diff --git a/LuisLauM.github.io.Rproj b/LuisLauM.github.io.Rproj index 8e3c2eb..1abdc87 100644 --- a/LuisLauM.github.io.Rproj +++ b/LuisLauM.github.io.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: a44bdcad-f072-4b27-b696-0c1b2ca08110 RestoreWorkspace: Default SaveWorkspace: Default diff --git a/blog/about-this-website/about-this-website.qmd b/blog/about-this-website/about-this-website.qmd index e14e145..112a1b5 100644 --- a/blog/about-this-website/about-this-website.qmd +++ b/blog/about-this-website/about-this-website.qmd @@ -67,6 +67,9 @@ I Didn't Have to Start from Scratch. Fortunately, there are many resources avail + +--- + # [ES] Desarrollando 'Beneath the surface 🌊' ## La idea diff --git a/blog/quarto-template-article/article-template.zip b/blog/quarto-template-article/article-template.zip index e12c618..d1ed157 100644 Binary files a/blog/quarto-template-article/article-template.zip and b/blog/quarto-template-article/article-template.zip differ diff --git a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/_extension.yml b/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/_extension.yml deleted file mode 100644 index 194f33b..0000000 --- a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/_extension.yml +++ /dev/null @@ -1,13 +0,0 @@ -title: Authors-block -authors: - - name: Lorenz A. Kapsner - orcid: 0000-0003-1866-860X - - name: Albert Krewinkel - orcid: 0000-0002-9455-0796 - - name: Robert Winkler -version: 0.2.1 -quarto-required: ">=1.3.0" -contributes: - filters: - - authors-block.lua - diff --git a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/authors-block.lua b/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/authors-block.lua deleted file mode 100644 index c7cc6c5..0000000 --- a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/authors-block.lua +++ /dev/null @@ -1,64 +0,0 @@ ---[[ -authors-block – affiliations block extension for quarto - -Copyright (c) 2023 Lorenz A. Kapsner - -Permission to use, copy, modify, and/or distribute this software for any purpose -with or without fee is hereby granted, provided that the above copyright notice -and this permission notice appear in all copies. - -THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH -REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND -FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, -INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER -TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF -THIS SOFTWARE. -]] - -local List = require 'pandoc.List' - --- [import] -local from_utils = require "utils" -local normalize_affiliations = from_utils.normalize_affiliations -local normalize_authors = from_utils.normalize_authors -local normalize_latex_authors = from_utils.normalize_latex_authors - -local from_authors = require "from_author_info_blocks" -local default_marks = from_authors.default_marks -local create_equal_contributors_block = from_authors.create_equal_contributors_block -local create_affiliations_blocks = from_authors.create_affiliations_blocks -local create_correspondence_blocks = from_authors.create_correspondence_blocks -local is_corresponding_author = from_authors.is_corresponding_author -local author_inline_generator = from_authors.author_inline_generator -local create_authors_inlines = from_authors.create_authors_inlines --- [/import] - --- This is the main-part -function Pandoc(doc) - local meta = doc.meta - local body = List:new{} - - local mark = function (mark_name) return default_marks[mark_name] end - - body:extend(create_equal_contributors_block(meta.authors, mark) or {}) - body:extend(create_affiliations_blocks(meta.affiliations) or {}) - body:extend(create_correspondence_blocks(meta.authors, mark) or {}) - body:extend(doc.blocks) - - for _i, author in ipairs(meta.authors) do - author.test = is_corresponding_author(author) - end - - meta.affiliations = normalize_affiliations(meta.affiliations) - meta.author = meta.authors:map(normalize_authors(meta.affiliations)) - - -- Overwrite authors with formatted values. We use a single, formatted - -- string for most formats. LaTeX output, however, looks nicer if we - -- provide a authors as a list. - meta.author = pandoc.MetaInlines(create_authors_inlines(meta.author, mark)) - -- Institute info is now baked into the affiliations block. - meta.affiliations = nil - - return pandoc.Pandoc(body, meta) -end diff --git a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/from_author_info_blocks.lua b/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/from_author_info_blocks.lua deleted file mode 100644 index 79edb1c..0000000 --- a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/from_author_info_blocks.lua +++ /dev/null @@ -1,197 +0,0 @@ --- https://github.com/pandoc/lua-filters/commit/ca72210b453cc0d045360e0ae36448d019d7dfbf ---[[ -affiliation-blocks – generate title components - -Copyright © 2017–2021 Albert Krewinkel - -Permission to use, copy, modify, and/or distribute this software for any purpose -with or without fee is hereby granted, provided that the above copyright notice -and this permission notice appear in all copies. - -THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH -REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND -FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, -INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER -TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF -THIS SOFTWARE. -]] - --- from @kapsner --- [import] -local from_utils = require "utils" -local has_key = from_utils.has_key --- [/import] -local M = {} - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua -local List = require 'pandoc.List' -local utils = require 'pandoc.utils' -local stringify = utils.stringify - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua -local default_marks -local default_marks = { - corresponding_author = FORMAT == 'latex' - and {pandoc.RawInline('latex', '*')} - or {pandoc.Str '✉'}, - equal_contributor = FORMAT == 'latex' - and {pandoc.RawInline('latex', '$\\dagger{}$')} - or {pandoc.Str '*'}, -} -M.default_marks = default_marks - --- modified by @kapsner --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua -local function is_equal_contributor(author) - if has_key(author, "attributes") then - return author.attributes["equal-contributor"] - end - return nil -end - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua ---- Create equal contributors note. -local function create_equal_contributors_block(authors, mark) - local has_equal_contribs = List:new(authors):find_if(is_equal_contributor) - if not has_equal_contribs then - return nil - end - local contributors = { - pandoc.Superscript(mark'equal_contributor'), - pandoc.Space(), - pandoc.Str 'These authors contributed equally to this work.' - } - return List:new{pandoc.Para(contributors)} -end -M.create_equal_contributors_block = create_equal_contributors_block - - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua -local function intercalate(lists, elem) - local result = List:new{} - for i = 1, (#lists - 1) do - result:extend(lists[i]) - result:extend(elem) - end - if #lists > 0 then - result:extend(lists[#lists]) - end - return result -end - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua ---- Check whether the given author is a corresponding author -local function is_corresponding_author(author) - if has_key(author, "attributes") then - if author.attributes["corresponding"] then - return author.email - end - end - return nil -end -M.is_corresponding_author = is_corresponding_author - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua ---- Generate a block element containing the correspondence information -local function create_correspondence_blocks(authors, mark) - local corresponding_authors = List:new{} - for _, author in ipairs(authors) do - if is_corresponding_author(author) then - local mailto = 'mailto:' .. utils.stringify(author.email) - local author_with_mail = List:new( - -- modified by @kapsner - author.name.literal .. List:new{pandoc.Space(), pandoc.Str '<'} .. - author.email .. List:new{pandoc.Str '>'} - ) - local link = pandoc.Link(author_with_mail, mailto) - table.insert(corresponding_authors, {link}) - end - end - if #corresponding_authors == 0 then - return nil - end - local correspondence = List:new{ - pandoc.Superscript(mark'corresponding_author'), - pandoc.Space(), - pandoc.Str'Correspondence:', - pandoc.Space() - } - local sep = List:new{pandoc.Str',', pandoc.Space()} - return { - pandoc.Para(correspondence .. intercalate(corresponding_authors, sep)) - } -end -M.create_correspondence_blocks = create_correspondence_blocks - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua ---- Create inlines for a single author (includes all author notes) -local function author_inline_generator (get_mark) - return function (author) - local author_marks = List:new{} - -- modified by @kapsner - if has_key(author, "attributes") then - if author.attributes["equal-contributor"] then - author_marks[#author_marks + 1] = get_mark 'equal_contributor' - end - end - local idx_str - for _, idx in ipairs(author.affiliations) do - if type(idx) ~= 'table' then - idx_str = tostring(idx) - else - idx_str = stringify(idx) - end - author_marks[#author_marks + 1] = {pandoc.Str(idx_str)} - end - if is_corresponding_author(author) then - author_marks[#author_marks + 1] = get_mark 'corresponding_author' - end - -- modified by @kapsner - if FORMAT:match 'latex' then - author.name.literal[#author.name.literal + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','})) - return author - else - local res = List.clone(author.name.literal) - res[#res + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','})) - return res - end - end -end -M.author_inline_generator = author_inline_generator - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua ---- Generate a list of inlines containing all authors. -local function create_authors_inlines(authors, mark) - local inlines_generator = author_inline_generator(mark) - local inlines = List:new(authors):map(inlines_generator) - local and_str = List:new{pandoc.Space(), pandoc.Str'and', pandoc.Space()} - - local last_author = inlines[#inlines] - inlines[#inlines] = nil - local result = intercalate(inlines, {pandoc.Str ',', pandoc.Space()}) - if #authors > 1 then - result:extend(List:new{pandoc.Str ","} .. and_str) - end - result:extend(last_author) - return result -end -M.create_authors_inlines = create_authors_inlines - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua ---- Generate a block list all affiliations, marked with arabic numbers. -local function create_affiliations_blocks(affiliations) - local affil_lines = List:new(affiliations):map( - function (affil, i) - local num_inlines = List:new{ - pandoc.Superscript{pandoc.Str(affil.number)}, - pandoc.Space() - } - return num_inlines .. affil.name - end - ) - return {pandoc.Para(intercalate(affil_lines, {pandoc.LineBreak()}))} -end -M.create_affiliations_blocks = create_affiliations_blocks - -return M diff --git a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/from_scholarly_metadata.lua b/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/from_scholarly_metadata.lua deleted file mode 100644 index 0ff7e81..0000000 --- a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/from_scholarly_metadata.lua +++ /dev/null @@ -1,59 +0,0 @@ ---[[ -ScholarlyMeta – normalize author/affiliation meta variables - -Copyright (c) 2017-2021 Albert Krewinkel, Robert Winkler - -Permission to use, copy, modify, and/or distribute this software for any purpose -with or without fee is hereby granted, provided that the above copyright notice -and this permission notice appear in all copies. - -THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH -REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND -FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, -INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER -TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF -THIS SOFTWARE. -]] - -local List = require 'pandoc.List' -local utils = require 'pandoc.utils' -local stringify = utils.stringify - -local M = {} - - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/scholarly-metadata/scholarly-metadata.lua ---- Returns a function which checks whether an object has the given ID. -local function has_id(id) - return function(x) return x.id == id end -end - - --- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/scholarly-metadata/scholarly-metadata.lua ---- Resolve institute placeholders to full named objects -local function resolve_institutes(institute, known_institutes) - local unresolved_institutes - if institute == nil then - unresolved_institutes = {} - elseif type(institute) == "string" or type(institute) == "number" then - unresolved_institutes = {institute} - else - unresolved_institutes = institute - end - - local result = List:new{} - for i, inst in ipairs(unresolved_institutes) do - -- this has been modified by @kapsner - --result[i] = - -- known_institutes[tonumber(inst)] or - -- known_institutes:find_if(has_id(pandoc.utils.stringify(inst))) or - -- to_named_object(inst) - intermed_val = known_institutes:find_if(has_id(stringify(inst))) - result[i] = pandoc.MetaString(stringify(intermed_val.index)) - end - return result -end -M.resolve_institutes = resolve_institutes - -return M \ No newline at end of file diff --git a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/utils.lua b/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/utils.lua deleted file mode 100644 index d0103ca..0000000 --- a/blog/quarto-template-article/article-template/_extensions/kapsner/authors-block/utils.lua +++ /dev/null @@ -1,62 +0,0 @@ ---[[ -authors-block – affiliations block extension for quarto - -Copyright (c) 2023 Lorenz A. Kapsner - -Permission to use, copy, modify, and/or distribute this software for any purpose -with or without fee is hereby granted, provided that the above copyright notice -and this permission notice appear in all copies. - -THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH -REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND -FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, -INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER -TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF -THIS SOFTWARE. -]] - -local List = require 'pandoc.List' -local utils = require 'pandoc.utils' -local stringify = utils.stringify - --- [import] -local from_scholarly = require "from_scholarly_metadata" -local resolve_institutes = from_scholarly.resolve_institutes --- [/import] - -local M = {} - --- from @kapsner -local function normalize_affiliations(affiliations) - local affiliations_norm = List:new(affiliations):map( - function(affil, i) - affil.index = pandoc.MetaInlines(pandoc.Str(tostring(i))) - affil.id = pandoc.MetaString(stringify(affil.id)) - return affil - end - ) - return affiliations_norm -end -M.normalize_affiliations = normalize_affiliations - --- from https://stackoverflow.com/a/2282547 -local function has_key(set, key) - return set[key] ~= nil -end -M.has_key = has_key - --- from @kapsner -local function normalize_authors(affiliations) - return function(auth) - auth.id = pandoc.MetaString(stringify(auth.name)) - auth.affiliations = resolve_institutes( - auth.affiliations, - affiliations - ) - return auth - end -end -M.normalize_authors = normalize_authors - -return M diff --git a/blog/quarto-template-article/article-template/_extensions/letter/_extension.yml b/blog/quarto-template-article/article-template/_extensions/letter/_extension.yml deleted file mode 100644 index a40584b..0000000 --- a/blog/quarto-template-article/article-template/_extensions/letter/_extension.yml +++ /dev/null @@ -1,11 +0,0 @@ -title: Letter template -author: Radovan Bast -version: 0.1.0 -contributes: - formats: - pdf: - template: template.tex - pdf-engine: pdflatex - format-resources: - - logo.png - - signature.png diff --git a/blog/quarto-template-article/article-template/_extensions/letter/logo.png b/blog/quarto-template-article/article-template/_extensions/letter/logo.png deleted file mode 100644 index 08b91f5..0000000 Binary files a/blog/quarto-template-article/article-template/_extensions/letter/logo.png and /dev/null differ diff --git a/blog/quarto-template-article/article-template/_extensions/letter/signature.png b/blog/quarto-template-article/article-template/_extensions/letter/signature.png deleted file mode 100644 index bba2f6e..0000000 Binary files a/blog/quarto-template-article/article-template/_extensions/letter/signature.png and /dev/null differ diff --git a/blog/quarto-template-article/article-template/_extensions/letter/template.tex b/blog/quarto-template-article/article-template/_extensions/letter/template.tex deleted file mode 100644 index d78017c..0000000 --- a/blog/quarto-template-article/article-template/_extensions/letter/template.tex +++ /dev/null @@ -1,63 +0,0 @@ -\documentclass[11pt,a4paper]{letter} - -% https://tex.stackexchange.com/a/257464 -\def\tightlist{} - -\usepackage{bera} -\usepackage{fontawesome} - -\usepackage{setspace} -\usepackage{geometry} -\geometry{a4paper, top=3cm, bottom=2cm, left=2cm, right=2cm} - -\usepackage{graphicx} - -\usepackage{hyperref} -\hypersetup{ - colorlinks=true, - linkcolor=blue, - filecolor=magenta, - urlcolor=blue, - } - -\usepackage[absolute,overlay]{textpos} -\setlength{\TPHorizModule}{1cm} -\setlength{\TPVertModule}{1cm} - -\date{\today} - -\begin{document} - -\begin{letter}{$for(address)$$address$$sep$\\$endfor$} - -$if(opening)$ - \opening{\textbf{$subject$} \\[1.0cm] $opening$} -$else$ - \opening{\textbf{$subject$} \\} -$endif$ - -$body$ - -\vspace{5mm} - -\closing{ - $closing$ -} - -\vspace{5mm} - -\begin{textblock}{10}(2.0,26.0) - \fontsize{9}{8} - \selectfont \sffamily - \color[gray]{0.4} - \begin{tabular}{@{}l@{}} - \textbf{Wencheng Lau-Medrano} \\ - Av. Jean Monnet, \\ - 34203 Sète, France \\[0.15cm] - \faicon{envelope} luis.laum@gmail.com - \end{tabular} -\end{textblock} - -\end{letter} - -\end{document} diff --git a/blog/quarto-template-article/article-template/article_v1.qmd b/blog/quarto-template-article/article-template/article_v1.qmd deleted file mode 100644 index 421e917..0000000 --- a/blog/quarto-template-article/article-template/article_v1.qmd +++ /dev/null @@ -1,90 +0,0 @@ ---- -title: "First look at the distribution of deactivated dFADs used by the French Indian Ocean tropical tuna purse-seine fishery" -authors: - - name: Wencheng Lau-Medrano - orcid: 0000-0002-7979-9710 - url: https://umr-marbec.fr/membre/luis-lau-medrano/ - affiliations: - - ref: marbec - - ref: ird - email: luis.laum@gmail.com - corresponding: true - - name: Daniel Gaertner - orcid: 0000-0002-1194-4432 - affiliations: - - ref: marbec - - ref: ird - - name: Francis Marsac - orcid: 0000-0002-3295-594X - affiliations: - - ref: marbec - - ref: ird - - name: Loreleï Guéry - orcid: 0000-0003-3004-8462 - affiliations: - - ref: cirad - - ref: phim - - name: David M. Kaplan - orcid: 0000-0001-6087-359X - affiliations: - - ref: marbec - - ref: ird - url: https://umr-marbec.fr/membre/david-kaplan/ -affiliations: - - id: marbec - name: MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Sète, France - - id: ird - name: Institut de Recherche pour le Développement (IRD), Av. Jean Monnet, 34203 Sète, France - - id: cirad - name: CIRAD, UMR PHIM, Montpellier, France - - id: phim - name: PHIM, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France -filters: - - authors-block -link-citations: true -bibliography: bibliography.bib -csl: ices-journal-of-marine-science.csl -format: - docx: - toc: false - number-sections: false - reference-doc: custom-reference-doc.docx -editor: source ---- - -```{r setup, include=FALSE} -# This options will be applied to all chunks -knitr::opts_chunk$set(echo = FALSE, - verbose = FALSE, - dev = "ragg_png", - out.width = "100%", - message = FALSE, - warning = FALSE, - dpi = 1500) -``` - -## Abstract - - -# Introduction - -# Methods - -# Results - -# Discussion - -# Acknowledgements - -# Author contribution - -# Data availability statement - -# Code availability - -# Funding - -# Competing interests - - -# References {-} \ No newline at end of file diff --git a/blog/quarto-template-article/article-template/bibliography.bib b/blog/quarto-template-article/article-template/bibliography.bib deleted file mode 100644 index d94a78d..0000000 --- a/blog/quarto-template-article/article-template/bibliography.bib +++ /dev/null @@ -1,442 +0,0 @@ -@article{dupaixChallengeAssessingEffects2024, - title = {The Challenge of Assessing the Effects of Drifting Fish Aggregating Devices on the Behaviour and Biology of Tropical Tuna}, - author = {Dupaix, Amaël and Ménard, Frédéric and Filmalter, John D. and Baidai, Yannick and Bodin, Nathalie and Capello, Manuela and Chassot, Emmanuel and Demarcq, Hervé and Deneubourg, Jean‐Louis and Fonteneau, Alain and Forget, Fabien and Forrestal, Francesca and Gaertner, Daniel and Hall, Martin and Holland, Kim N. and Itano, David and Kaplan, David Michael and Lopez, Jon and Marsac, Francis and Maufroy, Alexandra and Moreno, Gala and Muir, Jeff A. and Murua, Hilario and Roa‐Pascuali, Liliana and Pérez, Géraldine and Restrepo, Victor and Robert, Marianne and Schaefer, Kurt M. and Sempo, Grégory and Soria, Marc and Dagorn, Laurent}, - date = {2024-05}, - journaltitle = {Fish and Fisheries}, - shortjournal = {Fish and Fisheries}, - volume = {25}, - number = {3}, - pages = {381--400}, - issn = {1467-2960, 1467-2979}, - doi = {10.1111/faf.12813}, - url = {https://onlinelibrary.wiley.com/doi/10.1111/faf.12813}, - urldate = {2024-04-26}, - langid = {english} -} - -@article{escalleQuantifyingDriftingFish2021, - title = {Quantifying Drifting {{Fish Aggregating Device}} Use by the World's Largest Tuna Fishery}, - author = {Escalle, Lauriane and Hare, Steven R and Vidal, Tiffany and Brownjohn, Maurice and Hamer, Paul and Pilling, Graham}, - editor = {Browman, Howard}, - date = {2021-10-09}, - journaltitle = {ICES Journal of Marine Science}, - volume = {78}, - number = {7}, - pages = {2432--2447}, - issn = {1054-3139, 1095-9289}, - doi = {10.1093/icesjms/fsab116}, - url = {https://academic.oup.com/icesjms/article/78/7/2432/6307380}, - urldate = {2023-04-28}, - langid = {english} -} - -@report{faoReportThirtythirdSession2019, - title = {Report of the {{Thirty-third Session}} of the {{Committee}} on {{Fisheries}}: {{Rome}}, {{Italy}} 9-13 {{July}} 2018}, - shorttitle = {Report of the {{Thirty-third Session}} of the {{Committee}} on {{Fisheries}}}, - author = {FAO}, - date = {2019}, - number = {1249}, - institution = {FAO}, - location = {Rome}, - langid = {english}, - annotation = {Licence: CC BY-NC-SA 3.0 IGO} -} - -@book{faoVoluntaryGuidelinesMarking2019, - title = {Voluntary {{Guidelines}} on the {{Marking}} of {{Fishing Gear}}. {{Directives}} Volontaires Sur Le Marquage Des Engins de Pêche. {{Directrices}} Voluntarias Sobre El Marcado de Las Artes de Pesca}, - author = {FAO}, - date = {2019}, - publisher = {FAO}, - location = {Rome}, - url = {https://www.fao.org/documents/card/en/c/CA3546T/}, - urldate = {2023-04-26}, - isbn = {978-92-5-131312-1}, - annotation = {Licence: CC BY-NC-SA 3.0 IGO} -} - -@report{fonteneauManagingTropicalTuna2015, - type = {Collect. Vol. Sci. Pap.}, - title = {Managing Tropical Tuna Purse Seine Fisheries through Limiting the Number of Drifting Fish Aggregating Devices in the {{Indian Ocean}}: Food for Thought}, - author = {Fonteneau, Alain and Chassot, Emmanuel and Gaertner, Daniel}, - date = {2015}, - number = {71(1)}, - pages = {460--475}, - institution = {ICCAT}, - url = {https://www.semanticscholar.org/paper/MANAGING-TROPICAL-TUNA-PURSE-SEINE-FISHERIES-THE-OF-Fonteneau-Chassot/36767a2aee6b886d8c18de5d5fbed3d620bd5ac9}, - langid = {english} -} - -@inproceedings{gaertnerResultsAchievedFramework2016, - title = {Results Achieved within the Framework of the {{EU}} Research Project: {{Catch}}, {{Effort}}, and Ecosystem Impacts of {{FAD-fishing}} ({{CECOFAD}})}, - author = {Gaertner, Daniel and Ariz, Javier and Bez, Nicolas and Clermidy, Sonia and Moreno, Gala and Murua, Hilario and Soto, Maria and Marsac, Francis}, - date = {2016-10-17}, - series = {{{IOTC-2016-WPTT18-35}}}, - publisher = {IOTC}, - url = {https://iotc.org/documents/results-achieved-within-framework-eu-research-project-catch-effort-and-ecosystem-impacts}, - urldate = {2023-12-08}, - eventtitle = {18th {{Working Party}} on {{Tropical Tunas}} ({{IOTC}})} -} - -@dataset{gebco2023, - type = {Documents,Network Common Data Form}, - title = {The {{GEBCO}}\_2023 {{Grid}} - a Continuous Terrain Model of the Global Oceans and Land.}, - author = {{GEBCO Bathymetric Compilation Group 2023}}, - date = {2023}, - publisher = {[object Object]}, - doi = {10.5285/F98B053B-0CBC-6C23-E053-6C86ABC0AF7B}, - url = {https://www.bodc.ac.uk/data/published_data_library/catalogue/10.5285/f98b053b-0cbc-6c23-e053-6c86abc0af7b/}, - urldate = {2024-05-14}, - langid = {english}, - version = {1}, - keywords = {elevation,oceans} -} - -@article{gilmanHighestRiskAbandoned2021, - title = {Highest Risk Abandoned, Lost and Discarded Fishing Gear}, - author = {Gilman, Eric and Musyl, Michael and Suuronen, Petri and Chaloupka, Milani and Gorgin, Saeid and Wilson, Jono and Kuczenski, Brandon}, - date = {2021-03-30}, - journaltitle = {Scientific Reports}, - shortjournal = {Sci Rep}, - volume = {11}, - number = {1}, - pages = {7195}, - issn = {2045-2322}, - doi = {10.1038/s41598-021-86123-3}, - url = {https://www.nature.com/articles/s41598-021-86123-3}, - urldate = {2023-04-26}, - langid = {english} -} - -@article{gilmanStatusInternationalMonitoring2015, - title = {Status of International Monitoring and Management of Abandoned, Lost and Discarded Fishing Gear and Ghost Fishing}, - author = {Gilman, Eric}, - date = {2015-10}, - journaltitle = {Marine Policy}, - shortjournal = {Marine Policy}, - volume = {60}, - pages = {225--239}, - issn = {0308597X}, - doi = {10.1016/j.marpol.2015.06.016}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S0308597X1500175X}, - urldate = {2023-04-25}, - langid = {english} -} - -@article{hallierDriftingFishAggregation2008, - title = {Drifting Fish Aggregation Devices Could Act as an Ecological Trap for Tropical Tuna Species}, - author = {Hallier, J and Gaertner, D}, - date = {2008-01-17}, - journaltitle = {Marine Ecology Progress Series}, - shortjournal = {Mar. Ecol. Prog. Ser.}, - volume = {353}, - pages = {255--264}, - issn = {0171-8630, 1616-1599}, - doi = {10.3354/meps07180}, - url = {http://www.int-res.com/abstracts/meps/v353/p255-264/}, - urldate = {2022-10-06}, - langid = {english} -} - -@inproceedings{hallierReviewTunaFisheries1992, - title = {Review of Tuna Fisheries on Floating Objects in the {{Indian Ocean}}}, - booktitle = {Proceedings of the {{International Workshop}} on the {{Ecology}} and {{Fisheries}} for Tunas {{Associated}} with {{Floating Objects}}}, - author = {Hallier, Jean-Pierre and Parajua, Jesus I.}, - date = {1992-07-11}, - pages = {354--370}, - publisher = {NOAA Technical Report NMFS-SEFSC-334}, - location = {La Jolla, California, USA}, - langid = {english} -} - -@misc{iattcResolutionC2104Conservation2021, - title = {Resolution {{C-21-04}}, {{Conservation}} Measures for Tropical Tunas in the {{Eastern Pacific Ocean}} Suring 2022-2024}, - author = {IATTC}, - date = {2021-10}, - organization = {Inter-American Tropical Tuna Commission} -} - -@article{imzilenRecoverySeaAbandoned2022, - title = {Recovery at Sea of Abandoned, Lost or Discarded Drifting Fish Aggregating Devices}, - author = {Imzilen, Taha and Lett, Christophe and Chassot, Emmanuel and Maufroy, Alexandra and Goujon, Michel and Kaplan, David M.