Nothing
setClass("Medline",
representation(
Query = "character",
PMID = "character",
YearRevised = "numeric",
MonthRevised = "numeric",
DayRevised= "numeric",
YearPubDate = "numeric",
MonthPubDate = "character",
DayPubDate= "numeric",
YearArticleDate = "numeric",
MonthArticleDate = "numeric",
DayArticleDate= "numeric",
YearEntrez = "numeric",
MonthEntrez = "numeric",
DayEntrez= "numeric",
HourEntrez= "numeric",
MinuteEntrez= "numeric",
YearMedline = "numeric",
MonthMedline = "numeric",
DayMedline= "numeric",
HourMedline= "numeric",
MinuteMedline= "numeric",
YearReceived = "numeric",
MonthReceived = "numeric",
DayReceived= "numeric",
HourReceived= "numeric",
MinuteReceived= "numeric",
YearAccepted = "numeric",
MonthAccepted = "numeric",
DayAccepted= "numeric",
HourAccepted= "numeric",
MinuteAccepted= "numeric",
YearEpublish = "numeric",
MonthEpublish = "numeric",
DayEpublish= "numeric",
HourEpublish= "numeric",
MinuteEpublish= "numeric",
YearPpublish = "numeric",
MonthPpublish = "numeric",
DayPpublish= "numeric",
HourPpublish= "numeric",
MinutePpublish= "numeric",
YearPmc = "numeric",
MonthPmc = "numeric",
DayPmc = "numeric",
HourPmc = "numeric",
MinutePmc = "numeric",
YearPubmed = "numeric",
MonthPubmed = "numeric",
DayPubmed = "numeric",
HourPubmed = "numeric",
MinutePubmed = "numeric",
Author = "list",
ISSN= "character",
Title = "character",
ArticleTitle= "character",
ELocationID= "character",
AbstractText= "character",
Affiliation= "list",
Language= "character",
PublicationType= "character",
MedlineTA= "character",
NlmUniqueID= "character",
ISSNLinking= "character",
PublicationStatus= "character",
ArticleId= "character",
DOI = "character",
Volume= "character",
Issue= "character",
ISOAbbreviation= "character",
MedlinePgn= "character",
CopyrightInformation= "character",
Country= "character",
GrantID= "list",
COIStatement = "character",
Mesh="list",
Keywords="list",
Citations="list")
)
null_replace <- function(x) ifelse(is.null(x), NA, x)
list_null_replace <- function(x) if(class(x) == "NULL") NA else x
Medline <- function(object, query = character(0)){
TagIndex <- lapply(object, names)
# ARTICLE LIST FROM PUBMED QUERY
PMID <- sapply(object, function(x) null_replace(x[["PMID"]]),USE.NAMES=FALSE)
YearRevised <- sapply(object, function(x) null_replace(x[["YearRevised"]]),USE.NAMES=FALSE)
MonthRevised <- sapply(object, function(x) null_replace(x[["MonthRevised"]]),USE.NAMES=FALSE)
DayRevised <- sapply(object, function(x) null_replace(x[["DayRevised"]]),USE.NAMES=FALSE)
YearArticleDate <- sapply(object, function(x) null_replace(x[["YearArticleDate"]]),USE.NAMES=FALSE)
MonthArticleDate <- sapply(object, function(x) null_replace(x[["MonthArticleDate"]]),USE.NAMES=FALSE)
DayArticleDate <- sapply(object, function(x) null_replace(x[["DayArticleDate"]]),USE.NAMES=FALSE)
YearPubDate <-sapply(object, function(x) null_replace(x[["YearPubDate"]]),USE.NAMES=FALSE)
MonthPubDate <- sapply(object, function(x) null_replace(x[["MonthPubDate"]]),USE.NAMES=FALSE)
DayPubDate <- sapply(object, function(x) null_replace(x[["DayPubDate"]]),USE.NAMES=FALSE)
YearEntrez <- sapply(object, function(x) null_replace(x[["YearEntrez"]]),USE.NAMES=FALSE)
MonthEntrez <- sapply(object, function(x) null_replace(x[["MonthEntrez"]]),USE.NAMES=FALSE)
