In R4EPI/r4epi: Report templates and helper functions for applied epidemiology
Introduction to this template
This is a template which can be used to create a report from a retrospective
nutrition survey.
- There are sections for reading and cleaning data, calculating
anthropometric indicators based on z-score counts followed by
weighting and then survey analysis.
- For a more detailed explanation of this template, please visit https://r4epis.netlify.com/surveys
-
Feedback and suggestions are welcome at the GitHub issues page
-
Text within <! > will not show in your final document. These comments are used
to explain the template. You can delete them if you want.
Data analysis: Definitions and standards
We used the following definitions for the analysis of the survey results for Weight for Height z-scores (WHZ):
- Global acute malnutrition (GAM): a WHZ score of less than (<) -2 and/or oedema;
- Moderate acute malnutrition: WHZ score <-2 and ≥ -3 and no oedema;
- Severe acute malnutrition (SAM): WHZ score <-3 and/or oedema.
We used the following definitions for the analysis of the survey results for MUAC measurements:
- Global acute malnutrition (GAM): MUAC of <125mm and/or oedema;
- Moderate acute malnutrition: MUAC <125mm and >= 115mm and no oedema;
- Severe acute malnutrition (SAM): MUAC <115mm and/or oedema.
In order to estimate stunting in the surveyed population, we looked at Height for Age z-scores (HAZ) and used the following definitions:
- Stunting: HAZ score <-2;
- Moderate stunting: HAZ score >=-3 and <-2;
- Severe stunting: HAZ score <-3.
In order to estimate underweight in the surveyed population, we looked at Weight for Age z-scores (WAZ) and used the following definitions:
- Underweight: WAZ score < -2;
- moderate underweight: WAZ score >=-3 and <-2;
- Severe underweight: WAZ <-3
Exclusion of z-scores from Observed mean SMART flags included:
WHZ: <-5 or >5;
HAZ: <-6 or >6;
* WAZ: <-6 or >5.
Installing and loading required packages
## hide all code chunks in the output, but show errors
knitr::opts_chunk$set(echo = FALSE, error = TRUE, fig.width = 6*1.25, fig.height = 6)
## set default NA to - in output, define figure width/height
options(knitr.kable.NA = "-")
# Ensures the package "pacman" is installed
if (!require("pacman")) {
install.packages("pacman") }
# Install and load required packages for this template
pacman::p_load(
knitr, # create output docs
here, # find your files
rio, # for importing data
janitor, # clean/shape data
dplyr, # clean/shape data
tidyr, # clean/shape data
forcats, # manipulate and rearrange factors
stringr, # manipulate texts
ggplot2, # create plots and charts
apyramid, # plotting age pyramids
sitrep, # MSF field epi functions
anthro, # WHO Child Growth Standards (wrapper of survey)
survey, # for survey functions
srvyr, # dplyr wrapper for survey package
gtsummary, # produce tables
flextable, # for styling output tables
labelled, # add labels to variables
matchmaker, # recode datasets with dictionaries
parsedate # guessing dates
)
## set default text size to 16 for plots
## give classic black/white axes for plots
ggplot2::theme_set(theme_classic(base_size = 18))
## generates MSF standard dictionary for Kobo
study_data_dict <- msf_dict_survey("Nutrition")
## generates MSF standard dictionary for Kobo in long format (for recoding)
study_data_dict_long <- msf_dict_survey(disease = "Nutrition", compact = FALSE)
## generates a fake dataset for use as an example in this template
## this dataset already has household and individual levels merged
study_data_raw <- gen_data(dictionary = "Nutrition",
varnames = "name",
numcases = 1000)
### Read in data ---------------------------------------------------------------
## Excel file ------------------------------------------------------------------
## read in household data sheet
# study_data_hh <- rio::import(here::here("nutrition_survey.xlsx"),
# which = "nutrition_survey_erb", na = "")
## read in individual level data sheet
# study_data_indiv <- rio::import(here::here("nutrition_survey.xlsx",
# which = "r1", na = "")
## Excel file with password ----------------------------------------------------
## Use this section if your Excel has a password.
# install.packages(c("excel.link", "askpass"))
# library(excel.link)
# study_data_hh <- xl.read.file(here::here("nutrition_survey.xlsx"),
# xl.sheet = "nutrition_survey_erb",
# password = askpass::askpass(prompt = "please enter file password"))
# study_data_indiv <- xl.read.file(here::here("nutrition_survey.xlsx"),
# xl.sheet = "r1",
# password = askpass::askpass(prompt = "please enter file password"))
## Excel file ------------------------------------------------------------------
## to read in a specific sheet use "which"
# study_data_hh <- rio::import(here::here("nutrition_survey.xlsx"), which = "Sheet1")
## Excel file -- Specific range ------------------------------------------------
## you can specify a range in an excel sheet.
# study_data_hh <- rio::import(here::here("nutrition_survey.xlsx"), range = "B2:J102")
## Excel file with password ----------------------------------------------------
## use this section if your Excel has a password.
# install.packages(c("excel.link", "askpass"))
# library(excel.link)
# study_data_hh <- xl.read.file(here::here("nutrition_survey.xlsx"),
# xl.sheet = "Sheet1",
# password = askpass::askpass(prompt = "please enter file password"))
## CSV file --------------------------------------------------------------------
# study_data_hh <- rio::import(here::here("nutrition_survey.csv"))
## Stata data file -------------------------------------------------------------
# study_data_hh <- rio::import(here::here("nutrition_survey.dat"))
## join the individual and household data to form a complete data set
#study_data_raw <- left_join(study_data_hh, study_data_indiv, by = c("_index" = "_parent_index"))
## Data dictionary -------------------------------------------------------------
## read in a kobo data dictionary
## important to specify template is FALSE (otherwise you get the generic dict)
# study_data_dict <- msf_dict_survey(name = here::here("nutrition_survey_dict.xlsx"),
# template = FALSE)
## look at the dictionary by uncommenting the line below
# View(study_data_dict)
## Clean column names ----------------------------------------------------------
## This step fixes the column names so they are easy to use in R.
## make a copy of your orginal dataset and name it study_data_cleaned
study_data_cleaned <- study_data_raw
## Sometimes you want to rename specific variables
## The formula for this is rename(data, NEW_NAME = OLD_NAME).
## You can add multiple column name recodes by simply separating them with a comma
# study_data_cleaned <- rename(study_data_cleaned,
# violence_nature_other_details = violence_nature_other)
## define clean variable names using clean_names from the janitor package.
study_data_cleaned <- janitor::clean_names(study_data_cleaned)
## create a unique identifier by combining indeces of the two levels
## x and y are added on to the end of variables that are duplicated
## (in this case, parent and child index)
# study_data_cleaned <- study_data_cleaned %>%
# mutate(uid = str_glue("{index}_{index_y}"))
## MSF Survey Dictionary ----------------------------------------------------------
## generates MSF standard dictionary for Kobo
# study_data_dict <- msf_dict_survey("Nutrition")
## generates MSF standard dictionary for Kobo in long format (for recoding)
# study_data_dict_long <- msf_dict_survey(disease = "Nutrition", compact = FALSE)
## look at the standard dictionary by uncommenting the line below
# View(study_data_dict)
## You will need to recode your variables to match the data dictionary. This is
## addressed below.
## Clean column names ----------------------------------------------------------
## This step fixes the column names so they are easy to use in R.
## make a copy of your orginal dataset and name it study_data_cleaned
# study_data_cleaned <- study_data_raw
## define clean variable names using clean_names from the janitor package.
# study_data_cleaned <- janitor::clean_names(study_data_cleaned)
## Match column names ---------------------------------------------------------
## This step helps you match your variables to the standard variables.
## This step will require some patience. Courage!
## Use the function msf_dict_rename_helper() to create a template based on the
## standard dictionary. This will copy a rename command like the one above to your
## clipboard.
# msf_dict_rename_helper("nutrition", varnames = "name")
## Paste the result below and your column names to the matching variable.
## Be careful! You still need to be aware of what each variable means and what
## values it takes.
## If there are any variables that are in the MSF dictionary that are not in
## your data set, then you should comment them out, but be aware that some
## analyses may not run because of this.
## PASTE HERE
## Here is an EXAMPLE for changing a few specific names. function. In this
## example, we have the columns "gender" and "age" that we want to rename as
## "sex" and "age_years".
## The formula for this is rename(data, NEW_NAME = OLD_NAME).
# study_data_cleaned <- rename(study_data_cleaned,
# sex = gender, # TEXT
# age_years = age # INTEGER_POSITIVE
# )
## Read data -------------------------------------------------------------------
## This step reads in your population data from Excel.
## You may need to rename your columns.
# population_data <- rio::import(here::here("population.xlsx"), which = "Sheet1")
## repeat preparation steps as appropriate
## Enter counts directly -------------------------------------------------------
## Below is an example of how to enter population counts by groups.
# population_data_age <- gen_population(
# groups = c("0-2", "3-14", "15-29", "30-44", "45+"),
# counts = c(3600, 18110, 13600, 8080, 6600),
# strata = NULL) %>%
# rename(age_group = groups,
# population = n)
## Create counts from proportions ----------------------------------------------
## This step helps you estimate sub-group size with proportions.
## You need to replace the total_pop and proportions. You can change the groups
## to fit your needs.
## Here we repeat the steps for two regions (district A and B) then bind the two
## together
## generate population data by age groups in years for district A
population_data_age_district_a <- gen_population(total_pop = 10000, # set total population
groups = c("6-11", "12-23", "24-35", "36-47", "48-60"), # set groups
proportions = c(0.0164, 0.0164, 0.015, 0.015, 0.015), # set proportions for each group
strata = c("Male", "Female")) %>% # stratify by gender
rename(age_group = groups, # rename columns (NEW NAME = OLD NAME)
sex = strata,
population = n) %>%
mutate(health_district = "district_a") # add a column to identify region
## generate population data by age groups in years for district B
population_data_age_district_b <- gen_population(total_pop = 10000, # set total population
groups = c("6-11", "12-23", "24-35", "36-47", "48-60"), # set groups
proportions = c(0.0164, 0.0164, 0.015, 0.015, 0.015), # set proportions for each group
strata = c("Male", "Female")) %>% # stratify by gender
rename(age_group = groups, # rename columns (NEW NAME = OLD NAME)
sex = strata,
population = n) %>%
mutate(health_district = "district_b") # add a column to identify region
## bind region population data together to get overall population
population_data_age <- bind_rows(population_data_age_district_a,
population_data_age_district_b)
cluster_counts <- tibble(cluster = c("Village 1", "Village 2", "Village 3", "Village 4",
"Village 5", "Village 6", "Village 7", "Village 8",
"Village 9", "Village 10"),
households = c(700, 400, 600, 500, 300,
800, 700, 400, 500, 500))
## view the first ten rows of data
head(study_data_raw, n = 10)
## view your whole dataset interactivley (in an excel style format)
View(study_data_raw)
## overview of variable types and contents
str(study_data_raw)
## gives mean, median and max values of variables
## gives counts for categorical variables
## also gives number of NAs
summary(study_data_raw)
## view unique values contained in variables
## you can run this for any column -- just replace the column name
unique(study_data_raw$sex)
## check for logical inconsistencies
## for example check age <6 months and height >100 cm and return corresponding IDs
study_data_raw %>%
filter(age_month < 6 & height > 100) %>%
select("uid")
