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4 |
31 |
32 | $title-metadata.html()$
33 |
34 |
5 |
6 |
8 | $if(subtitle)$
9 |
30 |
6 | 
7 | $title$
8 | $if(subtitle)$
9 | $subtitle$
10 | $endif$ 11 |
12 | ISSN 2824-7795
15 |
19 | $endif$
20 | $if(categories)$
21 | $if(quarto-template-params.title-block-categories)$
22 |
16 | $description$
17 |
18 |
23 | $for(categories)$
24 |
27 | $endif$
28 | $endif$
29 | $categories$
25 | $endfor$
26 |
3 |
4 |
5 |
6 | $for(by-author)$
7 |
28 | $endif$
29 |
30 |
8 | $if(by-author.url)$$endif$$if(by-author.name.literal)$$by-author.name.literal$$endif$$if(by-author.url)$$endif$ $if(by-author.orcid)$ 
$endif$
9 |
10 |
11 | $if(by-author.affiliations)$
12 |
25 | $endif$
26 | $endfor$
27 | $endif$
9 |
31 | $if(by-affiliation)$
32 | $elseif(by-author)$
33 |
97 |
98 | $if(abstract)$
99 |
34 |
35 |
41 | $endif$
42 |
43 | $if(date)$
44 |
36 | $for(by-author)$
37 |
40 | $by-author.name.literal$ $if(by-author.orcid)$ $endif$
45 |
46 |
49 |
50 | $endif$
51 |
52 | $if(date-modified)$
53 |
54 |
55 |
58 |
59 | $endif$
60 |
61 | $if(doi)$
62 |
63 |
64 |
69 |
70 | $endif$
71 |
72 | $if(keywords)$
73 |
74 |
75 |
78 |
79 | $endif$
80 |
81 |
82 |
83 |
95 |
96 |
84 | $if(draft)$
85 | 
88 | $endif$
89 | $if(published)$
90 |
91 | 
92 | $endif$
93 |
94 | draft
86 | $else$ 87 |
88 | $endif$
89 | $if(published)$
90 |
91 |
92 | $endif$
93 |
100 |
105 | $endif$
106 |
--------------------------------------------------------------------------------
/_extensions/computo/partials/pdf/before-body.tex:
--------------------------------------------------------------------------------
1 | \definecolor{computo-blue}{HTML}{034E79}
2 |
3 | \begin{tikzpicture}[remember picture,overlay]
4 | \fill[computo-blue]
5 | (current page.north west) -- (current page.north east) --
6 | ([yshift=-5cm]current page.north east|-current page.north east) --
7 | ([yshift=-5cm]current page.north west|-current page.north west) -- cycle;
8 | \node[anchor=north west, xshift=.75cm,
9 | yshift=-.75cm] at (current page.north west) {\includegraphics[height=3cm]{logo_text_white}};
10 | \node[font=\sffamily\bfseries\color{white},anchor=north west, xshift=.75cm,
11 | yshift=-4.25cm] at (current page.north
12 | west) {\fontsize{10}{12}\selectfont ISSN 2824-7795};
13 | \node[font=\sffamily\bfseries\color{white},anchor=west,
14 | xshift=4.25cm,yshift=-2.75cm] at (current page.north west)
15 | {\begin{minipage}{15cm}
16 | \fontsize{25}{30}\selectfont
17 | $title$
18 | \vspace{.5cm}
19 | \\
20 | \fontsize{15}{18}\selectfont
21 | $subtitle$
22 | \end{minipage}};
23 | \end{tikzpicture}
24 |
25 | \vspace*{2.5cm}
26 | \begin{center}
27 | $for(by-author)$
28 | $if(by-author.name.literal)$$by-author.name.literal$$endif$$if(it.orcid)$~\orcidlink{$it.orcid$}$endif$$if(it.attributes.corresponding)$\footnote{Corresponding author: $if(it.email)$\href{mailto:$it.email$}{$it.email$}$endif$}$endif$\quad
29 | $for(by-author.affiliations)$
