---
title: "Vaccination survey short"
output: 
  word_document:
    keep_md: true
---



# Introduction to this template

This is a template which can be used to create a report from a vaccination 
coverage survey from the short dictionary. 

- There are sections for reading and cleaning data, followed by 
    weighting calculations and then survey analysis.  
- For a more detailed explanation of this template, please visit https://github.com/R4EPI/sitrep/  
- Feedback and suggestions are welcome at the [GitHub issues page](https://github.com/R4EPI/sitrep/issues)

- Text within <! > will not show in your final document. These comments are used
to explain the template. You can delete them if you want.

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This comment will not show up when you knit the document.
A comment with a title with slashes indicates a name of a code chunk.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->


## Installing and loading required packages 

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// setup \\\
--------------------------------------------------------------------------------
Several packages are required for different aspects of  analysis with *R*. 
You will need to install these before starting. 
These packages can be quite large and may take a while to download in the
field. If you have access to a USB key with these packages, it makes sense to
copy and paste the packages into your computer's R package library 
(run the command .libPaths() to see the folder path). 
For help installing packages, please visit https://github.com/R4EPI/sitrep/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
  

```{r setup, include = FALSE, results='hide', message=FALSE, warning=FALSE}
## 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)



# 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
  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
  lubridate,   # working with dates
  parsedate    # guessing dates
  )


## set default text size to 18 for plots
## give classic black/white axes for plots
ggplot2::theme_set(theme_classic(base_size = 18))
```




<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// read_fake_data \\\
--------------------------------------------------------------------------------
To play with this template, you can create fake data based off data
dictionary used for Kobo.
Comment out this chunk when you are using real data.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r read_fake_data, warning = FALSE, message = FALSE}


## generates MSF standard dictionary for Kobo 
study_data_dict <- msf_dict("Vaccination_short")

## generates MSF standard dictionary for Kobo in long format (for recoding)
study_data_dict_long <- msf_dict(dictionary = "Vaccination_short", 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 = "Vaccination_short", 
                           varnames = "name",
                           numcases = 1000)
```


<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
You should load your data as a linelist, where each row is one person. 

There are two options for reading data:
- Your data is from Kobo: use read_kobo_data
- Your data is NOT FROM Kobo and in Excel, CSV, or Stata format: 
use read_non_kobo_data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->


<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// read_kobo_data \\\
--------------------------------------------------------------------------------
This section is for data collected with Kobo.
It uses the standardized MSF data dictionary.

If you didn't use the standardized data dictionary, go to read_non_kobo_data.

Generally, survey datasets will have two levels:
One for household and one for individual (to combine see merge_data_levels).
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->


```{r read_kobo_data, warning = FALSE, message = FALSE}

### Read in data ---------------------------------------------------------------


## Excel file ------------------------------------------------------------------

## read in household data sheet
# study_data_hh <- rio::import(here::here("vaccination_survey.xlsx"), 
#                               which = "vaccination_survey_erb", na = "")

## read in individual level data sheet
# study_data_indiv <- rio::import(here::here("vaccination_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("vaccination_survey.xlsx"),
#                              xl.sheet = "vaccination_survey_erb",
#                              password = askpass::askpass(prompt = "please enter file password"))

# study_data_indiv <- xl.read.file(here::here("vaccination_survey.xlsx"),
#                              xl.sheet = "r1",
#                              password = askpass::askpass(prompt = "please enter file password"))
```


<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// merge_data_levels \\\
--------------------------------------------------------------------------------
For survey datasets with two levels (e.g. household and individual), 
these levels will need to be merged in to one dataset. 

This is done using a unique identifier for the household 
(which has to be repeated for each row in the individuals dataset) 
For a Kobo dataset this variable is "_index" at the household level, which 
matches the "_parent_index" at the individual level.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r merge_data_levels}

## 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"))
```



<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// prep_kobo_data \\\
--------------------------------------------------------------------------------
This section is to import your data dictionary and standardise variable names. 