DayEntrez <- sapply(object, function(x) null_replace(x[["DayEntrez"]]),USE.NAMES=FALSE)
MinuteEntrez <- sapply(object, function(x) null_replace(x[["MinuteEnrez"]]),USE.NAMES=FALSE)
HourEntrez <- sapply(object, function(x) null_replace(x[["HourEntrez"]]),USE.NAMES=FALSE)
YearMedline <- sapply(object, function(x) null_replace(x[["YearMedline"]]),USE.NAMES=FALSE)
MonthMedline <- sapply(object, function(x) null_replace(x[["MonthMedline"]]),USE.NAMES=FALSE)
DayMedline <- sapply(object, function(x) null_replace(x[["DayMedline"]]),USE.NAMES=FALSE)
MinuteMedline <- sapply(object, function(x) null_replace(x[["MinuteMedline"]]),USE.NAMES=FALSE)
HourMedline <- sapply(object, function(x) null_replace(x[["HourMedline"]]),USE.NAMES=FALSE)
YearReceived <- sapply(object, function(x) null_replace(x[["YearReceived"]]),USE.NAMES=FALSE)
MonthReceived <- sapply(object, function(x) null_replace(x[["MonthReceived"]]),USE.NAMES=FALSE)
DayReceived <- sapply(object, function(x) null_replace(x[["DayReceived"]]),USE.NAMES=FALSE)
MinuteReceived <- sapply(object, function(x) null_replace(x[["MinuteReceived"]]),USE.NAMES=FALSE)
HourReceived <- sapply(object, function(x) null_replace(x[["HourReceived"]]),USE.NAMES=FALSE)
YearEpublish <- sapply(object, function(x) null_replace(x[["YearEpublish"]]),USE.NAMES=FALSE)
MonthEpublish <- sapply(object, function(x) null_replace(x[["MonthEpublish"]]),USE.NAMES=FALSE)
DayEpublish <- sapply(object, function(x) null_replace(x[["DayEpublish"]]),USE.NAMES=FALSE)
MinuteEpublish <- sapply(object, function(x) null_replace(x[["MinuteEpublish"]]),USE.NAMES=FALSE)
HourEpublish <- sapply(object, function(x) null_replace(x[["HourEpublish"]]),USE.NAMES=FALSE)
YearPpublish <- sapply(object, function(x) null_replace(x[["YearPpublish"]]),USE.NAMES=FALSE)
MonthPpublish <- sapply(object, function(x) null_replace(x[["MonthPpublish"]]),USE.NAMES=FALSE)
DayPpublish <- sapply(object, function(x) null_replace(x[["DayPpublish"]]),USE.NAMES=FALSE)
MinutePpublish <- sapply(object, function(x) null_replace(x[["MinutePpublish"]]),USE.NAMES=FALSE)
HourPpublish <- sapply(object, function(x) null_replace(x[["HourPpublish"]]),USE.NAMES=FALSE)
YearPmc <- sapply(object, function(x) null_replace(x[["YearPmc"]]),USE.NAMES=FALSE)
MonthPmc <- sapply(object, function(x) null_replace(x[["MonthPmc"]]),USE.NAMES=FALSE)
DayPmc <- sapply(object, function(x) null_replace(x[["DayPmc"]]),USE.NAMES=FALSE)
MinutePmc <- sapply(object, function(x) null_replace(x[["MinutePmc"]]),USE.NAMES=FALSE)
HourPmc <- sapply(object, function(x) null_replace(x[["HourPmc"]]),USE.NAMES=FALSE)
YearPubmed <- sapply(object, function(x) null_replace(x[["YearPubmed"]]),USE.NAMES=FALSE)
MonthPubmed <- sapply(object, function(x) null_replace(x[["MonthPubmed"]]),USE.NAMES=FALSE)
DayPubmed <- sapply(object, function(x) null_replace(x[["DayPubmed"]]),USE.NAMES=FALSE)
MinutePubmed <- sapply(object, function(x) null_replace(x[["MinutePubmed"]]),USE.NAMES=FALSE)
HourPubmed <- sapply(object, function(x) null_replace(x[["HourPubmed"]]),USE.NAMES=FALSE)
YearAccepted <- sapply(object, function(x) null_replace(x[["YearAccepted"]]),USE.NAMES=FALSE)
MonthAccepted <- sapply(object, function(x) null_replace(x[["MonthAccepted"]]),USE.NAMES=FALSE)
DayAccepted <- sapply(object, function(x) null_replace(x[["DayAccepted"]]),USE.NAMES=FALSE)
