protocol_output.Rmd

---
output: word_document
params: 
    study_title: "Study title"
    authors: "Authors"
    
title: "`r paste0(params$study_title)`"
author: "`r paste0(params$authors)`"
subtitle: "– ODMAP Protocol –"
date: "`r Sys.Date()`"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, eval=TRUE, message=FALSE, warning=FALSE)
```

---

```{r, results = 'asis'}
section = ""
subsection = ""
odmap_dict_rmd = filter(odmap_dict,! element_id %in% c("o_title_1", "o_authorship_1", "o_authorship_2"))
for(i in 1:nrow(odmap_dict_rmd)){
  # Find out if new section header needs to be rendered
  section_new = odmap_dict_rmd$section_id[i]
  if(section_new != section & !(section_new %in% elem_hide[[input$o_objective_1]])){
    section = section_new
    knit_section(section)
  }
  
  # Find out if new subsection header needs to be rendered
  subsection_new = odmap_dict_rmd$subsection_id[i]
  if(subsection_new != subsection & !(subsection_new %in% elem_hide[[input$o_objective_1]])){
    subsection = subsection_new
    knit_subsection(subsection)
  }
  
  # Render elements
  switch(odmap_dict_rmd$element_type[i],
         text = knit_text(odmap_dict_rmd$element_id[i]),
         suggestion = knit_suggestion(odmap_dict_rmd$element_id[i]),
         objective = knit_suggestion(odmap_dict_rmd$element_id[i]),
         extent = knit_extent(odmap_dict_rmd$element_id[i]),
         model_algorithm = knit_suggestion(odmap_dict_rmd$element_id[i]),
         model_setting = knit_model_settings(odmap_dict_rmd$element_id[i]))
}
```