedBookData$History[[i]]$Year[[1]] 487 | Fields[["MonthPubmed"]] <- x$PubmedBookData$History[[i]]$Month[[1]] 488 | Fields[["DayPubmed"]] <- x$PubmedBookData$History[[i]]$Day[[1]] 489 | Fields[["MinutePubmed"]] <- x$PubmedBookData$History[[i]]$Minute[[1]] 490 | Fields[["HourPubmed"]] <- x$PubmedBookData$History[[i]]$Hour[[1]] 491 | } 492 | } 493 | 494 | Fields[["ISSN"]] <- x$BookDocument$Article$Journal$ISSN[[1]] 495 | Fields[["Volume"]] <- x$BookDocument$Article$Journal$JournalIssue$Volume[[1]] 496 | Fields[["Issue"]] <- x$BookDocument$Article$Journal$JournalIssue$Issue[[1]] 497 | Fields[["Title"]] <- x$BookDocument$Article$Journal$JournalIssue$Title[[1]] 498 | 499 | if(!is.null(x$BookDocument$ArticleTitle)) 500 | Fields[["ArticleTitle"]] <- paste(unlist(x$BookDocument[names(x$BookDocument) == "ArticleTitle"]), collapse = "") 501 | 502 | authors_editors <- x$BookDocument$Book[names(x$BookDocument$Book) == "AuthorList"] 503 | authors <- authors_editors[sapply(authors_editors, function(x) attr(x, "Type")) == "authors"] 504 | editors <- authors_editors[sapply(authors_editors, function(x) attr(x, "Type")) == "editors"] 505 | 506 | 507 | if(length(authors) != 0){ 508 | 509 | Authors <- do.call("rbind", lapply(authors[[1]], function(z){ 510 | 511 | if(any(names(z) == "CollectiveName") | (is.null(z$ForeName) & is.null(z$Initials))){ 512 | data.frame( 513 | CollectiveName = ifelse(is.null(z$CollectiveName), as.character(z$LastName[[1]]), as.character(z$CollectiveName[[1]])), 514 | LastName = NA, 515 | ForeName = NA, 516 | Initials = NA, 517 | stringsAsFactors=FALSE 518 | ) 519 | } 520 | else{ 521 | data.frame( 522 | CollectiveName = NA, 523 | LastName = ifelse(is.null(z$LastName[[1]]), NA, as.character(z$LastName[[1]])), 524 | ForeName = ifelse(is.null(z$ForeName[[1]]), NA, as.character(z$ForeName[[1]])), 525 | Initials = ifelse(is.null(z$Initials[[1]]), NA, as.character(z$Initials[[1]])), 526 | stringsAsFactors=FALSE 527 | ) 528 | } 529 | })) 530 | 531 | Authors$order <- 1:nrow(Authors) 532 | 533 | Fields[["Author"]] <- Authors 534 | 535 | Affiliations <- lapply(authors, function(z){ 536 | z$AffiliationInfo$Affiliation[[1]] 537 | }) 538 | 539 | names(Affiliations) <- 1:length(Affiliations) 540 | 541 | Fields[["Affiliation"]] <- unlist(Affiliations) 542 | } 543 | 544 | 545 | if(length(editors) != 0){ 546 | 547 | Editors <- do.call("rbind", lapply(editors[[1]], function(z){ 548 | 549 | data.frame( 550 | LastName = ifelse(is.null(z$LastName[[1]]), NA, as.character(z$LastName[[1]])), 551 | ForeName = ifelse(is.null(z$ForeName[[1]]), NA, as.character(z$ForeName[[1]])), 552 | Initials = ifelse(is.null(z$Initials[[1]]), NA, as.character(z$Initials[[1]])), 553 | stringsAsFactors=FALSE 554 | ) 555 | })) 556 | 557 | Editors$order <- 1:nrow(Editors) 558 | 559 | Fields[["BookEditors"]] <- Editors 560 | } 561 | 562 | elocations <- names(x$BookDocument$Article) 563 | 564 | if(any(elocations == "ELocationID")){ 565 | 566 | elocations <- x$BookDocument$Article[which(elocations == "ELocationID")] 567 | 568 | for(e in elocations){ 569 | if(attr(e, "EIdType") == "pii") 570 | Fields[["ELocationID"]] <- e[[1]] 571 | 572 | if(attr(e, "EIdType") == "doi") 573 | Fields[["DOI"]] <- e[[1]] 574 | } 575 | } 576 | 577 | if(!is.null(x$BookDocument$Abstract)){ 578 | AbstractText <- paste(unlist(x$BookDocument$Abstract[names(x$BookDocument$Abstract) == "AbstractText"]), collapse = " ") 579 | 580 | Fields[["AbstractText"]] <- AbstractText 581 | } 582 | 583 | Fields[["Language"]] <- x$BookDocument$Language[[1]] 584 | Fields[["PublicationType"]] <- x$BookDocument$Book$PublicationType[[1]] 585 | Fields[["Country"]] <- x$BookDocument$Article$Country[[1]] 586 | Fields[["MedlineTA"]] <- x$BookDocument$Article$MedlineTA[[1]] 587 | Fields[["NlmUniqueID"]] <- x$BookDocument$Article$NlmUniqueID[[1]] 588 | Fields[["ISSNLinking"]] <- x$BookDocument$Article$ISSNLinking[[1]] 