MinuteAccepted <- sapply(object, function(x) null_replace(x[["MinuteAccepted"]]),USE.NAMES=FALSE)
HourAccepted <- sapply(object, function(x) null_replace(x[["HourAccepted"]]),USE.NAMES=FALSE)
AbstractText <- lapply(object, function(x) list_null_replace(x[["AbstractText"]]))
Author <- lapply(object, function(x) list_null_replace(x[["Author"]]))
Affiliation <- lapply(object, function(x) list_null_replace(x[["Affiliation"]]))
names(AbstractText) <- PMID
names(Author) <- PMID
names(Affiliation) <- PMID
ISSN <- sapply(object, function(x) null_replace(x[["ISSN"]]),USE.NAMES=FALSE)
Title <- sapply(object, function(x) null_replace(x[["Title"]]),USE.NAMES=FALSE)
ArticleTitle <- sapply(object, function(x) null_replace(x[["ArticleTitle"]]),USE.NAMES=FALSE)
ELocationID <- sapply(object, function(x) null_replace(x[["ELocationID"]]),USE.NAMES=FALSE)
Language <- sapply(object, function(x) null_replace(x[["Language"]]),USE.NAMES=FALSE)
PublicationType <- sapply(object, function(x) null_replace(x[["PublicationType"]]),USE.NAMES=FALSE)
MedlineTA <- sapply(object, function(x) null_replace(x[["MedlineTA"]]),USE.NAMES=FALSE)
NlmUniqueID <- sapply(object, function(x) null_replace(x[["NlmUniqueID"]]),USE.NAMES=FALSE)
ISSNLinking <- sapply(object, function(x) null_replace(x[["ISSNLinking"]]),USE.NAMES=FALSE)
PublicationStatus <- sapply(object, function(x) null_replace(x[["PublicationStatus"]]),USE.NAMES=FALSE)
ArticleId <- sapply(object, function(x) null_replace(x[["ArticleId"]]),USE.NAMES=FALSE)
DOI <- sapply(object, function(x) null_replace(x[["DOI"]]),USE.NAMES=FALSE)
Volume <- sapply(object, function(x) null_replace(x[["Volume"]]),USE.NAMES=FALSE)
Issue <- sapply(object, function(x) null_replace(x[["Issue"]]),USE.NAMES=FALSE)
ISOAbbreviation <- sapply(object, function(x) null_replace(x[["ISOAbbreviation"]]),USE.NAMES=FALSE)
MedlinePgn <- sapply(object, function(x) null_replace(x[["MedlinePgn"]]),USE.NAMES=FALSE)
CopyrightInformation <- sapply(object, function(x) null_replace(x[["CopyrightInformation"]]),USE.NAMES=FALSE)
Country <- sapply(object, function(x) null_replace(x[["Country"]]),USE.NAMES=FALSE)
GrantID <- lapply(object, function(x) list_null_replace(x[["GrantID"]]))
COIStatement <- sapply(object, function(x) null_replace(x[["CoiStatement"]]),USE.NAMES=FALSE)
Mesh <- lapply(object, function(x) list_null_replace(x[["Mesh"]]))
Keywords <- lapply(object, function(x) list_null_replace(x[["Keywords"]]))
Citations <- lapply(object, function(x) list_null_replace(x[["Citations"]]))
names(GrantID) <- PMID
names(Mesh) <- PMID
names(Keywords) <- PMID
names(Citations) <- PMID
PMID <- as.character(PMID)
YearRevised <- as.numeric(YearRevised)
MonthRevised <- as.numeric(MonthRevised)
DayRevised <- as.numeric(DayRevised)
YearPubDate <- as.numeric(YearPubDate)
MonthPubDate <- as.character(MonthPubDate)
DayPubDate <- as.numeric(DayPubDate)
YearArticleDate <- as.numeric(YearArticleDate)
MonthArticleDate <- as.numeric(MonthArticleDate)
DayArticleDate <- as.numeric(DayArticleDate)
YearEntrez <- as.numeric(YearEntrez)
MonthEntrez <- as.numeric(MonthEntrez)
DayEntrez <- as.numeric(DayEntrez)
HourEntrez <- as.numeric(HourEntrez)
MinuteEntrez <- as.numeric(MinuteEntrez)
YearMedline <- as.numeric(YearMedline)
MonthMedline <- as.numeric(MonthMedline)
