In databrew/saint: SAINT

# Basic knitr options
library(knitr)
opts_chunk$set(comment = NA, 
               echo = FALSE, 
               warning = FALSE, 
               message = FALSE, 
               error = FALSE, 
               cache = FALSE,
               fig.width = 8.64,
               fig.height = 4.86,
               fig.path = 'figures/')

(... = list of options continues)

library(readxl)
library(dplyr)
library(knitr)
library(stringr)
library(kableExtra)
lang <- params$language
rel <- params$relevant
var <- params$include_variable_names
cn <- params$choice_names_too

# Read in the excel
df <- read_excel('../../../forms/saintperu/saintperu.xlsx')

# Read in the choices
choices <- read_excel('../../../forms/saintperu/saintperu.xlsx', sheet = 2)

# Join the questions and choices
out_list <- list()
for(i in 1:nrow(df)){
  this_row <- df[i,]
  has_choices <- grepl('select_multiple', this_row$type) | grepl('select_one', this_row$type)
  if(!has_choices){
    out <- this_row %>% mutate(choices = NA)
  } else {
    out <- this_row %>% mutate(list_name = unlist(strsplit(type, ' '))[2])
    left <- choices %>% filter(list_name == out$list_name)
    names(left) <- gsub('label', 'choices', names(left))
    left$choice_name <- left$name 
    left$name <- NULL
    out <- left_join(left, out)
  }
  out_list[[i]] <- out
}
out <- bind_rows(out_list)

# Clean up
if(is.null(lang)){
  out$Label <- out$label
  out$Hint <- out$hint
  out$Choices <- out$choices
} else {
  out$Label <- as.character(unlist(out[,paste0('label::', lang)]))
  out$Hint <- as.character(unlist(out[,paste0('hint::', lang)]))
  out$Choices <- as.character(unlist(out[,paste0('choices::', lang)]))
}
out$`Response Code` <- out$choice_name
out$Response <- out$Choices
keep_vars <- c('type', 'name', 'Label', 'Hint', 'Response', 'Response Code')

out <- out %>% dplyr::select(all_of(keep_vars))
clean_type <- function(x){
  unlist(lapply(strsplit(x, ' '), function(y){y[1]}))
}
out$type <- clean_type(out$type)
out <- out %>% filter(!type %in% c('begin', 'deviceid', 'end',
                                   'note', 'start', 'today', 'calculate'))
out <- out %>% dplyr::rename(Question = Label,
                             `Variable name` = name,
                             `Variable type` = type,
                             `Response choices` = Response,
                             `Response choice code` = `Response Code`)
out <- out %>% dplyr::select(Question, `Variable name`, `Variable type`, `Response choices`, `Response choice code`)

# Delete duplicate question names
rn <- as.character(c(1))
for(i in 2:nrow(out)){
  this <- out$Question[i]
  that <- out$Question[i-1]
  if(this == that){
    out$Question[i] <- ' '
    rn[i] <- ' '
  } else {
    rn[i] <- max(as.numeric(rn), na.rm = TRUE) + 1
  }
}
rn <- as.character(rn)

DT::datatable(out, rownames = rn, 
              options = list(
                           paging =TRUE,
                           pageLength =  nrow(out),
                           columnDefs = list(list(className = 'dt-right', targets = '_all'))
                           ))