Add packages listing

_header.html

@@ -8,7 +8,6 @@
 
 <!-- Matomo -->
 <script src="https://www.tesselle.org/scripts/unicorn.js"></script>
-<noscript><p><img src="https://analyseweb.huma-num.fr/matomo.php?idsite=332&rec=1" style="border:0" alt="" /></p></noscript>
 
 <!-- Mastodon -->
 <link rel="me" href="https://archaeo.social/@tesselle" />

_quarto.yml

@@ -10,72 +10,29 @@ website:
 
   favicon: /images/icons/favicon.ico
   image: /images/card.png
-  margin-header: |
-    ![](/images/tesselle.png)
-  open-graph:
-    image: https://www.tesselle.org/images/card.png
 
   search: false
   navbar:
-    background: "#ffd402ff"
     pinned: true
     right:
       - icon: house
         text: Homepage
         href: "https://www.tesselle.org"
-      - sidebar:packages
       - icon: github
         text: Github
         href: https://github.com/tesselle/
       - icon: download
         text: R-universe
         href: https://tesselle.r-universe.dev/
 
-  sidebar:
-    - id: packages
-      title: "Packages"
-      collapse-level: 1
-      contents:
-        - section: "Count data"
-          contents:
-            - text: tabula
-              url:  https://packages.tesselle.org/tabula/
-        - section: "Compositional data"
-          contents:
-            - text: nexus
-              url:  https://packages.tesselle.org/nexus/
-        - section: "Chronological data"
-          contents:
-            - text: aion
-              url:  https://packages.tesselle.org/aion/
-            - text: kairos
-              url:  https://packages.tesselle.org/kairos/
-        - section: "Multivariate data"
-          contents:
-            - text: arkhe
-              url:  https://packages.tesselle.org/arkhe/
-            - text: dimensio
-              url:  https://packages.tesselle.org/dimensio/
-        - section: "Signal processing"
-          contents:
-            - text: alkahest
-              url:  https://packages.tesselle.org/alkahest/
-        - section: "Data visualization"
-          contents:
-            - text: khroma
-              url:  https://packages.tesselle.org/khroma/
-            - text: isopleuros
-              url:  https://packages.tesselle.org/isopleuros/
-        - section: "Datasets"
-          contents:
-            - text: folio
-              url:  https://packages.tesselle.org/folio/
   page-footer:
     center: |
       <a href="https://www.u-bordeaux-montainge.fr"><img src="https://www.tesselle.org/images/logo-ubm.svg" class="logo-institution" /></a><a href="https://www.cnrs.fr"><img src="https://www.tesselle.org/images/logo-cnrs.svg" class="logo-institution" /></a>
       <br>The tesselle project is supported by <a href="https://www.archeosciences-bordeaux.fr/" target="_blank">Archéosciences Bordeaux</a>, the <a href="https://mshs.univ-toulouse.fr/" target="_blank"><abbr title="Centre de Recherche et d'Études pour l'Art Préhistorique">CREAP</abbr></a> and the <a href="https://www.huma-num.fr/" target="_blank"><abbr title="Très Grande Infrastructure de Recherche">TGIR</abbr> Huma-Num</a>.
+      <noscript><p><img src="https://analyseweb.huma-num.fr/matomo.php?idsite=332&rec=1" style="border:0" alt="" /></p></noscript>
 
 format:
   html:
-    theme: custom.scss
+    theme: cosmo
+    css: style.css
     include-in-header: _header.html

gallery.ejs

@@ -0,0 +1,39 @@
+
+```{=html}
+
+<% for (const item of items) { %>
+
+<h2><%- item.category %></h2>
+
+<p><%- item.description %></p>
+
+<div class="list grid" style="column-gap: 10px;">
+
+<% for (const tile of item.tiles) { %>
+  <div class="card border-2 rounded-3 g-col-12 g-col-sm-6 g-col-md-4 mb-2" <%= metadataAttrs(tile) %>>
+    <div class="card-header py-1 px-2 border-bottom border-1 bg-light">
+      <small class="card-text inline-block">
+        <a href="https://packages.tesselle.org/<%- tile.title %>/" class="listing-title"><%= tile.title %></a>
+        <a href="https://github.com/tesselle/<%- tile.title %>" title="View source code"
+          class="source-code card-text float-end inline-block">
+          <i class="bi-code-slash"></i>
+        </a>
+        <span class="text-muted listing-subtitle"><%= tile.subtitle %></span>
+      </small>
+    </div>
+    <a href="https://packages.tesselle.org/<%- tile.title %>/">
+      <img src="/images/<%- tile.title %>.png" alt="<%- tile.description %>" class="card-img-top"/>
+    </a>
+
+    <% if (tile.publicationdate) { %>
+      <b class="listing-publicationdate"><%= tile.publicationdate %></b>
+    <% } %>
+
+  </div>
+<% } %>
+
+</div>
+
+<% } %>
+
+```