30 | $if(it.department)$$it.department$$if(it.name)$, $endif$$endif$$if(it.name)$$it.name$$endif$$if(it.department)$\\$elseif(it.name)$\\$endif$
31 | $endfor$
32 | $endfor$
33 |
34 | \bigskip
35 |
36 | Date published: $date$ \quad Last modified: $date-modified$
37 | \end{center}
38 |
39 | \bigskip
40 | \begin{abstract}
41 | $abstract$
42 | \end{abstract}
43 |
44 | $if(keywords)$
45 | \noindent%
46 | {\it Keywords:} $for(keywords)$$it$$sep$, $endfor$
47 | \vfill
48 | $endif$
49 |
50 | $if(draft)$
51 | \linenumbers
52 | \DraftwatermarkOptions{stamp=true, colorspec=0.9, text={\rm submitted}}
53 | $else$
54 | \DraftwatermarkOptions{stamp=false}
55 | $endif$
56 |
57 |
--------------------------------------------------------------------------------
/_extensions/computo/partials/pdf/include-in-header.tex:
--------------------------------------------------------------------------------
1 | \usepackage{tikz}
2 | \usepackage{xcolor}
3 | \usepackage{tabularx}
4 | \usepackage{orcidlink}
5 | \usepackage{lineno}
6 | \usepackage{libertinus}
7 | \usepackage{draftwatermark}
8 |
9 |
--------------------------------------------------------------------------------
/_extensions/computo/shortcodes.lua:
--------------------------------------------------------------------------------
1 | --[[
2 | This file defines the shortcodes that your extension will make available
3 | https://quarto.org/docs/authoring/shortcodes.html#custom-shortcodes
4 | Quarto exports utils function that can be used in all filters. See
5 | https://github.com/quarto-dev/quarto-cli/blob/main/src/resources/pandoc/datadir/init.lua#L1522-L1576
6 | ]]--
7 |
8 | -- Example shortcode that provides a nicely formatted 'LaTeX' string
9 | function latex()
10 | if quarto.doc.isFormat("pdf") then
11 | return pandoc.RawBlock('tex', '{\\LaTeX}')
12 | elseif quarto.doc.isFormat("html") then
13 | return pandoc.Math('InlineMath', "\\LaTeX")
14 | else
15 | return pandoc.Span('LaTeX')
16 | end
17 | end
--------------------------------------------------------------------------------
/_quarto.yml:
--------------------------------------------------------------------------------
1 | project:
2 | title: "computo-quarto-extension"
3 | render:
4 | - computo-quarto-extension.qmd
5 | resources:
6 | - environment.yml
7 |
8 | title: "Computo Journal Format"
9 | subtitle: "To be used as template for contribution to Computo"
10 | date: 01/02/2023
11 | date-modified: last-modified
12 | author:
13 | - name: The Computo Team
14 | corresponding: true
15 | email: computo@sfds.asso.fr
16 | url: https://computo.sfds.asso.fr
17 | orcid: 0000-0000-0000-0000
18 | affiliations:
19 | - name: Société Française de Statistique
20 | department: Statistique
21 | address: IHP
22 | city: Paris
23 | country: France
24 | postal-code: 75005
25 | - name: a friend
26 | affiliations:
27 | - Another Affiliation
28 | description: |
29 | This document provides a template based on the quarto system for contributions to Computo. The github repository in itself provides a specific quarto extension useful for authors (and editors!).