}, - date = {2022-04-28}, - journaltitle = {Nature Sustainability}, - shortjournal = {Nat Sustain}, - volume = {5}, - number = {7}, - pages = {593--602}, - issn = {2398-9629}, - doi = {10.1038/s41893-022-00883-y}, - url = {https://www.nature.com/articles/s41893-022-00883-y}, - urldate = {2023-03-07}, - langid = {english} -} - -@article{imzilenSpatialManagementCan2021, - ids = {ImzilenSpatialmanagementcanaccepted}, - title = {Spatial Management Can Significantly Reduce {{dFAD}} Beachings in {{Indian}} and {{Atlantic Ocean}} Tropical Tuna Purse Seine Fisheries}, - author = {Imzilen, Taha and Lett, Christophe and Chassot, Emmanuel and Kaplan, David M.}, - date = {2021-02-01}, - journaltitle = {Biological Conservation}, - shortjournal = {Biological Conservation}, - volume = {254}, - pages = {108939}, - issn = {0006-3207}, - doi = {10.1016/j.biocon.2020.108939}, - url = {http://www.sciencedirect.com/science/article/pii/S0006320720309976}, - urldate = {2021-01-12}, - langid = {english}, - keywords = {Coral reefs,Fish aggregating device (FAD),Fishing debris,Marine pollution,Ocean currents} -} - -@inproceedings{iotcResolution17082017, - title = {Resolution 17/08: {{Procedures}} on a {{Fish Aggregating Devices}} ({{FADs}}) Management Plan, Including a Limitation on the Number of {{FADs}}, More Detailed Significations of Catch Reporting from {{FAD}} Sets, and the Development of Improved {{FAD}} Designs to Reduce the Incidence of Entanglement of Non-Target Species}, - author = {IOTC}, - date = {2017}, - series = {{{IOTC-2017-WPDCS13-INF02}}}, - eventtitle = {Working {{Party}} on {{Data Collection}} and {{Statistics}}} -} - -@article{kaplanUncertaintyEmpiricalEstimates2017, - title = {Uncertainty in Empirical Estimates of Marine Larval Connectivity}, - author = {Kaplan, David M. and Cuif, Marion and Fauvelot, Cécile and Vigliola, Laurent and Nguyen-Huu, Tri and Tiavouane, Josina and Lett, Christophe}, - editor = {Hidalgo, Manuel}, - date = {2017-07-01}, - journaltitle = {ICES Journal of Marine Science}, - volume = {74}, - number = {6}, - pages = {1723--1734}, - issn = {1054-3139, 1095-9289}, - doi = {10.1093/icesjms/fsw182}, - url = {https://academic.oup.com/icesjms/article/74/6/1723/2741993}, - urldate = {2023-09-27}, - langid = {english} -} - -@article{lennert-codyRecentPurseseineFAD2018, - title = {Recent Purse-Seine {{FAD}} Fishing Strategies in the Eastern {{Pacific Ocean}}: What Is the Appropriate Number of {{FADs}} at Sea?}, - shorttitle = {Recent Purse-Seine {{FAD}} Fishing Strategies in the Eastern {{Pacific Ocean}}}, - author = {Lennert-Cody, Cleridy E and Moreno, Gala and Restrepo, Victor and Román, Marlon H and Maunder, Mark N}, - editor = {Poos, Jan Jaap}, - date = {2018-10-01}, - journaltitle = {ICES Journal of Marine Science}, - volume = {75}, - number = {5}, - pages = {1748--1757}, - issn = {1054-3139, 1095-9289}, - doi = {10.1093/icesjms/fsy046}, - url = {https://academic.oup.com/icesjms/article/75/5/1748/4976455}, - urldate = {2022-10-24}, - langid = {english} -} - -@article{macmillanSpatiotemporalVariabilityDrifting2022, - title = {Spatio-Temporal Variability in Drifting {{Fish Aggregating Device}} ({{dFAD}}) Beaching Events in the {{Seychelles Archipelago}}}, - author = {MacMillan, Isla and Attrill, Martin J and Imzilen, Taha and Lett, Christophe and Walmsley, Simon and Chu, Clarus and Kaplan, David M}, - editor = {Rodil, Ivan}, - date = {2022-06-29}, - journaltitle = {ICES Journal of Marine Science}, - volume = {79}, - number = {5}, - pages = {1687--1700}, - issn = {1054-3139, 1095-9289}, - doi = {10.1093/icesjms/fsac091}, - url = {https://academic.oup.com/icesjms/article/79/5/1687/6591913}, - urldate = {2023-03-06}, - langid = {english} -} - -@inproceedings{marsacDriftingFADsUsed2000, - title = {Drifting {{FADs}} Used in Tuna Fisheries: An Ecological Trap?}, - author = {Marsac, F. and Fonteneau, A and Ménard, F}, - date = {2000}, - series = {Actes {{Colloques-IFREMER}}}, - volume = {28}, - pages = {537--552}, - publisher = {Le Gall, J.-Y., Cayré, P., Taquet M.}, - eventtitle = {Pêche Thonière et Dispositifs de Concentration de Poissons} -} - -@article{maufroyLargeScaleExaminationSpatioTemporal2015, - title = {Large-{{Scale Examination}} of {{Spatio-Temporal Patterns}} of {{Drifting Fish Aggregating Devices}} ({{dFADs}}) from {{Tropical Tuna Fisheries}} of the {{Indian}} and {{Atlantic Oceans}}}, - author = {Maufroy, Alexandra and Chassot, Emmanuel and Joo, Rocío and Kaplan, David Michael}, - editor = {Hays, Graeme}, - date = {2015-05-26}, - journaltitle = {PLOS ONE}, - shortjournal = {PLoS ONE}, - volume = {10}, - number = {5}, - pages = {e0128023}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0128023}, - url = {https://dx.plos.org/10.1371/journal.pone.0128023}, - urldate = {2022-10-05}, - langid = {english} -} - -@article{maufroyMassiveIncreaseUse2017, - title = {Massive Increase in the Use of Drifting {{Fish Aggregating Devices}} ({{dFADs}}) by Tropical Tuna Purse Seine Fisheries in the {{Atlantic}} and {{Indian}} Oceans}, - author = {Maufroy, Alexandra and Kaplan, David M. and Bez, Nicolas and Molina, De and Delgado, Alicia and Murua, Hilario and Floch, Laurent and Chassot, Emmanuel}, - date = {2017-01-01}, - journaltitle = {ICES Journal of Marine Science}, - shortjournal = {ICES J Mar Sci}, - volume = {74}, - number = {1}, - pages = {215--225}, - issn = {1054-3139}, - doi = {10.1093/icesjms/fsw175}, - url = {https://academic.oup.com/icesjms/article-abstract/74/1/215/2418180/Massive-increase-in-the-use-of-drifting-Fish}, - urldate = {2017-03-09}, - keywords = {data,fish aggregating device,fishing effort,fishing strategy,GPS buoys,observers’} -} - -@dataset{pacIOOS.DistanceNearestCoastline2012, - title = {Distance to {{Nearest Coastline}}: 0.01-{{Degree Grid}}}, - author = {OBPG and Stumpf, Richard P.}, - date = {2012}, - publisher = {Distributed by the Pacific Islands Ocean Observing System (PacIOOS)}, - url = {https://www.pacioos.hawaii.edu/metadata/dist2coast_1deg.html}, - urldate = {2024-01-16} -} - -@article{ponsBenefitsConcernsSolutions2023, - title = {Benefits, Concerns, and Solutions of Fishing for Tunas with Drifting Fish Aggregation Devices}, - author = {Pons, Maite and Kaplan, David and Moreno, Gala and Escalle, Lauriane and Abascal, Francisco and Hall, Martin and Restrepo, Victor and Hilborn, Ray}, - date = {2023-07-27}, - journaltitle = {Fish and Fisheries}, - shortjournal = {Fish and Fisheries}, - pages = {faf.12780}, - issn = {1467-2960, 1467-2979}, - doi = {10.1111/faf.12780}, - url = {https://onlinelibrary.wiley.com/doi/10.1111/faf.12780}, - urldate = {2023-07-31}, - langid = {english} -} - -@report{restrepoSummaryBycatchIssues2017, - type = {lSSF Technical Report}, - title = {A {{Summary}} of {{Bycatch Issues}} and {{ISSF Mitigation Initiatives To-Date}} in {{Purse Seine Fisheries}}, with Emphasis on {{FADs}}}, - author = {Restrepo, Victor and Dagorn, Laurent and Itano, David and Justel-Rubio, A and Forget, Fabien and Moreno, Gala}, - date = {2017}, - number = {2017-06}, - institution = {International Seafood Sustainability Foundation}, - location = {Washington, D.C., USA}, - langid = {english} -} - -@article{schwarzJollyseberModelMore2001, - title = {The {{Jolly-seber}} Model: {{More}} than Just Abundance}, - shorttitle = {The {{Jolly-seber}} Model}, - author = {Schwarz, Carl J.}, - date = {2001-06}, - journaltitle = {Journal of Agricultural, Biological, and Environmental Statistics}, - shortjournal = {JABES}, - volume = {6}, - number = {2}, - pages = {195--205}, - issn = {1085-7117, 1537-2693}, - doi = {10.1198/108571101750524706}, - url = {http://link.springer.com/10.1198/108571101750524706}, - urldate = {2023-09-27}, - langid = {english} -} - -@article{wangLargeScaleDeploymentFish2014, - title = {The {{Large-Scale Deployment}} of {{Fish Aggregation Devices Alters Environmentally-Based Migratory Behavior}} of {{Skipjack Tuna}} in the {{Western Pacific Ocean}}}, - author = {Wang, Xuefang and Chen, Yong and Truesdell, Samuel and Xu, Liuxiong and Cao, Jie and Guan, Wenjiang}, - editor = {Buckel, Jeffrey}, - date = {2014-05-21}, - journaltitle = {PLoS ONE}, - shortjournal = {PLoS ONE}, - volume = {9}, - number = {5}, - pages = {e98226}, - issn = {1932-6203}, - doi = {10.1371/journal.pone.0098226}, - url = {https://dx.plos.org/10.1371/journal.pone.0098226}, - urldate = {2023-07-31}, - langid = {english} -} - -@article{zudaireBiodegradableDriftingFish2023, - title = {Biodegradable Drifting Fish Aggregating Devices: {{Current}} Status and Future Prospects}, - shorttitle = {Biodegradable Drifting Fish Aggregating Devices}, - author = {Zudaire, Iker and Moreno, Gala and Murua, Jefferson and Hamer, Paul and Murua, Hilario and T. Tolotti, Mariana and Roman, Marlon and Hall, Martin and Lopez, Jon and Grande, Maitane and Merino, Gorka and Escalle, Lauriane and C. Basurko, Oihane and Capello, Manuela and Dagorn, Laurent and Ramos, Maria Lourdes and Abascal, Francisco J. and Báez, José Carlos and Pascual-Alayón, Pedro J. and Déniz, Santiago and Santiago, Josu}, - date = {2023-07}, - journaltitle = {Marine Policy}, - shortjournal = {Marine Policy}, - volume = {153}, - pages = {105659}, - issn = {0308597X}, - doi = {10.1016/j.marpol.2023.105659}, - url = {https://linkinghub.elsevier.com/retrieve/pii/S0308597X23001860}, - urldate = {2023-07-21}, - langid = {english} -} - -@report{zudaireFADWatchCollaborative2018, - title = {{{FAD Watch}}: A Collaborative Initiative to Minimize the