Add GitHub metadata

.github/workflows/render.yaml

@@ -3,7 +3,7 @@
 on:
   workflow_dispatch:
   schedule:
-    - cron:  '00 00 * * 1'
+    - cron:  '00 00 1 * *'
   push:
     branches: [main]
 
@@ -58,6 +58,8 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ always() }}
     needs: pkgdown
+    env:
+      GITHUB_PAT: ${{ secrets.TOKEN }}
     steps:
       - uses: actions/checkout@v4
 

DESCRIPTION

@@ -14,10 +14,12 @@ URL: https://github.com/tesselle/packages
 Depends: 
     R (>= 4.1.0)
 Imports:
+    httr2,
+    gh,
     knitr,
     quarto,
-    rjson,
-    rmarkdown
+    rmarkdown,
+    yaml
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

_header.html

@@ -1,3 +1,6 @@
+<!-- Font Awesome -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css" integrity="sha512-iecdLmaskl7CVkqkXNQ/ZH/XLlvWZOJyj7Yy7tcenmpD1ypASozpmT/E0iPtmFIB46ZmdtAc9eNBvH0H/ZpiBw==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+
 <!-- Matomo -->
 <script src="https://www.tesselle.org/scripts/unicorn.js"></script>
 

_utils.R

@@ -0,0 +1,31 @@
+# R-universe API
+uni_info <- function(what = c("Package", "Title", "Version", "Description")) {
+  api <- httr2::request("https://tesselle.r-universe.dev")
+  req <- httr2::req_url_path(api, "/api/packages/")
+  resp <- httr2::req_perform(req)
+  json <- httr2::resp_body_json(resp)
+
+  pkg <- lapply(X = json, `[`, what)
+  pkg <- lapply(pkg, as.data.frame)
+  pkg <- do.call(rbind, pkg)
+  pkg
+}
+
+# GitHub API
+gh_infos <- function(what = c("stargazers_count", "forks", "open_issues")) {
+  ## Repo infos
+  user_repo <- gh::gh(
+    endpoint = "/search/repositories",
+    q="user:tesselle topic:r-package",
+    .limit = Inf
+  )
+  items <- user_repo$items
+  if (length(items) < 1) return(NULL)
+  if (length(items) == 1 && items == "") return(NULL)
+
+  items <- lapply(items, `[`, c("name", what))
+  items <- lapply(items, as.data.frame)
+  items <- do.call(rbind, items)
+  items
+}
+