The Kobo data dictionary has variable names
in the "name" column of the survey sheet. Possible values for each variable are
specified in choices sheet. 
In the choices tab, "name" has the shortened value and the "label::english" and 
"label::french" columns have the appropriate long versions. 
Using the msf_dict function to import a Kobo dictionary excel file will 
re-format this for you so it can be used easily to recode. 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r prep_kobo_data}

## Data dictionary -------------------------------------------------------------


## read in a kobo data dictionary
## important to specify template is FALSE (otherwise you get the generic dict)
# study_data_dict <- read_dict(name = here::here("vaccination_survey_dict.xlsx"))

## 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 original dataset and name it study_data_cleaned
study_data_cleaned <- study_data_raw

## Sometimes you want to rename specific variables
## For example we want to add details to violance_natur_other
## This is because otherwise it will be duplicated after we clean names below
## 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,
#                              age_in_years = q10_age_yr,
#                              age_in_months = q55_age_mth)

## 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}"))
```


<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// read_population_data \\\
--------------------------------------------------------------------------------
This template uses population data to create survey weights. 

There are three options:
- You can read in a spreadsheet with age group, sex and region data.
- You can put in the specific populations into the gen_population function. 
- If you have the total or regional populations, you can estimate the age group
from proportions.

Below we show basic examples for reading data and entering counts - as well as 
a more complex version using proportions to get the age/sex breakdown in 
two separate regions. (Useful if doing a stratified survey)

Comment out the options you are not using.

Make sure that the groups fit those in your survey data!

Age group proportions are from the OCBA population denominators tool v1. The
proportions below are for sub-Saharan Africa in 2019. They are only an estimate!
If you have more specific proportions/data, you can use them below.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r read_population_data, warning = FALSE, message = FALSE}


## 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("0", "1", "2", "3", "4", "5+"), # set groups
  proportions = c(0.0164, 0.0164, 0.015, 0.015,
                  0.015, 0.1386), # 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("0", "1", "2", "3", "4", "5+"), # set groups
  proportions = c(0.0164, 0.0164, 0.015, 0.015,
                  0.015, 0.1386), # 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 \\\
--------------------------------------------------------------------------------
For cluster surveys you may want to add survey weights at the cluster level. 

This could be done as in the read_population_data chunk. 

Alternatively if there are only a few counts, these could be entered as below
in to a tibble. 

In any case you will need to have one column with a cluster identifier which 
matches your survey data, and another column with the number of households in 
each cluster. 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r cluster_counts}

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))
```




<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// browse_data \\\
--------------------------------------------------------------------------------

You'll want to look at your data. Here are a few ways you can explore.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r browse_data, eval = FALSE}
## view the first ten rows of data
head(study_data_raw, n = 10)

## view your whole dataset interactively (in an excel style format)
View(study_data_raw)

## overview of variable types and contents
str(study_data_raw)

## get summary: 
## mean, median and max values of variables
## 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 date inconsistencies 
## for example check vaccine age greater than current age and return corresponding IDs
study_data_raw %>% 
  filter(age_routine_vacc > age_months) %>% 
  select("uid")

## use the dfSummary function in combination with view
## note that view is not capitalised with this package
# summarytools::dfSummary(linelist_cleaned) %>%
#   summarytools::view()
```



<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This part of the script will create and clean variables in your data.

All your cleaning and variable creation should happen in these chunks.
That way, in case something goes wrong, you can push the small arrow at the top
of the chunk to re-run all the code chunks up to the current one.

The chunks are:
- standardise_dates  -- will set up and clean dates.
- create_age_group   -- creates the age group variables from age
- recode_dictionary  -- recode variables based on a data dictionary
- factor_vars        -- helps clean factor variables
- labelling_data     -- add variable labels to your dataset
- remove_unused_data -- dropping unused rows/columns
- survey_weights     -- calculating survey weights according to study design
- survey_design      -- create a survey object for weighted analysis 

You must adapt this section according to your data!
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->



<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// standardise_dates \\\
--------------------------------------------------------------------------------

This chunk will help you set up and clean your date variables.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r standardise_dates}

## 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-standard data -------------------------------------------------------------
## Use this section if you did not have dates defined in a Kobo data dictionary.

## 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"))

```




<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// create_age_group \\\ 
--------------------------------------------------------------------------------

This chunk will help you set up your age group variable.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r create_age_group}

## 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_years = as.integer(age_years), 
         age_months = as.integer(age_months))