DayMedline <- as.numeric(DayMedline)
HourMedline <- as.numeric(HourMedline)
MinuteMedline <- as.numeric(MinuteMedline)
YearAccepted <- as.numeric(YearAccepted)
YearReceived <- as.numeric(YearReceived)
YearEpublish <- as.numeric(YearEpublish)
YearPpublish <- as.numeric(YearPpublish)
YearPmc <- as.numeric(YearPmc)
YearPubmed <- as.numeric(YearPubmed)
MonthAccepted <- as.numeric(MonthAccepted)
MonthReceived <- as.numeric(MonthReceived)
MonthEpublish <- as.numeric(MonthEpublish)
MonthPpublish <- as.numeric(MonthPpublish)
MonthPmc <- as.numeric(MonthPmc)
MonthPubmed <- as.numeric(MonthPubmed)
DayAccepted <- as.numeric(DayAccepted)
DayReceived <- as.numeric(DayReceived)
DayEpublish <- as.numeric(DayEpublish)
DayPpublish <- as.numeric(DayPpublish)
DayPmc <- as.numeric(DayPmc)
DayPubmed <- as.numeric(DayPubmed)
HourAccepted <- as.numeric(HourAccepted)
HourReceived <- as.numeric(HourReceived)
HourEpublish <- as.numeric(HourEpublish)
HourPpublish <- as.numeric(HourPpublish)
HourPmc <- as.numeric(HourPmc)
HourPubmed <- as.numeric(HourPubmed)
MinuteAccepted <- as.numeric(MinuteAccepted)
MinuteReceived <- as.numeric(MinuteReceived)
MinuteEpublish <- as.numeric(MinuteEpublish)
MinutePpublish <- as.numeric(MinutePpublish)
MinutePmc <- as.numeric(MinutePmc)
MinutePubmed <- as.numeric(MinutePubmed)
ISSN <- as.character(ISSN)
Title <- as.character(Title)
ArticleTitle <- as.character(ArticleTitle)
ELocationID <- as.character(ELocationID)
AbstractText <- as.character(AbstractText)
Affiliation <- Affiliation
Language <- as.character(Language)
PublicationType <- as.character(PublicationType)
MedlineTA <- as.character(MedlineTA)
NlmUniqueID <- as.character(NlmUniqueID)
ISSNLinking <- as.character(ISSNLinking)
PublicationStatus <- as.character(PublicationStatus)
ArticleId <- as.character(ArticleId)
DOI <- as.character(DOI)
Volume <- as.character(Volume)
Issue <- as.character(Issue)
ISOAbbreviation <- as.character(ISOAbbreviation)
MedlinePgn <- as.character(MedlinePgn)
CopyrightInformation <- as.character(CopyrightInformation)
Country <- as.character(Country)
GrantID <- GrantID
COIStatement <- as.character(COIStatement)
new("Medline",
Query = query,
PMID = PMID,
YearRevised = YearRevised,
MonthRevised = MonthRevised ,
DayRevised = DayRevised,
YearPubDate = YearPubDate,
MonthPubDate = MonthPubDate ,
DayPubDate = DayPubDate,
YearArticleDate = YearArticleDate,
MonthArticleDate = MonthArticleDate ,
DayArticleDate = DayArticleDate,
YearEntrez = YearEntrez,
MonthEntrez = MonthEntrez ,
DayEntrez = DayEntrez,
HourEntrez = HourEntrez,
MinuteEntrez = MinuteEntrez,
YearMedline = YearMedline,
MonthMedline = MonthMedline ,
DayMedline = DayMedline,
HourMedline = HourMedline,
MinuteMedline = MinuteMedline,
YearAccepted = YearAccepted,
MonthAccepted = MonthAccepted ,
DayAccepted = DayAccepted,
HourAccepted = HourAccepted,
MinuteAccepted = MinuteAccepted,
YearReceived = YearReceived,
MonthReceived = MonthReceived,
DayReceived = DayReceived,
HourReceived = HourReceived,
MinuteReceived = MinuteReceived,
YearEpublish = YearEpublish,
MonthEpublish = MonthEpublish ,
DayEpublish = DayEpublish,
HourEpublish = HourEpublish,
MinuteEpublish = MinuteEpublish,
YearPpublish = YearPpublish,
MonthPpublish = MonthPpublish ,
DayPpublish = DayPpublish,
HourPpublish = HourPpublish,
MinutePpublish = MinutePpublish,