30 | keywords: [template, quarto, R, Python, reproductibility]
31 | doi: 10.xxxx/xxx-xxx
32 | citation:
33 | type: article-journal
34 | container-title: "Computo"
35 | doi: "10.xxxx/xxx-xxx"
36 | url: "https://github.com/computorg/computo-quarto-extension"
37 | issn: "2824-7795"
38 | abstract: |
39 | This is the abstract - Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur posuere vestibulum facilisis. Aenean pretium orci augue, quis lobortis libero accumsan eu. Nam mollis lorem sit amet pellentesque ullamcorper. Curabitur lobortis libero eget malesuada vestibulum. Nam nec nibh massa. Pellentesque porttitor cursus tellus. Mauris urna erat, rhoncus sed faucibus sit amet, venenatis eu ipsum.
40 | bibliography: references.bib
41 | google-scholar: true
42 | github-user: computorg
43 | repo: "computo-quarto-extension"
44 | draft: true # set to false once the build is running
45 | published: false # will be set to true once accepted
46 | format:
47 | computo-html: default
48 | computo-pdf: default
49 |
50 | diagram:
51 | engine:
52 | tikz:
53 | header-includes:
54 | - '\usetikzlibrary{arrows}'
55 |
56 |
--------------------------------------------------------------------------------
/computo-quarto-extension.qmd:
--------------------------------------------------------------------------------
1 | # About this document
2 |
3 | This document provides a template based on the [quarto system](https://quarto.org/) for contributions to **Computo** [@computo]. We show how `Python` [@perez2011python] or `R` [@R-base] code can be included.
4 |
5 | # Formatting
6 |
7 | This section covers basic formatting guidelines. [Quarto](https://quarto.org/) is a versatile formatting system for authoring HTML based on markdown, integrating {{< latex >}} and various code block interpreted either via Jupyter or Knitr (and thus deal with Python, R and many other langages). It relies on the [Pandoc Markdown](https://rmarkdown.rstudio.com/authoring_pandoc_markdown.html) markup language.
8 |
9 | :::{.callout-note}
10 | We will only give some formatting elements. Authors can refer to the [Quarto web page](https://quarto.org/) for a complete view of the formatting possibilities.
11 | :::
12 |
13 | :::{.callout-note}
14 | Quarto itself is a work-in-progress and a lot of bugs are constantly fixed or features added. As such, we recommend:
15 |
16 | - searching any encountered issue with renders in [the upstream quarto dev repo](https://github.com/quarto-dev/quarto-cli/issues)
17 | - using a [version of quarto > 1.2](https://github.com/quarto-dev/quarto-cli/releases)
18 | :::
19 |
20 | To render/compile a document, run `quarto render`. A document will be generated that includes both content as well as the output of any embedded code chunks within the document:
21 |
22 | ``` .bash
23 | quarto render content.qmd # will render to html
24 | ```
25 |
26 | ## Basic markdown formatting
27 |
28 | **Bold text** or _italic_
29 |
30 | - This is a list
31 | - With more elements
32 | - It isn't numbered.
33 |
34 | But we can also do a numbered list
35 |
36 | 1. This is my first item
37 | 2. This is my second item
38 | 3. This is my third item
39 |
40 | ## Mathematics
41 |
42 | ### Mathematical formulae
43 |
44 | [{{< latex >}}](https://www.latex-project.org/) code is natively supported[^katex], which makes it possible to use mathematical formulae:
45 |
46 | [^katex]: We use [katex](https://katex.org/) for this purpose.