## create an age group variable (combining those over 5 years) 
study_data_cleaned <- study_data_cleaned %>%
  mutate(age_group = factor(
    if_else(age_years >= 5,
      "5+",
      as.character(age_years)
    )
  ))


## create an age group variable by specifying categorical breaks (of years)
# study_data_cleaned <- study_data_cleaned %>% 
#   mutate(age_group = age_categories(age_years, 
#                                     breakers = c(0, 3, 15, 30, 45)
#                                     ))

## create age group variable for under 1 years based on months
study_data_cleaned <- study_data_cleaned %>%
  mutate(age_group_mon = age_categories(study_data_cleaned$age_months,
                                                 breakers = c(0, 6, 9, 12),
                                                 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, meaning:
## it will order your age_category from smallest to largest unit 
## i.e. days first then months then years (depending on which are given)
study_data_cleaned <- group_age_categories(study_data_cleaned, 
                                         years = age_group, 
                                         months = age_group_mon)


## years since diagnosis variable ----------------------------------------------

## adapt age at diagnosis and then create a new time_since variable
study_data_cleaned <- study_data_cleaned %>% 
  mutate(
    ## change the age at diagnosis variable to be in years 
    age_diagnosis = age_diagnosis / 12, 
    ## change those less than 1 year to be 0
    age_diagnosis = if_else(age_diagnosis < 1, 
                                 0, 
                                 age_diagnosis), 
    ## calculate the years between current age and age at diagnosis
    time_since = age_years - age_diagnosis)


## create a grouping variable for years since diagnosis
study_data_cleaned <- study_data_cleaned %>% 
  mutate(time_since_group = age_categories(time_since,
               lower = 0, upper = 5, by = 1))

## fix the labels for years under five
study_data_cleaned <- study_data_cleaned %>% 
  ## remove what comes after a dash (i.e. repeated year)
  mutate(time_since_group = str_remove(time_since_group, "-.*"))
    
```


<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// recode_dictionary \\\
--------------------------------------------------------------------------------
We can use the matchmaker package to recode our dataset using a data dictionary. 
So for example our variable for sex might have coded values of "m" and "f" but 
the label would be "Male" and "Female".
This corresponds to the option_name and option_label in Kobo dictionaries.
Currently, value labels cant be used for analysis so we have just recoded using 
the matchmaker package (in the recode_dictionary chunk). 
Variable labels can be used and so we will used the labelled package for that in 
the labelling_data code chunk. 
You could also have your data in French by specifying "option_label_french", 
if your data dictionary has that included (see the generic dictionary for example).  
NOTE: it is important to use matchmaker before working with factor vars 
(factor_vars) as it will swap things to characters based on the dictionary used
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r recode_dictionary}
## 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")
```

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// factor_vars \\\
--------------------------------------------------------------------------------

This chunk will help you clean factor variables.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r factor_vars}

## 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")

## 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"
  ))

## create a new variable by reordering the levels of a factor 
study_data_cleaned <- study_data_cleaned %>%
  mutate(no_consent = fct_relevel(no_consent_reason,
                                  "There is no benefit to me and my family", 
                                  "I do not have time", 
                                  "I have had a negative experience with a previous survey.",
                                  "Other")
        )


## create a character variable based off groups of a different variable 
## combine all vaccine variables in to one 
## keep the yes answers and change others to no 
## if missing in all three vars then stays NA
study_data_cleaned <- study_data_cleaned %>% 
  mutate(vaccination_status = case_when(
    is.na(msf_vacc) & 
      is.na(routine_vacc) & 
      is.na(sia_vacc)                  ~ NA_character_,
    msf_vacc     == "Yes, card"             ~ "Card", 
    routine_vacc == "Yes, card"             ~ "Card", 
    sia_vacc     == "Yes, card"             ~ "Card", 
    msf_vacc     == "Yes, verbal"           ~ "Verbal", 
    routine_vacc == "Yes, verbal"           ~ "Verbal", 
    sia_vacc     == "Yes, verbal"           ~ "Verbal",
    TRUE                                    ~ "Unvaccinated")
    )

## correct the order of levels in newly created var
study_data_cleaned <- study_data_cleaned %>% 
  mutate(vaccination_status = fct_relevel(vaccination_status, 
                                          "Card", 
                                          "Verbal", 
                                          "Unvaccinated")
  )