gallery.ejs

@@ -1,21 +1,25 @@
 
 ```{=html}
-<p class="fs-3">R packages of the <strong><a href="https://www.tesselle.org/">tesselle</a></strong> projet:</p>
-
-<div class="grid">
+<div class="list grid">
 <% for (const item of items) { %>
-  <div class="g-col-12 g-col-sm-6 g-col-md-4 mb-2">
-    <div class="card h-100 shadow-sm" <%= metadataAttrs(item) %>>
-      <img src="/images/<%- item.title %>.png" alt="<%- item.description %>" class="card-img-top rounded-top">
+  <div class="g-col-12 g-col-sm-6 g-col-md-4 mb-2" <%= metadataAttrs(item) %>>
+    <div class="card h-100 shadow-sm">
+      <img src="/images/<%- item.package %>.png" alt="<%- item.description %>" class="card-img-top rounded-top">
 
       <div class="card-body" style="position: relative;">
-        <h5 class="card-title listing-title"><%= item.title %></h5>
-        <h6 class="card-subtitle mb-2 text-body-secondary listing-subtitle"><%= item.subtitle %></h6>
+        <h5 class="card-title listing-package"><%= item.package %></h5>
+        <h6 class="card-subtitle mb-2 text-body-secondary"><%= item.title %></h6>
       </div>
-      <div class="card-footer bg-light">
+      <div class="card-footer bg-light py-3">
+        <div class="d-flex flex-row text-body-secondary text-center mb-2">
+          <div class="flex-fill listing-stargazers_count"><span class="fa-solid fa-star fa-lg" aria-hidden="true"></span> <%= item.stargazers_count %></div>
+          <div class="flex-fill listing-open_issues"><span class="fa-solid fa-circle-exclamation fa-lg" aria-hidden="true"></span> <%= item.open_issues %></div>
+          <div class="flex-fill listing-forks"><span class="fa-solid fa-code-fork fa-lg" aria-hidden="true"></span> <%= item.forks %></div>
+          <div class="flex-fill listing-version">v<%= item.version %></div>
+        </div>
         <div class="d-flex flex-row text-center">
-          <a href="https://packages.tesselle.org/<%- item.title %>/" class="card-link flex-fill">Documentation</a>
-          <a href="https://github.com/tesselle/<%- item.title %>" class="card-link flex-fill">Source code</a>
+          <a href="https://packages.tesselle.org/<%- item.package %>/" class="card-link flex-fill">Documentation</a>
+          <a href="https://github.com/tesselle/<%- item.package %>" class="card-link flex-fill">Source code</a>
         </div>
       </div>
     </div>

gallery.yml

@@ -1,90 +1,179 @@
-- title: tabula
-  subtitle: Analysis and Visualization of Archaeological Count Data
-  categories:
-    - 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.
-- title: nexus
-  subtitle: Sourcing Archaeological Materials by Chemical Composition
-  categories:
-    - compositional data
-  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.
-- title: kairos
-  subtitle: Analysis of Chronological Patterns from Archaeological Count Data
-  categories:
-    - count data
-    - chronological data
-  description: |
-    'kairos' 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
+- package: khroma
+  title: Colour Schemes for Scientific Data Visualization
+  version: 1.12.0
+  description: |-
+    Color schemes ready for each type of data (qualitative,
+    diverging or sequential), with colors that are distinct for all
+    people, including color-blind readers. This package provides an
+    implementation of Paul Tol (2018) and Fabio Crameri (2018)
+    <doi:10.5194/gmd-11-2541-2018> color schemes for use with
+    'graphics' or 'ggplot2'. It provides tools to simulate
+    color-blindness and to test how well the colors of any palette
+    are identifiable. Several scientific thematic schemes (geologic
+    timescale, land cover, FAO soils, etc.) are also implemented.
+  stargazers_count: 193
+  forks: 7
+  open_issues: 1
+- package: tabula
+  title: Analysis and Visualization of Archaeological Count Data
+  version: 3.1.0
+  description: |-
+    An easy way to examine archaeological count data. This
+    package 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.). It allows to
+    easily visualize count data and statistical thresholds: rank vs
+    abundance plots, heatmaps, Ford (1962) and Bertin (1977)
+    diagrams, etc.
+  stargazers_count: 34
+  forks: 5
+  open_issues: 0
+- package: kairos
+  title: |-
+    Analysis of Chronological Patterns from Archaeological Count
+    Data
+  version: 2.1.0
+  description: |-
+    A toolkit for absolute and relative 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
-  categories:
-    - chronological data
-  description: |
-    'aion' 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).
-- title: dimensio
-  subtitle: Multivariate Data Analysis
-  categories:
-    - multivariate data analysis
-  description: |
-    Simple Principal Components Analysis (PCA) and Correspondence Analysis
-    (CA) based on the Singular Value Decomposition (SVD). 'dimensio'
