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Copy pathsvaga-data-filtering.r
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svaga-data-filtering.r
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for (s in c(sp.colnames[[sp.position]],"Nonspecific")){
#non.svaga.object[[sp.position]][[s]]<-CD.species[CD.species$SYNDROMIC==s&CD.species$AGENS=="",]
CD.syndrome <- CD.species[CD.species$SYNDROMIC==s&CD.species$AGENS!="",
c("AGENS","PÅVISAD","INSÄNTMATERIAL","ANKOMSTDATUM")]
if(dim(CD.syndrome)[1]>0){
if(is.null(dim(svaga.object[[sp.position]][[s]])[1])){
CD.syndrome$AGENS<- str_replace(CD.syndrome$AGENS, "\\(\\+\\)", "")
syndromes.name=unique(c(colnames(svaga.object[[sp.position]][[s]]),CD.syndrome$AGENS))
a.all=raw_to_syndromicW(id=INSÄNTMATERIAL,
syndromes.var=AGENS,
syndromes.name=syndromes.name,
dates.var=ANKOMSTDATUM,
date.format = "%d/%m/%Y",
min.date=ISOweek2date(weekly.object[[sp.position]]@dates[1,1]),
max.date=new.data.end,
data=CD.syndrome)
CD.syndrome.pos=CD.syndrome[CD.syndrome$PÅVISAD=="Påvisad",]
a.pos=raw_to_syndromicW(id=INSÄNTMATERIAL,
syndromes.var=AGENS,
syndromes.name=syndromes.name,
dates.var=ANKOMSTDATUM,
date.format = "%d/%m/%Y",
min.date=ISOweek2date(weekly.object[[sp.position]]@dates[1,1]),
max.date=new.data.end,
data=CD.syndrome.pos)
svaga.object[[sp.position]][[s]] <- abind(a.all@observed,a.pos@observed,along=3)
}else{
if(dim(svaga.object[[sp.position]][[s]])[1]>=last.historical.row.week){
svaga.object[[sp.position]][[s]] <- svaga.object[[sp.position]][[s]][1:last.historical.row.week,,,drop=FALSE]
CD.syndrome$AGENS<- str_replace(CD.syndrome$AGENS, "\\(\\+\\)", "")
syndromes.name=unique(c(colnames(svaga.object[[sp.position]][[s]]),CD.syndrome$AGENS))
a.all=raw_to_syndromicW(id=INSÄNTMATERIAL,
syndromes.var=AGENS,
syndromes.name=syndromes.name,
dates.var=ANKOMSTDATUM,
date.format = "%d/%m/%Y",
min.date=new.data.start,
max.date=new.data.end,
data=CD.syndrome)
CD.syndrome.pos=CD.syndrome[CD.syndrome$PÅVISAD=="Påvisad",]
a.pos=raw_to_syndromicW(id=INSÄNTMATERIAL,
syndromes.var=AGENS,
syndromes.name=syndromes.name,
dates.var=ANKOMSTDATUM,
date.format = "%d/%m/%Y",
min.date=new.data.start,
max.date=new.data.end,
data=CD.syndrome.pos)
svaga.new.all <- rbindlist(list(as.data.frame(svaga.object[[sp.position]][[s]][,,1]),
as.data.frame(a.all@observed)),
fill=TRUE)
svaga.new.pos <- rbindlist(list(as.data.frame(svaga.object[[sp.position]][[s]][,,2]),
as.data.frame(a.pos@observed)),
fill=TRUE)
svaga.object[[sp.position]][[s]] <- abind(svaga.new.all,svaga.new.pos,along=3)
}else{
#svaga.object[[sp.position]][[s]]
svaga.object.ends <- ISOweek2date(weekly.object[[sp.position]]@dates[dim(svaga.object[[sp.position]][[s]])[1],1])+6
CD.syndrome$AGENS<- str_replace(CD.syndrome$AGENS, "\\(\\+\\)", "")
syndromes.name=unique(c(colnames(svaga.object[[sp.position]][[s]]),CD.syndrome$AGENS))
a.all=raw_to_syndromicW(id=INSÄNTMATERIAL,
syndromes.var=AGENS,
syndromes.name=syndromes.name,
dates.var=ANKOMSTDATUM,
date.format = "%d/%m/%Y",
min.date=svaga.object.ends+1,
max.date=new.data.end,
data=CD.syndrome)
CD.syndrome.pos=CD.syndrome[CD.syndrome$PÅVISAD=="Påvisad",]
a.pos=raw_to_syndromicW(id=INSÄNTMATERIAL,
syndromes.var=AGENS,
syndromes.name=syndromes.name,
dates.var=ANKOMSTDATUM,
date.format = "%d/%m/%Y",
min.date=svaga.object.ends+1,
max.date=new.data.end,
data=CD.syndrome.pos)
svaga.new.all <- rbindlist(list(as.data.frame(svaga.object[[sp.position]][[s]][,,1]),
as.data.frame(a.all@observed)),
fill=TRUE)
svaga.new.pos <- rbindlist(list(as.data.frame(svaga.object[[sp.position]][[s]][,,2]),
as.data.frame(a.pos@observed)),
fill=TRUE)
svaga.object[[sp.position]][[s]] <- abind(svaga.new.all,svaga.new.pos,along=3)
}
}
}
}