47 |
48 | will render
49 |
50 | $$
51 | f(x_1, \dots, x_n; \mu, \sigma^2) =
52 | \frac{1}{\sigma \sqrt{2\pi}} \exp{\left(- \frac{1}{2\sigma^2}\sum_{i=1}^n(x_i - \mu)^2\right)}
53 | $$
54 |
55 | It is also possible to cross-reference an equation, see @eq-mylabel:
56 |
57 | $$
58 | \begin{aligned}
59 | D_{x_N} & = \frac12
60 | \left[\begin{array}{cc}
61 | x_L^\top & x_N^\top \end{array}\right] \,
62 | \left[\begin{array}{cc} L_L & B \\ B^\top & L_N \end{array}\right] \,
63 | \left[\begin{array}{c}
64 | x_L \\ x_N \end{array}\right] \\
65 | & = \frac12 (x_L^\top L_L x_L + 2 x_N^\top B^\top x_L + x_N^\top L_N x_N),
66 | \end{aligned}
67 | $$ {#eq-mylabel}
68 |
69 | ### Theorems and other amsthem-like environments
70 |
71 | Quarto includes a nice support for theorems, with predefined prefix labels for theorems, lemmas, proposition, etc. see [this page](https://quarto.org/docs/authoring/cross-references.html#theorems-and-proofs). Here is a simple example:
72 |
73 | ::: {#thm-slln}
74 | ### Strong law of large numbers
75 |
76 | The sample average converges almost surely to the expected value:
77 |
78 | $$\overline{X}_n\ \xrightarrow{\text{a.s.}}\ \mu \qquad\textrm{when}\ n \to \infty.$$
79 | :::
80 |
81 | See @thm-slln.
82 |
83 | ## Code
84 |
85 | Quarto uses either Jupyter or knitr to render code chunks. This can be triggered in the yaml header, e.g., for Jupyter (should be installed on your computer) use
86 |
87 | ``` yaml
88 | ---
89 | title: "My Document"
90 | author "Jane Doe"
91 | jupyter: python3
92 | ---
93 | ```
94 |
95 | For knitr (R + knitr must be installed on your computer)
96 |
97 | ``` yaml
98 | ---
99 | title: "My Document"
100 | author "Jane Doe"
101 | ---
102 | ```
103 |
104 | You can use Jupyter for Python code and more. And R + KnitR for if you want to mix R with Python (via the package reticulate @R-reticulate).
105 |
106 | ### R
107 |
108 | `R` code [@R-base] chunks may be embedded as follows:
109 |
110 | ```{r r-code, echo=TRUE}
111 | x <- rnorm(10)
112 | ```
113 |
114 |
115 | ### Python
116 |
117 | ```{python}
118 | #| label: fig-plotly
119 | #| fig-cap: "A simple python plotly example"
120 | import plotly.express as px
121 | df = px.data.tips()
122 | fig = px.histogram(df, x="total_bill", y="tip", color="sex",
123 | marginal="box", # or violin, rug
124 | hover_data=df.columns)
125 | fig
126 | ```
127 |
128 | ## Figures
129 |
130 | Plots can be generated as follows and referenced. See plot @fig-gg:
131 |
132 | ```{r}
133 | #| label: fig-gg
134 | #| fig-cap: "A simple ggplot example"
135 | #| message: false
136 | library("ggplot2")
137 | p <- ggplot(mpg, aes(displ, hwy)) +
138 | geom_point() +
139 | geom_smooth() + theme_bw()
140 | p
141 | ```
142 |
143 | Interactive plots may also be produced in the HTML output of the document^[The pdf output is just a screenshot of the interactive plot from the html output]:
144 |
145 | ```{r}
146 | #| label: fig-ggplotly
147 | #| fig-cap: "A simple ggplotly interactive example"
148 | #| message: false
149 | #| warning: false
150 | library("plotly")
151 | ggplotly(p)
152 | ```
153 |
154 | It is also possible to create figures from static images:
155 |
156 | :::{#fig-logo}
157 |
158 | 
159 |
160 | SFdS logo (c.a. 2021)
161 |
162 | :::
163 |
164 | ## Tables
165 |
166 | ### Markdown syntax
167 |
168 | Tables (with label: `@tbl-mylabel` renders @tbl-mylabel) can be generated with markdown as follows