## use the dfSummary function in combination with view
## note that view is not capitalised with this package
# summarytools::dfSummary(study_data_cleaned) %>%
# summarytools::view()
## Kobo standard data --------------------------------------------------------
## If you got your data from Kobo, use this portion of the code.
## If not, comment this section out and use the below.
## make sure all date variables are formatted as dates
## get the names of variables which are dates
DATEVARS <- study_data_dict %>%
filter(type == "date") %>%
filter(name %in% names(study_data_cleaned)) %>%
## filter to match the column names of your data
pull(name) # select date vars
## find if there are date variables which are completely empty
EMPTY_DATEVARS <- purrr::map(DATEVARS, ~all(
is.na(study_data_cleaned[[.x]])
)) %>%
unlist() %>%
which()
## remove exclude the names of variables which are completely emptys
DATEVARS <- DATEVARS[-EMPTY_DATEVARS]
## change to dates
## use the parse_date() function to make a first pass at date variables.
## parse_date() produces a complicated format - so we use as.Date() to simplify
study_data_cleaned <- study_data_cleaned %>%
mutate(
across(.cols = all_of(DATEVARS),
.fns = ~parsedate::parse_date(.x) %>% as.Date()))
## Non-Kobo data -------------------------------------------------------------
## Use this section if you did not have Kobo data.
## use the parse_date() function to make a first pass at date variables.
## parse_date() produces a complicated format - so we use as.Date() to simplify
# study_data_cleaned <- study_data_cleaned %>%
# mutate(
# across(.cols = matches("date|Date"),
# .fns = ~parsedate::parse_date(.x) %>% as.Date()))
## Fix wrong dates -------------------------------------------------------------
## Some dates will be unrealistic or wrong.
## Here is an example of how to manually fix dates.
## Look at your data and edit as needed.
## set specific unrealistic dates to NA
# study_data_cleaned <- mutate(study_data_cleaned,
# date < as.Date("2017-11-01") ~ as.Date(NA),
# date == as.Date("2081-01-01") ~ as.Date("2018-01-01"))
## Age group variables ----------------------------------------------------------
## This step shows you how to create categorical variables from numeric variables.
## We have some intermediate steps on the way.
## make sure age is an integer
study_data_cleaned <- study_data_cleaned %>%
mutate(age_months = as.integer(age_months),
age_years = as.integer(age_months))
## add convert years to months (for those over 1 year)
study_data_cleaned <- study_data_cleaned %>%
mutate(age_months = if_else(
age_years >= 1,
as.integer(age_years * 12),
as.integer(age_months)
))
## create an age group variable (combining those over 24 months and those under)
study_data_cleaned <- study_data_cleaned %>%
mutate(age_group_bin = factor(
if_else(age_months >= 24,
"24-60",
"0-23"
)
))
## create age group variable for based on months
study_data_cleaned <- study_data_cleaned %>%
mutate(age_group = age_categories(study_data_cleaned$age_months,
breakers = c(6, 12, 24, 36, 48, 60),
ceiling = TRUE))
## alternatively, create an age group variable specify a sequence
# study_data_cleaned$age_group <- age_categories(study_data_cleaned$age,
# lower = 0,
# upper = 100,
# by = 10)
## If you already have an age group variable defined, you should manually
## arrange the categories
# study_data_cleaned$age_group <- factor(study_data_cleaned$age_group,
# c("0-4y", "5-14y", "15-29y", "30-44y", "45+y"))
## to combine different age categories use the following function
## this prioritises the smaller unit, i.e. if given months and years, will return months first
# study_data_cleaned <- group_age_categories(study_data_cleaned,
# years = age_group,
# months = age_group_mon)
## recode values with matchmaker package (value labels cant be used for analysis)
study_data_cleaned <- match_df(study_data_cleaned,
study_data_dict_long,
from = "option_name",
to = "option_label_english",
by = "name",
order = "option_order_in_set")
## Change a yes/no variable in to TRUE/FALSE
## create a new variable called consent
## where the old one is yes place TRUE in the new one
## (this could also be done with the if_else or case_when function -
## but this option is shorter)
study_data_cleaned <- study_data_cleaned %>%
mutate(consent = consent == "Yes")
## Change a character to factor - set the levels of a factor
study_data_cleaned <- study_data_cleaned %>%
mutate(sex = factor(sex,
levels = c("Female", "Male"))
)
## recode the levels of a factor
## put these in a second variable called sex_brief
## (this is necessary because the anthro package doesnt accept "Male"/"female")
study_data_cleaned <- study_data_cleaned %>%
mutate(sex_brief = fct_recode(sex,
"F" = "Female",
"M" = "Male")
)
# ## change the order of levels
# study_data_cleaned <- study_data_cleaned %>%
# mutate(soap = fct_relevel(soap,
# "Distribution",
# "Healthcentre",
# "Never")
# )
# ## create a new grouping for soap variable
# ## simplified, distribution or health centre then covered otherwise not covered
# study_data_cleaned <- study_data_cleaned %>%
# mutate(coverage = if_else(soap %in% c("Distribution", "Healthcentre"),
# "Covered",
# "Not covered")
# )
## Recode character variables
## This step shows how to fix misspellings in the geographic region variable.
## Ideally, you want these values to match and population data!
# study_data_cleaned <- study_data_cleaned %>%
# mutate(village_name = case_when(
# village_name == "Valliages 1" ~ "village 1",
# village_name == "Village1" ~ "village 1",
# village_name == "Town 3" ~ "village 3"
# village_name == "Town3" ~ "village 3",
# TRUE ~ as.character(village_name))
# ))
## create a character variable based off groups of a different variable
study_data_cleaned <- study_data_cleaned %>%
mutate(health_district = case_when(
cluster_number %in% c(1:5) ~ "district_a",
TRUE ~ "district_b"
))
## explicitly replace NA of a factor
# study_data_cleaned <- study_data_cleaned %>%
# mutate(coverage = fct_explicit_na(coverage, na_level = "Not Applicable"))
## if you had a multi-choice question and the missing values were given as a "."
## replace missing values in multi-choice questions to "" so that we can
## filter them out later.
# study_data_cleaned <- study_data_cleaned %>%
# mutate(
# across(
# .cols = contains("violence"), # all variables that contain the word "violence"
# .fns = ~fct_explicit_na(as.character(.), "") # replace missing values with ""
# )
# )
## fix factor levels -----------------------------------------------------------
## make sure there are the appropriate levels (names)
study_data_cleaned$no_consent_reason <- fct_recode(study_data_cleaned$no_consent_reason,
"No time" = "I do not have time",
"Previous negative experience" = "I have had a negative experience with a previous survey.",
"No perceived benefit" = "There is no benefit to me and my family"
)
## anthro zscores --------------------------------------------------------------
## retrieve zscores
zscore_results <- with(study_data_cleaned, anthro_zscores(
sex = as.character(sex_brief),
age = age_months,
is_age_in_month = TRUE,
weight = weight,
lenhei = height,
oedema = as.numeric(oedema),
armc = muac / 10 # convert to cm
))
## add columns from zscore_results columns to study dataset
study_data_cleaned <- bind_cols(study_data_cleaned, zscore_results)
## categorise children ---------------------------------------------------------
## weight for height z-scores
## * Global acute malnutrition (GAM): a WHZ score of less than (<) -2 and/or oedema;
## * Moderate acute malnutrition: WHZ score <-2 and ≥ -3 and no oedema;
## * Severe acute malnutrition (SAM): WHZ score <-3 and/or oedema.
study_data_cleaned <- study_data_cleaned %>%
mutate(
gam_whz = zwfl < -2 | oedema == "Yes",
mam_whz = zwfl >= -3 & zwei < -2,
sam_whz = zwfl < -3 | oedema == "Yes"
) %>%
## set flagged children to NA for each of the indicator variables
## if the flag for this indicator is not missing and is 1 then set indicator vars to NA
## else leave the indicator variable as it was
mutate(
across(
.cols = c(gam_whz, mam_whz, sam_whz), # select the indicator variables
.fns = ~if_else(!is.na(fwfl) & fwfl == 1, NA, .)) # NA if flagged, else leave as is
)
## stunting according to height for age z-scores
## * Stunting: HAZ score <-2;
## * Moderate stunting: HAZ score >=-3 and <-2;
## * Severe stunting: HAZ score <-3.
study_data_cleaned <- study_data_cleaned %>%
mutate(
stunting_haz = zlen < -2,
moderate_stunting_haz = zlen >= -3 & zlen < -2,
severe_stunting_haz = zlen < -3
) %>%
## set flagged children to NA for each of the indicator variables
## if the flag for this indicator is not missing and is 1 then set indicator vars to NA
## else leave the indicator variable as it was
mutate(
across(
.cols = c(stunting_haz,
moderate_stunting_haz,
severe_stunting_haz), # select the indicator variables
.funs = ~if_else(!is.na(flen) & flen == 1, NA, .))) # NA if flagged, else leave as is
## underweight according to height for age z-scores
## * Underweight: WAZ score < -2 OR oedema;
## * moderate underweight: WAZ score >=-3 and <-2;
## * Severe underweight: WAZ < -3 OR oedema
study_data_cleaned <- study_data_cleaned %>%
mutate(
underweight_waz = zwei < -2 | oedema == "Yes",
moderate_underweight_waz = zwei >= -3 & zwei < -2,
severe_underweight_waz = zwei < -3 | oedema == "Yes"
) %>%
## set flagged children to NA for each of the indicator variables
## if the flag for this indicator is not missing and is 1 then set indicator vars to NA
## else leave the indicator variable as it was
mutate(
across(
.cols = c(underweight_waz,
moderate_underweight_waz,
severe_underweight_waz), # select the indicator variables
.fns = ~if_else(!is.na(fwei) & fwei == 1, NA, .))) # NA if flagged, else leave as is
## according to MUAC
## * Global acute malnutrition (GAM): MUAC of <125mm and/or oedema;
## * Moderate acute malnutrirtion: MUAC <125mm and >= 115mm and no oedema;
## * Severe acute malnutrition (SAM): MUAC <115mm and/or oedema.
study_data_cleaned <- study_data_cleaned %>%
mutate(
gam_muac = muac < 125 | oedema == "Yes",
mam_muac = muac < 125 & muac >= 115 & oedema == "No",
sam_muac = muac < 115 | oedema == "Yes"
)
## group indicator variables ---------------------------------------------------
## define all the indicators of interest
## we will use this to run the same function over all variables later on
WHZ <- c("gam_whz",
"mam_whz",
"sam_whz")
HAZ <- c("stunting_haz",
"moderate_stunting_haz",
"severe_stunting_haz")
WAZ <- c("underweight_waz",
"moderate_underweight_waz",
"severe_underweight_waz")
MUAC <- c("gam_muac",
"mam_muac",
"sam_muac")
indicators <- c(WHZ, HAZ, WAZ, MUAC)
## turn all indicators in to factors
study_data_cleaned <- study_data_cleaned %>%
mutate(
across(
.cols = all_of(indicators), # all variables named in indicators
.fns = factor # turn into a factor
))
## turn all flags in to TRUE/FALSE variables
study_data_cleaned <- study_data_cleaned %>%
mutate(
across(
.cols = all_of(c("fwei", "flen", "fwfl")), # names of flag variables
.fns = as.logical # turn in to logical
))
## create variable names with labelled
## define a list of names and labels based on the dictionary
var_labels <- setNames(
## add variable labels as a list
as.list(study_data_dict$short_name),
## name the list with the current variable names
study_data_dict$name)
## add the variable labels to dataset
study_data_cleaned <- study_data_cleaned %>%
set_variable_labels(
## set the labels with the object defined above
.labels = var_labels,
## do not throw an error if some names dont match
## not all names in the dictionary appear in the dataset
.strict = FALSE)
## it is possible to update individual variables manually too
study_data_cleaned <- study_data_cleaned %>%
set_variable_labels(
## variable name = variable label
age_years = "Age (years)",
age_months = "Age (months)",
age_group = "Age group (months)",
age_group_bin = "Age category (months)",
flen = "HAZ",
fwei = "WAZ",
fwfl = "WHZ",
gam_muac = "GAM",
mam_muac = "MAM" ,
sam_muac = "SAM",
moderate_stunting_haz = "Moderate stunting",
severe_stunting_haz = "Severe stunting",
stunting_haz = "Stunting",
moderate_underweight_waz = "Moderate underweight",
severe_underweight_waz = "Severe underweight",
underweight_waz = "Underweight",
gam_whz = "GAM",
mam_whz = "MAM",
sam_whz = "SAM"
)
## Drop unused rows -----------------------------------------------------------
## store the cases that you drop so you can describe them (e.g. non-consenting)
dropped <- study_data_cleaned %>%
filter(!consent | age_months < 6 | age_months > 60 |
## note that whatever you use for weights cannot be missing!
village_name == "Other"| is.na(age_years) | is.na(sex))
## drop the unused rows from the survey data set
study_data_cleaned <- anti_join(study_data_cleaned, dropped, by = names(dropped))
