Initial commit

.github/workflows/publish.yml

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+on:
+  workflow_dispatch:
+  push:
+    branches: main
+
+name: Quarto Publish
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Render and Publish
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+/.quarto/
+.httr-oauth
+/docs/
+/_site/

Blog.qmd

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+---
+title: "Blog"
+listing:
+  contents: posts
+  type: default
+  sort: "date desc"
+  categories: true
+  feed: true
+---
+
+

Projects.qmd

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+---
+title: "Projects"
+listing:
+  contents: projects
+  type: grid
+  categories: false
+---
+
+
+

Publications.qmd

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+---
+title: "Publications"
+toc: true
+---
+
+### Articles
+
+- Quintero, Rodríguez‐Sánchez, Jordano (2022) [Reciprocity and interaction effectiveness in generalised mutualisms among free‐living species](https://doi.org/10.1111/ele.14141). *Ecology Letters* 26 (1): 132-146. [[PDF](https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.14141)]
+
+- Rodríguez-Sanchez, Pérez-Luque, Bartomeus, Varela (2016) [Ciencia reproducible: ¿qué, por qué, cómo?](https://doi.org/10.7818/ECOS.2016.25-2.11). *Ecosistemas* 25 (2): 83-92
+
+### Book chapters
+
+
+

R/doi2md.R

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+doi2md <- function(doi = NULL, style = NULL) {
+
+  doi <- gsub("https://doi.org/", "", doi)
+
+  dt <- rcrossref::cr_works(doi)$data
+
+  if (!is.null(style)) {
+    out <- rcrossref::cr_cn(doi, format = "text", style = "ecology-letters")
+  } else {
+
+    out <- paste(
+      paste(dt$author[[1]]$family, collapse = ", "),
+      paste0("(", substr(dt$created, start = 1, stop = 4), ")"),
+      paste0("[", dt$title, "](", "https://doi.org/", doi, ")."),
+      paste0("*", dt$container.title, "*"),
+      dt$volume,
+      paste0("(", dt$issue, "):"),
+      dt$page,
+      collapse = " "
+      )
+
+  }
+
+  cat(out)
+
+}
+
+
+
+

R/scholar_pubs.R

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+scholar_pubs <- function(id = NULL, file = "publications.qmd") {
+
+  scholar.df <- scholar::get_publications(id) |>
+    sort_by(~ list(-year))
+
+  pubs <- do.call("rbind", lapply(split(scholar.df, f = 1:nrow(scholar.df)), format_pub))
+
+  pubs <- paste("- ", format_pubs, collapse = "\n\n")
+
+  writeLines(c("---",
+               "title: Publications",
+               "---",
+               pubs),
+             con = "pubs.qmd")
+
+
+}
+
+format_pub <- function(pub) {
+  paste(pub$author, pub$year, pub$title, paste0("*", pub$journal, "*"), pub$number, sep = ". ")
+}
+
+

