library(tidyverse)
df_hptcog <-
readxl::read_xlsx("Diminish Structure MASTER FILE.xlsx") %>%
janitor::clean_names() %>%
rename(
sex = a1_gender,
ageyrs = a3_how_old_are_you,
resid = a6_please_indicate_the_location_of_your_residence,
educ = a8_what_is_the_highest_level_of_education_you_have_completed,
income = n2_on_average_what_is_the_monthly_income_for_the_entire_household_choose_one,
currently_smoke = b1_do_you_currently_smoke_any_tobacco_products_such_as_cigarettes_cigars_or_pipes_choose_one_if_no_go_to_b3,
past_smoked = b3_have_you_smoked_in_the_past_choose_one,
nhis = a4_do_you_have_a_valid_national_health_insurance_scheme_card,
dm = x4_diabetes_mellitus,
alcohol = c1_do_you_currently_use_alcoholic_beverage_such_as_beer_wine_spirits_palm_wine_or_akpeteshie_choose_one,
salt_add = d5_in_a_typical_week_how_often_is_salt_added_to_food_that_has_already_been_prepared_please_circle_the_correct_response,
physical_activity = e1_do_you_frequently_perform_physical_activities_that_cause_a_small_increase_in_breathing_or_make_your_heart_rate_go_up_such_as_fast_brisk_walking_jogging_bicycling_or_other_please_circle_the_correct_response,
dura_exercise = e2_how_much_time_in_minutes_do_you_spend_walking_fast_briskly_jogging_bicycling_or_any_other_form_of_exercise_on_a_typical_day,
fruits_per_week = d1_in_a_typical_week_on_how_many_days_in_the_past_week_have_you_had_fruits_if_zero_go_to_next_question_d4,
daily_fruits = d2_how_many_servings_of_fruit_do_you_eat_on_one_of_those_days ,
days_veges = d3_in_a_typical_week_on_how_many_days_in_the_past_week_have_you_had_vegetables,
daily_veges = d4_how_many_servings_of_vegetables_do_you_eat_on_one_of_those_days,
heart_failure = x2b_heart_failure_swelling_in_your_both_legs_shortness_of_breath_and_shortness_of_breath_when_lying_down,
stroke = x3_stroke_weakness_on_one_side_of_the_body,
dura_hpt = f1_how_many_months_years_ago_were_you_first_told_you_had_high_blood_pressure_months_years,
med_1 = x1_medication,
med_2 = x2_medication,
med_3 = x3_medication,
med_4 = x4_medication,
med_5 = x5_medication,
med_6 = x6_medication,
med_7 = x7_medication,
med_8 = x1_other_medication,
med_9 = x2_other_medication,
med_10 = x3_other_medication,
sbp1 = x1_systolic_blood_pressure_mm_hg,
sbp2 = x2_systolic_blood_pressure_mm_hg,
sbp3 = x3_systolic_blood_pressure_mm_hg,
sbp4 = x4_systolic_blood_pressure_mm_hg,
sbp5 = x5_systolic_blood_pressure_mm_hg,
sbp6 = x6_systolic_blood_pressure_mm_hg,
sbp7 = x7_systolic_blood_pressure_mm_hg,
sbp8 = x8_systolic_blood_pressure_mm_hg,
sbp9 = x9_systolic_blood_pressure_mm_hg,
sbp10 = x10_systolic,
dbp1 = x1_diastolic_blood_pressure_mm_hg,
dbp2 = x2_diastolic_blood_pressure_mm_hg,
dbp3 = x3_diastolic_blood_pressure_mm_hg,
dbp4 = x4_diastolic_blood_pressure_mm_hg,
dbp5 = x5_diastolic_blood_pressure_mm_hg,
dbp6 = x6_diastolic_blood_pressure_mm_hg,
dbp7 = x7_diastolic,
dbp8 = x8_diastolic_blood_pressure_mm_hg,
dbp9 = x9_diastolic_blood_pressure_mm_hg,
dbp10 = x10_diastolic
) %>%
mutate(
moca_tertile = gtools::quantcut(
moca_score,
q = 3,
labels = c("Lower Tercile", "Middle Tercile", "Upper Tercile")) %>%