## create a new grouping for vaccine status variable 
## simplified, card or verbal then yes otherwise no 
study_data_cleaned <- study_data_cleaned %>% 
  mutate(
    vaccination_status_simple = case_when(
      is.na(vaccination_status)                   ~ NA_character_,
      vaccination_status %in% c("Card", "Verbal") ~ "Vaccinated", 
      TRUE                                        ~ "Unvaccinated")
    )

## correct the order of levels in newly created var
study_data_cleaned <- study_data_cleaned %>% 
  mutate(vaccination_status_simple = fct_relevel(vaccination_status_simple, 
                                                 "Vaccinated", 
                                                 "Unvaccinated")
  )

## explicitly replace NA of a factor
study_data_cleaned <- study_data_cleaned %>%
  mutate(routine_vacc = fct_explicit_na(routine_vacc, na_level = "No answer"))

```


<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// labelling_data \\\
--------------------------------------------------------------------------------

We can use the labelled package to add tags to our variable names and values.  
This means that we can have both coded values and a cleaner written out form of
variable names and values; this makes our code easier to write but our output 
cleaner to look at (because we can use labels in tables/figures).

So for example our variable name would be "sex" but the label would be "Sex", and
the values would be "m" and "f" but the label would be "Male" and "Female".
This corresponds to the option_name and option_label in kobo dictionaries.

Currently, value labels cant be used for analysis so we have just recoded using 
the matchmaker package (in the recode_dictionary chunk). 
Variable labels can be used and so we will used the labelled package for that. 

NOTE: it is important to use matchmaker before working with factor vars 
(factor_vars) as it will swap things to characters based on the dictionary used
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r labelling_data}
## 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$label_english), 
  ## name the list with the current variable names
  study_data_dict$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_group     = "Age group (years)",
    age_months    = "Age (months)", 
    age_group_mon = "Age group (months)",
    age_category  = "Age category", 
    time_since_group = "Time since diagnosis (years)"
    )
```


<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// remove_unused_data \\\
--------------------------------------------------------------------------------

Your data might have empty rows or columns you want to remove.
You can also use this section to create temporary datasets so you can review
specific variables or rows.

You may want to drop rows with missing IDs (i.e. blank rows from excel) 
simply add a !is.na(uid) if using a Kobo dataset.

Those without consent need to be dropped too

It is important that you drop observations before adding survey weights!
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r remove_unused_data}
## Drop unused rows  -----------------------------------------------------------

## store the cases that you drop so you can describe them (e.g. non-consenting)
dropped <- study_data_cleaned %>% 
  filter(!consent| village_name == "other")

## use the dropped cases to remove 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")
```


<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// duplicates \\\
--------------------------------------------------------------------------------
This chunk removes duplicate cases based on case_number, sex and age_group. 
(you can edit to use whichever unique identifiers you think relevant)
There are two options for this. Option 1 simply keeps the first occurrence of a 
duplicated case. 
Option 2 gives you the ability to create a TRUE/FALSE variable to flag rows that
are duplicated - giving you more flexibility around browsing which ones to drop. 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r duplicates}
## 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(submission_time)) %>% 
#   ## only keep the earliest row 
#   slice(1)
```


<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// survey_weights \\\
--------------------------------------------------------------------------------

Create survey weights according to your study design. 

These require information on the source population and/or the clusters surveyed. 

There are three options, comment out those you do not use: 
- Stratified 
- Cluster 
- Stratified and cluster 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r survey_weights}

## 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 people 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)
```



<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// survey_design \\\
--------------------------------------------------------------------------------

Create survey object according to your study design. 

Used the same way as dataframes to calculate weight proportions etc. 

Make sure that all necessary variables are created before this. 

There are four options, comment out those you do not use: 
- Simple random 
- Stratified 
- Cluster 
- Stratified cluster

For this template - we will pretend that we cluster surveys in two seperate 
strata (health districts A and B). 
So to get overall estimates we need have combined cluster and strata weights. 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r survey_design}

## 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
                  )
```



<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// save_cleaned_data \\\
--------------------------------------------------------------------------------

You can save your cleaned dataset as an Excel. 
This automatically names your file "study_data_cleaned_DATE", where DATE is the
current date.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r save_cleaned_data}
# rio::export(study_data_cleaned,  here::here("data", str_glue("study_data_cleaned_{Sys.Date()}.xlsx")))
```



# Results

## Survey inclusion 


<!--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// inclusion_counts \\\
--------------------------------------------------------------------------------

The below chunks calculate values that are displayed with the inline text

Get the counts of clusters and households included 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-->

```{r inclusion_counts}

## 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 without consent to participate in the survey, 
the reasons for refusal are described below. 