gallery.yml

@@ -0,0 +1,104 @@
+- category: Count data
+  description: ""
+  tiles:
+    - title: tabula
+      subtitle: Analysis and Visualization of Archaeological Count Data
+      description: |
+        **tabula** provides
+        several tests and measures of diversity: heterogeneity and evenness
+        (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1,
+        Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson,
+        etc.). The package make it easy to visualize count data and statistical
+        thresholds: rank vs. abundance plots, heatmaps, Ford and Bertin diagrams.
+- category: Compositional data
+  description: ""
+  tiles:
+    - title: nexus
+      subtitle: Sourcing Archaeological Materials by Chemical Composition
+      description: |
+        **nexus** allows the exploration and analysis of compositional data in the
+        framework of Aitchison (1986). It provides tools for chemical
+        fingerprinting and source tracking of ancient materials.
+        **Initial development is in progress.**
+- category: Chronological data
+  description: ""
+  tiles:
+    - title: kairos
+      subtitle: Analysis of Chronological Patterns from Archaeological Count Data
+      description: |
+        A toolkit for absolute dating and analysis of chronological patterns.
+        This package includes functions for chronological modeling and dating of
+        archaeological assemblages from count data. It provides methods for
+        matrix seriation. It also allows to compute time point estimates and
+        density estimates of the occupation and duration of an archaeological
+        site.
+    - title: aion
+      subtitle: Archaeological Time Series
+      description: |
+        A toolkit for archaeological time series analysis. This package provides
+        a system of classes and methods to represent and work with
+        archaeological time series. Dates are represented as *rata die* and can
+        be converted to (virtualy) any calendar defined by Reingold (2018).
+- category: Multivariate data analysis
+  description: ""
+  tiles:
+    - title: dimensio
+      subtitle: Multivariate Data Analysis
+      description: |
+        Simple Principal Components Analysis (PCA) and Correspondence Analysis
+        (CA) based on the Singular Value Decomposition (SVD). This package
+        provides S4 classes and methods to compute, extract, summarize and
+        visualize results of multivariate data analysis. It also includes
+        methods for partial bootstrap validation described in Greenacre (1984)
+        and Lebart (2006).
+- category: Data visualization
+  description: ""
+  tiles:
+    - title: isopleuros
+      subtitle: Ternary Plots
+      description: |
+        This package allows to create ternary plot
+        using `graphics`. It provides functions to display the data in the
+        ternary space, to add or tune graphical elements and to display
+        statistical summaries. It also includes common ternary diagrams useful
+        for the archaeologist (e.g. soil texture charts, ceramic phase diagram).
+    - title: khroma
+      subtitle: Colour Schemes for Scientific Data Visualization
+      description: |
+        Colour schemes ready for each type of data (qualitative, diverging or
+        sequential), with colours that are distinct for all people, including
+        colour-blind readers. This package provides an implementation of Paul
+        Tol (2018) and Fabio Crameri (2018) colour schemes for use with
+        `graphics` or `ggplot2`. It provides tools to simulate colour-blindness
+        and to test how well the colours of any palette are identifiable.
+        Several scientific thematic schemes (geologic timescale, land cover,
+        FAO soils, etc.) are also implemented.
+- category: Tools
+  description: ""
+  tiles:
+    - title: alkahest
+      subtitle: Pre-Processing XY Data from Experimental Methods
+      description: |
+        A lightweight, dependency-free toolbox for pre-processing XY data from
+        experimental methods (i.e. any signal that can be measured along a
+        continuous variable). This package provides methods for baseline
+        estimation and correction, smoothing, normalization, integration and
+        peaks detection.
+    - title: arkhe
+      subtitle: Tools for Cleaning Rectangular Data
+      description: |
+        This
+        package allows to detect, count and replace values or delete
+        rows/columns according to a specific predicate. In addition, it provides
+        tools to check conditions and return informative error messages.
+- category: Datasets
+  description: ""
+  tiles:
+    - title: folio
+      subtitle: Datasets for Teaching Archaeology and Paleontology
+      description: |
+        **folio** provides several types of data
+        related to broad topics (cultural evolution, radiocarbon dating,
+        paleoenvironments, etc.), which can be used to illustrate statistical
+        methods in the classroom (multivariate data analysis, compositional
+        data analysis, diversity measurement, etc.).