## Drop columns ----------------------------------------------------------------
## OPTIONAL: This step shows you how you can remove certain variables.
## study_data_cleaned <- select(study_data_cleaned, -c("age_years", "sex"))
## OPTIONAL: if you want to inspect certain variables, you can select these by
## name or column number. This example creates a reduced dataset for the first
## three columns, age_years, and sex.
# study_data_reduced <- select(study_data_cleaned, c(1:3, "age_years", "sex")
## option 1: only keep the first occurrence of duplicate case
study_data_cleaned <- study_data_cleaned %>%
## find duplicates based on case number, sex and age group
## only keep the first occurrence
distinct(uid, sex, age_group, .keep_all = TRUE)
# ## option 2: create flagging variables for duplicates (then use to browse)
#
# study_data_cleaned <- study_data_cleaned %>%
# ## choose which variables to use for finding unique rows
# group_by(uid, sex, age_group) %>%
# mutate(
# ## get the number of times duplicate occurs
# num_dupes = n(),
# duped = if_else(num_dupes > 1 , TRUE, FALSE)
# )
#
# ## browse duplicates based on flagging variables
# study_data_cleaned %>%
# ## only keep rows that are duplicated
# filter(duped) %>%
# ## arrange by variables of interest
# arrange(uid, sex, age_group) %>%
# View()
#
# ## filter duplicates to only keep the row with the earlier entry
# study_data_cleaned %>%
# ## choose which variables to use for finding unique rows
# group_by(uid, sex, age_group) %>%
# ## sort to have the earliest date by person first
# arrange(as.Date(start)) %>%
# ## only keep the earliest row
# slice(1)
## stratified ------------------------------------------------------------------
## create a variable called "surv_weight_strata"
## contains weights for each individual - by age group, sex and health district
study_data_cleaned <- add_weights_strata(x = study_data_cleaned,
p = population_data_age,
surv_weight = "surv_weight_strata",
surv_weight_ID = "surv_weight_ID_strata",
age_group, sex, health_district)
## cluster ---------------------------------------------------------------------
## get the number of individuals interviewed per household
## adds a variable with counts of the household (parent) index variable
study_data_cleaned <- study_data_cleaned %>%
add_count(index, name = "interviewed")
## create cluster weights
study_data_cleaned <- add_weights_cluster(x = study_data_cleaned,
cl = cluster_counts,
eligible = number_children,
interviewed = interviewed,
cluster_x = village_name,
cluster_cl = cluster,
household_x = index,
household_cl = households,
surv_weight = "surv_weight_cluster",
surv_weight_ID = "surv_weight_ID_cluster",
ignore_cluster = FALSE,
ignore_household = FALSE)
## stratified and cluster ------------------------------------------------------
## create a survey weight for cluster and strata
study_data_cleaned <- study_data_cleaned %>%
mutate(surv_weight_cluster_strata = surv_weight_strata * surv_weight_cluster)
## simple random ---------------------------------------------------------------
survey_design_simple <- study_data_cleaned %>%
as_survey_design(ids = 1, # 1 for no cluster ids
weights = NULL, # No weight added
strata = NULL # sampling was simple (no strata)
)
## stratified ------------------------------------------------------------------
survey_design_strata <- study_data_cleaned %>%
as_survey_design(ids = 1, # 1 for no cluster ids
weights = surv_weight_strata, # weight variable created above
strata = health_district # sampling was stratified by district
)
## cluster ---------------------------------------------------------------------
survey_design_cluster <- study_data_cleaned %>%
as_survey_design(ids = village_name, # cluster ids
weights = surv_weight_cluster, # weight variable created above
strata = NULL # sampling was simple (no strata)
)
## stratified cluster ----------------------------------------------------------
survey_design <- study_data_cleaned %>%
as_survey_design(ids = village_name, # cluster ids
weights = surv_weight_cluster_strata, # weight variable created above
strata = health_district # sampling was stratified by district
)
rio::export(study_data_cleaned, here::here("data", str_glue("study_data_cleaned_{Sys.Date()}.xlsx")))
Results
Survey inclusion
## get counts of number of clusters
num_clus <- study_data_cleaned %>%
## trim data to unique clusters
distinct(cluster_number) %>%
## get number of rows (count how many unique)
nrow()
## get counts of number households
num_hh <- study_data_cleaned %>%
## get unique houses by cluster
distinct(cluster_number, household_number) %>%
## get number of rounds (count how many unique)
nrow()
We included r num_hh households across r num_clus clusters in this survey analysis.
Among the r nrow(dropped) individuals excluded from the survey analysis,
r fmt_count(dropped, consent) individuals were excluded for not being between
6 and 60 months and r fmt_count(dropped, !consent) were excluded
for lack of consent. The reasons for no consent are shown below.
## using the dataset with dropped individuals
dropped %>%
## only keep reasons for no consent
select(no_consent_reason) %>%
## make NAs a factor level called missing
## to make the proportion of the total, including the missings
mutate(no_consent_reason = fct_explicit_na(no_consent_reason,
na_level = "Missing")) %>%
## get counts and proportions
tbl_summary() %>%
## make variable names bold
bold_labels() %>%
# change to flextable format
as_flex_table() %>%
# make header text bold (using {flextable})
bold(part = "header") %>%
# make your table fit to the maximum width of the word document
set_table_properties(layout = "autofit")
## get counts of the number of households per cluster
clustersize <- study_data_cleaned %>%
## trim data to only unique households within each cluster
distinct(cluster_number, household_number) %>%
## count the number of households within each cluster
count(cluster_number) %>%
pull(n)
## get the median number of households per cluster
clustermed <- median(clustersize)
## get the min and max number of households per cluster
## paste these together seperated by a dash
clusterrange <- str_c(range(clustersize), collapse = "--")
## get counts of children per household
## do this by cluster as household IDs are only unique within clusters
hhsize <- study_data_cleaned %>%
count(cluster_number, household_number) %>%
pull(n)
## get median number of children per household
hhmed <- median(hhsize)
## get the min and max number of children per household
## paste these together seperated by a dash
hhrange <- str_c(range(hhsize), collapse = "--")
## get standard deviation
hhsd <- round(sd(hhsize), digits = 1)
The median number of households per cluster was
r clustermed, with a range of r clusterrange. The median number of children
per household was r hhmed (range: r hhrange, standard deviation: r hhsd).
Demographic information
In total we included r nrow(study_data_cleaned) in the survey analysis.
The age break down and a comparison with the source population is shown below.
## counts and props of the study population
ag <- tabyl(study_data_cleaned, age_group, show_na = FALSE) %>%
mutate(n_total = sum(n),
age_group = fct_inorder(age_group))
## counts and props of the source population
propcount <- population_data_age %>%
group_by(age_group) %>%
tally(population) %>%
mutate(percent = n / sum(n))
## bind together the columns of two tables, group by age, and perform a
## binomial test to see if n/total is significantly different from population
## proportion.
## suffix here adds to text to the end of columns in each of the two datasets
left_join(ag, propcount, by = "age_group", suffix = c("", "_pop")) %>%
group_by(age_group) %>%
## broom::tidy(binom.test()) makes a data frame out of the binomial test and
## will add the variables p.value, parameter, conf.low, conf.high, method, and
## alternative. We will only use p.value here. You can include other
## columns if you want to report confidence intervals
mutate(binom = list(broom::tidy(binom.test(n, n_total, percent_pop)))) %>%
unnest(cols = c(binom)) %>% # important for expanding the binom.test data frame
mutate(
across(.cols = contains("percent"),
.fns = ~.x * 100)) %>%
## Adjusting the p-values to correct for false positives
## (because testing multiple age groups). This will only make
## a difference if you have many age categories
mutate(p.value = p.adjust(p.value, method = "holm")) %>%
## Only show p-values over 0.001 (those under report as <0.001)
mutate(p.value = ifelse(p.value < 0.001, "<0.001", as.character(round(p.value, 3)))) %>%
## rename the columns appropriately
select(
"Age group" = age_group,
"Study population (n)" = n,
"Study population (%)" = percent,
"Source population (n)" = n_pop,
"Source population (%)" = percent_pop,
"P-value" = p.value
) %>%
# produce styled output table with auto-adjusted column widths with {flextable}
qflextable() %>%
# make header text bold (using {flextable})
bold(part = "header") %>%
# make your table fit to the maximum width of the word document
set_table_properties(layout = "autofit") %>%
## set to only show 1 decimal place
colformat_double(digits = 1)
## compute the median age
medage <- median(study_data_cleaned$age_months)
## paste the lower and uper quartile together
iqr <- str_c( # basically copy paste together the following
## calculate the 25% and 75% of distribution, with missings removed
quantile(
study_data_cleaned$age_months,
c(0.25, 0.75),
na.rm = TRUE),
## between lower and upper place an en-dash
collapse = "--")
## compute overall sex ratio
sex_ratio <- study_data_cleaned %>%
count(sex) %>%
pivot_wider(names_from = sex, values_from = n) %>%
mutate(ratio = round(Male/Female, digits = 3)) %>%
pull(ratio)
## compute sex ratios by age group
sex_ratio_age <- study_data_cleaned %>%
count(age_group, sex) %>%
pivot_wider(names_from = sex, values_from = n) %>%
mutate(ratio = round(Male/Female, digits = 3)) %>%
select(age_group, ratio)
## sort table by ascending ratio then select the lowest (first)
min_sex_ratio_age <- arrange(sex_ratio_age, ratio) %>% slice(1)
Among the r nrow(study_data_cleaned) surveyed individuals, there were
r fmt_count(study_data_cleaned, sex == "Female") females and
r fmt_count(study_data_cleaned, sex == "Male") males (unweighted). The male to
female ratio was r sex_ratio in the surveyed population. The lowest male to
female ratio was r min_sex_ratio_age$ratio
in the r min_sex_ratio_age$age_group month age group.
The median age of surveyed individuals was r medage years (Q1-Q3 of r iqr
years). Children under two years of age made up
r fmt_count(study_data_cleaned, age_group_bin == "0-23")of the surveyed
individuals.
The highest number of surveyed individuals (unweighted) were in the
r table(study_data_cleaned$age_group) %>% which.max() %>% names()
year age group.
Unweighted age distribution of household population by year age group and gender.
# get cross tabulated counts and proportions
study_data_cleaned %>%
tbl_cross(
row = age_group,
col = sex,
percent = "cell") %>%
# change to flextable format
as_flex_table() %>%
# make header text bold (using {flextable})
bold(part = "header") %>%
# make your table fit to the maximum width of the word document
set_table_properties(layout = "autofit")
There were r fmt_count(dropped, is.na(sex)) cases missing
information on sex and
r fmt_count(dropped, is.na(age_group)) missing age group.