YearPmc = YearPmc,
MonthPmc = MonthPmc ,
DayPmc = DayPmc,
HourPmc = HourPmc,
MinutePmc = MinutePmc,
YearPubmed = YearPubmed,
MonthPubmed = MonthPubmed ,
DayPubmed = DayPubmed,
HourPubmed = HourPubmed,
MinutePubmed = MinutePubmed,
ISSN = ISSN,
Title = Title,
Author = Author,
ArticleTitle = ArticleTitle,
ELocationID = ELocationID,
AbstractText = AbstractText,
Affiliation = Affiliation,
Language = Language,
PublicationType = PublicationType,
MedlineTA = MedlineTA,
NlmUniqueID = NlmUniqueID,
ISSNLinking = ISSNLinking,
PublicationStatus = PublicationStatus,
ArticleId = ArticleId,
DOI = DOI,
Volume = Volume,
Issue = Issue,
ISOAbbreviation = ISOAbbreviation,
MedlinePgn = MedlinePgn,
CopyrightInformation = CopyrightInformation,
Country = Country,
GrantID = GrantID,
COIStatement = COIStatement,
Mesh = Mesh,
Keywords = Keywords,
Citations = Citations
)
}
setMethod("print","Medline",function(x,...){
cat("PubMed query: ",x@Query,"\n\n")
cat("Records: ",length(x@PMID),"\n")
})
setMethod("show","Medline",function(object){
cat("PubMed query: ",object@Query,"\n\n")
cat("Records: ",length(object@PMID),"\n")
})
setMethod("Query","Medline",function(object) object@Query)
setMethod("PMID","Medline",function(object) object@PMID)
setMethod("YearRevised","Medline",function(object) object@YearRevised)
setMethod("MonthRevised","Medline",function(object) object@MonthRevised)
setMethod("DayRevised","Medline",function(object) object@DayRevised)
setMethod("YearPubDate","Medline",function(object) object@YearPubDate)
setMethod("MonthPubDate","Medline",function(object) object@MonthPubDate)
setMethod("DayPubDate","Medline",function(object) object@DayPubDate)
setMethod("YearArticleDate","Medline",function(object) object@YearArticleDate)
setMethod("MonthArticleDate","Medline",function(object) object@MonthArticleDate)
setMethod("DayArticleDate","Medline",function(object) object@DayArticleDate)
setMethod("YearEntrez","Medline",function(object) object@YearEntrez)
setMethod("MonthEntrez","Medline",function(object) object@MonthEntrez)
setMethod("DayEntrez","Medline",function(object) object@DayEntrez)
setMethod("HourEntrez","Medline",function(object) object@HourEntrez)
setMethod("MinuteEntrez","Medline",function(object) object@MinuteEntrez)
setMethod("YearMedline","Medline",function(object) object@YearMedline)
setMethod("MonthMedline","Medline",function(object) object@MonthMedline)
setMethod("DayMedline","Medline",function(object) object@DayMedline)
setMethod("HourMedline","Medline",function(object) object@HourMedline)
setMethod("MinuteMedline","Medline",function(object) object@MinuteMedline)
setMethod("YearAccepted","Medline",function(object) object@YearAccepted)
setMethod("MonthAccepted","Medline",function(object) object@MonthAccepted)
setMethod("DayAccepted","Medline",function(object) object@DayAccepted)
setMethod("HourAccepted","Medline",function(object) object@HourAccepted)
setMethod("MinuteAccepted","Medline",function(object) object@MinuteAccepted)
setMethod("YearReceived","Medline",function(object) object@YearReceived)
setMethod("MonthReceived","Medline",function(object) object@MonthReceived)
setMethod("DayReceived","Medline",function(object) object@DayReceived)
setMethod("HourReceived","Medline",function(object) object@HourReceived)