<!--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// consent_reasons \\\
--------------------------------------------------------------------------------

This chunk will create a table of dropped individuals by reason for no consent. 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-->

```{r consent_reasons}

## 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()
```



<!--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// cluster_hh_size \\\
--------------------------------------------------------------------------------

The below chunks calculate values that are displayed with the inline text

Get counts of households per cluster and individuals per household. 
From these create medians and standard deviations. 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-->

```{r cluster_hh_size}

## 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. 


<!--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// descriptive_sampling_bias \\\
--------------------------------------------------------------------------------

Compare the proportions in each age group between your sample and 
the source population. 

This is important to be able to highlight potential sampling bias. 
You could similarly repeat this looking at distributions by sex. 

Note that these p-values are just indicative, and a descriptive discussion (or
visualisation with age-pyramids below) of the distributions in your study sample 
compared to the source population is more
important than the binomial test itself. This is because increasing sample size
will more often than not lead to differences that may be irrelevant after weighting
your data. 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-->

```{r descriptive_sampling_bias, warning = FALSE}
## 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
  ) %>%
  qflextable()

```



<!--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// median_age_sex_ratios \\\
--------------------------------------------------------------------------------

The below chunk calculate values that are displayed inline

This returns the median age and sex ratios overall as well as by age group. 
It also pulls the age group with the highest sex ratio. 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-->

```{r median_age_sex_ratios}
## compute the median age 
medage <- median(study_data_cleaned$age_years)
## paste the lower and upper quartile together
iqr <- str_c(  # basically copy paste togehter the following
  ## calculate the 25% and 75% of distribution, with missings removed
  quantile(     
    study_data_cleaned$age_years, 
    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` year age group.
The median age of surveyed individuals was `r medage` years (Q1-Q3 of `r iqr`
years). Children under five years of age made up 
`r fmt_count(study_data_cleaned, age_years < 5)`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 population by year age group and gender.

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// describe_by_age_group_and_sex \\\
--------------------------------------------------------------------------------

This chunk will create an unweighted table of survey individuals by age group 
and sex.

Note that proportions are of the total sample (not within each gender) 
to change this, set percent = "column"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r describe_by_age_group_and_sex}

# get cross tabulated counts and proportions
study_data_cleaned %>% 
  tbl_cross( 
    row = age_group, 
    col = sex, 
    percent = "cell")
```



Unweighted age distribution of population by age category (month and year) and gender.

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// describe_by_age_category_and_sex \\\
--------------------------------------------------------------------------------

This chunk will create an unweighted table of survey individuals by age category 
and sex (i.e. a breakdown by months and years combined).

Note that proportions are of the total sample (not within each gender) 
to change this, set percent = "column"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r describe_by_age_category_and_sex}

# get cross tabulated counts and proportions
study_data_cleaned %>% 
  tbl_cross( 
    row = age_category, 
    col = sex, 
    percent = "cell")
```


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 \\\
--------------------------------------------------------------------------------

This chunk creates an unweighted (using study_data_cleaned) age/sex pyramid
of your cases.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r age_pyramid, warning=FALSE}

age_pyramid(study_data_cleaned, 
                 age_group, 
                 split_by = sex,
                 proportional = TRUE) + 
  labs(y = "Proportion", x = "Age group (years)") + # 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. 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r age_pyramid_strata, warning=FALSE}

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 (years)") +  # 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 \\\
--------------------------------------------------------------------------------

This chunk creates a weighted (using survey_design) age/sex pyramid
of your cases.

