Account for Data that is Missing Due to Nesting

This function adds entries for variables that are only missing due to nesting - rather than truely being missing. Variables that are adjusted are: cause of death, date of death, starting treatment date, treatment end date, year of BCG vaccination, and time since entry.

account_for_nested_missing(df)

Arguments

df	A dataframe containing cleaned ETS data as produced by tbinenglanddataclean.

Value

A dataframe that has nested missingness corrected for a subset of variables

Examples

## Code
account_for_nested_missing
#> function (df) 
#> {
#>     caserepdate <- NULL
#>     year <- NULL
#>     sex <- NULL
#>     age <- NULL
#>     phec <- NULL
#>     occat <- NULL
#>     ethgrp <- NULL
#>     ukborn <- NULL
#>     timesinceent <- NULL
#>     symptonset <- NULL
#>     datediag <- NULL
#>     startedtreat <- NULL
#>     starttreatdate <- NULL
#>     txenddate <- NULL
#>     pulmextrapulm <- NULL
#>     culture <- NULL
#>     sputsmear <- NULL
#>     anyres <- NULL
#>     prevdiag <- NULL
#>     bcgvacc <- NULL
#>     bcgvaccyr <- NULL
#>     overalloutcome <- NULL
#>     tomdeathrelat <- NULL
#>     dateofdeath <- NULL
#>     txenddate <- NULL
#>     natquintile <- NULL
#>     filt_df <- df %>% select(caserepdate, year, sex, age, phec, 
#>         occat, ethgrp, ukborn, timesinceent, symptonset, datediag, 
#>         startedtreat, starttreatdate, txenddate, pulmextrapulm, 
#>         culture, sputsmear, anyres, prevdiag, bcgvacc, bcgvaccyr, 
#>         overalloutcome, tomdeathrelat, dateofdeath, txenddate, 
#>         natquintile)
#>     nest_filt_df <- filt_df %>% mutate(tomdeathrelat = ifelse(overalloutcome == 
#>         "Died", tomdeathrelat %>% as.character, overalloutcome %>% 
#>         as.character) %>% factor) %>% mutate(dateofdeath = ifelse(overalloutcome == 
#>         "Died", dateofdeath, 1e+05)) %>% mutate(starttreatdate = ifelse(startedtreat == 
#>         "Started", starttreatdate, startedtreat)) %>% mutate(txenddate = ifelse(overalloutcome == 
#>         "Treatment completed", txenddate, overalloutcome)) %>% 
#>         mutate(bcgvaccyr = ifelse(bcgvacc == "Yes", bcgvaccyr %>% 
#>             as.character, bcgvacc) %>% factor) %>% mutate(dateofdeath = ifelse(overalloutcome %in% 
#>         "Died", dateofdeath, "N/A") %>% as.factor) %>% mutate(timesinceent = ifelse(ukborn %in% 
#>         "UK born", "N/A", timesinceent))
#> }
#> <bytecode: 0x55630bdb4050>
#> <environment: namespace:ETSMissing>