manuscript-template.qmd

---
title: Manuscript Template
author:
  - name: Author One
    orcid: 0000-0002-0760-5497
    corresponding: true
    email: youremail@email.com
    roles:
      - Investigation
      - Project administration
      - Software
      - Visualization
    affiliations:
      - name: CRNL
  - name: Author Two
    orcid: 0000-0002-7859-8394
    corresponding: false
    roles: []
    affiliations:
      - name: CRNL
keywords:
  - quarto
  - neuroscience
  - coffee
toc: true
toc-depth: 2
csl: "styles/current-biology.csl"
execute: 
  echo: false
format: docx
---
Version: {{< var version >}}
{{< include functions/_stats_format.qmd >}}

## General Information

This is a template meant to accelerate the adoption of Quarto. It does
not do much, besides providing an extensively configured header. The
header contains various fields that provide standard information about
the paper and some formatting rendering options. Check it out.

## References

It is quite easy to include citations. You can either use Crtl+Shit+F8
to call the utility of Quarto to add from your local Zotero (and other
sources), or you can populate manually your references.bib file and
write down citation keys directly [@abbasi2023]. Look at the end of this
file to see how the bibliography is inserted.

## Automatic inclusion of statistics

To include statistics automatically, you need to **include** additional
.qmd files. Here, we include the following file
`functions/_stats_format.qmd`. This allows us to write down statistics
in using the following expression: `{python} Ttest("stock")`.

Here is a result based on the output from Matlab's ttest() function,
displayed automatically: `{python} Ttest("stock")`

Here is another results based on the output from R lm() function:
`{python} Rlm("example","weight")`

One may also output directly text to display from Matlab, R, Python or Julia:
`{python} textStat("glmeExample","newprocess")`

`{python} Mcorr("totest","weight", "age")`

## Automatic inclusion of images

There are various ways to include images in a document. At the simplest,
you just need to reference the image path and possibly add some
formatting parameters. For example:

But we can also make use of Quarto layouts.

## Bibliography

::: {#refs}
:::

## Figures

### Insert pre-generated figure

![Example
Figure](_analyses/figures/writingTime.png){#fig-exampleImported
fig-align="center" width="50%" fig-cap-location="bottom"}

### Insert Python figure (matplotlib)

::: {width="100%"}
```{python}
#| fig-cap: 
#|   - "Example Python Figure with Caption. (A) Something. (B) Something else. (C) Yet another thing."
#| 
import matplotlib.pyplot as plt
import numpy as np

# example data
x = np.arange(0.1, 4, 0.1)
y1 = np.exp(-1.0 * x)
y2 = np.exp(-0.5 * x)

# example variable error bar values
y1err = 0.1 + 0.1 * np.sqrt(x)
y2err = 0.1 + 0.1 * np.sqrt(x/2)


fig, (ax0, ax1, ax2) = plt.subplots(nrows=1, ncols=3, sharex=True,
                                   figsize=(9, 4))

ax0.set_title('A', loc='left')
ax0.errorbar(x, y1, yerr=y1err)
ax0.errorbar(x, y2, yerr=y2err)

ax1.set_title('B', loc='left')
ax1.errorbar(x, y1, yerr=y1err, errorevery=6)
ax1.errorbar(x, y2, yerr=y2err, errorevery=6)

ax2.set_title('C', loc='left')
ax2.errorbar(x, y1, yerr=y1err, errorevery=(0, 6))
ax2.errorbar(x, y2, yerr=y2err, errorevery=(3, 6))

plt.show()
```
:::