# Age distributions

#### Caroline Ring

#### 2017-07-14

    library(httk)
    library(survey)
    #> Loading required package: grid
    #> Loading required package: Matrix
    #> Loading required package: survival
    #>
    #> Attaching package: 'survey'
    #> The following object is masked from 'package:graphics':
    #>
    #>     dotchart
    library(data.table)
    library(ggplot2)

Get lists of all possible race/ethnicity categories and gender categories.

    all.reth <- levels(nhanes_mec_svy$variables[, ridreth1])
    all.gendr <- levels(nhanes_mec_svy$variables[, riagendr])

Get smoothed density estimates for age in months, by cycle for each gender and race/ethnicity, using the `survey::svysmooth` function.

    grct <- 1
    smth.year <- vector(mode="list", length=10)
    for (gendr in all.gendr){
      for (r in all.reth){
        grsub <- subset(nhanes_mec_svy, riagendr==gendr & ridreth1==r & !is.na(ridexagm))
        smth.list <- vector(mode="list", length=3)
        ct <- 1
        for (y in grsub$variables[, levels(sddsrvyr)]){ #by cycle
          ysub <- subset(grsub, sddsrvyr==y)
          tmp <- svysmooth(~ridexagm,
                           ysub,
                           ngrid=960)$ridexagm
          smth.list[[ct]] <- c(tmp, list(year=rep(y, length(tmp$x))))
          ct <- ct + 1
        }
        tmp.year <- rbindlist(lapply(smth.list, as.data.table))
        tmp.year[, gender:=gendr]
        tmp.year[, reth:=r]
        smth.year[[grct]] <- tmp.year
        grct <- grct+1
      }
    }
    #bind with smoothed data for all cycles combined
    smth.all <- rbind(rbindlist(smth.year),
                      age_dist_smooth[, smth[[1]], by=.(gender, reth)])
    smth.all[, gender:=factor(gender, levels=all.gendr)]
    smth.all[, reth:=factor(reth, levels=all.reth)]

Plot smoothed density estimates of age, by cycle and lumped.

    #Plot
    colvect <- c(RColorBrewer::brewer.pal(3, "Set2"), "black")
    names(colvect) <- c('NHANES 2007-2008',
                        'NHANES 2009-2010',
                        'NHANES 2011-2012',
                        'Overall')
    p <- ggplot(data=smth.all) +
      geom_line(aes(x=x, y=y, color=year)) +
      scale_color_manual(values=colvect) +
      labs(x='Age, months',
           y='Smoothed density estimate') +
      facet_grid(reth~gender)+
      theme_bw() +
      theme(strip.background=element_blank())
    print(p)
    ggsave(filename="pdf_figures/age_smooth.pdf",
           plot=p,
           width=8.5,
           height=11)