format_nut_health_indicators: Format Nutrition and Health Indicators

In SaeedR1987/healthyr: REACH Nutrition & Health R Tools

Format Nutrition and Health Indicators

Description

This function allows for standardization of variable names and values for technical nutrition and health indicators. The function additionally calls helper functions to reformat, calculate indicators, and create data quality flags for each of the sets of indicators.

Usage

format_nut_health_indicators(
  df,
  file_path = NULL,
  use_flags_yn = NULL,
  hhid = NULL,
  date_of_dc = NULL,
  enum = NULL,
  cluster = NULL,
  id,
  date_of_birth = NULL,
  age_years_var = NULL,
  age_months_var = NULL,
  age_proxy_var = NULL,
  age_days = NULL,
  sex_var,
  oedema_var,
  plw_status_var = NULL,
  muac_var = NULL,
  weight_var = NULL,
  height_var = NULL,
  type_interview = NULL,
  wgss_seeing = NULL,
  wgss_hearing = NULL,
  wgss_walking = NULL,
  wgss_remembering = NULL,
  wgss_selfcare = NULL,
  wgss_communicating = NULL,
  health_barriers = NULL,
  delivery_location = NULL,
  birth_assistant = NULL,
  iycf_caregiver = NULL,
  iycf_1 = NULL,
  iycf_2 = NULL,
  iycf_3 = NULL,
  iycf_4 = NULL,
  iycf_5 = NULL,
  iycf_6a = NULL,
  iycf_6b = NULL,
  iycf_6b_num = NULL,
  iycf_6c = NULL,
  iycf_6c_num = NULL,
  iycf_6c_swt = NULL,
  iycf_6d = NULL,
  iycf_6d_num = NULL,
  iycf_6d_swt = NULL,
  iycf_6e = NULL,
  iycf_6f = NULL,
  iycf_6g = NULL,
  iycf_6h = NULL,
  iycf_6h_swt = NULL,
  iycf_6i = NULL,
  iycf_6j = NULL,
  iycf_6j_swt = NULL,
  iycf_7a = NULL,
  iycf_7a_num = NULL,
  iycf_7b = NULL,
  iycf_7c = NULL,
  iycf_7d = NULL,
  iycf_7e = NULL,
  iycf_7f = NULL,
  iycf_7g = NULL,
  iycf_7h = NULL,
  iycf_7i = NULL,
  iycf_7j = NULL,
  iycf_7k = NULL,
  iycf_7l = NULL,
  iycf_7m = NULL,
  iycf_7n = NULL,
  iycf_7o = NULL,
  iycf_7p = NULL,
  iycf_7q = NULL,
  iycf_7r = NULL,
  iycf_7s = NULL,
  iycf_8 = NULL,
  monthly_expenditures = NULL,
  period_expenditures = NULL,
  num_period_months = NULL,
  health_exp_col = NULL,
  food_exp_col = NULL,
  vaccine_card_yn = NULL,
  penta = NULL,
  penta_date1 = NULL,
  penta_date2 = NULL,
  penta_date3 = NULL,
  penta_count = NULL,
  measles = NULL,
  measles_date1 = NULL,
  measles_date2 = NULL,
  fcs_cereal = NULL,
  fcs_legumes = NULL,
  fcs_dairy = NULL,
  fcs_meat = NULL,
  fcs_veg = NULL,
  fcs_fruit = NULL,
  fcs_oil = NULL,
  fcs_sugar = NULL,
  hdds_cereals = NULL,
  hdds_tubers = NULL,
  hdds_veg = NULL,
  hdds_fruit = NULL,
  hdds_meat = NULL,
  hdds_eggs = NULL,
  hdds_fish = NULL,
  hdds_legumes = NULL,
  hdds_dairy = NULL,
  hdds_oils = NULL,
  hdds_sugars = NULL,
  hdds_condiments = NULL,
  hhs_nofoodhh_1 = NULL,
  hhs_nofoodhh_1a = NULL,
  hhs_sleephungry_2 = NULL,
  hhs_sleephungry_2a = NULL,
  hhs_alldaynight_3 = NULL,
  hhs_alldaynight_3a = NULL,
  rcsi_lesspreferred_1 = NULL,
  rcsi_borrowfood_2 = NULL,
  rcsi_limitportion_3 = NULL,
  rcsi_restrict_4 = NULL,
  rcsi_reducemeals5 = NULL,
  lcs_variables = NULL,
  livelihood_variables = NULL
)