factor(levels = c("Upper Tercile", "Middle Tercile", "Lower Tercile")
),
sex = factor(sex, levels = c("Male", "Female")),
resid = factor(resid, levels = c("Rural","Peri urban", "Urban")),
educ2 = fct_recode(
educ,
None = "Less than primary school",
None = "No formal schooling",
None = "Non-formal education",
Primary = "Primary school completed",
Secondary = "Secondary school completed",
Secondary = "High school completed",
Tertiary = "Post graduate degree",
Tertiary = "College /University completed") %>%
factor(
levels = c("None", "Primary", "Secondary", "Tertiary"),
ordered = FALSE),
income2 = case_when(
income == "90-100GHc" ~ "<100 GHc",
income == "<90 GHc" ~ "<100 GHc",
income == "100-500GHc" ~ "100-500GHc",
income == "500-1000 GHc" ~ "500-1000 GHc",
income == ">1000 GHc" ~ ">1000 GHc",
TRUE ~ "Unknown"
) %>%
factor(
levels = c("<100 GHc", "100-500GHc","500-1000 GHc",
">1000 GHc", "Unknown")
),
dm2 = case_when(dm == "Yes" ~ "Yes", dm == "No" ~ "No"),
ever_smoked = case_when(
currently_smoke == "Yes" | past_smoked == "Yes" ~ "Yes",
TRUE ~ "No"),
salt_add2 = case_when(
salt_add %in% c("Occasionally","Option 2", "Rarely", "Ver often") ~ "Yes",
salt_add %in% "Never" ~ "No"
),
heart_failure = ifelse(heart_failure=="REFUSED", NA, heart_failure),
stroke = ifelse(stroke=="REFUSED", NA, heart_failure),
body_weight = ifelse(body_weight < 20, body_weight + 60, body_weight),
bmi = body_weight/(height/100)^2,
across(med_1:med_10, ~toupper(.)),
nifedipine = case_when(
str_detect(med_1, "NIFE") | str_detect(med_2, "NIFE") |
str_detect(med_3, "NIFE") | str_detect(med_4, "NIFE") |
str_detect(med_5, "NIFE") | str_detect(med_6, "NIFE") |
str_detect(med_7, "NIFE") | str_detect(med_8, "NIFE") |
str_detect(med_9, "NIFE") | str_detect(med_10, "NIFE") ~ "Yes",
TRUE ~ "No"
),
amlodipine = case_when(
str_detect(med_1, "AMLO") | str_detect(med_2, "AMLO") |
str_detect(med_3, "AMLO") | str_detect(med_4, "AMLO") |
str_detect(med_5, "AMLO") | str_detect(med_6, "AMLO") |
str_detect(med_7, "AMLO") | str_detect(med_8, "AMLO") |
str_detect(med_9, "AMLO") | str_detect(med_10, "AMLO") ~ "Yes",
TRUE ~ "No"
),
losartan = case_when(
str_detect(med_1, "LOSA") | str_detect(med_2, "LOSA") |
str_detect(med_3, "LOSA") | str_detect(med_4, "LOSA") |
str_detect(med_5, "LOSA") | str_detect(med_6, "LOSA") |
str_detect(med_7, "LOSA") | str_detect(med_8, "LOSA") |
str_detect(med_9, "LOSA") | str_detect(med_10, "LOSA") ~ "Yes",
TRUE ~ "No"
),
lisinopril = case_when(
str_detect(med_1, "LISI") | str_detect(med_2, "LISI") |
str_detect(med_3, "LISI") | str_detect(med_4, "LISI") |
str_detect(med_5, "LISI") | str_detect(med_6, "LISI") |
str_detect(med_7, "LISI") | str_detect(med_8, "LISI") |
str_detect(med_9, "LISI") | str_detect(med_10, "LISI") ~ "Yes",
TRUE ~ "No"
),
bendro = case_when(
str_detect(med_1, "BENDR") | str_detect(med_2, "BENDR") |
str_detect(med_3, "BENDR") | str_detect(med_4, "BENDR") |
str_detect(med_5, "BENDR") | str_detect(med_6, "BENDR") |
str_detect(med_7, "BENDR") | str_detect(med_8, "BENDR") |
str_detect(med_9, "BENDR") | str_detect(med_10, "BENDR") ~ "Yes",
TRUE ~ "No"
),
methyldopa = case_when(