Unweighted age and gender distribution of household population covered by the
survey.
age_pyramid(study_data_cleaned,
age_group,
split_by = sex,
proportional = TRUE) +
labs(y = "Proportion", x = "Age group (months)") + # change axis labels
theme(legend.position = "bottom", # move legend to bottom
legend.title = element_blank(), # remove title
text = element_text(size = 18) # change text size
)
Unweighted age and gender distribution, stratified by health district,
of household population covered by the survey.
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// age_pyramid_strata \\
This chunk creates an unweighted (using study_data_cleaned) age/sex pyramid
of your cases, stratified by health district.
If you have a stratified survey design this may be useful for visualising
if you have an excess of representation in
either sex or gender in any of your survey strata.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
age_pyramid(study_data_cleaned,
age_group,
split_by = sex,
stack_by = health_district,
proportional = TRUE,
pal = c("red", "blue")) +
labs(y = "Proportion", x = "Age group (months)") + # change axis labels
theme(legend.position = "bottom", # move legend to bottom
legend.title = element_blank(), # remove title
text = element_text(size = 18) # change text size
)
Weighted age and gender distribution of household population covered by the survey.
age_pyramid(survey_design,
age_group,
split_by = sex,
proportion = TRUE) +
labs(y = "Proportion (weighted)", x = "Age group (months)") + # change axis labels
theme(legend.position = "bottom", # move legend to bottom
legend.title = element_blank(), # remove title
text = element_text(size = 18) # change text size
)
Quality of indicators collected
Box plot of Zscores for height-for-age, weight-for-age and weight-for-height
## pull variables together for plotting
temp_data <- study_data_cleaned %>%
## stack variable names in one column and values for vars in another
## call first column indicator and second column zscore
pivot_longer(cols = c(zwfl, zlen, zwei),
names_to = "Indicator",
values_to = "Zscore") %>%
## only keep variables of interest
select(Indicator, Zscore) %>%
## rename indicators to something more understandable
mutate(
Indicator = fct_recode(Indicator,
"HAZ" = "zlen",
"WAZ" = "zwei",
"WHZ" = "zwfl"
))
## use indicators on the x-axis and z-score on the y-axis
ggplot(temp_data, aes(x = Indicator, y = Zscore)) +
## plot as a box plot
geom_boxplot() +
## add a dotted horizontal line at 0 for reference
geom_hline(yintercept = 0, linetype = "dashed")
Box plot of Zscores for height-for-age, weight-for-age and weight-for-height by sex
## pull variables together for plotting
temp_data <- study_data_cleaned %>%
## stack variable names in one column and values for vars in another
## call first column indicator and second column zscore
pivot_longer(cols = c(zwfl, zlen, zwei),
names_to = "Indicator",
values_to = "Zscore") %>%
## only keep variables of interest
select(sex, Indicator, Zscore) %>%
## rename indicators to something more understandable
mutate(
Indicator = fct_recode(Indicator,
"HAZ" = "zlen",
"WAZ" = "zwei",
"WHZ" = "zwfl"
))
## use indicators on the x-axis and z-score on the y-axis
## colour according to sex
ggplot(temp_data, aes(x = Indicator, y = Zscore, fill = sex)) +
## plot as a boxplot
geom_boxplot() +
## add a dotted horizontal line at 0 for reference
geom_hline(yintercept = 0, linetype = "dashed") +
## remove the title of legend
theme(legend.title = element_blank())
Box plot of Zscores for height-for-age by age group
## use age group on the x-axis and height z-score on the y-axis
ggplot(study_data_cleaned, aes(x = age_group, y = zlen)) +
## plot as a boxplot
geom_boxplot() +
## add a dotted horizontal line at 0 for reference
geom_hline(yintercept = 0, linetype = "dashed") +
## change axis titles
labs(x = "Age group (Months)", y = "HAZ score")
Box plot of Zscores for weight-for-age by age group
## use age group on the x-axis and weight z-score on the y-axis
ggplot(study_data_cleaned, aes(x = age_group, y = zwei)) +
## plot as a boxplot
geom_boxplot() +
## add a dotted horizontal line at 0 for reference
geom_hline(yintercept = 0, linetype = "dashed") +
## change axis titles
labs(x = "Age group (Months)", y = "WAZ score")
Box plot of Zscores for weight-for-height by age group
## use age group on the x-axis and weight-height z-score on the y-axis
ggplot(study_data_cleaned, aes(x = age_group, y = zwfl)) +
## plot as a boxplot
geom_boxplot() +
## add a dotted horizontal line at 0 for reference
geom_hline(yintercept = 0, linetype = "dashed") +
## change axis titles
labs(x = "Age group (Months)", y = "WHZ score")
Unweighted z-curve of height-for-age among non-flagged children for this indicator
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// zcurve_haz \\
This chunk creates a z-curve of height-for-age compared to the WHO reference
population
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
study_data_cleaned %>%
## only consider z-scores that are not flagged
filter(flen == FALSE) %>%
## plot zcurve
zcurve(zlen)
Unweighted z-curve of weight-for-age among non-flagged children for this indicator
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// zcurve_haz \\
This chunk creates a z-curve of weight-for-age compared to the WHO reference
population
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
study_data_cleaned %>%
## only consider z-scores that are not flagged
filter(fwei == FALSE) %>%
## plot zcurve
zcurve(zwei)
Unweighted z-curve of weight-for-height among non-flagged children for this indicator
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// zcurve_whz \\
This chunk creates a z-curve of weighted-for-height compared to the WHO reference
population
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
study_data_cleaned %>%
## only consider z-scores that are not flagged
filter(fwfl == FALSE) %>%
## plot zcurve
zcurve(zwfl)
Unweighted counts and proportions of children missing or flagged for indicators
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// missing_flagged_indicators \\
This chunk creates an unweighted table of number children with missing or
flagged indicators
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
study_data_cleaned %>%
select(flen, fwei, fwfl) %>%
## mutate each of the flags be easier to enterprate
mutate(
across(everything(),
~case_when(
.x == TRUE ~ "Flagged",
.x == FALSE ~ "Included",
TRUE ~ "Missing"
))
) %>%
# Variable labels are removed by mutate(across(..)) for some reason
set_variable_labels(
## variable name = variable label
flen = "HAZ",
fwei = "WAZ",
fwfl = "WHZ"
) %>%
tbl_summary() %>%
# change to flextable format
as_flex_table() %>%
# make header text bold (using {flextable})
bold(part = "header") %>%
# make your table fit to the maximum width of the word document
set_table_properties(layout = "autofit")
In addition the number of children missing MUAC
was r fmt_count(study_data_cleaned, is.na(muac)).
Nutritional status based on indicators
Weighted prevalence of malnutrition based on MUAC, by age group (months)
and overall
overall <- survey_design %>%
## tabulate multiple variables with same values
select(all_of(MUAC)) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE)
age_strat <- survey_design %>%
## tabulate multiple variables with same values
select(all_of(MUAC), age_group) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE,
## stratify by age group
by = age_group)
## combine the overall and stratified tables
tbl_merge(list(overall, age_strat)) %>%
modify_spanning_header(
list(
## rename the spanning header
## you can see what the columns are called by putting in an object and inspecting table_body
stat_0_1 ~ "**Overall**",
c(stat_1_2,
stat_2_2,
stat_3_2,
stat_4_2,
stat_5_2) ~ "**Age group (months)**")) %>%
# change to flextable format
as_flex_table() %>%
# make header text bold (using {flextable})
bold(part = "header") %>%
# make your table fit to the maximum width of the word document
set_table_properties(layout = "autofit")
Weighted prevalence of malnutrition based on MUAC among children <87cm,
by age group (months) and overall
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// muac_age_group_filter \\
This chunk creates a weighted table of prevalence based on MUAC for age groups
and for the overall population among children under 87cm tall (using filter).
This happens in three stages:
- Table for overall
- Table for age groups
- Bind the two together as rows
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
overall <- survey_design %>%
## only keep children less than 87cm
filter(height < 87) %>%
## tabulate multiple variables with same values
select(all_of(MUAC)) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE)
age_strat <- survey_design %>%
## only keep children less than 87cm
filter(height < 87) %>%
## tabulate multiple variables with same values
select(all_of(MUAC), age_group) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE,
## stratify by age group
by = age_group)
## combine the overall and stratified tables
tbl_merge(list(overall, age_strat)) %>%
modify_spanning_header(
list(
## rename the spanning header
## you can see what the columns are called by putting in an object and inspecting table_body
stat_0_1 ~ "**Overall**",
c(stat_1_2,
stat_2_2,
stat_3_2,
stat_4_2,
stat_5_2) ~ "**Age group (months)**")) %>% #
# change to flextable format
as_flex_table() %>%
# make header text bold (using {flextable})
bold(part = "header") %>%
# make your table fit to the maximum width of the word document
set_table_properties(layout = "autofit")
Weighted prevalence of malnutrition based on height-for-age z-score categories,
by age group (months) and overall
overall <- survey_design %>%
## tabulate multiple variables with same values
select(all_of(HAZ)) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE)
age_strat <- survey_design %>%
## tabulate multiple variables with same values
select(all_of(HAZ), age_group) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE,
## stratify by age group
by = age_group)
## combine the overall and stratified tables
tbl_merge(list(overall, age_strat)) %>%
modify_spanning_header(
list(
## rename the spanning header
## you can see what the columns are called by putting in an object and inspecting table_body
stat_0_1 ~ "**Overall**",
c(stat_1_2,
stat_2_2,
stat_3_2,
stat_4_2,
stat_5_2) ~ "**Age group (months)**")) %>%
# change to flextable format
as_flex_table() %>%
# make header text bold (using {flextable})
bold(part = "header") %>%
# make your table fit to the maximum width of the word document
set_table_properties(layout = "autofit")
Weighted prevalence of malnutrition based on weight-for-age z-score categories,
by age group (months) and overall
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// waz_age_group \\
This chunk creates a weighted table of prevalence based on weight-for-age
z-scores for age groups and for the overall population.
This happens in three stages:
- Table for overall
- Table for age groups
- Bind the two together as rows
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
overall <- survey_design %>%
## tabulate multiple variables with same values
select(all_of(WAZ)) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE)
age_strat <- survey_design %>%
## tabulate multiple variables with same values
select(all_of(WAZ), age_group) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE,
## stratify by age group
by = age_group)
## combine the overall and stratified tables
tbl_merge(list(overall, age_strat)) %>%
modify_spanning_header(
list(
## rename the spanning header
## you can see what the columns are called by putting in an object and inspecting table_body
stat_0_1 ~ "**Overall**",
c(stat_1_2,
stat_2_2,
stat_3_2,
stat_4_2,
stat_5_2) ~ "**Age group (months)**")) %>%
# change to flextable format
as_flex_table() %>%
# make header text bold (using {flextable})
bold(part = "header") %>%
# make your table fit to the maximum width of the word document
set_table_properties(layout = "autofit")
Weighted prevalence of malnutrition based on weight-for-height z-score categories,
by age group (months) and overall
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// whz_age_group \\
This chunk creates a weighted table of prevalence based on weight-for-height
z-scores for age groups and for the overall population.