README.md

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+# Template for academic website made with Quarto
+
+A template for academic websites made with [Quarto](https://quarto.org) and hosted on GitHub.
+
+This is all configured so you only need to edit the source files in Quarto (.qmd). The website is generated and hosted automatically by GitHub.
+
+Example website: https://pakillo.github.io/academic-website-template-Quarto/
+
+## Using this template
+
+1. Click on green button "Use this template" -> "Create a new repository"
+
+2. Important: check 'Include all branches' when creating the repository (because we will need the 'gh-pages' branch to host the website).
+
+3. Choose a name for your repository
+
+4. Once your repo is created, remember to update the links and info in `_quarto.yml`, `index.qmd`, etc.
+
+5. With every new commit pushed to the 'main branch' the website will be updated automatically (using GitHub Actions). If that is not working, go to Settings -> GitHub Pages and check that it is configured as explained [here](https://quarto.org/docs/publishing/github-pages.html#source-branch). Otherwise the Quarto rendering might be failing. Try running 'quarto render' locally in your computer for debugging.
+
+
+### Tips
+
+In the 'R' folder there are a couple of R functions to help you populate the Publications page.
+
+- `doi2md` will take a DOI (e.g. from a published paper) and produce the Markdown text ready to paste into `Publications.qmd`. For example, running `doi2md("10.1111/ele.14141")` returns this text that you can directly paste into `Publications.qmd` (requires internet connection for retrieving the publication metadata):
+
+  Quintero, Rodríguez‐Sánchez, Jordano (2022) [Reciprocity and interaction effectiveness in generalised mutualisms among free‐living species](https://doi.org/10.1111/ele.14141). *Ecology Letters* 26 (1): 132-146
+
+- `scholar_pubs` will take a Google Scholar ID (e.g. mine is "LQQrHeEAAAAJ") and will generate a Quarto file (named "publications.qmd" by default) with your full publication list as available in your Google Scholar profile. Note you could of course write similar functions to retrieve publications dynamically from your ORCID profile, Zotero database, etc.
+
+
+

_extensions/mcanouil/iconify/LICENSE

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+MIT License
+
+Copyright (c) 2024 Mickaël Canouil
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

_extensions/mcanouil/iconify/_extension.yml

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+title: Iconify support
+author: Mickaël Canouil
+version: 2.1.2
+quarto-required: ">=1.2.280"
+contributes:
+  shortcodes:
+    - iconify.lua