Arguments

df	Inputs a dataframe with nutrition and health data of interest.
file_path	Optional input of a character file path. If included will save an excel sheet of the new dataframe.
use_flags_yn	Optional input if you want to exclude flagged values from the final indicator calculations. If "yes" then records with data quality flags will be treated differently in the calculations.
hhid	Input of a character value specifying the column name for household id. Can use the uuid here as well.
date_of_dc	Input of a character value specifying the column name for date of data collection.
enum	Input of a character value specifying the column name for enumerator or team id.
cluster	Input of a character value specifying the column name for cluster number or id.
id	Input of a character value specifying the column name for an individual id within the household.
date_of_birth	Input of a character value specifying the column name for date of birth
age_years_var	Input of a character value specifying the column name for age in years of the individual
age_months_var	Input of a character value specifying the column name for age in months of the individual
age_proxy_var	Input of a character value specifying the column name for proxy age of children. That is, whether the child is 6-23 months of age, or 24-59 months of age. For use with some MUAC only related data collection.
age_days	Input of a character value specifying the column name for age in days of children under-5 years of age
sex_var	Input of a character value specifying the column name for sex of the individual.
oedema_var	Input of a character value specifying the column name for nutritional oedema
plw_status_var	Input of a character value specifying the column name for pregnant and/or breastfeeding status for women of reproductive age
muac_var	Input of a character value specifying the column name for MUAC measurements in mm or cm
weight_var	Input of a character value specifying the column name for weight measurements in kilograms
height_var	Input of a character value specifying the column name for length and/or height measurements in cm
type_interview	Input of a character value specifying the column name for direct or proxy interviews for Washington Group questions
wgss_seeing	Input of a character value specifying the column name for seeing domain of Washington Group Short Set of questions
wgss_hearing	Input of a character value specifying the column name for hearing domain of Washington Group Short Set of questions
wgss_walking	Input of a character value specifying the column name for walking domain of Washington Group Short Set of questions
wgss_remembering	Input of a character value specifying the column name for remembering domain of Washington Group Short Set of questions
wgss_selfcare	Input of a character value specifying the column name for self-care domain of Washington Group Short Set of questions
wgss_communicating	Input of a character value specifying the column name for communicating domain of Washington Group Short Set of questions
health_barriers	Inputs a character vector of column names for self-reported health barriers.
delivery_location	Input of a character value specifying the column name for child delivery location
birth_assistant	Input of a character value specifying the column name for who attended the woman's birth
iycf_caregiver	Input of a character value specifying the column name for if the primary caregiver or mother of the child was interviewed for the IYCF questions (y/n)
iycf_1	Input of a character value specifying the column name for ever breastfed (y.n)
iycf_2	Input of a character value specifying the column name for how long after birth breastfed
iycf_3	Input of a character value specifying the column name for given anything to eat/drink in first 2 days after delivery
iycf_4	Input of a character value specifying the column name for breastfed yesterday during the day or night (y/n)
iycf_5	Input of a character value specifying the column name for drink anything from bottle with a nipple (y/n)
iycf_6a	Input of a character value specifying the column name for plain water
iycf_6b	Input of a character value specifying the column name for infant formula (y/n)
iycf_6b_num	Input of a character value specifying the column name for infant formula (number)
iycf_6c	Input of a character value specifying the column name for milk from animals, fresh tinned powder (y/n)
iycf_6c_num	Input of a character value specifying the column name for milk form animals, fresh, tinned, pwder (number)
iycf_6c_swt	Input of a character value specifying the column name for milk was sweetened (y/n)