index.qmd

@@ -1,13 +1,12 @@
 ---
-title: "R Packages & Archaeology"
-description: |
-  **tesselle** is a collection of [R](https://www.r-project.org/) packages for 
-  research and teaching in archaeology. These packages focus on quantitative 
-  analysis methods developed for archaeology. The **tesselle** packages are 
-  designed to work seamlessly together and to complement general-purpose and 
-  other specialized statistical packages. Learn more at 
-  [tesselle.org](https://www.tesselle.org).
-title-block-banner: true
+pagetitle: "R Packages & Archaeology"
+resources: 
+  - "sitemapindex.xml"
+  - "packages.json"
+listing:
+  - id: gallery
+    template: gallery.ejs
+    contents: gallery.yml
 ---
 
 ```{r}
@@ -18,11 +17,7 @@ repo <- utils::contrib.url("https://tesselle.r-universe.dev")
 pkg <- utils::available.packages(contriburl = repo)
 pkg <- as.data.frame(pkg)
 url_pkg <- sprintf("https://packages.tesselle.org/%s", pkg$Package)
-```
 
-```{r}
-#| label: sitemap 
-#| echo: false
 ## Build sitemap index
 loc <- paste0(url_pkg, "/sitemap.xml")
 map <- sprintf("  <sitemap>\n    <loc>%s</loc>\n  </sitemap>", loc)
@@ -34,17 +29,13 @@ cat(
   '  </sitemap>',
   map,
   '</sitemapindex>',
-  file = "_site/sitemapindex.xml",
+  file = "sitemapindex.xml",
   sep = "\n",
   append = FALSE
 )
-```
 
-```{r}
-#| label: search 
-#| echo: false
 ## Build search index
-search_pkg <- search_ref <- list()
+search_pkg <- list()
 for (i in seq_along(url_pkg)) {
   path <- url_pkg[[i]]
   tmp <- try(
@@ -55,21 +46,22 @@ for (i in seq_along(url_pkg)) {
     for (j in seq_along(tmp)) {
       ## Add package name
       tmp[[j]]$package <- pkg$Package[[i]]
-      
-      ## Get references
-      if (!is.null(tmp[[j]]$what) && tmp[[j]]$what == "References") {
-        search_ref <- c(search_ref, tmp[j])
-        # tmp[[j]] <- NULL 
-      }
     }
     search_pkg <- c(search_pkg, tmp)
   }
 }
-cat(rjson::toJSON(search_pkg), file = "_site/packages.json", append = FALSE)
-cat(rjson::toJSON(search_ref), file = "_site/references.json", append = FALSE)
+cat(rjson::toJSON(search_pkg), file = "packages.json", append = FALSE)
 ```
 
-## Read the doc
+::: {#hero-banner .column-screen}
+::: {.grid .column-page}
+::: {.headline .g-col-lg-6 .g-col-12 .g-col-md-12}
+# Welcome
+[**tesselle**](https://packages.tesselle.org) is a collection of [R](https://www.r-project.org/) packages for research and teaching in archaeology. These packages focus on quantitative analysis methods developed for archaeology. The **tesselle** packages are designed to work seamlessly together and to complement general-purpose and other specialized statistical packages.
+:::
+
+::: {.g-col-lg-6 .g-col-12 .g-col-md-12}
+# Read the doc
 
 Quickly discover relevant content by searching the documentation or exploring the [project bibliography](https://www.zotero.org/groups/2894473/tesselle/library).
 
@@ -79,3 +71,10 @@ Quickly discover relevant content by searching the documentation or exploring th
 <input type="search" class="form-control" aria-label="Search for..." name="search-packages" data-search-index="/packages.json" id="search-packages" placeholder="e.g. seriation" autocomplete="off">
 </div>
 </form>
+:::
+
+:::
+:::
+
+::: {#gallery .column-page}
+:::