This happens in three stages:
- Table for overall
- Table for age groups
- Bind the two together as rows
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
overall <- survey_design %>%
## tabulate multiple variables with same values
select(all_of(WHZ)) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE)
age_strat <- survey_design %>%
## tabulate multiple variables with same values
select(all_of(WHZ), age_group) %>%
## only show the row with TRUE
tbl_svysummary(missing = "no",
value = everything() ~ TRUE,
## stratify by age group
by = age_group)
## combine the overall and stratified tables
tbl_merge(list(overall, age_strat)) %>%
modify_spanning_header(
list(
## rename the spanning header
## you can see what the columns are called by putting in an object and inspecting table_body
stat_0_1 ~ "**Overall**",
c(stat_1_2,
stat_2_2,
stat_3_2,
stat_4_2,
stat_5_2) ~ "**Age group (months)**")) %>%
# change to flextable format
as_flex_table() %>%
# make header text bold (using {flextable})
bold(part = "header") %>%
# make your table fit to the maximum width of the word document
set_table_properties(layout = "autofit")
R4EPI/r4epi documentation built on Feb. 13, 2023, 3:25 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Introduction to this template
This is a template which can be used to create a report from a retrospective nutrition survey.
- There are sections for reading and cleaning data, calculating
anthropometric indicators based on z-score counts followed by
weighting and then survey analysis. - For a more detailed explanation of this template, please visit https://r4epis.netlify.com/surveys
-
Feedback and suggestions are welcome at the GitHub issues page
-
Text within <! > will not show in your final document. These comments are used to explain the template. You can delete them if you want.
Data analysis: Definitions and standards
We used the following definitions for the analysis of the survey results for Weight for Height z-scores (WHZ):
- Global acute malnutrition (GAM): a WHZ score of less than (<) -2 and/or oedema;
- Moderate acute malnutrition: WHZ score <-2 and ≥ -3 and no oedema;
- Severe acute malnutrition (SAM): WHZ score <-3 and/or oedema.
We used the following definitions for the analysis of the survey results for MUAC measurements:
- Global acute malnutrition (GAM): MUAC of <125mm and/or oedema;
- Moderate acute malnutrition: MUAC <125mm and >= 115mm and no oedema;
- Severe acute malnutrition (SAM): MUAC <115mm and/or oedema.
In order to estimate stunting in the surveyed population, we looked at Height for Age z-scores (HAZ) and used the following definitions:
- Stunting: HAZ score <-2;
- Moderate stunting: HAZ score >=-3 and <-2;
- Severe stunting: HAZ score <-3.
In order to estimate underweight in the surveyed population, we looked at Weight for Age z-scores (WAZ) and used the following definitions:
- Underweight: WAZ score < -2;
- moderate underweight: WAZ score >=-3 and <-2;
- Severe underweight: WAZ <-3
Exclusion of z-scores from Observed mean SMART flags included:
WHZ: <-5 or >5;
HAZ: <-6 or >6;
* WAZ: <-6 or >5.
Installing and loading required packages
## hide all code chunks in the output, but show errors knitr::opts_chunk$set(echo = FALSE, error = TRUE, fig.width = 6*1.25, fig.height = 6) ## set default NA to - in output, define figure width/height options(knitr.kable.NA = "-") # Ensures the package "pacman" is installed if (!require("pacman")) { install.packages("pacman") } # Install and load required packages for this template pacman::p_load( knitr, # create output docs here, # find your files rio, # for importing data janitor, # clean/shape data dplyr, # clean/shape data tidyr, # clean/shape data forcats, # manipulate and rearrange factors stringr, # manipulate texts ggplot2, # create plots and charts apyramid, # plotting age pyramids sitrep, # MSF field epi functions anthro, # WHO Child Growth Standards (wrapper of survey) survey, # for survey functions srvyr, # dplyr wrapper for survey package gtsummary, # produce tables flextable, # for styling output tables labelled, # add labels to variables matchmaker, # recode datasets with dictionaries parsedate # guessing dates ) ## set default text size to 16 for plots ## give classic black/white axes for plots ggplot2::theme_set(theme_classic(base_size = 18))
## generates MSF standard dictionary for Kobo study_data_dict <- msf_dict_survey("Nutrition") ## generates MSF standard dictionary for Kobo in long format (for recoding) study_data_dict_long <- msf_dict_survey(disease = "Nutrition", compact = FALSE) ## generates a fake dataset for use as an example in this template ## this dataset already has household and individual levels merged study_data_raw <- gen_data(dictionary = "Nutrition", varnames = "name", numcases = 1000)
### Read in data --------------------------------------------------------------- ## Excel file ------------------------------------------------------------------ ## read in household data sheet # study_data_hh <- rio::import(here::here("nutrition_survey.xlsx"), # which = "nutrition_survey_erb", na = "") ## read in individual level data sheet # study_data_indiv <- rio::import(here::here("nutrition_survey.xlsx", # which = "r1", na = "") ## Excel file with password ---------------------------------------------------- ## Use this section if your Excel has a password. # install.packages(c("excel.link", "askpass")) # library(excel.link) # study_data_hh <- xl.read.file(here::here("nutrition_survey.xlsx"), # xl.sheet = "nutrition_survey_erb", # password = askpass::askpass(prompt = "please enter file password")) # study_data_indiv <- xl.read.file(here::here("nutrition_survey.xlsx"), # xl.sheet = "r1", # password = askpass::askpass(prompt = "please enter file password"))
## Excel file ------------------------------------------------------------------ ## to read in a specific sheet use "which" # study_data_hh <- rio::import(here::here("nutrition_survey.xlsx"), which = "Sheet1") ## Excel file -- Specific range ------------------------------------------------ ## you can specify a range in an excel sheet. # study_data_hh <- rio::import(here::here("nutrition_survey.xlsx"), range = "B2:J102") ## Excel file with password ---------------------------------------------------- ## use this section if your Excel has a password. # install.packages(c("excel.link", "askpass")) # library(excel.link) # study_data_hh <- xl.read.file(here::here("nutrition_survey.xlsx"), # xl.sheet = "Sheet1", # password = askpass::askpass(prompt = "please enter file password")) ## CSV file -------------------------------------------------------------------- # study_data_hh <- rio::import(here::here("nutrition_survey.csv")) ## Stata data file ------------------------------------------------------------- # study_data_hh <- rio::import(here::here("nutrition_survey.dat"))
## join the individual and household data to form a complete data set #study_data_raw <- left_join(study_data_hh, study_data_indiv, by = c("_index" = "_parent_index"))
## Data dictionary ------------------------------------------------------------- ## read in a kobo data dictionary ## important to specify template is FALSE (otherwise you get the generic dict) # study_data_dict <- msf_dict_survey(name = here::here("nutrition_survey_dict.xlsx"), # template = FALSE) ## look at the dictionary by uncommenting the line below # View(study_data_dict) ## Clean column names ---------------------------------------------------------- ## This step fixes the column names so they are easy to use in R. ## make a copy of your orginal dataset and name it study_data_cleaned study_data_cleaned <- study_data_raw ## Sometimes you want to rename specific variables ## The formula for this is rename(data, NEW_NAME = OLD_NAME). ## You can add multiple column name recodes by simply separating them with a comma # study_data_cleaned <- rename(study_data_cleaned, # violence_nature_other_details = violence_nature_other) ## define clean variable names using clean_names from the janitor package. study_data_cleaned <- janitor::clean_names(study_data_cleaned) ## create a unique identifier by combining indeces of the two levels ## x and y are added on to the end of variables that are duplicated ## (in this case, parent and child index) # study_data_cleaned <- study_data_cleaned %>% # mutate(uid = str_glue("{index}_{index_y}"))
## MSF Survey Dictionary ---------------------------------------------------------- ## generates MSF standard dictionary for Kobo # study_data_dict <- msf_dict_survey("Nutrition") ## generates MSF standard dictionary for Kobo in long format (for recoding) # study_data_dict_long <- msf_dict_survey(disease = "Nutrition", compact = FALSE) ## look at the standard dictionary by uncommenting the line below # View(study_data_dict) ## You will need to recode your variables to match the data dictionary. This is ## addressed below. ## Clean column names ---------------------------------------------------------- ## This step fixes the column names so they are easy to use in R. ## make a copy of your orginal dataset and name it study_data_cleaned # study_data_cleaned <- study_data_raw ## define clean variable names using clean_names from the janitor package. # study_data_cleaned <- janitor::clean_names(study_data_cleaned) ## Match column names --------------------------------------------------------- ## This step helps you match your variables to the standard variables. ## This step will require some patience. Courage! ## Use the function msf_dict_rename_helper() to create a template based on the ## standard dictionary. This will copy a rename command like the one above to your ## clipboard. # msf_dict_rename_helper("nutrition", varnames = "name") ## Paste the result below and your column names to the matching variable. ## Be careful! You still need to be aware of what each variable means and what ## values it takes. ## If there are any variables that are in the MSF dictionary that are not in ## your data set, then you should comment them out, but be aware that some ## analyses may not run because of this. ## PASTE HERE ## Here is an EXAMPLE for changing a few specific names. function. In this ## example, we have the columns "gender" and "age" that we want to rename as ## "sex" and "age_years". ## The formula for this is rename(data, NEW_NAME = OLD_NAME). # study_data_cleaned <- rename(study_data_cleaned, # sex = gender, # TEXT # age_years = age # INTEGER_POSITIVE # )
## Read data ------------------------------------------------------------------- ## This step reads in your population data from Excel. ## You may need to rename your columns. # population_data <- rio::import(here::here("population.xlsx"), which = "Sheet1") ## repeat preparation steps as appropriate ## Enter counts directly ------------------------------------------------------- ## Below is an example of how to enter population counts by groups. # population_data_age <- gen_population( # groups = c("0-2", "3-14", "15-29", "30-44", "45+"), # counts = c(3600, 18110, 13600, 8080, 6600), # strata = NULL) %>% # rename(age_group = groups, # population = n) ## Create counts from proportions ---------------------------------------------- ## This step helps you estimate sub-group size with proportions. ## You need to replace the total_pop and proportions. You can change the groups ## to fit your needs. ## Here we repeat the steps for two regions (district A and B) then bind the two ## together ## generate population data by age groups in years for district A population_data_age_district_a <- gen_population(total_pop = 10000, # set total population groups = c("6-11", "12-23", "24-35", "36-47", "48-60"), # set groups proportions = c(0.0164, 0.0164, 0.015, 0.015, 0.015), # set proportions for each group strata = c("Male", "Female")) %>% # stratify by gender rename(age_group = groups, # rename columns (NEW NAME = OLD NAME) sex = strata, population = n) %>% mutate(health_district = "district_a") # add a column to identify region ## generate population data by age groups in years for district B population_data_age_district_b <- gen_population(total_pop = 10000, # set total population groups = c("6-11", "12-23", "24-35", "36-47", "48-60"), # set groups proportions = c(0.0164, 0.0164, 0.015, 0.015, 0.015), # set proportions for each group strata = c("Male", "Female")) %>% # stratify by gender rename(age_group = groups, # rename columns (NEW NAME = OLD NAME) sex = strata, population = n) %>% mutate(health_district = "district_b") # add a column to identify region ## bind region population data together to get overall population population_data_age <- bind_rows(population_data_age_district_a, population_data_age_district_b)
cluster_counts <- tibble(cluster = c("Village 1", "Village 2", "Village 3", "Village 4", "Village 5", "Village 6", "Village 7", "Village 8", "Village 9", "Village 10"), households = c(700, 400, 600, 500, 300, 800, 700, 400, 500, 500))