iycf_6d	Input of a character value specifying the column name for yoghurt drinks (y/n)
iycf_6d_num	Input of a character value specifying the column name for yoghurt drinks (number)
iycf_6d_swt	Input of a character value specifying the column name for yoghurt drink was sweetened (y/n)
iycf_6e	Input of a character value specifying the column name for chocolate flavoured drinks, including from syrup / powders (y/n)
iycf_6f	Input of a character value specifying the column name for Fruit juice or fruit-flavoured drinks including those made from syrups or powders? (y/n)
iycf_6g	Input of a character value specifying the column name for sodas, malt drinks, sports and energy drinks (y/n)
iycf_6h	Input of a character value specifying the column name for tea, coffee, herbal drinks (y/n)
iycf_6h_swt	Input of a character value specifying the column name for tea coffee herbal drinks were sweetened (y/n)
iycf_6i	Input of a character value specifying the column name for clear broth / soup (y/n)
iycf_6j	Input of a character value specifying the column name for other liquids (y/n)
iycf_6j_swt	Input of a character value specifying the column name for other drinks were sweetened (y/n)
iycf_7a	Input of a character value specifying the column name for yoghurt (NOT yoghurt drinks) (y/n)
iycf_7a_num	Input of a character value specifying the column name for yoghurt (NOT yoghurt drinks) (number)
iycf_7b	Input of a character value specifying the column name for porridge, bread, rice, nooodles (y/n)
iycf_7c	Input of a character value specifying the column name for vitamin a rich vegetables (pumpkin, carrots, sweet red peppers, squash or yellow/orange sweet potatoes) (y/n)
iycf_7d	Input of a character value specifying the column name for white starches (plaintains, white potatoes, white yams, manioc, cassava) (y/n)
iycf_7e	Input of a character value specifying the column name for dark green leafy vegetables (y/n)
iycf_7f	Input of a character value specifying the column name for other vegetables (y/n)
iycf_7g	Input of a character value specifying the column name for vitamin a rich fruits (ripe mangoes, ripe papayas) (y/n)
iycf_7h	Input of a character value specifying the column name for other fruits (y/n)
iycf_7i	Input of a character value specifying the column name for organ meats (liver ,kidney, heart) (y/n)
iycf_7j	Input of a character value specifying the column name for processed meats (sausages, hot dogs, ham, bacon, salami, canned meat) (y/n)
iycf_7k	Input of a character value specifying the column name for any other meats (beef, chicken, pork, goat, chicken, duck) (y/n)
iycf_7l	Input of a character value specifying the column name for eggs (y/n)
iycf_7m	Input of a character value specifying the column name for fish (fresh or dried fish or shellfish) (y/n)
iycf_7n	Input of a character value specifying the column name for legumes (beans, peas, lentils, seeds, chickpeas) (y/n)
iycf_7o	Input of a character value specifying the column name for cheeses (hard or soft cheeses) (y/n)
iycf_7p	Input of a character value specifying the column name for sweets (chocolates, candies, pastries, cakes) (y.n)
iycf_7q	Input of a character value specifying the column name for fried or empty carbs (chips, crisps, french fries, fried dough, instant noodles) (y/n)
iycf_7r	Input of a character value specifying the column name for Any other solid, semi-solid, or soft foods
iycf_7s	Input of a character value specifying the column name for did child eat solid/semi-solid foods (y/n) for list based questionnaires
iycf_8	Input of a character value specifying the column name for times child ate solid/semi-solid foods (number)
monthly_expenditures	Inputs a character vector of column names for monthly expenditures over 30 days
period_expenditures	Inputs a character vector of column names for period expenditures of a period of time
num_period_months	Inputs a number for the number of months of the period expenditures for health expediture calculations
health_exp_col	Inputs a character value specifying the column name for health expenditures
food_exp_col	Inputs a character value specifying the column name for food expenditures
vaccine_card_yn	Inputs a character value specifying the column name for vaccine card yes no question
penta	Inputs a character value specifying the column name for pentavalent vaccine
penta_date1	Inputs a character value specifying the column name for date of penta dose 1
penta_date2	Inputs a character value specifying the column name for date of penta dose 2
penta_date3	Inputs a character value specifying the column name for date of penta dose 3
penta_count	Inputs a character value specifying the column name for number of penta doses reported