Impact of {{FADs}} in Coastal Ecosystems}, - author = {Zudaire, Iker and Santiago, Josu and Grande, Maitane and Murua, Hilario and Adam, Pierre-André and Nogués, Pep and Collier, Thomas and Morgan, Matthew and Khan, Nasreen and Baguette, François and Moron, Julio and Moniz, Isadora and Herrera, Miguel}, - date = {2018}, - number = {IOTC-2018-WPEB14-12}, - pages = {21}, - institution = {IOTC} -} - -@Manual{rpkg_base, - title = {R: A Language and Environment for Statistical Computing}, - author = {{R Core Team}}, - organization = {R Foundation for Statistical Computing}, - address = {Vienna, Austria}, - year = {2024}, - url = {https://www.R-project.org/}, -} - -@Manual{rpkg_dplyr, - title = {dplyr: A Grammar of Data Manipulation}, - author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan}, - year = {2023}, - note = {R package version 1.1.4}, - url = {https://CRAN.R-project.org/package=dplyr}, -} - -@Manual{rpkg_tidyr, - title = {tidyr: Tidy Messy Data}, - author = {Hadley Wickham and Davis Vaughan and Maximilian Girlich}, - year = {2024}, - note = {R package version 1.3.1}, - url = {https://CRAN.R-project.org/package=tidyr}, -} - -@Manual{rpkg_survival, - title = {A Package for Survival Analysis in R}, - author = {Terry M Therneau}, - year = {2024}, - note = {R package version 3.6-4}, - url = {https://CRAN.R-project.org/package=survival}, -} - -@Book{rpkg_ggplot2, - author = {Hadley Wickham}, - title = {ggplot2: Elegant Graphics for Data Analysis}, - publisher = {Springer-Verlag New York}, - year = {2016}, - isbn = {978-3-319-24277-4}, - url = {https://ggplot2.tidyverse.org}, -} - -@Manual{rpkg_terra, - title = {terra: Spatial Data Analysis}, - author = {Robert J. Hijmans}, - year = {2024}, - note = {R package version 1.7-78}, - url = {https://CRAN.R-project.org/package=terra}, -} - -@Book{rpkg_sf, - author = {Edzer Pebesma and Roger Bivand}, - title = {{Spatial Data Science: With applications in R}}, - year = {2023}, - publisher = {{Chapman and Hall/CRC}}, - url = {https://r-spatial.org/book/}, - doi = {10.1201/9780429459016}, -} diff --git a/blog/quarto-template-article/article-template/custom-reference-doc.docx b/blog/quarto-template-article/article-template/custom-reference-doc.docx deleted file mode 100644 index 9e6c805..0000000 Binary files a/blog/quarto-template-article/article-template/custom-reference-doc.docx and /dev/null differ diff --git a/blog/quarto-template-article/article-template/ices-journal-of-marine-science.csl b/blog/quarto-template-article/article-template/ices-journal-of-marine-science.csl deleted file mode 100644 index 7a91961..0000000 --- a/blog/quarto-template-article/article-template/ices-journal-of-marine-science.csl +++ /dev/null @@ -1,223 +0,0 @@ - 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In this example, the output will always be a file in MS Word format, which is widely accepted by several scientific journals. In the following, I will indicate the list of required software (which you should already have installed) and then I will explain the use and handling of each file contained in the template. +![](images/clipboard-1818852471.png) -# [ES] Empezando a trabajar con `marbec-gpu` +## Pre-requisites + +- Reference template: . There you will find the files needed to execute what is shown in this post, which may change as this post is updated. + +- R, RStudio y Zotero: / / + +- Quarto: In recent years, RStudio already includes a recent version of Quarto, but if you do not have the software or want to try versions other than the default, you can download them from . + +- Zotero-Quarto-RStudio integration: Citation management will make use of the tools explained in [my previous post](https://luislaum.github.io/blog/zotero-quarto-rstudio/zotero-quarto-rstudio.html), so **I recommend you to read and do what is explained there**. + +- Some experience in writing documents using Quarto (or R markdown). The best way to learn how to use Quarto is using it and find what you need to get what you need from online manuals (e.g. from [Quarto](https://quarto.org/)), [videos on YT](https://youtu.be/_f3latmOhew?feature=shared) or questions on several forums (e.g. [Stackoverflow](https://stackoverflow.com/questions/tagged/quarto)) and blogs. + +::: {.callout-tip title="Files and way of working"} +Although each researcher has a different way of organizing the files of their projects, it is HIGHLY recommended to work each one within the same folder (where we have configured an RStudio project), where there are separate folders for raw data, preprocessed data, output data, figures, code, external documents (reports, permissions, etc.), presentations, among others. For our example, it will be assumed that we are working in the root directory of our project itself, but ideally we should have a subfolder in dedicated to contain only the files related to the article (or articles) coming out of a project. This will be quite useful later on when revisions start coming in and not end up with dozens of confusingly named files scattered around our directory. + +![](images/clipboard-2838852447.png) +::: + +## `_extensions` folder + +Quarto extensions are basically scripts that add additional functionality and are developed and supported by the community. Quarto has a standalone environment philosophy, so, unlike R, the installation of the extensions must be done **local** in each project where we are going to run our Quarto script. For the purposes of this post, we are going to use an extension called [**kapsner/authors-block**](https://github.com/kapsner/authors-block), which **is already included** in the reference repository (inside the `/_extensions` folder), but it is always good to take a look at the original repository to see if they have incorporated any interesting improvements. + +## `bibliography.bib` file + +This file will contain the metadata of the bibliographic references that we will cite in our main file. It is not necessary to create it manually, that will be taken care of by the Zotero-rbbt tools, as detailed [in our respective post](https://luislaum.github.io/blog/zotero-quarto-rstudio/zotero-quarto-rstudio.html). + +## `ices-journal-of-marine-science.csl` file + +A **CSL** (Citation Style Language) file defines how citations and references should be formatted in a document, allowing bibliographic management programs (such as Zotero) to automate this process. These files are essential in writing scientific articles because they ensure that citations and references conform precisely to the style standards required by a journal or institution, such as APA, MLA or Vancouver. By using a CSL file, authors can easily switch between styles without having to manually rewrite their references, which saves time, reduces errors, and ensures consistency in citation formatting throughout the paper. + +Usually, each journal tells authors which style to follow when writing their citations, for which in many cases they share the respective `.csl` file; however, if we cannot find the correct file, there are [repositories such as this one](https://github.com/citation-style-language/styles) where hundreds of `.csl` files for different journals are stored and maintained. Look for the one that best fits the journal to which you will submit your manuscript. + +## `custom-reference-doc.docx` file + +Usually, a manuscript file does not need to have an ornate or sophisticated format, but it is possible that some journals, our advisor or reviewers may request some formatting details in our MS Word output file. This is where Quarto makes use of a simple but powerful solution: the use of a reference file-format. + +The `custom-reference-doc.docx` file is nothing more than a Word file that explicitly shows how each element will be displayed according to the style we have chosen. Anything we edit in this file will be used by Quarto to format our final document. To explain at length how to edit this file would take a whole post and right now there are many sources where this process is already explained, [this post for example](https://andrewpwheeler.com/2024/06/21/my-word-template-for-quarto/). What is important to keep in mind is that every change we make must be done at the level of MS Word's Format and Style options. While it might seem very annoying to have to work in Word, the good news is that it is not something we will do continuously, but only a couple of times during our project (if someone requests some special formatting in our manuscript). Personally, the shared file has been enough for my advisors, the reviewers and editors of 2 different journals (ICES JMS and Fisheries Research of Elsevier). + +## The main file: `article_v1.qmd` + +The initial part of the script of this template consists of a `header` (in YAML format) where the general options of our document will be shown: + +- `title`, between double quotes `" "`. +- `authors`, where we will be able to include data such as names, surnames and affiliation (which is the most important information), as well as ORCID code, reference URL, etc. +- `affiliations`, this is where we will indicate an identifier (which we will use as a reference for the authors) and the full name of the affiliation, as we want it to appear in the document. +- `filters`, where