-    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).
-- title: isopleuros
-  subtitle: Ternary Plots
-  categories:
-    - data visualization
-  description: |
-    'isopleuros' 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
-  categories:
-    - 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. 'khroma' 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.
-- title: alkahest
-  subtitle: Pre-Processing XY Data from Experimental Methods
-  categories:
-    - tools
-  description: |
-    'alkahest' is 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: folio
-  subtitle: Datasets for Teaching Archaeology and Paleontology
-  categories:
-    - datasets
-  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.).
+  stargazers_count: 14
+  forks: 1
+  open_issues: 6
+- package: folio
+  title: Datasets for Teaching Archaeology and Paleontology
+  version: 1.4.0
+  description: |-
+    Datasets for teaching quantitative approaches and modeling
+    in archaeology and paleontology. This package 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.).
+  stargazers_count: 11
+  forks: 0
+  open_issues: 1
+- package: dimensio
+  title: Multivariate Data Analysis
+  version: 0.7.0
+  description: |-
+    Simple Principal Components Analysis (PCA) and (Multiple)
+    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,
+    ISBN: 978-0-12-299050-2) and Lebart et al. (2006, ISBN:
+    978-2-10-049616-7).
+  stargazers_count: 10
+  forks: 0
+  open_issues: 1
+- package: aion
+  title: Archaeological Time Series
+  version: 1.0.3
+  description: |-
+    A toolkit for archaeological time series. 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 (virtually) any calendar defined
+    by Reingold and Dershowitz (2018) <doi:10.1017/9781107415058>.
+    This packages offers a simple API that can be used by other
+    specialized packages.
+  stargazers_count: 10
+  forks: 0
+  open_issues: 1
+- package: arkhe
+  title: Tools for Cleaning Rectangular Data
+  version: 1.6.0
+  description: |-
+    A dependency-free collection of simple functions for
+    cleaning rectangular data. This package allows to detect, count
+    and replace values or discard rows/columns using a predicate
+    function. In addition, it provides tools to check conditions
+    and return informative error messages.
+  stargazers_count: 10
+  forks: 0
+  open_issues: 0
+- package: isopleuros
+  title: Ternary Plots
+  version: 1.2.0
+  description: |-
+    Ternary plots made simple. This package allows to create
+    ternary plots 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 which are useful for the archaeologist
+    (e.g. soil texture charts, ceramic phase diagram).
+  stargazers_count: 8
+  forks: 1
+  open_issues: 0
+- package: tesselle
+  title: Easily Install and Load 'tesselle' Packages
+  version: 1.4.0
+  description: |-
+    Easy install and load key packages from the 'tesselle'
+    suite in a single step. The 'tesselle' suite is a collection of
+    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. These packages can be used to
+    explore and analyze common data types in archaeology: count
+    data, compositional data and chronological data. Learn more
+    about 'tesselle' at <https://www.tesselle.org>.
+  stargazers_count: 6
+  forks: 0
+  open_issues: 0
+- package: nexus
+  title: Sourcing Archaeological Materials by Chemical Composition
+  version: 0.2.0
+  description: |-
+    Exploration and analysis of compositional data in the
+    framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This
+    package provides tools for chemical fingerprinting and source
+    tracking of ancient materials.
+  stargazers_count: 4
+  forks: 0
+  open_issues: 2
+- package: alkahest
+  title: Pre-Processing XY Data from Experimental Methods
+  version: 1.1.1
+  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. Baseline
+    correction methods includes polynomial fitting as described in
+    Lieber and Mahadevan-Jansen (2003)
+    <doi:10.1366/000370203322554518>, Rolling Ball algorithm after
+    Kneen and Annegarn (1996) <doi:10.1016/0168-583X(95)00908-6>,
+    SNIP algorithm after Ryan et al. (1988)
+    <doi:10.1016/0168-583X(88)90063-8>, 4S Peak Filling after
+    Liland (2015) <doi:10.1016/j.mex.2015.02.009> and more.
+  stargazers_count: 4
+  forks: 0
+  open_issues: 0
+- package: ananke
+  title: Quantitative Chronology in Archaeology
+  version: 0.0.0.9000
+  description: What the package does (one paragraph).
+  stargazers_count: 0
+  forks: 0
+  open_issues: 0
+- package: kinesis
+  title: '''Shiny'' Applications for the ''tesselle'' Packages'
+  version: 0.0.0.9003
+  description: |-
+    A collection of 'shiny' applications for the 'tesselle'
+    packages.
+  stargazers_count: 0
+  forks: 0
+  open_issues: 1
+