169 |
170 | ```markdown
171 | | Tables | Are | Cool |
172 | |----------|:-------------:|------:|
173 | | col 1 is | left-aligned | $1600 |
174 | | col 2 is | centered | $12 |
175 | | col 3 is | right-aligned | $1 |
176 | : my table caption {#tbl-mylabel}
177 | ```
178 |
179 | | Tables | Are | Cool |
180 | |----------|:-------------:|------:|
181 | | col 1 is | left-aligned | $1600 |
182 | | col 2 is | centered | $12 |
183 | | col 3 is | right-aligned | $1 |
184 | : my table caption {#tbl-mylabel}
185 |
186 | ### List-table filter
187 |
188 | We also integrate the [list tables](https://github.com/pandoc-ext/list-table) filter from Pandoc, so that you may alternatively use this format , easier to write and maintain:
189 |
190 | ```markdown
191 | :::list-table
192 | * - row 1, column 1
193 | - row 1, column 2
194 | - row 1, column 3
195 |
196 | * - row 2, column 1
197 | -
198 | - row 2, column 3
199 |
200 | * - row 3, column 1
201 | - row 3, column 2
202 | :::
203 | ```
204 |
205 | :::list-table
206 | * - row 1, column 1
207 | - row 1, column 2
208 | - row 1, column 3
209 |
210 | * - row 2, column 1
211 | -
212 | - row 2, column 3
213 |
214 | * - row 3, column 1
215 | - row 3, column 2
216 | :::
217 |
218 | ### Table generated from code
219 |
220 | Table can also be generated by some code, for instance with ```knitr``` here:
221 |
222 | ```{r cars}
223 | knitr::kable(summary(cars), caption = "Table caption.")
224 | ```
225 |
226 | ## Algorithms
227 |
228 | A solution to typeset pseudocode just like you would do with {{< latex >}}, yet with HTML output is to rely on the JavaScript [pseudocode.js](https://github.com/SaswatPadhi/pseudocode.js). Your pseudocode is written inside a [Code Block](https://quarto.org/docs/authoring/markdown-basics.html#source-code) with the `pseudocode` class. Do not forget the class tag, that will trigger the rendering process of your pseudo-code. The result is as follows^[For proper pdf rendering, use [Camel cased](https://en.wikipedia.org/wiki/Camel_case) names for all `algorithmic` keywords, not upper case ones, like the examples in `pseudocode.js`’s documentation, which are not compatible with LaTeX.]:
229 |
230 | ````markdown
231 | ```pseudocode
232 | #| label: alg-quicksort
233 | #| html-indent-size: "1.2em"
234 | #| html-comment-delimiter: "//"
235 | #| html-line-number: true
236 | #| html-line-number-punc: ":"
237 | #| html-no-end: false
238 | #| pdf-placement: "htb!"
239 | #| pdf-line-number: true
240 |
241 | \begin{algorithm}
242 | \caption{Quicksort}
243 | \begin{algorithmic}
244 | \Procedure{Quicksort}{$A, p, r$}
245 | \If{$p < r$}
246 | \State $q = $ \Call{Partition}{$A, p, r$}
247 | \State \Call{Quicksort}{$A, p, q - 1$}
248 | \State \Call{Quicksort}{$A, q + 1, r$}
249 | \EndIf
250 | \EndProcedure
251 | \Procedure{Partition}{$A, p, r$}
252 | \State $x = A[r]$
253 | \State $i = p - 1$
254 | \For{$j = p, \dots, r - 1$}
255 | \If{$A[j] < x$}
256 | \State $i = i + 1$
257 | \State exchange
258 | $A[i]$ with $A[j]$
259 | \EndIf
260 | \State exchange $A[i]$ with $A[r]$
261 | \EndFor
262 | \EndProcedure
263 | \end{algorithmic}
264 | \end{algorithm}
265 | ```
266 | ````
267 |
268 | ```pseudocode
269 | #| label: alg-quicksort
270 | #| html-indent-size: "1.2em"
271 | #| html-comment-delimiter: "//"
272 | #| html-line-number: true
273 | #| html-line-number-punc: ":"
274 | #| html-no-end: false
275 | #| pdf-placement: "htb!"