we will list the *Fourth extensions` that we want to be loaded at the beginning of the document (and that will be looked for in the `/_extensions` folder). +- `link-citations`, where we can define (true/false) if we want the bibliographic citations in the final document to link to the corresponding reference in the final Bibliography section. +- `bibliography`, where we will indicate the file where our bibliographic references are in BibTeX format. +- `csl`, where we indicate the file that Quarto will use to establish the citation format for bibliographic references. +- `format`, where specific parameters of the output file will be specified. For this example, everything is set to get a MS Word file (`.docx`) that will use our `custom-reference-doc.docx` style reference file. The `toc` parameter (which refers to *Table Of Contents*) allows to display or not the table of contents at the beginning of the document. The `numer-sections` parameter allows to enable/disable the use of numbering in the sections of our manuscript. + +### *Setup chunk* + +The chunk shown at the beginning of the `qmd` file contains some parameters that should be set, so that you do not have to do it independently in each subsequent chunk. **Hey**, this is a SUGGESTED configuration, you can (and should) modify it as required by your project or the reviewers. + +```{r} +#| eval: false + +knitr::opts_chunk$set(echo = FALSE, + verbose = FALSE, + message = FALSE, + warning = FALSE, + dev = "ragg_png", + out.width = "100%", + dpi = 1500) +``` + +* `echo = FALSE`: Causes the executed code NOT to be displayed verbatim in the document. + +* `verbose = FALSE`: Useful for suppressing detailed messages about progress, intermediate steps or partial results of code within chunks to keep outputs cleaner. + +* `message = FALSE`/`warning = FALSE`: used to suppress warning messages or information that functions may generate during code execution, preventing them from appearing in the document output. This helps to keep the output cleaner and focused on the essential results. + +* `dev = "ragg_png"`: specifies that the graphics device used to generate the images is [ragg](https://ragg.r-lib.org/), an efficient and modern engine that produces graphics in PNG format with high quality and performance. + +* `out.width = "100%"`: sets that the width of the generated images or graphics will occupy 100% of the width of the container (e.g., the page or column where it is displayed), automatically adjusting to the available size. + +* `dpi = 1500`: sets the resolution of the images generated in the document, specifically in dots per inch. A value of 1500 dpi indicates a very high resolution, which results in sharper and more detailed images, but also heavier, so it will be the user's responsibility to determine the optimum value as specified by each magazine. + +### Writing in Quarto + +What follows is basically to write our manuscript as if it were just another report in Quarto, taking advantage of the power of chunks to recreate the analyses needed to generate each figure, table or value. Here it is important to recommend that each value that comes from an analysis of our information (i.e. that does not come directly from a bibliographic citation) should be generated from explicit code in our document. + +For example, let us imagine that I am working with the `mtcars` table (from R) and I want to write the following text-result: + +> The car models `r rownames(mtcars)[order(mtcars$mpg, decreasing = TRUE)[1:2]] |> paste(collapse = " and ")` were those with the highest miles per gallon value. + +The text inside our qmd file should look like this: + +```{verbatim} +The car models `r rownames(mtcars)[order(mtcars$mpg, decreasing = TRUE)[1:2]] |> paste(collapse = " and ")` were those with the highest miles per gallon value. +``` + +As you can see, within the paragraph itself I am running a chunk with a data sorting and extraction operation. While this may seem more cumbersome, it allows that if at some point we were to modify some pre-processing process of the initial data, the results will be generated automatically, without the need for us to do these small calculations again. + +::: {.callout-important} +Obviously, the texts related to the interpretation of the results should be reviewed whenever we know that we have made an important change in our initial data. +::: + +There are multiple websites (blogs and forums) where we can learn how to format our results or presentation. Some examples are: + +* [Markdown Basics](https://quarto.org/docs/authoring/markdown-basics.html) + +* [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/) + +* [R markdown](https://rmarkdown.rstudio.com/index.html) + +* [knitr](https://yihui.org/knitr/) + +* [Bookdown](https://bookdown.org/) + +* [Hello Quarto](https://quarto-tdg.org/overview.html) + +* [Quarto Q&A](https://github.com/quarto-dev/quarto-cli/discussions/categories/q-a). This site is particularly interesting because it is the Q&A section of the Quarto repository itself, so it is always good to take a look at its search engine and check if someone else had similar difficulties as us. We can also leave a ticket with our query if we don't find a match. + + + +## Extra file: `letter_editor.Rmd` + +The letter to the editor is a key component when submitting a scientific article to a journal, as it serves as a first presentation of the work to the editors and helps to highlight its relevance, originality and contribution to the field. Its usefulness lies in quickly capturing the editor's attention by summarizing the objectives, main findings and importance of the study, which facilitates the initial evaluation of the manuscript. In addition, it allows the author to briefly explain why the article is appropriate for the journal in question, showing alignment with its focus and audience. A well-written letter can positively influence the editor's decision to send the article for review, thus expediting the evaluation process. + +Although in this template I do not share an example of writing this letter (only the R markdown format), it is possible to find multiple related posts in various forums or blogs. The use of this file is quite intuitive, just fill in the fields and render the document. By the way, it requires the prior installation of the [komaletter package](https://cran.r-project.org/package=komaletter). + +--- + +# \[ES\] Escribiendo un artículo solo con Quarto y Zotero (y R) + +Este tutorial parte de una carpeta-plantilla en donde están los archivos necesarios para escribir el manuscrito completo para un artículo científico (aplicable a casi cualquier revista) usando únicamente herramientas de Quarto, RStudio, Zotero y R. En este ejemplo, el output será siempre un archivo en formato MS Word, que es ampliamente aceptado por diversas revistas científicas. A continuación, indicaré la lista de software requerido (que debn tener ya instalado) y luego iré explicando el uso y manejo de cada archivo contenido en la plantilla. + +![](images/clipboard-1818852471.png) ## Requerimientos -* RStudio: +- Plantilla de referencia: . Ahí se encuentran los archivos necesarios para ejecutar lo mostrado en este post, los cuales podrán ir variando conforme este post se actualice. + +- R, RStudio y Zotero: / / + +- Quarto: En los últimos años, RStudio ya incluye una versión reciente de Quarto, pero si usted no cuenta con el software o desea probar versiones distintas a la que llega por defecto, puede descargarlas desde . + +- Integración Zotero-Quarto-RStudio: El manejo de citas se debe hacer a través de las herramientas explicadas en [mi post anterior](https://luislaum.github.io/blog/zotero-quarto-rstudio/zotero-quarto-rstudio.html), así que **les recomiendo leerlo previamente e implementar lo explicado ahí**. -* Quarto: En los últimos años, RStudio ya incluye una versión reciente de Quarto, pero si usted desea probar versiones preliminare, puede descargarlas desde . +- Experiencia en la escritura de documentos usando Quarto (o R markdown). La mejor manera de aprender a usar Quarto es usándolo e ir hallando lo necesario para obtener lo que necesitamos a partir de manuales en línea (e.g. desde la propia web de [Quarto](https://quarto.org/)), [vídeos en YT](https://youtu.be/_f3latmOhew?feature=shared) o preguntas en diversos foros (e.g. [Stackoverflow](https://stackoverflow.com/questions/tagged/quarto)). -* Lenguajes de programación: En mi experiencia, he podido probar esta plantilla usando código en R, pero eso no limita su uso con otros lenguajes de programación (espero). +::: {.callout-tip title="Archivos, orden y modo de trabajo"} +Si bien cada investigador tiene una manera distinta de organizar los archivos de sus proyectos, es MUY recomendable trabajar cada uno dentro de una misma carpeta (en donde tengamos configurado un proyecto de RStudio), en donde haya carpetas diferenciadas para los datos de entrada en bruto (raw), los preprocesados, los de salida, las figuras, el código, los documentos externos (informes, permisos, etc.), las presentaciones, entre otros. Para nuestro ejemplo, se asumirá que estamos trabajando en el propio directorio raíz de nuestro proyecto, pero idealmente deberíamos tener una subcarpeta en dedicada a contener únicamente los