## view the first ten rows of data head(study_data_raw, n = 10) ## view your whole dataset interactivley (in an excel style format) View(study_data_raw) ## overview of variable types and contents str(study_data_raw) ## gives mean, median and max values of variables ## gives counts for categorical variables ## also gives number of NAs summary(study_data_raw) ## view unique values contained in variables ## you can run this for any column -- just replace the column name unique(study_data_raw$sex) ## check for logical inconsistencies ## for example check age <6 months and height >100 cm and return corresponding IDs study_data_raw %>% filter(age_month < 6 & height > 100) %>% select("uid") ## use the dfSummary function in combination with view ## note that view is not capitalised with this package # summarytools::dfSummary(study_data_cleaned) %>% # summarytools::view()
## Kobo standard data -------------------------------------------------------- ## If you got your data from Kobo, use this portion of the code. ## If not, comment this section out and use the below. ## make sure all date variables are formatted as dates ## get the names of variables which are dates DATEVARS <- study_data_dict %>% filter(type == "date") %>% filter(name %in% names(study_data_cleaned)) %>% ## filter to match the column names of your data pull(name) # select date vars ## find if there are date variables which are completely empty EMPTY_DATEVARS <- purrr::map(DATEVARS, ~all( is.na(study_data_cleaned[[.x]]) )) %>% unlist() %>% which() ## remove exclude the names of variables which are completely emptys DATEVARS <- DATEVARS[-EMPTY_DATEVARS] ## change to dates ## use the parse_date() function to make a first pass at date variables. ## parse_date() produces a complicated format - so we use as.Date() to simplify study_data_cleaned <- study_data_cleaned %>% mutate( across(.cols = all_of(DATEVARS), .fns = ~parsedate::parse_date(.x) %>% as.Date())) ## Non-Kobo data ------------------------------------------------------------- ## Use this section if you did not have Kobo data. ## use the parse_date() function to make a first pass at date variables. ## parse_date() produces a complicated format - so we use as.Date() to simplify # study_data_cleaned <- study_data_cleaned %>% # mutate( # across(.cols = matches("date|Date"), # .fns = ~parsedate::parse_date(.x) %>% as.Date())) ## Fix wrong dates ------------------------------------------------------------- ## Some dates will be unrealistic or wrong. ## Here is an example of how to manually fix dates. ## Look at your data and edit as needed. ## set specific unrealistic dates to NA # study_data_cleaned <- mutate(study_data_cleaned, # date < as.Date("2017-11-01") ~ as.Date(NA), # date == as.Date("2081-01-01") ~ as.Date("2018-01-01"))
## Age group variables ---------------------------------------------------------- ## This step shows you how to create categorical variables from numeric variables. ## We have some intermediate steps on the way. ## make sure age is an integer study_data_cleaned <- study_data_cleaned %>% mutate(age_months = as.integer(age_months), age_years = as.integer(age_months)) ## add convert years to months (for those over 1 year) study_data_cleaned <- study_data_cleaned %>% mutate(age_months = if_else( age_years >= 1, as.integer(age_years * 12), as.integer(age_months) )) ## create an age group variable (combining those over 24 months and those under) study_data_cleaned <- study_data_cleaned %>% mutate(age_group_bin = factor( if_else(age_months >= 24, "24-60", "0-23" ) )) ## create age group variable for based on months study_data_cleaned <- study_data_cleaned %>% mutate(age_group = age_categories(study_data_cleaned$age_months, breakers = c(6, 12, 24, 36, 48, 60), ceiling = TRUE)) ## alternatively, create an age group variable specify a sequence # study_data_cleaned$age_group <- age_categories(study_data_cleaned$age, # lower = 0, # upper = 100, # by = 10) ## If you already have an age group variable defined, you should manually ## arrange the categories # study_data_cleaned$age_group <- factor(study_data_cleaned$age_group, # c("0-4y", "5-14y", "15-29y", "30-44y", "45+y")) ## to combine different age categories use the following function ## this prioritises the smaller unit, i.e. if given months and years, will return months first # study_data_cleaned <- group_age_categories(study_data_cleaned, # years = age_group, # months = age_group_mon)
## recode values with matchmaker package (value labels cant be used for analysis) study_data_cleaned <- match_df(study_data_cleaned, study_data_dict_long, from = "option_name", to = "option_label_english", by = "name", order = "option_order_in_set")
## Change a yes/no variable in to TRUE/FALSE ## create a new variable called consent ## where the old one is yes place TRUE in the new one ## (this could also be done with the if_else or case_when function - ## but this option is shorter) study_data_cleaned <- study_data_cleaned %>% mutate(consent = consent == "Yes") ## Change a character to factor - set the levels of a factor study_data_cleaned <- study_data_cleaned %>% mutate(sex = factor(sex, levels = c("Female", "Male")) ) ## recode the levels of a factor ## put these in a second variable called sex_brief ## (this is necessary because the anthro package doesnt accept "Male"/"female") study_data_cleaned <- study_data_cleaned %>% mutate(sex_brief = fct_recode(sex, "F" = "Female", "M" = "Male") ) # ## change the order of levels # study_data_cleaned <- study_data_cleaned %>% # mutate(soap = fct_relevel(soap, # "Distribution", # "Healthcentre", # "Never") # ) # ## create a new grouping for soap variable # ## simplified, distribution or health centre then covered otherwise not covered # study_data_cleaned <- study_data_cleaned %>% # mutate(coverage = if_else(soap %in% c("Distribution", "Healthcentre"), # "Covered", # "Not covered") # ) ## Recode character variables ## This step shows how to fix misspellings in the geographic region variable. ## Ideally, you want these values to match and population data! # study_data_cleaned <- study_data_cleaned %>% # mutate(village_name = case_when( # village_name == "Valliages 1" ~ "village 1", # village_name == "Village1" ~ "village 1", # village_name == "Town 3" ~ "village 3" # village_name == "Town3" ~ "village 3", # TRUE ~ as.character(village_name)) # )) ## create a character variable based off groups of a different variable study_data_cleaned <- study_data_cleaned %>% mutate(health_district = case_when( cluster_number %in% c(1:5) ~ "district_a", TRUE ~ "district_b" )) ## explicitly replace NA of a factor # study_data_cleaned <- study_data_cleaned %>% # mutate(coverage = fct_explicit_na(coverage, na_level = "Not Applicable")) ## if you had a multi-choice question and the missing values were given as a "." ## replace missing values in multi-choice questions to "" so that we can ## filter them out later. # study_data_cleaned <- study_data_cleaned %>% # mutate( # across( # .cols = contains("violence"), # all variables that contain the word "violence" # .fns = ~fct_explicit_na(as.character(.), "") # replace missing values with "" # ) # ) ## fix factor levels ----------------------------------------------------------- ## make sure there are the appropriate levels (names) study_data_cleaned$no_consent_reason <- fct_recode(study_data_cleaned$no_consent_reason, "No time" = "I do not have time", "Previous negative experience" = "I have had a negative experience with a previous survey.", "No perceived benefit" = "There is no benefit to me and my family" )
## anthro zscores -------------------------------------------------------------- ## retrieve zscores zscore_results <- with(study_data_cleaned, anthro_zscores( sex = as.character(sex_brief), age = age_months, is_age_in_month = TRUE, weight = weight, lenhei = height, oedema = as.numeric(oedema), armc = muac / 10 # convert to cm )) ## add columns from zscore_results columns to study dataset study_data_cleaned <- bind_cols(study_data_cleaned, zscore_results) ## categorise children --------------------------------------------------------- ## weight for height z-scores ## * Global acute malnutrition (GAM): a WHZ score of less than (<) -2 and/or oedema; ## * Moderate acute malnutrition: WHZ score <-2 and ≥ -3 and no oedema; ## * Severe acute malnutrition (SAM): WHZ score <-3 and/or oedema. study_data_cleaned <- study_data_cleaned %>% mutate( gam_whz = zwfl < -2 | oedema == "Yes", mam_whz = zwfl >= -3 & zwei < -2, sam_whz = zwfl < -3 | oedema == "Yes" ) %>% ## set flagged children to NA for each of the indicator variables ## if the flag for this indicator is not missing and is 1 then set indicator vars to NA ## else leave the indicator variable as it was mutate( across( .cols = c(gam_whz, mam_whz, sam_whz), # select the indicator variables .fns = ~if_else(!is.na(fwfl) & fwfl == 1, NA, .)) # NA if flagged, else leave as is ) ## stunting according to height for age z-scores ## * Stunting: HAZ score <-2; ## * Moderate stunting: HAZ score >=-3 and <-2; ## * Severe stunting: HAZ score <-3. study_data_cleaned <- study_data_cleaned %>% mutate( stunting_haz = zlen < -2, moderate_stunting_haz = zlen >= -3 & zlen < -2, severe_stunting_haz = zlen < -3 ) %>% ## set flagged children to NA for each of the indicator variables ## if the flag for this indicator is not missing and is 1 then set indicator vars to NA ## else leave the indicator variable as it was mutate( across( .cols = c(stunting_haz, moderate_stunting_haz, severe_stunting_haz), # select the indicator variables .funs = ~if_else(!is.na(flen) & flen == 1, NA, .))) # NA if flagged, else leave as is ## underweight according to height for age z-scores ## * Underweight: WAZ score < -2 OR oedema; ## * moderate underweight: WAZ score >=-3 and <-2; ## * Severe underweight: WAZ < -3 OR oedema study_data_cleaned <- study_data_cleaned %>% mutate( underweight_waz = zwei < -2 | oedema == "Yes", moderate_underweight_waz = zwei >= -3 & zwei < -2, severe_underweight_waz = zwei < -3 | oedema == "Yes" ) %>% ## set flagged children to NA for each of the indicator variables ## if the flag for this indicator is not missing and is 1 then set indicator vars to NA ## else leave the indicator variable as it was mutate( across( .cols = c(underweight_waz, moderate_underweight_waz, severe_underweight_waz), # select the indicator variables .fns = ~if_else(!is.na(fwei) & fwei == 1, NA, .))) # NA if flagged, else leave as is ## according to MUAC ## * Global acute malnutrition (GAM): MUAC of <125mm and/or oedema; ## * Moderate acute malnutrirtion: MUAC <125mm and >= 115mm and no oedema; ## * Severe acute malnutrition (SAM): MUAC <115mm and/or oedema. study_data_cleaned <- study_data_cleaned %>% mutate( gam_muac = muac < 125 | oedema == "Yes", mam_muac = muac < 125 & muac >= 115 & oedema == "No", sam_muac = muac < 115 | oedema == "Yes" ) ## group indicator variables --------------------------------------------------- ## define all the indicators of interest ## we will use this to run the same function over all variables later on WHZ <- c("gam_whz", "mam_whz", "sam_whz") HAZ <- c("stunting_haz", "moderate_stunting_haz", "severe_stunting_haz") WAZ <- c("underweight_waz", "moderate_underweight_waz", "severe_underweight_waz") MUAC <- c("gam_muac", "mam_muac", "sam_muac") indicators <- c(WHZ, HAZ, WAZ, MUAC) ## turn all indicators in to factors study_data_cleaned <- study_data_cleaned %>% mutate( across( .cols = all_of(indicators), # all variables named in indicators .fns = factor # turn into a factor )) ## turn all flags in to TRUE/FALSE variables study_data_cleaned <- study_data_cleaned %>% mutate( across( .cols = all_of(c("fwei", "flen", "fwfl")), # names of flag variables .fns = as.logical # turn in to logical ))
## create variable names with labelled ## define a list of names and labels based on the dictionary var_labels <- setNames( ## add variable labels as a list as.list(study_data_dict$short_name), ## name the list with the current variable names study_data_dict$name) ## add the variable labels to dataset study_data_cleaned <- study_data_cleaned %>% set_variable_labels( ## set the labels with the object defined above .labels = var_labels, ## do not throw an error if some names dont match ## not all names in the dictionary