276 | #| pdf-line-number: true
277 |
278 | \begin{algorithm}
279 | \caption{Quicksort}
280 | \begin{algorithmic}
281 | \Procedure{Quicksort}{$A, p, r$}
282 | \If{$p < r$}
283 | \State $q = $ \Call{Partition}{$A, p, r$}
284 | \State \Call{Quicksort}{$A, p, q - 1$}
285 | \State \Call{Quicksort}{$A, q + 1, r$}
286 | \EndIf
287 | \EndProcedure
288 | \Procedure{Partition}{$A, p, r$}
289 | \State $x = A[r]$
290 | \State $i = p - 1$
291 | \For{$j = p, \dots, r - 1$}
292 | \If{$A[j] < x$}
293 | \State $i = i + 1$
294 | \State exchange
295 | $A[i]$ with $A[j]$
296 | \EndIf
297 | \State exchange $A[i]$ with $A[r]$
298 | \EndFor
299 | \EndProcedure
300 | \end{algorithmic}
301 | \end{algorithm}
302 | ```
303 |
304 | @alg-quicksort is extracted from Chapter 7, Introduction to Algorithms (3rd edition).
305 |
306 | ## Diagrams
307 |
308 | In addition of [quarto supported diagrams](https://quarto.org/docs/authoring/diagrams.html), we also support [tikz](https://www.overleaf.com/learn/latex/TikZ_package) diagrams. The following example^[This is the new syntax for cross-references since quarto 1.4, see [Crossreferenceable elements](https://quarto.org/docs/prerelease/1.4/crossref.html)] is rendered as follows.
309 |
310 | ````markdown
311 | :::{#fig-tikz}
312 |
313 | ``` tikz
314 | %%| filename: ../figure-tikz/fig-tikz
315 | \begin{tikzpicture}[node distance=2cm, auto, thick, scale=2, every node/.style={transform shape}]
316 | \node (P) {$P$};
317 | \node (B) [right of=P] {$B$};
318 | \node (A) [below of=P] {$A$};
319 | \node (C) [below of=B] {$C$};
320 | \node (P1) [node distance=1.4cm, left of=P, above of=P] {$\hat{P}$};
321 | \draw[->] (P) to node {$f$} (B);
322 | \draw[->] (P) to node [swap] {$g$} (A);
323 | \draw[->] (A) to node [swap] {$f$} (C);
324 | \draw[->] (B) to node {$g$} (C);
325 | \draw[->, bend right] (P1) to node [swap] {$\hat{g}$} (A);
326 | \draw[->, bend left] (P1) to node {$\hat{f}$} (B);
327 | \draw[->, dashed] (P1) to node {$k$} (P);
328 | \end{tikzpicture}
329 | ```
330 |
331 | A simple example of a commutative diagram with $\texttt{tikz}$.
332 |
333 | :::
334 | ````
335 |
336 | :::{#fig-tikz}
337 |
338 | ``` tikz
339 | %%| filename: ../figure-tikz/fig-tikz
340 | \begin{tikzpicture}[node distance=2cm, auto, thick, scale=2, every node/.style={transform shape}]
341 | \node (P) {$P$};
342 | \node (B) [right of=P] {$B$};
343 | \node (A) [below of=P] {$A$};
344 | \node (C) [below of=B] {$C$};
345 | \node (P1) [node distance=1.4cm, left of=P, above of=P] {$\hat{P}$};
346 | \draw[->] (P) to node {$f$} (B);
347 | \draw[->] (P) to node [swap] {$g$} (A);
348 | \draw[->] (A) to node [swap] {$f$} (C);
349 | \draw[->] (B) to node {$g$} (C);
350 | \draw[->, bend right] (P1) to node [swap] {$\hat{g}$} (A);
351 | \draw[->, bend left] (P1) to node {$\hat{f}$} (B);
352 | \draw[->, dashed] (P1) to node {$k$} (P);
353 | \end{tikzpicture}
354 | ```
355 |
356 | A simple example of a commutative diagram with $\texttt{tikz}$.