setMethod("MinuteReceived","Medline",function(object) object@MinuteReceived)
setMethod("YearEpublish","Medline",function(object) object@YearEpublish)
setMethod("MonthEpublish","Medline",function(object) object@MonthEpublish)
setMethod("DayEpublish","Medline",function(object) object@DayEpublish)
setMethod("HourEpublish","Medline",function(object) object@HourEpublish)
setMethod("MinuteEpublish","Medline",function(object) object@MinuteEpublish)
setMethod("YearPpublish","Medline",function(object) object@YearPpublish)
setMethod("MonthPpublish","Medline",function(object) object@MonthPpublish)
setMethod("DayPpublish","Medline",function(object) object@DayPpublish)
setMethod("HourPpublish","Medline",function(object) object@HourPpublish)
setMethod("MinutePpublish","Medline",function(object) object@MinutePpublish)
setMethod("YearPmc","Medline",function(object) object@YearPmc)
setMethod("MonthPmc","Medline",function(object) object@MonthPmc)
setMethod("DayPmc","Medline",function(object) object@DayPmc)
setMethod("HourPmc","Medline",function(object) object@HourPmc)
setMethod("MinutePmc","Medline",function(object) object@MinutePmc)
setMethod("YearPubmed","Medline",function(object) object@YearPubmed)
setMethod("MonthPubmed","Medline",function(object) object@MonthPubmed)
setMethod("DayPubmed","Medline",function(object) object@DayPubmed)
setMethod("HourPubmed","Medline",function(object) object@HourPubmed)
setMethod("MinutePubmed","Medline",function(object) object@MinutePubmed)
setMethod("Author","Medline",function(object) object@Author)
setMethod("ISSN","Medline",function(object) object@ISSN)
setMethod("Title","Medline",function(object) object@Title)
setMethod("ArticleTitle","Medline",function(object) object@ArticleTitle)
setMethod("ELocationID","Medline",function(object) object@ELocationID)
setMethod("AbstractText","Medline",function(object) object@AbstractText)
setMethod("Affiliation","Medline",function(object) object@Affiliation)
setMethod("Language","Medline",function(object) object@Language)
setMethod("PublicationType","Medline",function(object) object@PublicationType)
setMethod("MedlineTA","Medline",function(object) object@MedlineTA)
setMethod("NlmUniqueID","Medline",function(object) object@NlmUniqueID)
setMethod("ISSNLinking","Medline",function(object) object@ISSNLinking)
setMethod("PublicationStatus","Medline",function(object) object@PublicationStatus)
setMethod("ArticleId","Medline",function(object) object@ArticleId)
setMethod("DOI","Medline",function(object) object@DOI)
setMethod("Volume","Medline",function(object) object@Volume)
setMethod("Issue","Medline",function(object) object@Issue)
setMethod("ISOAbbreviation","Medline",function(object) object@ISOAbbreviation)
setMethod("MedlinePgn","Medline",function(object) object@MedlinePgn)
setMethod("CopyrightInformation","Medline",function(object) object@CopyrightInformation)
setMethod("Country","Medline",function(object) object@Country)
setMethod("GrantID","Medline",function(object) object@GrantID)
setMethod("COIStatement","Medline",function(object) object@COIStatement)
setMethod("Mesh","Medline",function(object) object@Mesh)
setMethod("Keywords","Medline",function(object) object@Keywords)
setMethod("Citations","Medline",function(object) object@Citations)
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