appear in the dataset .strict = FALSE) ## it is possible to update individual variables manually too study_data_cleaned <- study_data_cleaned %>% set_variable_labels( ## variable name = variable label age_years = "Age (years)", age_months = "Age (months)", age_group = "Age group (months)", age_group_bin = "Age category (months)", flen = "HAZ", fwei = "WAZ", fwfl = "WHZ", gam_muac = "GAM", mam_muac = "MAM" , sam_muac = "SAM", moderate_stunting_haz = "Moderate stunting", severe_stunting_haz = "Severe stunting", stunting_haz = "Stunting", moderate_underweight_waz = "Moderate underweight", severe_underweight_waz = "Severe underweight", underweight_waz = "Underweight", gam_whz = "GAM", mam_whz = "MAM", sam_whz = "SAM" )
## Drop unused rows ----------------------------------------------------------- ## store the cases that you drop so you can describe them (e.g. non-consenting) dropped <- study_data_cleaned %>% filter(!consent | age_months < 6 | age_months > 60 | ## note that whatever you use for weights cannot be missing! village_name == "Other"| is.na(age_years) | is.na(sex)) ## drop the unused rows from the survey data set study_data_cleaned <- anti_join(study_data_cleaned, dropped, by = names(dropped)) ## Drop columns ---------------------------------------------------------------- ## OPTIONAL: This step shows you how you can remove certain variables. ## study_data_cleaned <- select(study_data_cleaned, -c("age_years", "sex")) ## OPTIONAL: if you want to inspect certain variables, you can select these by ## name or column number. This example creates a reduced dataset for the first ## three columns, age_years, and sex. # study_data_reduced <- select(study_data_cleaned, c(1:3, "age_years", "sex")
## option 1: only keep the first occurrence of duplicate case study_data_cleaned <- study_data_cleaned %>% ## find duplicates based on case number, sex and age group ## only keep the first occurrence distinct(uid, sex, age_group, .keep_all = TRUE) # ## option 2: create flagging variables for duplicates (then use to browse) # # study_data_cleaned <- study_data_cleaned %>% # ## choose which variables to use for finding unique rows # group_by(uid, sex, age_group) %>% # mutate( # ## get the number of times duplicate occurs # num_dupes = n(), # duped = if_else(num_dupes > 1 , TRUE, FALSE) # ) # # ## browse duplicates based on flagging variables # study_data_cleaned %>% # ## only keep rows that are duplicated # filter(duped) %>% # ## arrange by variables of interest # arrange(uid, sex, age_group) %>% # View() # # ## filter duplicates to only keep the row with the earlier entry # study_data_cleaned %>% # ## choose which variables to use for finding unique rows # group_by(uid, sex, age_group) %>% # ## sort to have the earliest date by person first # arrange(as.Date(start)) %>% # ## only keep the earliest row # slice(1)
## stratified ------------------------------------------------------------------ ## create a variable called "surv_weight_strata" ## contains weights for each individual - by age group, sex and health district study_data_cleaned <- add_weights_strata(x = study_data_cleaned, p = population_data_age, surv_weight = "surv_weight_strata", surv_weight_ID = "surv_weight_ID_strata", age_group, sex, health_district) ## cluster --------------------------------------------------------------------- ## get the number of individuals interviewed per household ## adds a variable with counts of the household (parent) index variable study_data_cleaned <- study_data_cleaned %>% add_count(index, name = "interviewed") ## create cluster weights study_data_cleaned <- add_weights_cluster(x = study_data_cleaned, cl = cluster_counts, eligible = number_children, interviewed = interviewed, cluster_x = village_name, cluster_cl = cluster, household_x = index, household_cl = households, surv_weight = "surv_weight_cluster", surv_weight_ID = "surv_weight_ID_cluster", ignore_cluster = FALSE, ignore_household = FALSE) ## stratified and cluster ------------------------------------------------------ ## create a survey weight for cluster and strata study_data_cleaned <- study_data_cleaned %>% mutate(surv_weight_cluster_strata = surv_weight_strata * surv_weight_cluster)
## simple random --------------------------------------------------------------- survey_design_simple <- study_data_cleaned %>% as_survey_design(ids = 1, # 1 for no cluster ids weights = NULL, # No weight added strata = NULL # sampling was simple (no strata) ) ## stratified ------------------------------------------------------------------ survey_design_strata <- study_data_cleaned %>% as_survey_design(ids = 1, # 1 for no cluster ids weights = surv_weight_strata, # weight variable created above strata = health_district # sampling was stratified by district ) ## cluster --------------------------------------------------------------------- survey_design_cluster <- study_data_cleaned %>% as_survey_design(ids = village_name, # cluster ids weights = surv_weight_cluster, # weight variable created above strata = NULL # sampling was simple (no strata) ) ## stratified cluster ---------------------------------------------------------- survey_design <- study_data_cleaned %>% as_survey_design(ids = village_name, # cluster ids weights = surv_weight_cluster_strata, # weight variable created above strata = health_district # sampling was stratified by district )
rio::export(study_data_cleaned, here::here("data", str_glue("study_data_cleaned_{Sys.Date()}.xlsx")))
Results
Survey inclusion
## get counts of number of clusters num_clus <- study_data_cleaned %>% ## trim data to unique clusters distinct(cluster_number) %>% ## get number of rows (count how many unique) nrow() ## get counts of number households num_hh <- study_data_cleaned %>% ## get unique houses by cluster distinct(cluster_number, household_number) %>% ## get number of rounds (count how many unique) nrow()
We included r num_hh households across r num_clus clusters in this survey analysis.
Among the r nrow(dropped) individuals excluded from the survey analysis,
r fmt_count(dropped, consent) individuals were excluded for not being between
6 and 60 months and r fmt_count(dropped, !consent) were excluded
for lack of consent. The reasons for no consent are shown below.
## using the dataset with dropped individuals dropped %>% ## only keep reasons for no consent select(no_consent_reason) %>% ## make NAs a factor level called missing ## to make the proportion of the total, including the missings mutate(no_consent_reason = fct_explicit_na(no_consent_reason, na_level = "Missing")) %>% ## get counts and proportions tbl_summary() %>% ## make variable names bold bold_labels() %>% # change to flextable format as_flex_table() %>% # make header text bold (using {flextable}) bold(part = "header") %>% # make your table fit to the maximum width of the word document set_table_properties(layout = "autofit")
## get counts of the number of households per cluster clustersize <- study_data_cleaned %>% ## trim data to only unique households within each cluster distinct(cluster_number, household_number) %>% ## count the number of households within each cluster count(cluster_number) %>% pull(n) ## get the median number of households per cluster clustermed <- median(clustersize) ## get the min and max number of households per cluster ## paste these together seperated by a dash clusterrange <- str_c(range(clustersize), collapse = "--") ## get counts of children per household ## do this by cluster as household IDs are only unique within clusters hhsize <- study_data_cleaned %>% count(cluster_number, household_number) %>% pull(n) ## get median number of children per household hhmed <- median(hhsize) ## get the min and max number of children per household ## paste these together seperated by a dash hhrange <- str_c(range(hhsize), collapse = "--") ## get standard deviation hhsd <- round(sd(hhsize), digits = 1)
The median number of households per cluster was
r clustermed, with a range of r clusterrange. The median number of children
per household was r hhmed (range: r hhrange, standard deviation: r hhsd).
Demographic information
In total we included r nrow(study_data_cleaned) in the survey analysis.
The age break down and a comparison with the source population is shown below.
## counts and props of the study population ag <- tabyl(study_data_cleaned, age_group, show_na = FALSE) %>% mutate(n_total = sum(n), age_group = fct_inorder(age_group)) ## counts and props of the source population propcount <- population_data_age %>% group_by(age_group) %>% tally(population) %>% mutate(percent = n / sum(n)) ## bind together the columns of two tables, group by age, and perform a ## binomial test to see if n/total is significantly different from population ## proportion. ## suffix here adds to text to the end of columns in each of the two datasets left_join(ag, propcount, by = "age_group", suffix = c("", "_pop")) %>% group_by(age_group) %>% ## broom::tidy(binom.test()) makes a data frame out of the binomial test and ## will add the variables p.value, parameter, conf.low, conf.high, method, and ## alternative. We will only use p.value here. You can include other ## columns if you want to report confidence intervals mutate(binom = list(broom::tidy(binom.test(n, n_total, percent_pop)))) %>% unnest(cols = c(binom)) %>% # important for expanding the binom.test data frame mutate( across(.cols = contains("percent"), .fns = ~.x * 100)) %>% ## Adjusting the p-values to correct for false positives ## (because testing multiple age groups). This will only make ## a difference if you have many age categories mutate(p.value = p.adjust(p.value, method = "holm")) %>% ## Only show p-values over 0.001 (those under report as <0.001) mutate(p.value = ifelse(p.value < 0.001, "<0.001", as.character(round(p.value, 3)))) %>% ## rename the columns appropriately select( "Age group" = age_group, "Study population (n)" = n, "Study population (%)" = percent, "Source population (n)" = n_pop, "Source population (%)" = percent_pop, "P-value" = p.value ) %>% # produce styled output table with auto-adjusted column widths with {flextable} qflextable() %>% # make header text bold (using {flextable}) bold(part = "header") %>% # make your table fit to the maximum width of the word document set_table_properties(layout = "autofit") %>% ## set to only show 1 decimal place colformat_double(digits = 1)
## compute the median age medage <- median(study_data_cleaned$age_months) ## paste the lower and uper quartile together iqr <- str_c( # basically copy paste together the following ## calculate the 25% and 75% of distribution, with missings removed quantile( study_data_cleaned$age_months, c(0.25, 0.75), na.rm = TRUE), ## between lower and upper place an en-dash collapse = "--") ## compute overall sex ratio sex_ratio <- study_data_cleaned %>% count(sex) %>% pivot_wider(names_from = sex, values_from = n) %>% mutate(ratio = round(Male/Female, digits = 3)) %>% pull(ratio) ## compute sex ratios by age group sex_ratio_age <- study_data_cleaned %>% count(age_group, sex) %>% pivot_wider(names_from = sex, values_from = n) %>% mutate(ratio = round(Male/Female, digits = 3)) %>% select(age_group, ratio) ## sort table by ascending ratio then select the lowest (first) min_sex_ratio_age <- arrange(sex_ratio_age, ratio) %>% slice(1)
Among the r nrow(study_data_cleaned) surveyed individuals, there were
r fmt_count(study_data_cleaned, sex == "Female") females and
r fmt_count(study_data_cleaned, sex == "Male") males (unweighted). The male to
female ratio was r sex_ratio in the surveyed population. The lowest male to
female ratio was r min_sex_ratio_age$ratio
in the r min_sex_ratio_age$age_group month age group.
The median age of surveyed individuals was r medage years (Q1-Q3 of r iqr
years). Children under two years of age made up
r fmt_count(study_data_cleaned, age_group_bin == "0-23")of the surveyed
individuals.
The highest number of surveyed individuals (unweighted) were in the
r table(study_data_cleaned$age_group) %>% which.max() %>% names()
year age group.
Unweighted age distribution of household population by year age group and gender.
# get cross tabulated counts and proportions study_data_cleaned %>% tbl_cross( row = age_group, col = sex, percent = "cell") %>% # change to flextable format as_flex_table() %>% # make header text bold (using {flextable}) bold(part = "header") %>% # make your table fit to the maximum width of the word document set_table_properties(layout = "autofit")
There were r fmt_count(dropped, is.na(sex)) cases missing
information on sex and
r fmt_count(dropped, is.na(age_group)) missing age group.
