R/read_WHS_2009.R
In STAPM/hseclean: Health Survey Data Wrangling
Defines functions
read_WHS_2009
Documented in
read_WHS_2009
#' Read the Welsh Health Survey 2009 \lifecycle{maturing}
#'
#' Reads and does basic cleaning on the Welsh Health Survey 2009.
#'
#' @template read-data-description
#'
#' @template read-data-args
#'
#' @importFrom data.table :=
#'
#' @return Returns a data table.
#'
#' @export
#'
#' @examples
#'
#' \dontrun{
#'
#'
#' }
read_WHS_2009 <- function(
root = c("X:/", "/Volumes/Shared/")[1],
file = "HAR_PR/PR/Consumption_TA/HSE/Welsh Health Survey (WHS)/2009/UKDA-6589-tab/tab/welsh_health_09_adult2_archiving.tab"
) {
data <- data.table::fread(
paste0(root, file),
na.strings = c("NA", "", "-1", "-2", "-6", "-7", "-8", "-9", "-90", "-90.0", "-99", "N/A"))
data.table::setnames(data, names(data), tolower(names(data)))
alc_vars <- Hmisc::Cs(
#### alc_drink_now_allages
nodrink, freqalc, freqalc3, everdr,
# last 7 days
alcdrink, alcdrbi, alcdrbi0,
alcoday, #heaviest day
# normal strength beer
normpint, normlcan, normscan, # amount - pint / large cans&bottles / small cans&bottles
npinuni, nlcauni, nscauni, # units (derived)
# strong beer
strpint, strlcan, strscan,
spinuni, slcauni, sscauni,
# wine
winelar, winesta, winesma, winebot, # amount - large glass, standard glass, small glass, bottles
wluni, wstuni, wsmuni, wbuni, # units (derived)
# spirits
spirit, # amount
# sherry/fortified wine
fwine, # amount
# RTDs
alcopops,
alcouni,
## other alcohlic drinks
# (1)
oth1gla, oth1pin, oth1lcan, oth1scan,
# (2)
oth2gla, oth2pin, oth2lcan, oth2scan,
## derived units on heaviest day
units, units0,
alc4, # Level of maximal daily alc cosumption
alc5, # Maximum drank last week
alcagbi, # Max daily consumption - above guidelines [binary]
alcbibi # Max daily consumption - binge [binary]
)
#
# smk_vars <- tolower(Hmisc::Cs(smok, smokec, smoked, smokee, smokstat, smokex,
# smouthom, smoutoth, smokout,
# sminhome, sminoph, smincar, sminothe,
# smokin, triedgup, trygupbi, compsm, likegup, likgupbi,
# gupnum, guphlthp, guphtlhg, guprelil, gupfam, gupfin, gupchi, gupban, gupoth,
# expouth, expoutot, expinh, expinhot, expincar, expinoth, exouall, exounam, exinall, exinnsm, expoall, exponsm,
# ecigevbi, ecignbi, ecigesmo, ecigeex, ecigenev, ecigenon, ecignsmo, ecignex, ecignnev, ecignnon,
# stpsmk, stpsmk1m, stpsmk1y))
# smk_vars <- tolower(Hmisc::Cs(Smoke, SmAge, Dvsmokec, Dvsmokstat))
smk_vars <- tolower(Hmisc::Cs(smok, smokec, smoked, smokee, smokstat, smokex))
# SmAge only measured in some years
# key smoking variables are
# Smoke Smoking - Which one of these best describes you -99 Refused
# -98 Interview terminated early
# -88 Not selected in sub-sample
# -9 Don't Know (SPONTANEOUS ONLY)
# -8 Question not asked due to routing
# 1 I smoke daily
# 2 I smoke occasionally but not every day
# 3 I used to smoke daily but do not smoke at all now
# 4 I used to smoke occasionally but do not smoke at all now
# 5 I have never smoked
# SmAge Smoking - How old were you when you started smoking? -99 Refused
# -98 Interview terminated early
# -88 Not selected in sub-sample
# -9 Don't Know (SPONTANEOUS ONLY)
# -8 Question not asked due to routing
# Dvsmokec Derived variable - Currently smoke either daily or