str_detect(med_1, "DOPA") | str_detect(med_2, "DOPA") |
str_detect(med_3, "DOPA") | str_detect(med_4, "DOPA") |
str_detect(med_5, "DOPA") | str_detect(med_6, "DOPA") |
str_detect(med_7, "DOPA") | str_detect(med_8, "DOPA") |
str_detect(med_9, "DOPA") | str_detect(med_10, "DOPA")~ "Yes",
TRUE ~ "No"
),
hydralazine = case_when(
str_detect(med_1, "HYDRALA") | str_detect(med_2, "HYDRALA") |
str_detect(med_3, "HYDRALA") | str_detect(med_4, "HYDRALA") |
str_detect(med_5, "HYDRALA") | str_detect(med_6, "HYDRALA") |
str_detect(med_7, "HYDRALA") | str_detect(med_8, "HYDRALA") |
str_detect(med_9, "HYDRALA") | str_detect(med_10, "HYDRALA")~ "Yes",
TRUE ~ "No"
),
metformin = case_when(
str_detect(med_1, "METFO") | str_detect(med_2, "METFO") |
str_detect(med_3, "METFO") | str_detect(med_4, "METFO") |
str_detect(med_5, "METFO") | str_detect(med_6, "METFO") |
str_detect(med_7, "METFO") | str_detect(med_8, "METFO") |
str_detect(med_9, "METFO") | str_detect(med_10, "METFO")~ "Yes",
TRUE ~ "No"
),
aspirin = case_when(
str_detect(med_1, "ASPIR") | str_detect(med_2, "ASPIR") |
str_detect(med_3, "ASPIR") | str_detect(med_4, "ASPIR") |
str_detect(med_5, "ASPIR") | str_detect(med_6, "ASPIR") |
str_detect(med_7, "ASPIR") | str_detect(med_8, "ASPIR") |
str_detect(med_9, "ASPIR") | str_detect(med_10, "ASPIR")~ "Yes",
TRUE ~ "No"
),
gliclazide = case_when(
str_detect(med_1, "GLICL") | str_detect(med_2, "GLICL") |
str_detect(med_3, "GLICL") | str_detect(med_4, "GLICL") |
str_detect(med_5, "GLICL") | str_detect(med_6, "GLICL") |
str_detect(med_7, "GLICL") | str_detect(med_8, "GLICL") |
str_detect(med_9, "GLICL") | str_detect(med_10, "GLICL")~ "Yes",
TRUE ~ "No"
),
atorvastatin = case_when(
str_detect(med_1, "ATORV") | str_detect(med_2, "ATORV") |
str_detect(med_3, "ATORV") | str_detect(med_4, "ATORV") |
str_detect(med_5, "ATORV") | str_detect(med_6, "ATORV") |
str_detect(med_7, "ATORV") | str_detect(med_8, "ATORV") |
str_detect(med_9, "ATORV") | str_detect(med_10, "ATORV")~ "Yes",
TRUE ~ "No"
),
pioglitazone = case_when(
str_detect(med_1, "PIOG") | str_detect(med_2, "PIOG") |
str_detect(med_3, "PIOG") | str_detect(med_4, "PIOG") |
str_detect(med_5, "PIOG") | str_detect(med_6, "PIOG") |
str_detect(med_7, "PIOG") | str_detect(med_8, "PIOG") |
str_detect(med_9, "PIOG") | str_detect(med_10, "PIOG")~ "Yes",
TRUE ~ "No"
),
atenolol = case_when(
str_detect(med_1, "ATENOLOL") | str_detect(med_2, "ATENOLOL") |
str_detect(med_3, "ATENOLOL") | str_detect(med_4, "ATENOLOL") |
str_detect(med_5, "ATENOLOL") | str_detect(med_6, "ATENOLOL") |
str_detect(med_7, "ATENOLOL") | str_detect(med_8, "ATENOLOL") |
str_detect(med_9, "ATENOLOL") | str_detect(med_10, "ATENOLOL")~ "Yes",
TRUE ~ "No"
),
bisoprolol = case_when(
str_detect(med_1, "BISOPROLOL") | str_detect(med_2, "BISOPROLOL") |
str_detect(med_3, "BISOPROLOL") | str_detect(med_4, "BISOPROLOL") |
str_detect(med_5, "BISOPROLOL") | str_detect(med_6, "BISOPROLOL") |
str_detect(med_7, "BISOPROLOL") | str_detect(med_8, "BISOPROLOL") |
str_detect(med_9, "BISOPROLOL") | str_detect(med_10, "BISOPROLOL")~ "Yes",
TRUE ~ "No"
),
glimepiride = case_when(