_extensions/mcanouil/iconify/iconify.lua

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+--[[
+# MIT License
+#
+# Copyright (c) Mickaël Canouil
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+]]
+
+local function ensure_html_deps()
+  quarto.doc.add_html_dependency({
+    name = 'iconify',
+    version = '2.1.0',
+    scripts = {"iconify-icon.min.js"}
+  })
+end
+
+local function is_empty(s)
+  return s == nil or s == ''
+end
+
+local function is_valid_size(size)
+  if is_empty(size) then
+    return ''
+  end
+  local size_table = {
+    ["tiny"]         = "0.5em",
+    ["scriptsize"]   = "0.7em",
+    ["footnotesize"] = "0.8em",
+    ["small"]        = "0.9em",
+    ["normalsize"]   = "1em",
+    ["large"]        = "1.2em",
+    ["Large"]        = "1.5em",
+    ["LARGE"]        = "1.75em",
+    ["huge"]         = "2em",
+    ["Huge"]         = "2.5em",
+    ["1x"]           = "1em",
+    ["2x"]           = "2em",
+    ["3x"]           = "3em",
+    ["4x"]           = "4em",
+    ["5x"]           = "5em",
+    ["6x"]           = "6em",
+    ["7x"]           = "7em",
+    ["8x"]           = "8em",
+    ["9x"]           = "9em",
+    ["10x"]          = "10em",
+    ["2xs"]          = "0.625em",
+    ["xs"]           = "0.75em",
+    ["sm"]           = "0.875em",
+    ["lg"]           = "1.25em",
+    ["xl"]           = "1.5em",
+    ["2xl"]          = "2em"
+  }
+  for key, value in pairs(size_table) do
+    if key == size then
+      return 'font-size: ' .. value .. ';'
+    end
+  end
+  return 'font-size: ' .. size .. ';'
+end
+
+return {
+  ["iconify"] = function(args, kwargs)
+    -- detect html (excluding epub which won't handle fa)
+    if quarto.doc.is_format("html:js") then
+      ensure_html_deps()
+      local icon = pandoc.utils.stringify(args[1])
+      local set = "fluent-emoji"
+
+      if #args > 1 and string.find(pandoc.utils.stringify(args[2]), ":") then
+        quarto.log.warning(
+          'Use "set:icon" or "set icon" syntax, not both! ' ..
+          'Using "set:icon" syntax and discarding first argument!'
+        )
+        icon = pandoc.utils.stringify(args[2])
+      end
+
+      if string.find(icon, ":") then
+        set = string.sub(icon, 1, string.find(icon, ":") - 1)
+        icon = string.sub(icon, string.find(icon, ":") + 1)
+      elseif #args > 1 then
+        set = icon
+        icon = pandoc.utils.stringify(args[2])
+      end
+
+      local attributes = ' icon="' .. set .. ':' .. icon .. '"'
+      local default_label = 'Icon ' .. icon .. ' from ' .. set .. ' Iconify.design set.'
+
+      local size = is_valid_size(pandoc.utils.stringify(kwargs["size"]))
+      if not is_empty(size) then
+        attributes = attributes .. ' style="' .. size .. '"'
+      end
+
+      local aria_label = pandoc.utils.stringify(kwargs["label"])
+      if is_empty(aria_label) then
+        aria_label =  ' aria-label="' .. default_label .. '"'
+      else
+        aria_label =  ' aria-label="' .. aria_label .. '"'
+      end
+
+      local title = pandoc.utils.stringify(kwargs["title"])
+      if is_empty(title) then
+        title =  ' title="' .. default_label .. '"'
+      else
+        title =  ' title="' .. title .. '"'
+      end
+
+      attributes = attributes .. aria_label .. title
+
+      local width = pandoc.utils.stringify(kwargs["width"])
+      if not is_empty(width) and is_empty(size) then
+        attributes = attributes .. ' width="' .. width .. '"'
+      end
+      local height = pandoc.utils.stringify(kwargs["height"])
+      if not is_empty(height) and is_empty(size)  then
+        attributes = attributes .. ' height="' .. height .. '"'
+      end
+      local flip = pandoc.utils.stringify(kwargs["flip"])
+      if not is_empty(flip) then
+        attributes = attributes .. ' flip="' .. flip.. '"'
+      end
+      local rotate = pandoc.utils.stringify(kwargs["rotate"])
+      if not is_empty(rotate) then
+        attributes = attributes .. ' rotate="' .. rotate .. '"'
+      end
+
+      local inline = pandoc.utils.stringify(kwargs["inline"])
+      if is_empty(inline) or inline ~= "false" then
+        attributes = ' inline ' .. attributes
+      end
+
+
+      return pandoc.RawInline(
+        'html',
+        '<iconify-icon role="img"' .. attributes .. '></iconify-icon>'
+      )
+    else
+      return pandoc.Null()
+    end
+  end
+}

_freeze/Publications/execute-results/html.json

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+{
+  "hash": "4c54ef892ed009981305dbb188974a63",
+  "result": {
+    "engine": "knitr",
+    "markdown": "---\ntitle: \"Publications\"\n---\n\n\n\nAbout this site\n\n\n\n::: {.cell}\n\n```{.r .cell-code}\n1 + 1\n```\n\n::: {.cell-output .cell-output-stdout}\n\n```\n[1] 2\n```\n\n\n:::\n:::\n",
+    "supporting": [],
+    "filters": [
+      "rmarkdown/pagebreak.lua"
+    ],
+    "includes": {},
+    "engineDependencies": {},
+    "preserve": {},
+    "postProcess": true
+  }
+}

_freeze/Team/execute-results/html.json

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+{
+  "hash": "5af09650b9cd602b66b7d09482728273",
+  "result": {
+    "engine": "knitr",
+    "markdown": "---\ntitle: \"Team\"\n---\n\n\n\nAbout this site\n\n\n\n::: {.cell}\n\n```{.r .cell-code}\n1 + 1\n```\n\n::: {.cell-output .cell-output-stdout}\n\n```\n[1] 2\n```\n\n\n:::\n:::\n",
+    "supporting": [],
+    "filters": [
+      "rmarkdown/pagebreak.lua"
+    ],
+    "includes": {},
+    "engineDependencies": {},
+    "preserve": {},
+    "postProcess": true
+  }
+}