occasionally -99 Refused
# -98 Interview terminated early
# -88 Not selected in sub-sample
# -9 Don't Know (SPONTANEOUS ONLY)
# -8 Question not asked due to routing
# 0 No
# 1 Yes
#
# Dvsmokstat Derived variable - Smoking status -99 Refused
# -98 Interview terminated early
# -88 Not selected in sub-sample
# -9 Don't Know (SPONTANEOUS ONLY)
# -8 Question not asked due to routing
# 1 Smoker
# 2 Ex-smoker
# 3 Never smoked
#
# health_vars <- Hmisc::Cs(dvillchap1, dvillchap2, dvillchap3, dvillchap4, dvillchap5,
# dvillchap6, dvillchap7, dvillchap8, dvillchap9, dvillchap10,
# dvillchap11, dvillchap12, dvillchap13, dvillchap14, dvillchap15)
health_vars <- Hmisc::Cs(llti, lltibi,
llticd1, llticd2, llticd3, llticd4,
lltich1, lltich2, lltich3, lltich4, mental)
### there's also a comprehensive set of binary variables and whether they have received treatment for it,
### as well as SF12 and SF36 scores
other_vars <- Hmisc::Cs(
# weight, height and bmi
htcm, wtkg, bmi2,
tenure3,
#psu,
#strata, # stratification unit
# sampleadultweight,
archhsn, archpsn, ## scrambled household and person serials
wt_hhold, wt_adult, ## Household and Individual NR weight
#
#incresp,
# Education
#educend,
qualhi, # Highest educational qualification - revised 2008 [derived]
# Occupation
nssec8, nssec5, nssec3,
work, # work status
employ, # whether in employment
ecstat3, # econ status 3 class
ecstat, # econ status
# # Family
# marstat,
hhchild,
# demographic
age5yrm, # derived 5 year age cat with 75+ merged
region,
# dvethnicity,
# dvwimdovr5,
sex)
names <- c(other_vars, health_vars, alc_vars, smk_vars)
names <- tolower(names)
data <- data[ , names, with = F]
# data.table::setnames(data,
#
# c(#"dvwimdovr5","dvethnicity","gender",
#
# ##### alcohol weekly consumption vars
# "dnfreq","dnev","dnocc",
#
# # frequency of drink type over 12 months
# "dnoftbr","dnoftstbr","dnoftspir","dnoftsher","dnoftwine","dnoftapop",
# # normal strength beer
# "dnubrmeas1", "dnubrmeas2", "dnubrmeas3", "dnubrmeas4",
# "dnubrhalf", "dnubrsmc", "dnubrlgc", "dnubrbot",
# # strong beer
# "dnustbrmeas1", "dnustbrmeas2", "dnustbrmeas3", "dnustbrmeas4",
# "dnustbrhalf", "dnustbrsmc", "dnustbrlgc", "dnustbrbot",
# # wine
# "dnuwinemeas", "dnuwine",
# # sherry
# "dnusher",
# # spirits
# "dnuspir",
# # RTDs
# "dnapopmeas1", "dnapopmeas2", "dnapopmeas3",
# "dnuapopsmc", "dnuapopstbot", "dnuapoplgbot",
#
# ##### alcohol binge vars
# "dn7dn", "dnsame", "dn7dmost",
# "dntype1", "dntype2", "dntype3", "dntype4", "dntype5", "dntype6",
#
# # normal strength beer
# "dnbrhalf", "dnbrsmc", "dnbrlgc", "dnbrbot",
# # strong beer
# "dnstbrhalf", "dnstbrsmc", "dnstbrlgc", "dnstbrbot",
# # wine
# "dnwinebot", "dnwinelgg", "dnwinestg", "dnwinesmg",
# # sherry
# "dnsher",
# # spirits
# "dnspir",
# # RTDs
# "dnaplgbot", "dnapstbot", "dnapsmc",
#
# #### derived variable for weekly units
# "dvunitswk0",
#
#
# ## health vars
# "dvillchap1", "dvillchap2", "dvillchap3", "dvillchap4", "dvillchap5",
# "dvillchap6", "dvillchap7", "dvillchap8", "dvillchap9", "dvillchap10",
# "dvillchap11", "dvillchap12", "dvillchap13", "dvillchap14", "dvillchap15"),
#
# c(#"wimd","dvethnicity","sex",
#
# ##### alcohol weekly consumption vars
# "dnoft","dnevr","dnany",
#
# # frequency of drink type over 