measles	Inputs a character value specifying the column name for measles vaccine
measles_date1	Inputs a character value specifying the column name for date of measles dose 1
measles_date2	Inputs a character value specifying the column name for date of measles dose 2
fcs_cereal	Input of a character value specifying the column name for number of days of cereals food consumption in the household
fcs_legumes	Input of a character value specifying the column name for number of days of legumes food consumption in the household
fcs_dairy	Input of a character value specifying the column name for number of days of dairy food consumption in the household
fcs_meat	Input of a character value specifying the column name for number of days of meats food consumption in the household
fcs_veg	Input of a character value specifying the column name for number of days of vegetables food consumption in the household
fcs_fruit	Input of a character value specifying the column name for number of days of fruits food consumption in the household
fcs_oil	Input of a character value specifying the column name for number of days of oils food consumption in the household
fcs_sugar	Input of a character value specifying the column name for number of days of sugars food consumption in the household
hdds_cereals	Input of a character value specifying the column name for yes/no if cereals consumed yesterday in the household
hdds_tubers	Input of a character value specifying the column name for yes/no if tubers consumed yesterday in the household
hdds_veg	Input of a character value specifying the column name for yes/no if vegetables consumed yesterday in the household
hdds_fruit	Input of a character value specifying the column name for yes/no if fruits consumed yesterday in the household
hdds_meat	Input of a character value specifying the column name for yes/no if meats consumed yesterday in the household
hdds_eggs	Input of a character value specifying the column name for yes/no if eggs consumed yesterday in the household
hdds_fish	Input of a character value specifying the column name for yes/no if fish consumed yesterday in the household
hdds_legumes	Input of a character value specifying the column name for yes/no if legumes consumed yesterday in the household
hdds_dairy	Input of a character value specifying the column name for yes/no if dairy consumed yesterday in the household
hdds_oils	Input of a character value specifying the column name for yes/no if oils consumed yesterday in the household
hdds_sugars	Input of a character value specifying the column name for yes/no if sugars consumed yesterday in the household
hdds_condiments	Input of a character value specifying the column name for yes/no if condiments consumed yesterday in the household
hhs_nofoodhh_1	Input of a character value specifying the column name for household hunger scale question 1
hhs_nofoodhh_1a	Input of a character value specifying the column name for household hunger scale question 2
hhs_sleephungry_2	Input of a character value specifying the column name for household hunger scale question 3
hhs_sleephungry_2a	Input of a character value specifying the column name for household hunger scale question 4
hhs_alldaynight_3	Input of a character value specifying the column name for household hunger scale question 5
hhs_alldaynight_3a	Input of a character value specifying the column name for household hunger scale question 6
rcsi_lesspreferred_1	Input of a character value specifying the column name for rcsi less preffered foods
rcsi_borrowfood_2	Input of a character value specifying the column name for rcsi borrow foods
rcsi_limitportion_3	Input of a character value specifying the column name for rcsi limit portion size
rcsi_restrict_4	Input of a character value specifying the column name for rcsi restrict consumption for adults
rcsi_reducemeals5	Input of a character value specifying the column name for rcsi reduce meals per day
lcs_variables	Inputs a character vector of column names specifying all the livelihood coping strategy columns.
livelihood_variables	Inputs a character vector of column names specifying all the livelihood activities for which income is received. These should be numerical columns with estimated income per livelihood activity. As per MSNA core indicator bank 2023.

Value

Returns a data frame with standardized variable names and values, additional columns for calculated indicators, and additional columns for data quality flags.

Examples

## Not run: format_nut_health_indicators(df = dfanthro, age_months = "age_in_months",
muac_var = "muac", ...)
## End(Not run)

SaeedR1987/healthyr documentation built on July 4, 2023, 11:17 p.m.