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index.Rmd
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index.Rmd
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---
title: '**Dynamic Functional Connectivity**'
subtitle: A tutorial
author:
- Lucas G. S. França ^[King's College London, [email protected]]
- Sunniva Fenn-Moltu ^[King's College London, [email protected]]
- Dafnis Batalle ^[King's College London, [email protected]]
output:
html_document:
theme: cerulean
highlight: pygments
toc: yes
toc_depth: 3
toc_float: yes
number_sections: no
df_print: kable
code_folding: hide
code_download: yes
word_document:
reference_docx: utils/Template_Word.docx
highlight: pygments
toc: no
toc_depth: 3
df_print: kable
number_sections: yes
rmarkdown::html_vignette:
toc: yes
toc_depth: 3
pdf_document:
toc: yes
toc_depth: '2'
latex_engine: xelatex
editor_options:
chunk_output_type: inline
bibliography: utils/bibliography.bib
csl: utils/apa.csl
---
<!--
!!!! IMPORTANT: run `source("utils/render.R")` to publish instead of clicking on 'Knit'
-->
```{r setup, warning=FALSE, message=TRUE, include=FALSE}
source("utils/config.R")
fast <- FALSE # Make this false to skip the chunks
```
# Introduction
```{r badges, echo=FALSE, message=TRUE, warning=FALSE, results='asis'}
# This chunk is a bit complex so don't worry about it: it's made to add badges to the HTML versions
# NOTE: You have to replace the links accordingly to have working "buttons" on the HTML versions
if (!knitr::is_latex_output() && knitr::is_html_output()) {
cat("
[](https://creativecommons.org/licenses/by-sa/4.0/)
[](https://github.com/CoDe-Neuro/dfc_chapter)
[](https://code-neuro.github.io/dfc_chapter/)
[](https://github.com/CoDe-Neuro/dfc_chapter/raw/main/word_and_pdf/SupplementaryMaterials.docx)
[](https://github.com/CoDe-Neuro/TemplateResults/blob/main/word_and_pdf/SupplementaryMaterials.pdf)")
}
```
This document was prepared on `r format(Sys.Date())`.
# Fig 1
```{r fig1, echo=FALSE, out.width = "50%", message=TRUE, warning=FALSE}
# Let's include a demo GIF (this doesn't work in PDF documents)
if (!knitr::is_latex_output()) {
knitr::include_graphics("figures/fig1.png")
}
```
# Fig 2
```{r fig2, echo=FALSE, message=TRUE, warning=FALSE}
# Let's include a demo GIF (this doesn't work in PDF documents)
if (!knitr::is_latex_output()) {
knitr::include_graphics("figures/fig2.svg")
}
```
Adapted from: https://en.wikipedia.org/wiki/Voxel#/media/File:Voxels.svg
# Fig 3
```{r fig3, echo=FALSE, message=TRUE, warning=FALSE}
# Let's include a demo GIF (this doesn't work in PDF documents)
if (!knitr::is_latex_output()) {
knitr::include_graphics("figures/fig3.png")
}
```
# Fig 4
```{r fig4, echo=FALSE, message=TRUE, warning=FALSE}
# Let's include a demo GIF (this doesn't work in PDF documents)
if (!knitr::is_latex_output()) {
knitr::include_graphics("figures/fig4.png")
}
```
# Fig 5
```{r fig5, echo=FALSE, message=TRUE, warning=FALSE}
# Let's include a demo GIF (this doesn't work in PDF documents)
if (!knitr::is_latex_output()) {
knitr::include_graphics("figures/fig5.svg")
}
```
# Fig 6
```{r fig6, echo=FALSE, message=TRUE, warning=FALSE}
# Let's include a demo GIF (this doesn't work in PDF documents)
if (!knitr::is_latex_output()) {
knitr::include_graphics("figures/fig6.png")
}
```
# Fig 7
```{r fig7, echo=FALSE, message=TRUE, warning=FALSE}
# Let's include a demo GIF (this doesn't work in PDF documents)
if (!knitr::is_latex_output()) {
knitr::include_graphics("figures/fig7.png")
}
```
```{r child=if (fast == FALSE) 'slide.Rmd'}
```
```{r child=if (fast == FALSE) 'cofluct.Rmd'}
```
```{r child=if (fast == FALSE) 'phase.Rmd'}
```
```{r child=if (fast == FALSE) 'leida.Rmd'}
```
# Package References
```{r warning=FALSE, message=FALSE, results='asis'}
report::cite_packages(sessionInfo())
```