12 months
# "nbeer","sbeer","spirits","sherry","wine","pops",
# # normal strength beer
# "nbeerm1", "nbeerm2", "nbeerm3", "nbeerm4",
# "nbeerq1", "nbeerq2", "nbeerq3", "nbeerq4",
# # strong beer
# "sbeerm1", "sbeerm2", "sbeerm3", "sbeerm4",
# "sbeerq1", "sbeerq2", "sbeerq3", "sbeerq4",
# # wine
# "bwineq2", "wineq",
# # sherry
# "sherryq",
# # spirits
# "spiritsq",
# # RTDs
# "popsly11", "popsly12", "popsly13",
# "popsq111", "popsq112", "popsq113",
#
# ##### alcohol binge vars
# "d7many", "drnksame", "whichday",
# "d7typ1", "d7typ2", "d7typ3", "d7typ4", "d7typ5", "d7typ6",
#
# # normal strength beer
# "nberqhp7", "nberqsm7", "nberqlg7", "nberqbt7",
# # strong beer
# "sberqhp7", "sberqsm7", "sberqlg7", "sberqbt7",
# # wine
# "wbtlgz", "wgls250ml", "wgls175ml", "wgls125ml",
# # sherry
# "sherqgs7",
# # spirits
# "spirqme7",
# # RTDs
# "popsqlg7", "popsqstb7", "popsqsm7",
#
# #### derived variable for weekly units
# "dv_wk_units",
#
# ## health vars
# "compm1", "compm2", "compm3", "compm4", "compm5",
# "compm6", "compm7", "compm8", "compm9", "compm10",
# "compm11", "compm12", "compm13", "compm14", "compm15")
# )
# Tidy survey weights and only keep the sub-sample that answered smoking
# and drinking related questions (in 2016/17 this is all respondents, but
# only a subsample in future years)
data <- data[!is.na(wt_adult)]
setnames(data, "wt_adult", "wt_int")
#data[age < 16, wt_int := NA]
# Set PSU and cluster
#data[ , psu := paste0("2009_", 1)]
#data[ , cluster := paste0("2009_", 1)]
data[ , year := 2009]
data[ , country := "Wales"]
return(data[])
}
STAPM/hseclean documentation built on June 9, 2025, 4:50 a.m.
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Defines functions read_WHS_2009
Documented in read_WHS_2009
#' Read the Welsh Health Survey 2009 \lifecycle{maturing}
#'
#' Reads and does basic cleaning on the Welsh Health Survey 2009.
#'
#' @template read-data-description
#'
#' @template read-data-args
#'
#' @importFrom data.table :=
#'
#' @return Returns a data table.
#'
#' @export
#'
#' @examples
#'
#' \dontrun{
#'
#'
#' }
read_WHS_2009 <- function(
root = c("X:/", "/Volumes/Shared/")[1],
file = "HAR_PR/PR/Consumption_TA/HSE/Welsh Health Survey (WHS)/2009/UKDA-6589-tab/tab/welsh_health_09_adult2_archiving.tab"
) {
data <- data.table::fread(
paste0(root, file),
na.strings = c("NA", "", "-1", "-2", "-6", "-7", "-8", "-9", "-90", "-90.0", "-99", "N/A"))
data.table::setnames(data, names(data), tolower(names(data)))
alc_vars <- Hmisc::Cs(
#### alc_drink_now_allages
nodrink, freqalc, freqalc3, everdr,
# last 7 days
alcdrink, alcdrbi, alcdrbi0,
alcoday, #heaviest day
# normal strength beer
normpint, normlcan, normscan, # amount - pint / large cans&bottles / small cans&bottles
npinuni, nlcauni, nscauni, # units (derived)
# strong beer
strpint, strlcan, strscan,
spinuni, slcauni, sscauni,
# wine
winelar, winesta, winesma, winebot, # amount - large glass, standard glass, small glass, bottles
wluni, wstuni, wsmuni, wbuni, # units (derived)
# spirits
spirit, # amount
# sherry/fortified wine
fwine, # amount
# RTDs
alcopops,
alcouni,
## other alcohlic drinks
# (1)
oth1gla, oth1pin, oth1lcan, oth1scan,
# (2)
oth2gla, oth2pin, oth2lcan, oth2scan,
## derived units on heaviest day
units, units0,