589 | Fields[["PublicationStatus"]] <- x$PubmedBookData$PublicationStatus[[1]] 590 | Fields[["ArticleId"]] <- x$BookDocument$ArticleIdList$ArticleId[[1]] 591 | Fields[["ISOAbbreviation"]] <- x$BookDocument$Article$Journal$ISOAbbreviation[[1]] 592 | Fields[["MedlinePgn"]] <- x$BookDocument$Article$Pagination$MedlinePgn[[1]] 593 | Fields[["CopyrightInformation"]] <- x$BookDocument$Abstract$CopyrightInformation[[1]] 594 | Fields[["BookPublisher"]] <- x$BookDocument$Book$Publisher$PublisherName[[1]] 595 | Fields[["BookPublisherLocation"]] <- x$BookDocument$Book$Publisher$PublisherLocation[[1]] 596 | Fields[["BookTitle"]] <- x$BookDocument$Book$BookTitle[[1]] 597 | Fields[["BookBeginningDate"]] <- x$BookDocument$Book$BeginningDate$Year[[1]] 598 | Fields[["BookEndingDate"]] <- x$BookDocument$Book$EndingDate$Year[[1]] 599 | Fields[["BookMedium"]] <- x$BookDocument$Book$Medium[[1]] 600 | 601 | 602 | if(!is.null(x$BookDocument$GrantList)){ 603 | 604 | Grants <- do.call("rbind", lapply(x$BookDocument$GrantList, function(z){ 605 | data.frame( 606 | GrantID = ifelse(is.null(z$GrantID[[1]]), NA, z$GrantID[[1]]), 607 | Agency = ifelse(is.null(z$Agency[[1]]), NA, z$Agency[[1]]), 608 | stringsAsFactors = F 609 | ) 610 | })) 611 | 612 | Fields[["GrantID"]] <- Grants 613 | } 614 | 615 | Fields[["COIStatement"]] <- x$BookDocument$CoiStatement[[1]] 616 | 617 | if(!is.null(x$BookDocument$KeywordList)){ 618 | keywords <- x$BookDocument$KeywordList[names(x$BookDocument$KeywordList) == "Keyword"] 619 | Fields[["Keywords"]] <- unlist(keywords) 620 | } 621 | 622 | 623 | if(!is.null(x$BookDocument$MeshHeadingList$MeshHeading)){ 624 | Mesh <- data.frame( 625 | Heading = unlist(x$BookDocument$MeshHeadingList), 626 | Type = ifelse(grepl("DescriptorName", names(unlist(x$BookDocument$MeshHeadingList))),"Descriptor","Qualifier"), 627 | stringsAsFactors = F 628 | ) 629 | 630 | Fields[["Mesh"]] <- Mesh 631 | } 632 | 633 | 634 | if(!is.null(x$PubmedBookData$ReferenceList)){ 635 | References <- lapply(x$PubmedBookData$ReferenceList, function(z){ 636 | paste(unlist(z), collapse = "") 637 | }) 638 | 639 | Fields[["Citations"]] <- References 640 | } 641 | 642 | Fields 643 | } 644 | -------------------------------------------------------------------------------- /R/Medline.R: -------------------------------------------------------------------------------- 1 | setClass("Medline", 2 | representation( 3 | Query = "character", 4 | PMID = "character", 5 | 6 | YearRevised = "numeric", 7 | MonthRevised = "numeric", 8 | DayRevised= "numeric", 9 | 10 | YearPubDate = "numeric", 11 | MonthPubDate = "character", 12 | DayPubDate= "numeric", 13 | 14 | YearArticleDate = "numeric", 15 | MonthArticleDate = "numeric", 16 | DayArticleDate= "numeric", 17 | 18 | 19 | YearEntrez = "numeric", 20 | MonthEntrez = "numeric", 21 | DayEntrez= "numeric", 22 | HourEntrez= "numeric", 23 | MinuteEntrez= "numeric", 24 | 25 | 26 | YearMedline = "numeric", 27 | MonthMedline = "numeric", 28 | DayMedline= "numeric", 29 | HourMedline= "numeric", 30 | MinuteMedline= "numeric", 31 | 32 | YearReceived = "numeric", 33 | MonthReceived = "numeric", 34 | DayReceived= "numeric", 35 | HourReceived= "numeric", 36 | MinuteReceived= "numeric", 37 | 38 | YearAccepted = "numeric", 39 | MonthAccepted = "numeric", 40 | DayAccepted= "numeric", 41 | HourAccepted= "numeric", 42 | MinuteAccepted= "numeric", 43 | 44 | YearEpublish = "numeric", 45 | MonthEpublish = "numeric", 46 | DayEpublish= "numeric", 47 | HourEpublish= "numeric", 48 | MinuteEpublish= "numeric", 49 | 50 | YearPpublish = "numeric", 51 | MonthPpublish = "numeric", 52 | DayPpublish= "numeric", 53 | HourPpublish= "numeric", 54 | MinutePpublish= "numeric", 55 | 56 | YearPmc = "numeric", 57 | MonthPmc = "numeric", 58 | DayPmc = "numeric", 59 | HourPmc = "numeric", 60 | MinutePmc = "numeric", 61 | 62 | YearPubmed = "numeric", 63 | MonthPubmed = "numeric", 64 | DayPubmed = "numeric", 65 | HourPubmed = "numeric", 66 | MinutePubmed = "numeric", 67 | 68 | Author = "list", 69 | ISSN= "character", 70 | Title = "character", 71 | ArticleTitle= "character", 72 | ELocationID= "character", 73 | AbstractText= "character", 74 | Affiliation= "list", 75 | Language= "character", 76 | PublicationType= "list", 77 | MedlineTA= "character", 78 | NlmUniqueID= "character", 79 | ISSNLinking= "character", 80 | PublicationStatus= "character", 81 | ArticleId= "character", 82 | DOI = "character", 83 | Volume= "character", 84 | Issue= "character", 85 | ISOAbbreviation= "character", 86 | MedlinePgn= "character", 87 | CopyrightInformation= "character", 88 | Country= "character", 89 | GrantID= "list", 90 | COIStatement = "character", 91 | Mesh="list", 92 | Keywords="list", 93 | Citations="list", 94 | BookPublisher= "character", 95 | BookPublisherLocation= "character", 96 | BookTitle= "character", 97 | BookBeginningDate= "numeric", 98 | BookEndingDate= "numeric", 99 | BookEditors= "list", 100 | BookMedium = "character" 101 | ) 102 | ) 103 | 104 | null_replace <- function(x) ifelse(is.null(x), NA, x) 105 | 106 | list_null_replace <- function(x) if(class(x) == "NULL") NA else x 107 | 108 | Medline <- function(object, query = character(0)){ 109 | 110 | TagIndex <- lapply(object, names) 111 | 112 | # ARTICLE LIST FROM PUBMED QUERY 113 | PMID <- sapply(object, function(x) null_replace(x[["PMID"]]),USE.NAMES=FALSE) 114 | 115 | YearRevised <- sapply(object, function(x) null_replace(x[["YearRevised"]]),USE.NAMES=FALSE) 116 | 117 | MonthRevised <- sapply(object, function(x) null_replace(x[["MonthRevised"]]),USE.NAMES=FALSE) 118 | 119 | DayRevised <- sapply(object, function(x) null_replace(x[["DayRevised"]]),USE.NAMES=FALSE) 120 | 121 | YearArticleDate <- sapply(object, function(x) null_replace(x[["YearArticleDate"]]),USE.NAMES=FALSE) 122 | 123 | MonthArticleDate <- sapply(object, function(x) null_replace(x[["MonthArticleDate"]]),USE.NAMES=FALSE) 124 | 125 | 126 | DayArticleDate <- sapply(object, function(x) null_replace(x[["DayArticleDate"]]),USE.NAMES=FALSE) 127 | 128 | 129 | YearPubDate <-sapply(object, function(x) null_replace(x[["YearPubDate"]]),USE.NAMES=FALSE) 130 | 131 | MonthPubDate <- sapply(object, function(x) null_replace(x[["MonthPubDate"]]),USE.NAMES=FALSE) 132 | 133 | DayPubDate <- sapply(object, function(x) null_replace(x[["DayPubDate"]]),USE.NAMES=FALSE) 134 | 135 | 136 | YearEntrez <- sapply(object, function(x) null_replace(x[["YearEntrez"]]),USE.NAMES=FALSE) 137 | 138 | MonthEntrez <- sapply(object, function(x) null_replace(x[["MonthEntrez"]]),USE.NAMES=FALSE) 139 | 140 | DayEntrez <- sapply(object, function(x) null_replace(x[["DayEntrez"]]),USE.NAMES=FALSE) 141 | 142 | MinuteEntrez <- sapply(object, function(x) null_replace(x[["MinuteEnrez"]]),USE.NAMES=FALSE) 143 | 144 | HourEntrez <- sapply(object, function(x) null_replace(x[["HourEntrez"]]),USE.NAMES=FALSE) 145 | 146 | 147 | YearMedline <- sapply(object, function(x) null_replace(x[["YearMedline"]]),USE.NAMES=FALSE) 148 | 149 | MonthMedline <- sapply(object, function(x) null_replace(x[["MonthMedline"]]),USE.NAMES=FALSE) 150 | 151 | DayMedline <- sapply(object, function(x) null_replace(x[["DayMedline"]]),USE.NAMES=FALSE) 152 | 153 | MinuteMedline <- sapply(object, function(x) null_replace(x[["MinuteMedline"]]),USE.NAMES=FALSE) 154 | 155 | HourMedline <- sapply(object, function(x) null_replace(x[["HourMedline"]]),USE.NAMES=FALSE) 156 | 157 | YearReceived <- sapply(object, function(x) null_replace(x[["YearReceived"]]),USE.NAMES=FALSE) 158 | 159 | MonthReceived <- sapply(object, function(x) null_replace(x[["MonthReceived"]]),USE.NAMES=FALSE) 160 | 161 | DayReceived <- sapply(object, function(x) null_replace(x[["DayReceived"]]),USE.NAMES=FALSE) 162 | 163 | MinuteReceived <- sapply(object, function(x) null_replace(x[["MinuteReceived"]]),USE.NAMES=FALSE) 164 | 165 | HourReceived <- sapply(object, function(x) null_replace(x[["HourReceived"]]),USE.NAMES=FALSE) 166 | 167 | YearEpublish <- sapply(object, function(x) null_replace(x[["YearEpublish"]]),USE.NAMES=FALSE) 168 | 169 | MonthEpublish <- sapply(object, function(x) null_replace(x[["MonthEpublish"]]),USE.NAMES=FALSE) 170 | 171 | DayEpublish <- sapply(object, function(x) null_replace(x[["DayEpublish"]]),USE.NAMES=FALSE) 172 | 173 | MinuteEpublish <- sapply(object, function(x) null_replace(x[["MinuteEpublish"]]),USE.NAMES=FALSE) 174 | 175 | HourEpublish <- sapply(object, function(x) null_replace(x[["HourEpublish"]]),USE.NAMES=FALSE) 176 | 177 | YearPpublish <- sapply(object, function(x) null_replace(x[["YearPpublish"]]),USE.NAMES=FALSE) 178 | 179 | MonthPpublish <- sapply(object, function(x) null_replace(x[["MonthPpublish"]]),USE.NAMES=FALSE) 180 | 181 | DayPpublish <- sapply(object, function(x) null_replace(x[["DayPpublish"]]),USE.NAMES=FALSE) 182 | 183 | MinutePpublish <- sapply(object, function(x) null_replace(x[["MinutePpublish"]]),USE.NAMES=FALSE) 184 | 185 | HourPpublish <- sapply(object, function(x) null_replace(x[["HourPpublish"]]),USE.NAMES=FALSE) 186 | 187 | 188 | YearPmc <- sapply(object, function(x) null_replace(x[["YearPmc"]]),USE.NAMES=FALSE) 189 | 190 | MonthPmc <- sapply(object, function(x) null_replace(x[["MonthPmc"]]),USE.NAMES=FALSE) 191 | 192 | DayPmc <- sapply(object, function(x) null_replace(x[["DayPmc"]]),USE.NAMES=FALSE) 193 | 194 | MinutePmc <- sapply(object, function(x) null_replace(x[["MinutePmc"]]),USE.NAMES=FALSE) 195 | 196 | HourPmc <- sapply(object, function(x) null_replace(x[["HourPmc"]]),USE.NAMES=FALSE) 197 | 198 | YearPubmed <- sapply(object, function(x) null_replace(x[["YearPubmed"]]),USE.NAMES=FALSE) 199 | 200 | MonthPubmed <- sapply(object, function(x) null_replace(x[["MonthPubmed"]]),USE.NAMES=FALSE) 201 | 202 | DayPubmed <- sapply(object, function(x) null_replace(x[["DayPubmed"]]),USE.NAMES=FALSE) 203 | 204 | MinutePubmed <- sapply(object, function(x) null_replace(x[["MinutePubmed"]]),USE.NAMES=FALSE) 205 | 206 | HourPubmed <- sapply(object, function(x) null_replace(x[["HourPubmed"]]),USE.NAMES=FALSE) 207 | 208 | YearAccepted <- sapply(object, function(x) null_replace(x[["YearAccepted"]]),USE.NAMES=FALSE) 209 | 210 | MonthAccepted <- sapply(object, function(x) null_replace(x[["MonthAccepted"]]),USE.NAMES=FALSE) 211 | 212 | DayAccepted <- sapply(object, function(x) null_replace(x[["DayAccepted"]]),USE.NAMES=FALSE) 213 | 214 | MinuteAccepted <- sapply(object, function(x) null_replace(x[["MinuteAccepted"]]),USE.NAMES=FALSE) 215 | 216 | HourAccepted <- sapply(object, function(x) null_replace(x[["HourAccepted"]]),USE.NAMES=FALSE) 217 | 218 | AbstractText <- lapply(object, function(x) list_null_replace(x[["AbstractText"]])) 219 | Author <- lapply(object, function(x) list_null_replace(x[["Author"]])) 220 | Affiliation <- lapply(object, function(x) list_null_replace(x[["Affiliation"]])) 221 | 222 | names(AbstractText) <- PMID 223 | names(Author) <- PMID 224 | names(Affiliation) <- PMID 225 | 226 | BookPublisher <- sapply(object, function(x) null_replace(x[["BookPublisher"]]),USE.NAMES=FALSE) 227 | BookPublisherLocation <- sapply(object, function(x) null_replace(x[["BookPublisherLocation"]]),USE.NAMES=FALSE) 228 | BookTitle <- sapply(object, function(x) null_replace(x[["BookTitle"]]),USE.NAMES=FALSE) 229 | BookBeginningDate <- sapply(object, function(x) null_replace(x[["BookBeginningDate"]]),USE.NAMES=FALSE) 230 | BookEndingDate <- sapply(object, function(x) null_replace(x[["BookEndingDate"]]),USE.NAMES=FALSE) 231 | BookMedium <- sapply(object, function(x) null_replace(x[["BookMedium"]]),USE.NAMES=FALSE) 232 | 233 | Editors <- lapply(object, function(x) list_null_replace(x[["BookEditors"]])) 234 | names(Editors) <- PMID 235 | 236 | ISSN <- sapply(object, function(x) null_replace(x[["ISSN"]]),USE.NAMES=FALSE) 237 | Title <- sapply(object, function(x) null_replace(x[["Title"]]),USE.NAMES=FALSE) 238 | ArticleTitle <- sapply(object, function(x) null_replace(x[["ArticleTitle"]]),USE.NAMES=FALSE) 239 | ELocationID <- sapply(object, function(x) null_replace(x[["ELocationID"]]),USE.NAMES=FALSE) 240 | Language <- sapply(object, function(x) null_replace(x[["Language"]]),USE.NAMES=FALSE) 241 | PublicationType <- lapply(object, function(x) list_null_replace(x[["PublicationType"]])) 242 | MedlineTA <- sapply(object, function(x) null_replace(x[["MedlineTA"]]),USE.NAMES=FALSE) 243 | NlmUniqueID <- sapply(object, function(x) null_replace(x[["NlmUniqueID"]]),USE.NAMES=FALSE) 244 | ISSNLinking <- sapply(object, function(x) null_replace(x[["ISSNLinking"]]),USE.NAMES=FALSE) 245 | PublicationStatus <- sapply(object, function(x) null_replace(x[["PublicationStatus"]]),USE.NAMES=FALSE) 246 | ArticleId <- sapply(object, function(x) null_replace(x[["ArticleId"]]),USE.NAMES=FALSE) 247 | DOI <- sapply(object, function(x) null_replace(x[["DOI"]]),USE.NAMES=FALSE) 248 | Volume <- sapply(object, function(x) null_replace(x[["Volume"]]),USE.NAMES=FALSE) 249 | Issue <- sapply(object, function(x) null_replace(x[["Issue"]]),USE.NAMES=FALSE) 250 | ISOAbbreviation <- sapply(object, function(x) null_replace(x[["ISOAbbreviation"]]),USE.NAMES=FALSE) 251 | MedlinePgn <- sapply(object, function(x) null_replace(x[["MedlinePgn"]]),USE.NAMES=FALSE) 252 | CopyrightInformation <- sapply(object, function(x) null_replace(x[["CopyrightInformation"]]),USE.NAMES=FALSE) 253 | Country <- sapply(object, function(x) null_replace(x[["Country"]]),USE.NAMES=FALSE) 254 | GrantID <- lapply(object, function(x) list_null_replace(x[["GrantID"]])) 255 | COIStatement <- sapply(object, function(x) null_replace(x[["CoiStatement"]]),USE.NAMES=FALSE) 256 | 257 | Mesh <- lapply(object, function(x) list_null_replace(x[["Mesh"]])) 258 | Keywords <- lapply(object, function(x) list_null_replace(x[["Keywords"]])) 259 | Citations <- lapply(object, function(x) list_null_replace(x[["Citations"]])) 260 | 261 | names(GrantID) <- PMID 262 | names(Mesh) <- PMID 263 | names(Keywords) <- PMID 264 | names(Citations) <- PMID 265 | names(PublicationType) <- PMID 266 | 267 | PMID <- as.character(PMID) 268 | 269 | YearRevised <- as.numeric(YearRevised) 270 | MonthRevised <- as.numeric(MonthRevised) 271 | DayRevised <- as.numeric(DayRevised) 272 | YearPubDate <- as.numeric(YearPubDate) 273 | MonthPubDate <- as.character(MonthPubDate) 274 | DayPubDate <- as.numeric(DayPubDate) 275 | YearArticleDate <- as.numeric(YearArticleDate) 276 | MonthArticleDate <- as.numeric(MonthArticleDate) 277 | DayArticleDate <- as.numeric(DayArticleDate) 278 | 279 | YearEntrez <- as.numeric(YearEntrez) 280 | MonthEntrez <- as.numeric(MonthEntrez) 281 | DayEntrez <- as.numeric(DayEntrez) 282 | HourEntrez <- as.numeric(HourEntrez) 283 | MinuteEntrez <- as.numeric(MinuteEntrez) 284 | YearMedline <- as.numeric(YearMedline) 285 | MonthMedline <- as.numeric(MonthMedline) 286 | DayMedline <- as.numeric(DayMedline) 287 | HourMedline <- as.numeric(HourMedline) 288 | MinuteMedline <- as.numeric(MinuteMedline) 289 | 290 | YearAccepted <- as.numeric(YearAccepted) 291 | YearReceived <- as.numeric(YearReceived) 292 | YearEpublish <- as.numeric(YearEpublish) 293 | YearPpublish <- as.numeric(YearPpublish) 294 | YearPmc <- as.numeric(YearPmc) 295 | YearPubmed <- as.numeric(YearPubmed) 296 | 297 | MonthAccepted <- as.numeric(MonthAccepted) 298 | MonthReceived <- as.numeric(MonthReceived) 299 | MonthEpublish <- as.numeric(MonthEpublish) 300 | MonthPpublish <- as.numeric(MonthPpublish) 301 | MonthPmc <- as.numeric(MonthPmc) 302 | MonthPubmed <- as.numeric(MonthPubmed) 303 | 304 | DayAccepted <- as.numeric(DayAccepted) 305 | DayReceived <- as.numeric(DayReceived) 306 | DayEpublish <- as.numeric(DayEpublish) 307 | DayPpublish <- as.numeric(DayPpublish) 308 | DayPmc <- as.numeric(DayPmc) 309 | DayPubmed <- as.numeric(DayPubmed) 310 | 311 | HourAccepted <- as.numeric(HourAccepted) 312 | HourReceived <- as.numeric(HourReceived) 313 | HourEpublish <- as.numeric(HourEpublish) 314 | HourPpublish <- as.numeric(HourPpublish) 315 | HourPmc <- as.numeric(HourPmc) 316 | HourPubmed <- as.numeric(HourPubmed) 317 | 318 | MinuteAccepted <- as.numeric(MinuteAccepted) 319 | MinuteReceived <- as.numeric(MinuteReceived) 320 | MinuteEpublish <- as.numeric(MinuteEpublish) 321 | MinutePpublish <- as.numeric(MinutePpublish) 322 | MinutePmc <- as.numeric(MinutePmc) 323 | MinutePubmed <- as.numeric(MinutePubmed) 324 | 325 | ISSN <- as.character(ISSN) 326 | Title <- as.character(Title) 327 | ArticleTitle <- as.character(ArticleTitle) 328 | ELocationID <- as.character(ELocationID) 329 | AbstractText <- as.character(AbstractText) 330 | Affiliation <- Affiliation 331 | Language <- as.character(Language) 332 | PublicationType <- PublicationType 333 | MedlineTA <- as.character(MedlineTA) 334 | NlmUniqueID <- as.character(NlmUniqueID) 335 | ISSNLinking <- as.character(ISSNLinking) 336 | PublicationStatus <- as.character(PublicationStatus) 337 | ArticleId <- as.character(ArticleId) 338 | DOI <- as.character(DOI) 339 | Volume <- as.character(Volume) 340 | Issue <- as.character(Issue) 341 | ISOAbbreviation <- as.character(ISOAbbreviation) 342 | MedlinePgn <- as.character(MedlinePgn) 343 | CopyrightInformation <- as.character(CopyrightInformation) 344 | Country <- as.character(Country) 345 | GrantID <- GrantID 346 | COIStatement <- as.character(COIStatement) 347 | 348 | BookPublisher <- as.character(BookPublisher) 349 | BookPublisherLocation <- as.character(BookPublisherLocation) 350 | BookTitle <- as.character(BookTitle) 351 | BookBeginningDate <- as.numeric(BookBeginningDate) 352 | BookEndingDate <- as.numeric(BookEndingDate) 353 | BookMedium <- as.character(BookMedium) 354 | 355 | new("Medline", 356 | Query = query, 357 | PMID = PMID, 358 | YearRevised = YearRevised, 359 | MonthRevised = MonthRevised , 360 | DayRevised = DayRevised, 361 | YearPubDate = YearPubDate, 362 | MonthPubDate = MonthPubDate , 363 | DayPubDate = DayPubDate, 364 | YearArticleDate = YearArticleDate, 365 | MonthArticleDate = MonthArticleDate , 366 | DayArticleDate = DayArticleDate, 367 | YearEntrez = YearEntrez, 368 | MonthEntrez = MonthEntrez , 369 | DayEntrez = DayEntrez, 370 | HourEntrez = HourEntrez, 371 | MinuteEntrez = MinuteEntrez, 372 | YearMedline = YearMedline, 373 | MonthMedline = MonthMedline , 374 | DayMedline = DayMedline, 375 | HourMedline = HourMedline, 376 | MinuteMedline = MinuteMedline, 377 | YearAccepted = YearAccepted, 378 | MonthAccepted = MonthAccepted , 379 | DayAccepted = DayAccepted, 380 | HourAccepted = HourAccepted, 381 | MinuteAccepted = MinuteAccepted, 382 | YearReceived = YearReceived, 383 | MonthReceived = MonthReceived, 384 | DayReceived = DayReceived, 385 | HourReceived = HourReceived, 386 | MinuteReceived = MinuteReceived, 387 | YearEpublish = YearEpublish, 388 | MonthEpublish = MonthEpublish , 389 | DayEpublish = DayEpublish, 390 | HourEpublish = HourEpublish, 391 | MinuteEpublish = MinuteEpublish, 392 | YearPpublish = YearPpublish, 393 | MonthPpublish = MonthPpublish , 394 | DayPpublish = DayPpublish, 395 | HourPpublish = HourPpublish, 396 | MinutePpublish = MinutePpublish, 397 | YearPmc = YearPmc, 398 | MonthPmc = MonthPmc , 399 | DayPmc = DayPmc, 400 | HourPmc = HourPmc, 401 | MinutePmc = MinutePmc, 402 | YearPubmed = YearPubmed, 403 | MonthPubmed = MonthPubmed , 404 | DayPubmed = DayPubmed, 405 | HourPubmed = HourPubmed, 406 | MinutePubmed = MinutePubmed, 407 | ISSN = ISSN, 408 | Title = Title, 409 | Author = Author, 410 | ArticleTitle = ArticleTitle, 411 | ELocationID = ELocationID, 412 | AbstractText = AbstractText, 413 | Affiliation = Affiliation, 414 | Language = Language, 415 | PublicationType = PublicationType, 416 | MedlineTA = MedlineTA, 417 | NlmUniqueID = NlmUniqueID, 418 | ISSNLinking = ISSNLinking, 419 | PublicationStatus = PublicationStatus, 420 | ArticleId = ArticleId, 421 | DOI = DOI, 422 | Volume = Volume, 423 | Issue = Issue, 424 | ISOAbbreviation = ISOAbbreviation, 425 | MedlinePgn = MedlinePgn, 426 | CopyrightInformation = CopyrightInformation, 427 | Country = Country, 428 | GrantID = GrantID, 429 | COIStatement = COIStatement, 430 | Mesh = Mesh, 431 | Keywords = Keywords, 432 | Citations = Citations, 433 | BookPublisher = BookPublisher, 434 | BookPublisherLocation = BookPublisherLocation, 435 | BookTitle = BookTitle, 436 | BookBeginningDate = BookBeginningDate, 437 | BookEndingDate = BookEndingDate, 438 | BookMedium = BookMedium, 439 | BookEditors = Editors 440 | ) 441 | } 442 | 443 | 444 | setMethod("print","Medline",function(x,...){ 445 | cat("PubMed query: ",x@Query,"\n\n") 446 | cat("Records: ",length(x@PMID),"\n") 447 | }) 448 | 449 | setMethod("show","Medline",function(object){ 450 | cat("PubMed query: ",object@Query,"\n\n") 451 | cat("Records: ",length(object@PMID),"\n") 452 | }) 453 | 454 | setMethod("Query","Medline",function(object) object@Query) 455 | setMethod("PMID","Medline",function(object) object@PMID) 456 | setMethod("YearRevised","Medline",function(object) object@YearRevised) 457 | setMethod("MonthRevised","Medline",function(object) object@MonthRevised) 458 | setMethod("DayRevised","Medline",function(object) object@DayRevised) 459 | setMethod("YearPubDate","Medline",function(object) object@YearPubDate) 460 | setMethod("MonthPubDate","Medline",function(object) object@MonthPubDate) 461 | setMethod("DayPubDate","Medline",function(object) object@DayPubDate) 462 | setMethod("YearArticleDate","Medline",function(object) object@YearArticleDate) 463 | setMethod("MonthArticleDate","Medline",function(object) object@MonthArticleDate) 464 | setMethod("DayArticleDate","Medline",function(object) object@DayArticleDate) 465 | setMethod("YearEntrez","Medline",function(object) object@YearEntrez) 466 | setMethod("MonthEntrez","Medline",function(object) object@MonthEntrez) 467 | setMethod("DayEntrez","Medline",function(object) object@DayEntrez) 468 | setMethod("HourEntrez","Medline",function(object) object@HourEntrez) 469 | setMethod("MinuteEntrez","Medline",function(object) object@MinuteEntrez) 470 | setMethod("YearMedline","Medline",function(object) object@YearMedline) 471 | setMethod("MonthMedline","Medline",function(object) object@MonthMedline) 472 | setMethod("DayMedline","Medline",function(object) object@DayMedline) 473 | setMethod("HourMedline","Medline",function(object) object@HourMedline) 474 | setMethod("MinuteMedline","Medline",function(object) object@MinuteMedline) 475 | setMethod("YearAccepted","Medline",function(object) object@YearAccepted) 476 | setMethod("MonthAccepted","Medline",function(object) object@MonthAccepted) 477 | setMethod("DayAccepted","Medline",function(object) object@DayAccepted) 478 | setMethod("HourAccepted","Medline",function(object) object@HourAccepted) 479 | setMethod("MinuteAccepted","Medline",function(object) object@MinuteAccepted) 480 | setMethod("YearReceived","Medline",function(object) object@YearReceived) 481 | setMethod("MonthReceived","Medline",function(object) object@MonthReceived) 482 | setMethod("DayReceived","Medline",function(object) object@DayReceived) 483 | setMethod("HourReceived","Medline",function(object) object@HourReceived) 484 | setMethod("MinuteReceived","Medline",function(object) object@MinuteReceived) 485 | setMethod("YearEpublish","Medline",function(object) object@YearEpublish) 486 | setMethod("MonthEpublish","Medline",function(object) object@MonthEpublish) 487 | setMethod("DayEpublish","Medline",function(object) object@DayEpublish) 