archivos relacionados al artículo (o artículos) que salen de un proyecto. Esto será bastante útil posteriormente, cuando empiecen a llegar las revisiones y no terminar con decenas de archivos con nombre confusos y desperdigados por nuestro directorio. -* Repositorio de referencia: . Ahí se encuentran los archivos necesarios para ejecutar lo mostrado en este post: script principal en formato Quarto (archivos `article_v1.qmd` y `letter_editor.qmd`), referencias bibliográficas en formato BibTeX (archivo `bibliography.bib`), formato de citación (para este ejemplo, archivo `ices-journal-of-marine-science.csl`) y plantilla en MS Word (archivo `custom-reference-doc.docx`). Los archivos podrán ir variando conforme este post se actualice. +![](images/clipboard-2838852447.png) +::: -* Experiencia en la escritura de documentos usando Quarto (o R markdown). La mejor manera de aprender a usar Quarto es usándolo e ir hallando lo necesario para obtener lo que necesitamos a partir de manuales en línea (e.g. desde la propia web de [Quarto](https://quarto.org/)), [vídeos en YT](https://youtu.be/_f3latmOhew?feature=shared) o preguntas en diversos foros (e.g. [Stackoverflow](https://stackoverflow.com/questions/tagged/quarto)). +## Carpeta `_extensions` -* Integración Zotero-Quarto-RStudio: Para insertar citas bibliográficas, se recomienda seguir los pasos de [mi post anterior](). +Las extensiones de Quarto son básicamente scripts que añaden funcionalidades adicionales y que son desarrolladas y soportadas por la comunidad. Quarto maneja una filosofía de entornos independientes, por lo que, a diferencia de R, la instalación de las extensiones de hacerse de manera **local** en cada proyecto en que vayamos a ejecutar nuestro script de Quarto. Para efectos del presente post, vamos a utilizar una extensión llamada [**kapsner/authors-block**](https://github.com/kapsner/authors-block), la cual **ya viene incluidas** en el repositorio de referencia (dentro de la carpeta `/_extensions`), pero siempre es bueno darse una vuelta por el repositorio original para saber si han incorporado alguna mejora interesante. -## Pasos previos y algunos consejos +## Archivo `bibliography.bib` -### Archivos, orden y modo de trabajo +Este archivo contendrá la metadata de las referencias bibliográficas que citaremos en nuestro archivo principal. No es necesario crearlo manualmente, de eso se encargará las herramientas de Zotero-rbbt, tal como se detalla [en nuestro post respectivo](https://luislaum.github.io/blog/zotero-quarto-rstudio/zotero-quarto-rstudio.html). -Si bien cada investigador (persona) tiene una manera distinta de ordenar los archivos de un proyecto, una de las primeras recomendaciones que puedo hacer es la de definir un proyecto en RStudio en donde al menos haya una carpeta diferenciada en donde se almacenará el contenido del artículo que vamos a escribir. Para nuestro ejemplo, utilizaremos el esquema del propio repositorio en donde está almacenada la plantilla. Es decir, se asumirá que partimos desde una carpeta general en donde están almacenado nuestros datos, figuras, código, resultados y demás, y en donde una de las subcarpetas (llamada `article`) es en donde se almacenará todo lo necesario para generar el artículo. +## Archivo `ices-journal-of-marine-science.csl` -### *Quarto extensions* +Un archivo **CSL** (Citation Style Language) define cómo se deben formatear las citas y las referencias en un documento, permitiendo que programas de gestión bibliográfica (como Zotero) automaticen este proceso. Estos archivos son fundamentales en la escritura de artículos científicos porque garantizan que las citas y referencias se adapten de manera precisa a las normas de estilo exigidas por una revista o institución, como APA, MLA o Vancouver. Al utilizar un archivo CSL, los autores pueden cambiar fácilmente entre estilos sin necesidad de reescribir manualmente sus referencias, lo que ahorra tiempo, reduce errores y asegura la consistencia en el formato de citación a lo largo del documento. -Las extensiones de Quarto son básicamente scripts que añaden funcionalidades adicionales y que son soportadas por la comunidad. Quarto maneja una filosofía de entornos independientes, por lo que, a diferencia de R, la instalación de las extensiones de hacerse de manera local en cada proyecto en que vayamos a ejecutar nuestro script de Quarto. Para efectos del presente post, vamos a utilizar una extensión llamada **kapsner/authors-block**, la cual **ya viene incluidas** en el [repositorio de referencia](https://github.com/LuisLauM/quarto-template-scientific-article/article-template.zip) (dentro de la carpeta `/_extensions`). +Usualmente, cada revista indica a los autores qué estilo deben seguir al momento de redactar sus citas, para lo cual en muchos casos comparten el respectivo archivo `.csl`; sin embargo, si no logramos hallar el archivo correcto, existen [repositorios como este](https://github.com/citation-style-language/styles) en donde se almacenan y mantienen cientos de archivos `.csl` para diferentes revistas. Busca el que más se ajuste a la revista a la que someterás tu manuscrito. -## Plantilla principal (de artículo científico) +## Archivo `custom-reference-doc.docx` -### Header +Usualmente, un archivo de manuscrito no requiere tener un formato ornamentado o sofisticado, pero es posible que algunas revistas, nuestro asesor o los revisores soliciten algunos detalles de formato en nuestro archivo de salida en MS Word. Aquí es donde Quarto hace uso de una solución sencilla, pero potente: el uso de un archivo-formato de referencia. + +El archivo `custom-reference-doc.docx` no es más que un archivo en Word en donde se muestra de forma explícita la manera en cómo se mostrará cada elemento según el estilo que hayamos elegido. Cualquier cosa que editemos en ese archivo será utilizada por Quarto para darle formato a nuestro documento final. Explicar en extenso cómo editar este archivo tomaría un post entero y ahora mismo existen muchas fuentes en donde ya se explica este proceso, [este post por ejemplo](https://andrewpwheeler.com/2024/06/21/my-word-template-for-quarto/). Lo que sí es importante tener en cuenta es que cada cambio que hagamos debe hacerse a nivel de las opciones de Formato y Estilo de MS Word. Si bien podría parecer muy molesto tener que trabajar en Word, la buena noticia es que no es algo que haremos continuamente, sino solo un par de veces durante nuestro proyecto (si es que alguien solicita algún formato especial en nuestro manuscrito). En lo personal, con el archivo compartido ha sido suficiente para mis asesores, los revisores y editores de 2 revistas distintas (ICES JMS y Fisheries Research de Elsevier). + +## Archivo principal `article_v1.qmd` La parte inicial del script de esta plantilla se compone un `header` (en formato YAML) en donde se mostrará las opciones generales de nuestro documento: -* `title` (entre comillas) -* `authors`, en donde podremos incluir datos como nombre, código ORCID, URL de referencia y afiliación. -* `affiliations` en donde se requiere que indiquemos un identificador (que usaremos como referencia para los autores) y el nombre (`name`) completo de la afiliación, tal como querramos que aparezca en el documento. -* `filters`, en donde listaremos las *Quarto extensions* que deseamos que se carguen al inicio del documento (y que se buscarán en la carpeta `/_extensions`). -* `link-citations`, en donde podremos definir (true/false) si deseamos que las citas bibliográficas en el documento final se enlacen a la referencia correspondiente en la sección final de Bibliografía. -* `bibliography`, en donde indicaremos el archivo en donde se hallan nuestras referencias bibliográficas en formato BibTeX. -* `csl`, en donde indicaremos el archivo que utilizará Quarto para establecer el formato de citación de referencias bibliográficas. -* `format`, en donde se indicará parámetros específicos del archivo de salida. Para este ejemplo, todo está configurado para obtener un archivo en MS Word (`.docx`). +- `title`, entre comillas dobles `" "`. +- `authors`, en donde podremos incluir datos como nombres, apellidos y afiliación (que es la información más importante), así como código ORCID, URL de referencia, etc. +- `affiliations`, aquí es donde indicaremos un identificador (que usaremos como referencia para los autores) y el nombre (`name`) completo de la afiliación, tal como querramos que aparezca en el documento. +- `filters`, en donde listaremos las *Quarto extensions* que deseamos que se carguen al inicio del documento (y que se buscarán en la carpeta `/_extensions`). +- `link-citations`, en donde podremos definir (true/false) si deseamos que las citas bibliográficas en el documento final se enlacen a la referencia correspondiente en la sección final de Bibliografía. +- `bibliography`, en donde indicaremos el archivo en donde se hallan nuestras referencias bibliográficas en formato BibTeX. +- `csl`, en donde indicaremos el archivo que utilizará Quarto para establecer el formato de citación de referencias bibliográficas. +- `format`, en donde se indicará parámetros específicos del archivo de salida. Para este ejemplo, todo está configurado para obtener un archivo en MS Word (`.docx`) que utilizará nuestro archivo de referencia de estilo `custom-reference-doc.docx`. El