alc4, # Level of maximal daily alc cosumption
alc5, # Maximum drank last week
alcagbi, # Max daily consumption - above guidelines [binary]
alcbibi # Max daily consumption - binge [binary]
)
#
# smk_vars <- tolower(Hmisc::Cs(smok, smokec, smoked, smokee, smokstat, smokex,
# smouthom, smoutoth, smokout,
# sminhome, sminoph, smincar, sminothe,
# smokin, triedgup, trygupbi, compsm, likegup, likgupbi,
# gupnum, guphlthp, guphtlhg, guprelil, gupfam, gupfin, gupchi, gupban, gupoth,
# expouth, expoutot, expinh, expinhot, expincar, expinoth, exouall, exounam, exinall, exinnsm, expoall, exponsm,
# ecigevbi, ecignbi, ecigesmo, ecigeex, ecigenev, ecigenon, ecignsmo, ecignex, ecignnev, ecignnon,
# stpsmk, stpsmk1m, stpsmk1y))
# smk_vars <- tolower(Hmisc::Cs(Smoke, SmAge, Dvsmokec, Dvsmokstat))
smk_vars <- tolower(Hmisc::Cs(smok, smokec, smoked, smokee, smokstat, smokex))
# SmAge only measured in some years
# key smoking variables are
# Smoke Smoking - Which one of these best describes you -99 Refused
# -98 Interview terminated early
# -88 Not selected in sub-sample
# -9 Don't Know (SPONTANEOUS ONLY)
# -8 Question not asked due to routing
# 1 I smoke daily
# 2 I smoke occasionally but not every day
# 3 I used to smoke daily but do not smoke at all now
# 4 I used to smoke occasionally but do not smoke at all now
# 5 I have never smoked
# SmAge Smoking - How old were you when you started smoking? -99 Refused
# -98 Interview terminated early
# -88 Not selected in sub-sample
# -9 Don't Know (SPONTANEOUS ONLY)
# -8 Question not asked due to routing
# Dvsmokec Derived variable - Currently smoke either daily or occasionally -99 Refused
# -98 Interview terminated early
# -88 Not selected in sub-sample
# -9 Don't Know (SPONTANEOUS ONLY)
# -8 Question not asked due to routing
# 0 No
# 1 Yes
#
# Dvsmokstat Derived variable - Smoking status -99 Refused
# -98 Interview terminated early
# -88 Not selected in sub-sample
# -9 Don't Know (SPONTANEOUS ONLY)
# -8 Question not asked due to routing
# 1 Smoker
# 2 Ex-smoker
# 3 Never smoked
#
# health_vars <- Hmisc::Cs(dvillchap1, dvillchap2, dvillchap3, dvillchap4, dvillchap5,
# dvillchap6, dvillchap7, dvillchap8, dvillchap9, dvillchap10,
# dvillchap11, dvillchap12, dvillchap13, dvillchap14, dvillchap15)
health_vars <- Hmisc::Cs(llti, lltibi,
llticd1, llticd2, llticd3, llticd4,
lltich1, lltich2, lltich3, lltich4, mental)
### there's also a comprehensive set of binary variables and whether they have received treatment for it,
### as well as SF12 and SF36 scores
other_vars <- Hmisc::Cs(
# weight, height and bmi
htcm, wtkg, bmi2,
tenure3,
#psu,
#strata, # stratification unit
# sampleadultweight,
archhsn, archpsn, ## scrambled household and person serials
wt_hhold, wt_adult, ## Household and Individual NR weight
#
#incresp,
# Education
#educend,
qualhi, # Highest educational qualification - revised 2008 [derived]
# Occupation
nssec8, nssec5, nssec3,
work, # work status
employ, # whether in employment
ecstat3, # econ status 3 class
ecstat, # econ status
# # Family
# marstat,
hhchild,
# demographic
age5yrm, # derived 5 year age cat with 75+ merged
region,
# dvethnicity,
# dvwimdovr5,
sex)
names <- c(other_vars, health_vars, alc_vars, smk_vars)
names <- tolower(names)
