R/hei_2010_PerPerson_ssum.R

In yikeshu0611/nhanesR: Tools for "NHANES" Database

hei_2010_PerPerson_ssum <- function(years,
                                    dietary='tot',
                                    varLabel=FALSE,
                                    energy=TRUE,
                                    component=TRUE,
                                    density=FALSE){
    if (dietary=='iff') join <- c('seqn','iline') else join <- 'seqn'

    # day=1
    fped <- fped_read(years = years,day = 1,dietary = dietary,version = 2010)
    tsv <- nhs_tsv(sprintf('drx%s|dr1%s',dietary,dietary),years = years,cat = FALSE)
    dt <- nhs_read(tsv,'wtdr4yr','wtdrd1',
                   "drxtkcal,drxikcal,dr1tkcal,dr2tkcal,dr1ikcal,dr2ikcal:kcal",
                   "drxtsfat,drxisfat,dr1tsfat,dr2tsfat,dr1isfat,dr2isfat:sfat",
                   "drxtalco,drxialco,dr1talco,dr2talco,dr1ialco,dr2ialco:alco",
                   "drdtsodi,drdisodi,dr1tsodi,dr1isodi,dr2tsodi,dr2isodi:sodi",
                   "drxtmfat,drximfat,dr1tmfat,dr2tmfat,dr1imfat,dr2imfat:mfat",
                   "drxtpfat,drxipfat,dr1tpfat,dr2tpfat,dr1ipfat,dr2ipfat:pfat",
                   codebook = FALSE,varLabel = FALSE,cat = FALSE)
    colnames(dt) <- rename_line(colnames(dt))
    colnames(dt) <- rename_fdcd(colnames(dt))
    dt <- drop_col(dt,'fdcd')

    dt$monopoly <- dt$mfat + dt$pfat
    maxalcgr <- 13*(dt$kcal/1000)
    dt$exalccal <- ifelse(dt$alco <= maxalcgr,0,7*( dt$alco - maxalcgr))
    indat <- dplyr::inner_join(dt,fped,join)
    indat$emptycal10 <- indat$addsugc + indat$solfatc + indat$exalccal
    indat1 <- indat

    # day=2
    fped <- fped_read(years = years,day = 2,dietary = dietary,version = 2010)
    tsv <- nhs_tsv(sprintf('drx%s|dr2%s',dietary,dietary),years = years,cat = FALSE)
    dt <- nhs_read(tsv,
                   "drxtkcal,drxikcal,dr1tkcal,dr2tkcal,dr1ikcal,dr2ikcal:kcal",
                   "drxtsfat,drxisfat,dr1tsfat,dr2tsfat,dr1isfat,dr2isfat:sfat",
                   "drxtalco,drxialco,dr1talco,dr2talco,dr1ialco,dr2ialco:alco",
                   "drdtsodi,drdisodi,dr1tsodi,dr1isodi,dr2tsodi,dr2isodi:sodi",
                   "drxtmfat,drximfat,dr1tmfat,dr2tmfat,dr1imfat,dr2imfat:mfat",
                   "drxtpfat,drxipfat,dr1tpfat,dr2tpfat,dr1ipfat,dr2ipfat:pfat",
                   codebook = FALSE,varLabel = FALSE,cat = FALSE,Year = FALSE)
    colnames(dt) <- rename_line(colnames(dt))
    colnames(dt) <- rename_fdcd(colnames(dt))
    dt <- drop_col(dt,'fdcd')

    dt$monopoly <- dt$mfat + dt$pfat
    maxalcgr <- 13*(dt$kcal/1000)
    dt$exalccal <- ifelse(dt$alco <= maxalcgr,0,7*( dt$alco - maxalcgr))
    indat <- dplyr::inner_join(dt,fped,join)
    indat$emptycal10 <- indat$addsugc + indat$solfatc + indat$exalccal
    indat2 <- indat


    indat <- dplyr::inner_join(indat1,indat2,join)

    if (!is.null(seqn)) indat <- indat[indat$seqn %in% seqn,]

    choice <- colnames(indat2)[-c(1:length(join))]
    for (i in choice) {
        which <- which(colnames(indat) %in% paste0(i,c('.x','.y')))
        indat$last <- rowSums(indat[,which],na.rm = TRUE)
        indat <- indat[,-which]
        colnames(indat)[ncol(indat)] <- i
    }
    colnames(indat) |> do::increase()
    ck <- indat$Year %in% c('1999-2000','2001-2002')
    indat[ck,choice] <- indat[ck,choice]/2 # these four years is the same


    # leg2010a
    afterleg <- leg2010a(indat = indat,
                         kcal = 'kcal',
                         allmeat ='pf_total',
                         seaplant = 'seaplant',
                         v_total = 'v_total',
                         v_drkgr = 'v_drkgr',
                         legumes = 'v_legumes')
    hei_2010(
        indat = afterleg,
        kcal='kcal',
        lv_total='legume_added_v_total',
        lbeangrn='legume_added_beangrn',
        f_total='f_total',
        wholefrt='f_whole',
        g_whl='g_whole',
        d_total='d_total',
        lallmeat='legume_added_allmeat',
        lseaplant='legume_added_seaplant',
        monopoly='monopoly',
        sfat='sfat',
        sodi='sodi',
        g_nwhl='g_refined',
        emptycal10='emptycal10',
        varLabel = varLabel,
        energy = energy,
        component = component,
        density = density,
        join=join
    )
}