Note - if this is substantially different to your unweighted 
pyramid, then it may suggest some sampling bias (similarly to the table comparing 
sample and source population distributions by binomial test). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r age_pyramid_survey, warning=FALSE}

age_pyramid(survey_design,
                 age_group,
                 split_by = sex, 
                 proportional = TRUE) +
  labs(y = "Proportion", x = "Age group (years)") +  # 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
       )
```



## Vaccination coverage

Weighted vaccination coverage; accepting equal validity from self-reported and 
card-reported vaccination status

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// vaccination_coverage_overall \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for vaccination 
coverage while accepting equal validity from self- and card-reporting. 

Note that this includes a design effect. 

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r vaccination_coverage_overall}

survey_design %>% 
  select(vaccination_status_simple) %>% 
  tbl_svysummary(statistic = everything() ~ "{n} ({p}%) [{deff}]") %>% 
  ## add the weighted total
  add_n() %>%
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      n ~ "**Weighted total (N)**",
      stat_0 ~ "**Weighted Count (n)**"
    )
    )

```


Weighted vaccination coverage; distinguishing between vaccination cards and 
verbal confirmation 

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// vaccination_coverage_overall_detail \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for vaccination 
coverage while distinguishing validity from self- and card-reporting. 

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r vaccination_coverage_overall_detail}

survey_design %>% 
  select(vaccination_status) %>% 
  tbl_svysummary() %>% 
  ## add the weighted total
  add_n() %>%
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      n ~ "**Weighted total (N)**",
      stat_0 ~ "**Weighted Count (n)**"
    )
    )
```



Weighted vaccination coverage by health district; accepting equal validity from
self-reported and card-reported vaccination status 

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// vaccination_coverage_strata \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for vaccination 
coverage while accepting equal validity from self- and card-reporting, 
stratified by health district. 

Note that this includes a design effect. 

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r vaccination_coverage_strata}

survey_design %>% 
  select(vaccination_status_simple, health_district) %>%
  tbl_svysummary(by = health_district) %>% 
  ## add the weighted total
  add_n() %>%   
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      n ~ "**Weighted total (N)**",
      stat_1 ~ "**District A Weighted Count (n)** \n N={n}", 
      stat_2 ~ "**District B Weighted Count (n)** \n N={n}" 
    )
    )

```





Weighted vaccination coverage by sex; accepting equal validity from self-reported 
and card-reported vaccination status

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// vaccination_coverage_sex \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for vaccination 
coverage while accepting equal validity from self- and card-reporting; broken 
down by sex. 

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r vaccination_coverage_sex}

survey_design %>% 
  select(vaccination_status_simple, sex) %>%
  tbl_svysummary(by = sex) %>% 
  ## add the weighted total
  add_n() %>%   
  ## add in confidence intervals
  add_ci() %>%  
  ## modify the column headers
  modify_header(
    list(
      n ~ "**Weighted total (N)**",
      stat_1 ~ "**Male Weighted Count (n)** \n N={n}", 
      stat_2 ~ "**Female Weighted Count (n)** \n N={n}" 
    )
    )
```



Weighted vaccination coverage by sex; distinguishing between vaccination cards 
and verbal confirmation

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// vaccination_coverage_sex_detail \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for vaccination 
coverage while distinguishing validity from self- and card-reporting; broken 
down by sex. 

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r vaccination_coverage_sex_detail}

survey_design %>% 
  select(vaccination_status, sex) %>%
  tbl_svysummary(by = sex) %>% 
  ## add the weighted total
  add_n() %>%   
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      n ~ "**Weighted total (N)**",
      stat_1 ~ "**Male Weighted Count (n)** \n N={n}", 
      stat_2 ~ "**Female Weighted Count (n)** \n N={n}" 
    )
    )

```



Weighted vaccination coverage by age group; accepting equal validity from self-reported and card-reported vaccination status

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// vaccination_coverage_age_group \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for vaccination 
coverage while accpeting equal validity from self- and card-reporting; broken 
down by age group.  