357 |
358 | :::
359 |
360 | You may refer to it as @fig-tikz.
361 |
362 | ## Handling references {#sec-references}
363 |
364 | ### Bibliographic references
365 |
366 | References are displayed as footnotes using [BibTeX](http://www.bibtex.org/), e.g. `[@computo]` will be displayed
367 | as [@computo], where `computo` is the bibtex key for this specific entry. The bibliographic information is automatically retrieved from
368 | the `.bib` file specified in the header of this document (here:`references.bib`).
369 |
370 | ### Other cross-references
371 |
372 | As already (partially) seen, Quarto includes a mecanism similar to the bibliographic references for sections, equations, theorems, figures,
373 | lists, etc. Have a look at [this page](https://quarto.org/docs/authoring/cross-references.html).
374 |
375 | ## To go further
376 |
377 | :::{.callout-note}
378 | ### One last note
379 | To go into more involved details, you can also simply check the source code of this document (button at the top), or have a look at the source of our [t-sne remake example](https://computo.sfds.asso.fr/published-paper-tsne/).
380 | :::
381 |
382 |
383 | ## Bibliography {.unnumbered}
384 |
385 | ::: {#refs}
386 | :::
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/environment.yml:
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1 | name: computo-quarto-extension
2 | channels:
3 | - conda-forge
4 | dependencies:
5 | - python=3.12
6 | - jupyter
7 | - plotly
8 | - numpy
9 | - pandas
10 | - python-kaleido
11 |
12 |
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/figures/sfds.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/computorg/computo-quarto-extension/d82f4fdea3376e12dff441b1f7d767e4cb972ff4/figures/sfds.png
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/references.bib:
--------------------------------------------------------------------------------
1 | @article{computo,
2 | title = {Computo: reproducible computational/algorithmic contributions in statistics and machine learning},
3 | author = {{Computo Team}},
4 | year = {2021},
5 | journal = {computo}
6 | }
7 |
8 | @Manual{R-base,
9 | title = {R: A Language and Environment for Statistical Computing},
10 | author = {{R Core Team}},
11 | organization = {R Foundation for Statistical Computing},
12 | address = {Vienna, Austria},
13 | year = {2020},
14 | url = {https://www.R-project.org/},
15 | }
16 |
17 | @Manual{R-reticulate,
18 | title = {reticulate: Interface to Python},
19 | author = {Kevin Ushey and JJ Allaire and Yuan Tang},
20 | year = {2020},
21 | note = {R package version 1.18},
22 | url = {https://github.com/rstudio/reticulate},
23 | }
24 |
25 | @article{perez2011python,
26 | title = {Python: an ecosystem for scientific computing},
27 | author = {Perez, Fernando and Granger, Brian E and Hunter, John D},
28 | journal = {Computing in Science \\& Engineering},
29 | volume = {13},
30 | number = {2},
31 | pages = {13--21},
32 | year = {2011},
33 | publisher = {AIP Publishing}
34 | }
35 |
36 |
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/renv/.gitignore:
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1 | library/
2 | local/
3 | cellar/
4 | lock/
5 | python/
6 | sandbox/
7 | staging/
8 | activate.R
9 | settings.json
--------------------------------------------------------------------------------
/setup-env-ci.sh:
--------------------------------------------------------------------------------
1 | sudo apt-get install -y libcurl4-openssl-dev libpng-dev
2 |
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/setup-render-ci.sh:
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1 | sudo apt-get install -y inkscape
2 | quarto install chromium
3 | mkdir -p ~/.local/bin
4 | ~/.TinyTeX/bin/x86_64-linux/tlmgr option sys_bin ~/.local/bin
5 | ~/.TinyTeX/bin/x86_64-linux/tlmgr path add
6 | ~/.TinyTeX/bin/x86_64-linux/tlmgr update --self
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101 |
104 | $labels.abstract$
102 | $abstract$
103 |