str_detect(med_1, "GLIM") | str_detect(med_2, "GLIM") |
str_detect(med_3, "GLIM") | str_detect(med_4, "GLIM") |
str_detect(med_5, "GLIM") | str_detect(med_6, "GLIM") |
str_detect(med_7, "GLIM") | str_detect(med_8, "GLIM") |
str_detect(med_9, "GLIM") | str_detect(med_10, "GLIM")~ "Yes",
TRUE ~ "No"
),
furosemide = case_when(
str_detect(med_1, "FUROS") | str_detect(med_2, "FUROS") |
str_detect(med_3, "FUROS") | str_detect(med_4, "FUROS") |
str_detect(med_5, "FUROS") | str_detect(med_6, "FUROS") |
str_detect(med_7, "FUROS") | str_detect(med_8, "FUROS") |
str_detect(med_9, "FUROS") | str_detect(med_10, "FUROS")~ "Yes",
TRUE ~ "No"
),
glibenclamide = case_when(
str_detect(med_1, "GLIB") | str_detect(med_2, "GLIB") |
str_detect(med_3, "GLIB") | str_detect(med_4, "GLIB") |
str_detect(med_5, "GLIB") | str_detect(med_6, "GLIB") |
str_detect(med_7, "GLIB") | str_detect(med_8, "GLIB") |
str_detect(med_9, "GLIB") | str_detect(med_10, "GLIB")~ "Yes",
TRUE ~ "No"
),
labetalol = case_when(
str_detect(med_1, "LABET") | str_detect(med_2, "LABET") |
str_detect(med_3, "LABET") | str_detect(med_4, "LABET") |
str_detect(med_5, "LABET") | str_detect(med_6, "LABET") |
str_detect(med_7, "LABET") | str_detect(med_8, "LABET") |
str_detect(med_9, "LABET") | str_detect(med_10, "LABET")~ "Yes",
TRUE ~ "No"
),
mixtard = case_when(
str_detect(med_1, "MIXTARD") | str_detect(med_2, "MIXTARD") |
str_detect(med_3, "MIXTARD") | str_detect(med_4, "MIXTARD") |
str_detect(med_5, "MIXTARD") | str_detect(med_6, "MIXTARD") |
str_detect(med_7, "MIXTARD") | str_detect(med_8, "MIXTARD") |
str_detect(med_9, "MIXTARD") | str_detect(med_10, "MIXTARD")~ "Yes",
TRUE ~ "No"
),
spironolactone = case_when(
str_detect(med_1, "SPIRONO") | str_detect(med_2, "SPIRONO") |
str_detect(med_3, "SPIRONO") | str_detect(med_4, "SPIRONO") |
str_detect(med_5, "SPIRONO") | str_detect(med_6, "SPIRONO") |
str_detect(med_7, "SPIRONO") | str_detect(med_8, "SPIRONO") |
str_detect(med_9, "SPIRONO") | str_detect(med_10, "SPIRONO")~ "Yes",
TRUE ~ "No"
),
acei = factor(lisinopril, levels = c("No", "Yes")),
arb = factor(losartan, levels = c("No", "Yes")),
bb = case_when(
atenolol == "Yes" ~ "Yes",
bisoprolol == "Yes" ~ "Yes",
labetalol == "Yes" ~ "Yes",
TRUE ~ "No") %>%
factor(),
ccb = case_when(
amlodipine == "Yes" ~ "Yes",
nifedipine == "Yes" ~ "Yes",
TRUE ~ "No") %>%
factor(),
diuretics = case_when(
spironolactone == "Yes" ~ "Yes",
furosemide == "Yes" ~ "Yes",
bendro == "Yes" ~ "Yes",
TRUE ~ "No") %>%
factor(),
antidiabetics = (gliclazide=="Yes") + (glimepiride == "Yes") +
(glibenclamide == "Yes") + (metformin == "Yes") +
(mixtard == "Yes"),
sulphonylurea = case_when(
gliclazide == "Yes" ~ "Yes",
glimepiride == "Yes" ~ "Yes",
glibenclamide == "Yes" ~ "Yes",
TRUE ~ "No") %>%
factor(),
antihypertensives = (nifedipine == "Yes") + (hydralazine == "Yes") +
(amlodipine == "Yes") + (losartan == "Yes") +
(lisinopril == "Yes") + (bendro == "Yes") +
(methyldopa == "Yes") + (atenolol == "Yes") +
(bisoprolol == "Yes") + (furosemide == "Yes") +
(labetalol == "Yes") + (spironolactone == "Yes"),
across(c(sbp1,dbp4, dbp7, dbp8, dbp9), ~as.numeric(.)),
low_moca = case_when(
