Nothing
Lexispoints <-
function (Bdata,transition,title,cov,legend)
{ z<- check.par (Bdata)
# require (Epi)
if (missing(cov)) cov=NA
if (missing(title)) title <- "Title missing"
if (missing(legend)) legend <- "topleft"
# year <- data.frame(YearTrans(Bdata))
Bdata2 <- date_b(Bdata=Bdata,selectday=1,format.out="year")
zx <- TransitionAB(Bdata2,transition) # zx: nrow = number of transition selected
Bdata2 <- subset(Bdata2,!is.na(zx$year))
ID <- zx$id
entry <- subset(Bdata2$start,Bdata2$ID%in%ID)
exit <- subset (zx$year,!is.na(zx$year)) # event of interest
birth <- subset(Bdata2$born,Bdata2$ID%in%ID)
istrans <- rep(1,length(ID))
#zbb <- subset(Bdata2,!is.na(zx$year))
Lcoh1 <- Lexis( id = ID,
entry = list( CalTime=entry ),
exit = list( CalTime=exit, Age=exit-birth ),
exit.status = istrans,
data=Bdata2[Bdata2$ID%in%ID,], # zbb,
merge=TRUE) # 1900 added for x-axis
# lex.dur = exit - entry
# CalTime = Lcoh1[,1] = date at entry (1900+)
# Age = age at ENTRY
# if (date_in_month_or_year == 1) moye <- 12 else moye <- 1
moye <- 1
AgeLow1 <- 5*trunc(min(na.omit(exit-birth)/(5*moye)))
AgeHigh1 <- 5*(trunc(max(na.omit(exit-birth)/(5*moye)))+1)
PerLow1 <- 5* trunc(min(na.omit(exit)/(5*moye)))
PerHigh1 <- 5* (trunc(max(na.omit(exit)/(5*moye)))+1)
PerHigh1[PerHigh1-PerLow1 < AgeHigh1-AgeLow1] <- PerLow1 + AgeHigh1 - AgeLow1
AgeHigh1[AgeHigh1-AgeLow1 < PerHigh1-PerLow1] <- AgeLow1 + PerHigh1 - PerLow1
Lexis.diagram (age=c(AgeLow1,AgeHigh1),alab="Age",date=c(PerLow1,PerHigh1),dlab="Calendar Time",
int=5,lab.int=5,col.life="black",lwd.grid=1,las=1,main=title)
color <- palette (rainbow(7))
Lcoh1$one <- 1
if (is.na(cov))
{ poscov <- which (colnames(Lcoh1)%in%"one")
covcat <- 1 } else
{ poscov <- which (colnames(Lcoh1)%in%cov)
covcat <- sort(unique(Lcoh1[,poscov]))
}
for (i in 1:length(covcat))
{ points(Lcoh1$CalTime[Lcoh1[,poscov]==covcat[i]]+Lcoh1$lex.dur[Lcoh1[,poscov]==covcat[i]],
Lcoh1$Age[Lcoh1[,poscov]==covcat[i]]+Lcoh1$lex.dur[Lcoh1[,poscov]==covcat[i]],
pch=c(NA,16)[Lcoh1$lex.Xst[Lcoh1[,poscov]==covcat[i]]+1], col=color[i], cex=0.5 )
}
legend(legend, title=cov,legend=covcat[1:length(covcat)],pch=16,col=color[1:length(covcat)],bg="white")
return (Lcoh=Lcoh1)
}
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