488 | setMethod("HourEpublish","Medline",function(object) object@HourEpublish) 489 | setMethod("MinuteEpublish","Medline",function(object) object@MinuteEpublish) 490 | setMethod("YearPpublish","Medline",function(object) object@YearPpublish) 491 | setMethod("MonthPpublish","Medline",function(object) object@MonthPpublish) 492 | setMethod("DayPpublish","Medline",function(object) object@DayPpublish) 493 | setMethod("HourPpublish","Medline",function(object) object@HourPpublish) 494 | setMethod("MinutePpublish","Medline",function(object) object@MinutePpublish) 495 | setMethod("YearPmc","Medline",function(object) object@YearPmc) 496 | setMethod("MonthPmc","Medline",function(object) object@MonthPmc) 497 | setMethod("DayPmc","Medline",function(object) object@DayPmc) 498 | setMethod("HourPmc","Medline",function(object) object@HourPmc) 499 | setMethod("MinutePmc","Medline",function(object) object@MinutePmc) 500 | setMethod("YearPubmed","Medline",function(object) object@YearPubmed) 501 | setMethod("MonthPubmed","Medline",function(object) object@MonthPubmed) 502 | setMethod("DayPubmed","Medline",function(object) object@DayPubmed) 503 | setMethod("HourPubmed","Medline",function(object) object@HourPubmed) 504 | setMethod("MinutePubmed","Medline",function(object) object@MinutePubmed) 505 | setMethod("Author","Medline",function(object) object@Author) 506 | setMethod("ISSN","Medline",function(object) object@ISSN) 507 | setMethod("Title","Medline",function(object) object@Title) 508 | setMethod("ArticleTitle","Medline",function(object) object@ArticleTitle) 509 | setMethod("ELocationID","Medline",function(object) object@ELocationID) 510 | setMethod("AbstractText","Medline",function(object) object@AbstractText) 511 | setMethod("Affiliation","Medline",function(object) object@Affiliation) 512 | setMethod("Language","Medline",function(object) object@Language) 513 | setMethod("PublicationType","Medline",function(object) object@PublicationType) 514 | setMethod("MedlineTA","Medline",function(object) object@MedlineTA) 515 | setMethod("NlmUniqueID","Medline",function(object) object@NlmUniqueID) 516 | setMethod("ISSNLinking","Medline",function(object) object@ISSNLinking) 517 | setMethod("PublicationStatus","Medline",function(object) object@PublicationStatus) 518 | setMethod("ArticleId","Medline",function(object) object@ArticleId) 519 | setMethod("DOI","Medline",function(object) object@DOI) 520 | setMethod("Volume","Medline",function(object) object@Volume) 521 | setMethod("Issue","Medline",function(object) object@Issue) 522 | setMethod("ISOAbbreviation","Medline",function(object) object@ISOAbbreviation) 523 | setMethod("MedlinePgn","Medline",function(object) object@MedlinePgn) 524 | setMethod("CopyrightInformation","Medline",function(object) object@CopyrightInformation) 525 | setMethod("Country","Medline",function(object) object@Country) 526 | setMethod("GrantID","Medline",function(object) object@GrantID) 527 | setMethod("COIStatement","Medline",function(object) object@COIStatement) 528 | setMethod("Mesh","Medline",function(object) object@Mesh) 529 | setMethod("Keywords","Medline",function(object) object@Keywords) 530 | setMethod("Citations","Medline",function(object) object@Citations) 531 | setMethod("BookPublisher", "Medline", function(object) object@BookPublisher) 532 | setMethod("BookPublisherLocation", "Medline", function(object) object@BookLocation) 533 | setMethod("BookTitle", "Medline", function(object) object@BookTitle) 534 | setMethod("BookBeginningDate", "Medline", function(object) object@BookBeginningDate) 535 | setMethod("BookEndingDate", "Medline", function(object) object@BookEndingDate) 536 | setMethod("BookMedium", "Medline", function(object) object@BookMedium) 537 | setMethod("BookEditors", "Medline", function(object) object@BookEditors) 538 | --------------------------------------------------------------------------------