data <- data[ , names, with = F]
# data.table::setnames(data,
#
# c(#"dvwimdovr5","dvethnicity","gender",
#
# ##### alcohol weekly consumption vars
# "dnfreq","dnev","dnocc",
#
# # frequency of drink type over 12 months
# "dnoftbr","dnoftstbr","dnoftspir","dnoftsher","dnoftwine","dnoftapop",
# # normal strength beer
# "dnubrmeas1", "dnubrmeas2", "dnubrmeas3", "dnubrmeas4",
# "dnubrhalf", "dnubrsmc", "dnubrlgc", "dnubrbot",
# # strong beer
# "dnustbrmeas1", "dnustbrmeas2", "dnustbrmeas3", "dnustbrmeas4",
# "dnustbrhalf", "dnustbrsmc", "dnustbrlgc", "dnustbrbot",
# # wine
# "dnuwinemeas", "dnuwine",
# # sherry
# "dnusher",
# # spirits
# "dnuspir",
# # RTDs
# "dnapopmeas1", "dnapopmeas2", "dnapopmeas3",
# "dnuapopsmc", "dnuapopstbot", "dnuapoplgbot",
#
# ##### alcohol binge vars
# "dn7dn", "dnsame", "dn7dmost",
# "dntype1", "dntype2", "dntype3", "dntype4", "dntype5", "dntype6",
#
# # normal strength beer
# "dnbrhalf", "dnbrsmc", "dnbrlgc", "dnbrbot",
# # strong beer
# "dnstbrhalf", "dnstbrsmc", "dnstbrlgc", "dnstbrbot",
# # wine
# "dnwinebot", "dnwinelgg", "dnwinestg", "dnwinesmg",
# # sherry
# "dnsher",
# # spirits
# "dnspir",
# # RTDs
# "dnaplgbot", "dnapstbot", "dnapsmc",
#
# #### derived variable for weekly units
# "dvunitswk0",
#
#
# ## health vars
# "dvillchap1", "dvillchap2", "dvillchap3", "dvillchap4", "dvillchap5",
# "dvillchap6", "dvillchap7", "dvillchap8", "dvillchap9", "dvillchap10",
# "dvillchap11", "dvillchap12", "dvillchap13", "dvillchap14", "dvillchap15"),
#
# c(#"wimd","dvethnicity","sex",
#
# ##### alcohol weekly consumption vars
# "dnoft","dnevr","dnany",
#
# # frequency of drink type over 12 months
# "nbeer","sbeer","spirits","sherry","wine","pops",
# # normal strength beer
# "nbeerm1", "nbeerm2", "nbeerm3", "nbeerm4",
# "nbeerq1", "nbeerq2", "nbeerq3", "nbeerq4",
# # strong beer
# "sbeerm1", "sbeerm2", "sbeerm3", "sbeerm4",
# "sbeerq1", "sbeerq2", "sbeerq3", "sbeerq4",
# # wine
# "bwineq2", "wineq",
# # sherry
# "sherryq",
# # spirits
# "spiritsq",
# # RTDs
# "popsly11", "popsly12", "popsly13",
# "popsq111", "popsq112", "popsq113",
#
# ##### alcohol binge vars
# "d7many", "drnksame", "whichday",
# "d7typ1", "d7typ2", "d7typ3", "d7typ4", "d7typ5", "d7typ6",
#
# # normal strength beer
# "nberqhp7", "nberqsm7", "nberqlg7", "nberqbt7",
# # strong beer
# "sberqhp7", "sberqsm7", "sberqlg7", "sberqbt7",
# # wine
# "wbtlgz", "wgls250ml", "wgls175ml", "wgls125ml",
# # sherry
# "sherqgs7",
# # spirits
# "spirqme7",
# # RTDs
# "popsqlg7", "popsqstb7", "popsqsm7",
#
# #### derived variable for weekly units
# "dv_wk_units",
#
# ## health vars
# "compm1", "compm2", "compm3", "compm4", "compm5",
# "compm6", "compm7", "compm8", "compm9", "compm10",
# "compm11", "compm12", "compm13", "compm14", "compm15")
# )
# Tidy survey weights and only keep the sub-sample that answered smoking
# and drinking related questions (in 2016/17 this is all respondents, but
# only a subsample in future years)
data <- data[!is.na(wt_adult)]
setnames(data, "wt_adult", "wt_int")
#data[age < 16, wt_int := NA]
# Set PSU and cluster
#data[ , psu := paste0("2009_", 1)]
#data[ , cluster := paste0("2009_", 1)]
data[ , year := 2009]
data[ , country := "Wales"]
return(data[])
}
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