moca_tertile == "Lower Tercile" ~ "Yes",
TRUE ~ "No"
) %>%
factor()
) %>%
rowwise() %>%
mutate(
sbp_sd = sd(
c(sbp1, sbp2, sbp3, sbp4, sbp5, sbp6, sbp7, sbp8, sbp9, sbp10),
na.rm=T),
dbp_sd = sd(
c(dbp1, dbp2, dbp3, dbp4, dbp5, dbp6, dbp7, dbp8, dbp9, dbp10),
na.rm=T),
sbp_mean = mean(
c(sbp1, sbp2, sbp3, sbp4, sbp5, sbp6, sbp7, sbp8, sbp9, sbp10),
na.rm=T),
dbp_mean = mean(
c(dbp1, dbp2, dbp3, dbp4, dbp5, dbp6, dbp7, dbp8, dbp9, dbp10),
na.rm=T)
) %>%
ungroup() %>%
mutate(
controlled_bp = case_when(
(sbp_mean < 140) & (dbp_mean < 90) ~ "Controlled",
(sbp_mean >= 140) | (dbp_mean >= 90) ~ "Uncontrolled") %>%
factor(levels = c("Controlled","Uncontrolled"))
) %>%
select(
ageyrs, sex, resid, educ, educ2, income, income2, dm2, currently_smoke,
ever_smoked, past_smoked, alcohol,nhis, moca_score, salt_add2,
physical_activity, dura_exercise, fruits_per_week, salt_add, daily_fruits,
days_veges, daily_veges, heart_failure, stroke, bmi, waist_circumference,
dura_hpt, nifedipine:spironolactone, moca_tertile, starts_with("med_"),
acei, arb, bb, ccb, diuretics, methyldopa, hydralazine, antidiabetics,
metformin, sulphonylurea, pioglitazone, mixtard, atorvastatin, aspirin,
antihypertensives, hill_and_bone_score, starts_with("sbp"),
starts_with("dbp"), body_weight, height, low_moca, sbp_mean, dbp_mean,
controlled_bp
)
labelled::var_label(df_hptcog) <-
list(
sex = "Sex",
ageyrs = "Age in years",
resid = "Residence",
educ = "Educational level",
educ2 = "Educational level",
income = "Income",
income2 = "Income",
currently_smoke = "Currently smoke",
past_smoked = "Ever Smoked",
nhis = "Have valid NHIS",
moca_score = "MOCA Score",
dm2 = "Diabetes Mellitus",
ever_smoked = "Ever smoked",
alcohol = "Alcohol intake",
salt_add = "Salt added to food",
salt_add2 = "Salt added to food",
physical_activity = "Physical activity",
dura_exercise = "Daily minutes exercising",
fruits_per_week = "Days of Fruit per week",
daily_fruits = "Daily Fruit servings",
days_veges = "Days/week vegetables",
daily_veges = "Daily vegetable servings",
heart_failure = "Heart failure",
stroke = "Stroke",
bmi = "BMI",
waist_circumference = "Waist Circunference",
dura_hpt = "Duration of hypertension in years",
med_1 = "Medications 1",
med_2 = "Medications 2",
med_3 = "Medications 3",
med_4 = "Medications 4",
med_5 = "Medications 5",
med_6 = "Medications 6",
med_7 = "Medications 7",
med_8 = "Medications 8",
med_9 = "Medications 9",
med_10 = "Medications 10",
acei = "ACE-Inhibitors",
arb = "ARB use",
bb = "Beta-Blockers use",
ccb = "Calcium Channel Blockers",
diuretics = "Diuretics",
methyldopa = "Methyldopa",
hydralazine = "Hydralazine",
antidiabetics = "No. of antidiabetics",
metformin = "Metformin",
sulphonylurea = "Sulphonylurea",
pioglitazone = "Thiazolidinedione",
mixtard = "Insulin",
atorvastatin = "Statin",
aspirin = "Antiplatelet",
antihypertensives = "No. of Antihypertensive",
hill_and_bone_score = "Hillbone score",
sbp_sd = "Systolic variability",
dbp_sd = "Diastolic variability",
sbp_mean = "Systolic Blood Pressure",
dbp_mean = "Diastolic Blood Pressure",
controlled_bp = "Controlled Blood Pressure"
)