parámetro `toc` (que hace referencia a *Table Of Contents*) permite mostrar o no la tabla de contenidos al inicio del documento. El parámetro `numer-sections` permite activar/desactivar el uso de numeración en las secciones de nuestro manuscrito. + +### *Setup chunk* + +El chunk que se muestra al inicio del archivo `qmd` contiene algunos parámetros que conviene fijar, para no tener que hacerlo independientemente en cada chunk posterior. **Ojo**, esta es una configuración SUGERIDA, usted podrá (y deberá) modificarla según lo requiera su proyecto o los revisores. + +```{r} +#| eval: false + +knitr::opts_chunk$set(echo = FALSE, + verbose = FALSE, + message = FALSE, + warning = FALSE, + dev = "ragg_png", + out.width = "100%", + dpi = 1500) +``` + +* `echo = FALSE`: Hace que el código ejecutado NO se muestre textualmente en el documento. + +* `verbose = FALSE`: Útil para suprimir mensajes detallados sobre el progreso, los pasos intermedios o los resultados parciales del código dentro de los chunks y mantener salidas más limpias. + +* `message = FALSE`/`warning = FALSE`: se utiliza para suprimir los mensajes de advertencia o información que las funciones pueden generar durante la ejecución del código, evitando que estos aparezcan en la salida del documento. Esto ayuda a mantener la salida más limpia y enfocada en los resultados esenciales. + +* `dev = "ragg_png"`: especifica que el dispositivo gráfico utilizado para generar las imágenes es [ragg](https://ragg.r-lib.org/), un motor eficiente y moderno que produce gráficos en formato PNG con alta calidad y rendimiento. + +* `out.width = "100%"`: establece que el ancho de las imágenes o gráficos generados ocupará el 100% del ancho del contenedor (por ejemplo, la página o columna donde se muestra), ajustándose automáticamente al tamaño disponible. + +* `dpi = 1500`: establece la resolución de las imágenes generadas en el documento, específicamente en puntos por pulgada (dots per inch). Un valor de 1500 dpi indica una resolución muy alta, lo que resulta en imágenes más nítidas y detalladas, pero también más pesadas, por lo que será responsabilidad del usuario determinar el valor óptimo junto a lo especificado por cada revista. + +### Redactar en Quarto + +Lo que sigue es básicamente redactar nuestro manuscrito somo si se tratara de un reporte más en Quarto, aprovechando el poder de los chunks para recrear los análisis necesarios para generar cada figura, tabla o valor. Aquí es importante recomendar que cada valor que provenga de un análisis de nuestra información (i.e. que no provenga diractamente de una cita bibliográfica) debe ser generado a partir de código explícito en nuestro documento. + +Por ejemplo, imaginemos que estoy trabajando con la tabla `mtcars` (de R) y deseo redactar el siguiente texto-resultado: + +> Los modelos `r rownames(mtcars)[order(mtcars$mpg, decreasing = TRUE)[1:2]] |> paste(collapse = " y ")` fueron aquellos con mayor valor de millas por galón. + +El texto dentro de nuestro archivo qmd dbería lucir del siguiente modo: + +```{verbatim} +Los modelos `r rownames(mtcars)[order(mtcars$mpg, decreasing = TRUE)[1:2]] |> paste(collapse = " y ")` fueron los que mostraron los primeros según la variable de millas por galón. +``` + +Como se observa, dentro del propio párrafo estoy ejecutando un chunk con una operación de ordenamiento y extracción de datos. Si bien esto puede parecer más engorroso, permite que si en algún momento tuviéramos que modificar algún proceso de preprocesamiento de los datos iniciales, los resultados se generarán automáticamente, sin necesidad de que tengamos que volver a hacer estos pequeños cálculos nuevamente. + +::: {.callout-important} +Evidentemente, los textos relacionados a la interpretación de los resultados deben ser revisados cada vez que sepamos que hemos realizado un cambio importante en nuestros datos iniciales. +::: + +Existen múltiples sitios web (blogs y foros) en donde podemos aprender a darle el formato que nuestros resultados o presentación requieren. Algunos ejemplos son: + +* [Markdown Basics](https://quarto.org/docs/authoring/markdown-basics.html) + +* [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/) + +* [R markdown](https://rmarkdown.rstudio.com/index.html) + +* [knitr](https://yihui.org/knitr/) + +* [Bookdown](https://bookdown.org/) +* [Hello Quarto](https://quarto-tdg.org/overview.html) -### First *chunk* +* [Quarto Q&A](https://github.com/quarto-dev/quarto-cli/discussions/categories/q-a). Este sitio es particularmente interesante porque se trata de la sección de Q&A del propio repositorio de Quarto, por lo que siempre es bueno darnos una vuelta por su buscador y revisar si alguien más tuvo similares dificultades que nosotros. Así mismo, podemos dejar un ticket con nuestra consulta si es que no encontramos coincidencias. -Un *chunk* es una sección dentro del documento que se haya escrita en algún formato particular asociado a código (bash, R, Python, SQL, etc.). La sintaxis general dentro de un archivo de Quarto es la siguiente: +## Archivo adicional `letter_editor.Rmd` +La carta al editor es un componente clave al someter un artículo científico a una revista, ya que sirve como una primera presentación del trabajo a los editores y ayuda a destacar su relevancia, originalidad y contribución al campo. Su utilidad radica en captar rápidamente la atención del editor al resumir los objetivos, los principales hallazgos y la importancia del estudio, lo que facilita la evaluación inicial del manuscrito. Además, permite al autor explicar brevemente por qué el artículo es adecuado para la revista en cuestión, mostrando alineación con su enfoque y audiencia. Una carta bien redactada puede influir positivamente en la decisión del editor de enviar el artículo a revisión, agilizando así el proceso de evaluación. +Si bien en esta plantilla no comparto un ejemplo de redacción de esta carta (solo el formato en R markdown), es posible hallar múltiples post relacionados en diversos foros o blogs. El uso de este archivo es bastante intuitivo, solo basta con rellenar los campos y renderizar el documento. Por cierto, se requiere la instalación previa del [paquete komaletter](https://cran.r-project.org/package=komaletter). -## Plantilla adicional (de carta al editor) diff --git a/blog/zotero-quarto-rstudio/zotero-quarto-rstudio.qmd b/blog/zotero-quarto-rstudio/zotero-quarto-rstudio.qmd index a566d61..fd2bab9 100644 --- a/blog/zotero-quarto-rstudio/zotero-quarto-rstudio.qmd +++ b/blog/zotero-quarto-rstudio/zotero-quarto-rstudio.qmd @@ -92,7 +92,7 @@ Great, we're all set! It's time to test our changes. 2. Next, we will create an empty file where our bibliographic citations will be stored (for our example, we will name it **references.bib**). Then, in the header of our Quarto file (also called the YAML section), we will add a line where we will indicate the path to this created file: -````{md} +````{verbatim} --- title: "test_rbbt" format: html @@ -102,8 +102,8 @@ bibliography: references.bib 3. Also, to ensure that **rbbt** does NOT attempt to include references to figures, tables, equations, or other non-bibliographic elements, we will include the following code within a chunk at the beginning of our document: -````{md} -#| echo: false +````{r} +#| eval: false # Get current filepath currentFilePath <- this.path::this.path() @@ -141,6 +141,8 @@ It is highly recommended to enable the *Render on Save* option (located at the t All the material needed to run this tutorial can be found in my repository, following this link [link](https://github.com/LuisLauM/LuisLauM.github.io/tree/main/blog/zotero-quarto-rstudio/test-rbbt.zip). ::: +--- + # \[ES\] Zotero + Quarto + RStudio y algo más Quarto se está volviendo cada vez más una poderosa alternativa para la generación de diversos tipos de documentos y reportes. Por su parte, Zotero es uno de los administradores de citas bibliográficas más extendido y utilizado, no solo por ser software libre, sino también porque la comunidad a su alrededor ha ido desarrollando muchos *plug-ins* que permiten incrementar sus capacidades fuera de lo ofrecido por sus propios desarrolladores. Finalmente, RStudio es uno de los IDE preferidos en la comunidad de programadores en R, R markdown y Quarto, por su simplicidad y potencia, pero también por permitir la incorporación de *addins* (la analogía de *plug-ings*) a través de paquetes de R. @@ -220,7 +222,7 @@ Añadir atajos de teclado en RStudio es muy sencillo, basta con ir al menú **To 2. Seguidamente, crearemos un archivo vacío en donde se guardarán nuestras citas bibliográficas (para nuestro ejemplo, le pondremos el nombre **references.bib**). Luego, en la cabecera de nuestro archivo de Quarto (llamada también la sección YAML), añadiremos una línea en donde indicaremos la ruta a este archivo creado: -````{md} +````{verbatim} --- title: "test_rbbt" format: html @@ -230,8 +232,8 @@ bibliography: references.bib 3. Así mismo, para asegurarnos de que **rbbt** NO intente incluir las referencias a figuras, tablas, ecuaciones, u otros elementos no bibliográficos, incluiremos el siguiente código dentro de un chunk al inicio de nuestro documento: -````{md} -#| echo: false +````{r} +#| eval: false # Get current filepath currentFilePath <- this.path::this.path()