repeatability_script_pdf.Rmd

---
title: "Gait Repeatability Study"
author: "Erik Waskiewicz"
date: "15/08/2018"
output: 
  pdf_document:
    latex_engine: xelatex
header-includes: 
  - \usepackage{rotating}
  - \usepackage{color}
  - \usepackage[dvipsnames]{xcolor}
  - \usepackage{fontspec}
  - \setmainfont{Arial}
editor_options: 
  chunk_output_type: console
---

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

## -------------------- INSTRUCTIONS ----------------------------------

# 1. Create directory for study and write file path in brackets below
setwd('<filepath>/gait-repeatability')

# 2. Move this script into new study directory
# 3. Edit title, author and date in lines 2-4 above. Do not alter any other code above.
# 4. Copy raw data into new directory named 'raw_data' within the study directory. Check that filepaths below point to the data.
study_sides = list(
  c('Left', 'raw_data/<Name of file>'),
  c('Right', 'raw_data/<Name of file>')
)

# 5. Change settings below, see readme for details
# 6. Once finished, save file and click knit

# ----------------------- Settings -----------------------------------
study_participants = list(
  c('Participant 1', '<Participant identifier>')
)
study_assessors = list(
  c('A1', '<Assessor identifier>'),
  c('A2', '<Assessor identifier>'),
  c('A3', '<Assessor identifier>')
)
study_sessions = list(
  c('Session 1', '01'),
  c('Session 2', '02'),
  c('Session 3', '03'),
  c('Session 4', '04')
)
study_parameters = list(
  c('Foot pitch', 'Foot Pitch Angles', 'X', -80, 30, 20),
  c('Foot progression', 'Foot Pitch Angles', 'Z', -25, 25, 10),
  c('Ankle dorsiflexion', 'Ankle Angles', 'X', -25, 15, 5),
  c('Ankle inversion', 'Ankle Angles', 'Y', 0, 30, 5),
  c('Knee flexion', 'Knee Angles', 'X', -15, 70, 10),
  c('Knee adduction', 'Knee Angles', 'Y', -15, 10, 5),
  c('Knee rotation', 'Knee Angles', 'Z', -22, 12, 10),
  c('Hip flexion', 'Hip Angles', 'X', -20, 40, 10),
  c('Hip adduction', 'Hip Angles', 'Y', -15, 10, 5),
  c('Hip rotation', 'Hip Angles', 'Z', -30, 10, 10),
  c('Pelvic tilt', 'Pelvic Angles', 'X', 0, 20, 5),
  c('Pelvic obliquity', 'Pelvic Angles', 'Y', -6, 6, 2),
  c('Pelvic rotation', 'Pelvic Angles', 'Z', -10, 12, 5)
)

## Load functions - make sure this points to the repeatability functions file
source('<filepath>/repeatability_functions.R')

# --------------------------------------------------------------------

# Don't edit from here onwards!

######################################################################
dir.create('results')
```

```{r data_sorting, results='asis'}
main_summary()
sorted_data <- main_sorting(study_sides)
```

```{r main_analysis, results='asis', fig.width=9, fig.height=11.5}
grp_df <- main_analysis_latex(sorted_data, study_parameters, study_sides, study_sessions, study_assessors)
```
  
```{r plot_GRP, results='asis', fig.width=9, fig.height=4}
main_grp_latex(grp_df, study_assessors)
```