Unweighted age and gender distribution of household population covered by the survey.
age_pyramid(study_data_cleaned, age_group, split_by = sex, proportional = TRUE) + labs(y = "Proportion", x = "Age group (months)") + # change axis labels theme(legend.position = "bottom", # move legend to bottom legend.title = element_blank(), # remove title text = element_text(size = 18) # change text size )
Unweighted age and gender distribution, stratified by health district, of household population covered by the survey. <!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /// age_pyramid_strata \\
This chunk creates an unweighted (using study_data_cleaned) age/sex pyramid of your cases, stratified by health district.
If you have a stratified survey design this may be useful for visualising if you have an excess of representation in either sex or gender in any of your survey strata. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
age_pyramid(study_data_cleaned, age_group, split_by = sex, stack_by = health_district, proportional = TRUE, pal = c("red", "blue")) + labs(y = "Proportion", x = "Age group (months)") + # change axis labels theme(legend.position = "bottom", # move legend to bottom legend.title = element_blank(), # remove title text = element_text(size = 18) # change text size )
Weighted age and gender distribution of household population covered by the survey.
age_pyramid(survey_design, age_group, split_by = sex, proportion = TRUE) + labs(y = "Proportion (weighted)", x = "Age group (months)") + # change axis labels theme(legend.position = "bottom", # move legend to bottom legend.title = element_blank(), # remove title text = element_text(size = 18) # change text size )
Quality of indicators collected
Box plot of Zscores for height-for-age, weight-for-age and weight-for-height
## pull variables together for plotting temp_data <- study_data_cleaned %>% ## stack variable names in one column and values for vars in another ## call first column indicator and second column zscore pivot_longer(cols = c(zwfl, zlen, zwei), names_to = "Indicator", values_to = "Zscore") %>% ## only keep variables of interest select(Indicator, Zscore) %>% ## rename indicators to something more understandable mutate( Indicator = fct_recode(Indicator, "HAZ" = "zlen", "WAZ" = "zwei", "WHZ" = "zwfl" )) ## use indicators on the x-axis and z-score on the y-axis ggplot(temp_data, aes(x = Indicator, y = Zscore)) + ## plot as a box plot geom_boxplot() + ## add a dotted horizontal line at 0 for reference geom_hline(yintercept = 0, linetype = "dashed")
Box plot of Zscores for height-for-age, weight-for-age and weight-for-height by sex
## pull variables together for plotting temp_data <- study_data_cleaned %>% ## stack variable names in one column and values for vars in another ## call first column indicator and second column zscore pivot_longer(cols = c(zwfl, zlen, zwei), names_to = "Indicator", values_to = "Zscore") %>% ## only keep variables of interest select(sex, Indicator, Zscore) %>% ## rename indicators to something more understandable mutate( Indicator = fct_recode(Indicator, "HAZ" = "zlen", "WAZ" = "zwei", "WHZ" = "zwfl" )) ## use indicators on the x-axis and z-score on the y-axis ## colour according to sex ggplot(temp_data, aes(x = Indicator, y = Zscore, fill = sex)) + ## plot as a boxplot geom_boxplot() + ## add a dotted horizontal line at 0 for reference geom_hline(yintercept = 0, linetype = "dashed") + ## remove the title of legend theme(legend.title = element_blank())
Box plot of Zscores for height-for-age by age group
## use age group on the x-axis and height z-score on the y-axis ggplot(study_data_cleaned, aes(x = age_group, y = zlen)) + ## plot as a boxplot geom_boxplot() + ## add a dotted horizontal line at 0 for reference geom_hline(yintercept = 0, linetype = "dashed") + ## change axis titles labs(x = "Age group (Months)", y = "HAZ score")
Box plot of Zscores for weight-for-age by age group
## use age group on the x-axis and weight z-score on the y-axis ggplot(study_data_cleaned, aes(x = age_group, y = zwei)) + ## plot as a boxplot geom_boxplot() + ## add a dotted horizontal line at 0 for reference geom_hline(yintercept = 0, linetype = "dashed") + ## change axis titles labs(x = "Age group (Months)", y = "WAZ score")
Box plot of Zscores for weight-for-height by age group
## use age group on the x-axis and weight-height z-score on the y-axis ggplot(study_data_cleaned, aes(x = age_group, y = zwfl)) + ## plot as a boxplot geom_boxplot() + ## add a dotted horizontal line at 0 for reference geom_hline(yintercept = 0, linetype = "dashed") + ## change axis titles labs(x = "Age group (Months)", y = "WHZ score")
Unweighted z-curve of height-for-age among non-flagged children for this indicator <!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /// zcurve_haz \\
This chunk creates a z-curve of height-for-age compared to the WHO reference population ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
study_data_cleaned %>% ## only consider z-scores that are not flagged filter(flen == FALSE) %>% ## plot zcurve zcurve(zlen)
Unweighted z-curve of weight-for-age among non-flagged children for this indicator <!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /// zcurve_haz \\
This chunk creates a z-curve of weight-for-age compared to the WHO reference population ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
study_data_cleaned %>% ## only consider z-scores that are not flagged filter(fwei == FALSE) %>% ## plot zcurve zcurve(zwei)
Unweighted z-curve of weight-for-height among non-flagged children for this indicator <!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /// zcurve_whz \\
This chunk creates a z-curve of weighted-for-height compared to the WHO reference population ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
study_data_cleaned %>% ## only consider z-scores that are not flagged filter(fwfl == FALSE) %>% ## plot zcurve zcurve(zwfl)
Unweighted counts and proportions of children missing or flagged for indicators <!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /// missing_flagged_indicators \\
This chunk creates an unweighted table of number children with missing or flagged indicators ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
study_data_cleaned %>% select(flen, fwei, fwfl) %>% ## mutate each of the flags be easier to enterprate mutate( across(everything(), ~case_when( .x == TRUE ~ "Flagged", .x == FALSE ~ "Included", TRUE ~ "Missing" )) ) %>% # Variable labels are removed by mutate(across(..)) for some reason set_variable_labels( ## variable name = variable label flen = "HAZ", fwei = "WAZ", fwfl = "WHZ" ) %>% tbl_summary() %>% # change to flextable format as_flex_table() %>% # make header text bold (using {flextable}) bold(part = "header") %>% # make your table fit to the maximum width of the word document set_table_properties(layout = "autofit")
In addition the number of children missing MUAC
was r fmt_count(study_data_cleaned, is.na(muac)).
Nutritional status based on indicators
Weighted prevalence of malnutrition based on MUAC, by age group (months) and overall
overall <- survey_design %>% ## tabulate multiple variables with same values select(all_of(MUAC)) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE) age_strat <- survey_design %>% ## tabulate multiple variables with same values select(all_of(MUAC), age_group) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE, ## stratify by age group by = age_group) ## combine the overall and stratified tables tbl_merge(list(overall, age_strat)) %>% modify_spanning_header( list( ## rename the spanning header ## you can see what the columns are called by putting in an object and inspecting table_body stat_0_1 ~ "**Overall**", c(stat_1_2, stat_2_2, stat_3_2, stat_4_2, stat_5_2) ~ "**Age group (months)**")) %>% # change to flextable format as_flex_table() %>% # make header text bold (using {flextable}) bold(part = "header") %>% # make your table fit to the maximum width of the word document set_table_properties(layout = "autofit")
Weighted prevalence of malnutrition based on MUAC among children <87cm, by age group (months) and overall <!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /// muac_age_group_filter \\
This chunk creates a weighted table of prevalence based on MUAC for age groups and for the overall population among children under 87cm tall (using filter).
This happens in three stages: - Table for overall - Table for age groups - Bind the two together as rows ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
overall <- survey_design %>% ## only keep children less than 87cm filter(height < 87) %>% ## tabulate multiple variables with same values select(all_of(MUAC)) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE) age_strat <- survey_design %>% ## only keep children less than 87cm filter(height < 87) %>% ## tabulate multiple variables with same values select(all_of(MUAC), age_group) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE, ## stratify by age group by = age_group) ## combine the overall and stratified tables tbl_merge(list(overall, age_strat)) %>% modify_spanning_header( list( ## rename the spanning header ## you can see what the columns are called by putting in an object and inspecting table_body stat_0_1 ~ "**Overall**", c(stat_1_2, stat_2_2, stat_3_2, stat_4_2, stat_5_2) ~ "**Age group (months)**")) %>% # # change to flextable format as_flex_table() %>% # make header text bold (using {flextable}) bold(part = "header") %>% # make your table fit to the maximum width of the word document set_table_properties(layout = "autofit")
Weighted prevalence of malnutrition based on height-for-age z-score categories, by age group (months) and overall
overall <- survey_design %>% ## tabulate multiple variables with same values select(all_of(HAZ)) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE) age_strat <- survey_design %>% ## tabulate multiple variables with same values select(all_of(HAZ), age_group) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE, ## stratify by age group by = age_group) ## combine the overall and stratified tables tbl_merge(list(overall, age_strat)) %>% modify_spanning_header( list( ## rename the spanning header ## you can see what the columns are called by putting in an object and inspecting table_body stat_0_1 ~ "**Overall**", c(stat_1_2, stat_2_2, stat_3_2, stat_4_2, stat_5_2) ~ "**Age group (months)**")) %>% # change to flextable format as_flex_table() %>% # make header text bold (using {flextable}) bold(part = "header") %>% # make your table fit to the maximum width of the word document set_table_properties(layout = "autofit")
Weighted prevalence of malnutrition based on weight-for-age z-score categories, by age group (months) and overall <!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /// waz_age_group \\
This chunk creates a weighted table of prevalence based on weight-for-age z-scores for age groups and for the overall population.
This happens in three stages: - Table for overall - Table for age groups - Bind the two together as rows ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
overall <- survey_design %>% ## tabulate multiple variables with same values select(all_of(WAZ)) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE) age_strat <- survey_design %>% ## tabulate multiple variables with same values select(all_of(WAZ), age_group) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE, ## stratify by age group by = age_group) ## combine the overall and stratified tables tbl_merge(list(overall, age_strat)) %>% modify_spanning_header( list( ## rename the spanning header ## you can see what the columns are called by putting in an object and inspecting table_body stat_0_1 ~ "**Overall**", c(stat_1_2, stat_2_2, stat_3_2, stat_4_2, stat_5_2) ~ "**Age group (months)**")) %>% # change to flextable format as_flex_table() %>% # make header text bold (using {flextable}) bold(part = "header") %>% # make your table fit to the maximum width of the word document set_table_properties(layout = "autofit")
Weighted prevalence of malnutrition based on weight-for-height z-score categories, by age group (months) and overall <!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /// whz_age_group \\
This chunk creates a weighted table of prevalence based on weight-for-height z-scores for age groups and for the overall population.
This happens in three stages: - Table for overall - Table for age groups - Bind the two together as rows ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
overall <- survey_design %>% ## tabulate multiple variables with same values select(all_of(WHZ)) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE) age_strat <- survey_design %>% ## tabulate multiple variables with same values select(all_of(WHZ), age_group) %>% ## only show the row with TRUE tbl_svysummary(missing = "no", value = everything() ~ TRUE, ## stratify by age group by = age_group) ## combine the overall and stratified tables tbl_merge(list(overall, age_strat)) %>% modify_spanning_header( list( ## rename the spanning header ## you can see what the columns are called by putting in an object and inspecting table_body stat_0_1 ~ "**Overall**", c(stat_1_2, stat_2_2, stat_3_2, stat_4_2, stat_5_2) ~ "**Age group (months)**")) %>% # change to flextable format as_flex_table() %>% # make header text bold (using {flextable}) bold(part = "header") %>% # make your table fit to the maximum width of the word document set_table_properties(layout = "autofit")
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