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r vaccination_coverage_age_group}

survey_design %>% 
  select(vaccination_status_simple, age_group) %>%
  ## Note that here we swap the stratifier 
  ## this way age group becomes the rows, so we need to calculate percent by row
  tbl_svysummary(by = vaccination_status_simple, 
                 percent = "row") %>% 
  ## add the weighted total
  add_n() %>%   
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      n ~ "**Weighted total (N)**",
      stat_1 ~ "**Vaccinated Weighted Count (n)** \n N={n}", 
      stat_2 ~ "**Unvaccinated Weighted Count (n)** \n N={n}" 
    )
    )
```



Weighted vaccination coverage by age group; distinguishing between vaccination 
cards and verbal confirmation 

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// vaccination_coverage_sex_detail \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for vaccination 
coverage while distinguishing validity from self- and card-reporting; broken 
down by age group.  

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r vaccination_coverage_age_group_detail}
 
survey_design %>% 
  select(vaccination_status, age_group) %>%
  ## Note that here we swap the stratifier 
  ## this way age group becomes the rows, so we need to calculate percent by row
  tbl_svysummary(by = vaccination_status, 
                 percent = "row") %>% 
  ## add the weighted total
  add_n() %>%   
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      n ~ "**Weighted total (N)**",
      stat_1 ~ "**Card Weighted Count (n)** \n N={n}", 
      stat_2 ~ "**Verbal Weighted Count (n)** \n N={n}", 
      stat_3 ~ "**Unvaccinated Weighted Count (n)** \n N={n}" 
    )
    )
```


## Reasons for not vaccinating 

Weighted counts and proportions for reasons not vaccinated in routine circumstances, individually, among those not vaccinated
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// no_vacc_reason_routine \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for reasons 
not vaccinated during routine immunisation activitites. 

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r no_vacc_reason_routine}

survey_design %>% 
  ## filter for those not vaccinated 
  filter(!routine_vacc %in% c("Yes, card", "Yes, verbal")) %>%
  select(reason_route_vacc) %>% 
  tbl_svysummary() %>% 
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      stat_0 ~ "**Weighted Count (n) \n (N={round(N, digits = 0)})**"
    )
    )

```


Weighted counts and proportions for reasons not vaccinated in campaign circumstances, individually, among those not vaccinated
<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// no_vacc_reason_campaign_sia_combo \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for reasons 
not vaccinated during campaign immunisation activitites. 

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r no_vacc_reason_campaign}

## campaign reasons 
survey_design %>% 
  ## filter for not vaccinated 
  filter(!msf_vacc %in% c("Yes, card", "Yes, verbal")) %>%
  select(reason_msf_vacc) %>% 
  tbl_svysummary() %>% 
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      stat_0 ~ "**Campaign Weighted Count (n) \n (N={round(N, digits = 0)})**"
    )
    )
```

Weighted counts and proportions for reasons not vaccinated in supplemented 
immunisation activities, among those not vaccinated

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// no_vacc_reason_sia \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for reasons 
not vaccinated during supplemented immunisation activitites. 

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
```{r no_vacc_reason_sia}

## sia reasons 
survey_design %>% 
  ## filter for not vaccinated 
  filter(!sia_vacc %in% c("Yes, card", "Yes, verbal")) %>%
  select(reason_sia_vacc) %>% 
  tbl_svysummary() %>% 
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      stat_0 ~ "**Supplementary Weighted Count (n) \n (N={round(N, digits = 0)})**"
    )
    )
```

## Measles infection 

Weighted counts and proportions for previous diagnosis of measles

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// measles_diagnosis \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for whether 
children have a previous diagnosis of measles

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r measles_diagnosis}

survey_design %>% 
  select(diagnosis_disease) %>% 
  tbl_svysummary() %>% 
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      stat_0 ~ "**Weighted Count (n) \n (N={round(N, digits = 0)})**"
    )
    )


```

Weighted counts and proportions for years since previous diagnosis of measles, 
among those who reported previous measles diagnosis

<!-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/// time_since_diagnosis \\\
--------------------------------------------------------------------------------

The below chunk creates a weighted table of counts proportions for time since  
children had a previous diagnosis of measles (i.e. difference in current age 
and age at infection)

Note that low counts or short observation times may lead to a confidence interval 
that crosses zero (i.e. negative) for ratios. These should be interpreted
as if no deaths or recoded to zero (impossible to have negative deaths). 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->

```{r time_since_diagnosis}

survey_design %>% 
  filter(diagnosis_disease == "Yes") %>% 
  select(time_since_group) %>% 
  tbl_svysummary() %>% 
  ## add in confidence intervals
  add_ci() %>% 
  ## modify the column headers
  modify_header(
    list(
      stat_0 ~ "**Weighted Count (n) \n (N={round(N, digits = 0)})**"
    )
    )

```



