diff --git a/_header.html b/_header.html index 3b831a33f..9ed878f03 100644 --- a/_header.html +++ b/_header.html @@ -8,7 +8,6 @@ - diff --git a/_quarto.yml b/_quarto.yml index d0695cd0f..ae66a5326 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -10,20 +10,14 @@ 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/ @@ -31,51 +25,14 @@ website: 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: |
The tesselle project is supported by Archéosciences Bordeaux, the CREAP and the TGIR Huma-Num. + format: html: - theme: custom.scss + theme: cosmo + css: style.css include-in-header: _header.html diff --git a/custom.scss b/custom.scss deleted file mode 100644 index 3e5cbd076..000000000 --- a/custom.scss +++ /dev/null @@ -1,70 +0,0 @@ -/*-- scss:defaults --*/ -$theme: "cosmo" !default; - -@import url('https://fonts.googleapis.com/css2?family=Ubuntu:wght@400;600;700&display=swap'); -@import url('https://fonts.googleapis.com/css2?family=Roboto:wght@300;400;700&display=swap'); - -$headings-font-family: "ubuntu", sans-serif; -$font-family-base: "roboto", sans-serif; -$font-family-sans-serif: "roboto", sans-serif; - -/*-- Additional custom styles --*/ -p { - font-family: $font-family-sans-serif; -} - -/* Add any additional CSS rules below */ -.quarto-title-banner { - color: black !important; - background-color: white !important; -} -.quarto-title-banner a { - color: black !important; - text-decoration: underline !important; -} - -/* Forms */ -form { - margin: 1em 0.5em; -} - -/* from https://github.com/r-lib/pkgdown/blob/51268b0d9cb0588d7a6404a2b8ef4ee19c435e89/inst/assets/BS4/pkgdown.css */ -.algolia-autocomplete { - width: 100%; -} -.algolia-autocomplete .aa-hint { - color: #999; -} -.algolia-autocomplete .aa-dropdown-menu { - width: max(100%, 20rem); - background-color: #fff; - border: 1px solid var(--gray); - border-radius: 0.2rem; - margin-top: 2px; - - max-height: 50vh; - overflow-y: auto; -} -.algolia-autocomplete .aa-dropdown-menu .aa-suggestion { - cursor: pointer; - padding: 5px 4px; - border-bottom: 1px #ddd solid; - /* font-size: 0.9rem; */ - color: #5E5E5E; - -} - -.search-details { - /* font-size: 0.9rem; */ - color: #0054AD; - display: inline; - font-weight: bolder; -} -.algolia-autocomplete .aa-dropdown-menu .aa-suggestion.aa-cursor { - background-color: #B2D7FF; -} - -/* Logo */ -.logo-institution { - height: 72px; -} diff --git a/gallery.ejs b/gallery.ejs new file mode 100644 index 000000000..64f32a267 --- /dev/null +++ b/gallery.ejs @@ -0,0 +1,39 @@ + +```{=html} + +<% for (const item of items) { %> + +

<%- item.category %>

+ +

<%- item.description %>

+ +
+ +<% for (const tile of item.tiles) { %> +
> +
+ + <%= tile.title %> + + + + <%= tile.subtitle %> + +
+ + <%- tile.description %> + + + <% if (tile.publicationdate) { %> + <%= tile.publicationdate %> + <% } %> + +
+<% } %> + +
+ +<% } %> + +``` diff --git a/gallery.yml b/gallery.yml new file mode 100644 index 000000000..e971cc694 --- /dev/null +++ b/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.). diff --git a/images/aion.png b/images/aion.png new file mode 100644 index 000000000..4c4919ad8 Binary files /dev/null and b/images/aion.png differ diff --git a/images/alkahest.png b/images/alkahest.png new file mode 100644 index 000000000..946c7e05e Binary files /dev/null and b/images/alkahest.png differ diff --git a/images/arkhe.png b/images/arkhe.png new file mode 100644 index 000000000..efb816c1b Binary files /dev/null and b/images/arkhe.png differ diff --git a/images/dimensio.png b/images/dimensio.png new file mode 100644 index 000000000..a19b3e7a5 Binary files /dev/null and b/images/dimensio.png differ diff --git a/images/folio.png b/images/folio.png new file mode 100644 index 000000000..ec900aa53 Binary files /dev/null and b/images/folio.png differ diff --git a/images/isopleuros.png b/images/isopleuros.png new file mode 100644 index 000000000..21a8fdd1b Binary files /dev/null and b/images/isopleuros.png differ diff --git a/images/kairos.png b/images/kairos.png new file mode 100644 index 000000000..d7be22390 Binary files /dev/null and b/images/kairos.png differ diff --git a/images/khroma.png b/images/khroma.png new file mode 100644 index 000000000..4743a9657 Binary files /dev/null and b/images/khroma.png differ diff --git a/images/nexus.png b/images/nexus.png new file mode 100644 index 000000000..0f77b9e0b Binary files /dev/null and b/images/nexus.png differ diff --git a/images/tabula.png b/images/tabula.png new file mode 100644 index 000000000..b3c3a6c26 Binary files /dev/null and b/images/tabula.png differ diff --git a/index.qmd b/index.qmd index 4999a03dd..1baf9b5f1 100644 --- a/index.qmd +++ b/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$Package) -``` -```{r} -#| label: sitemap -#| echo: false ## Build sitemap index loc <- paste0(url_pkg, "/sitemap.xml") map <- sprintf(" \n %s\n ", loc) @@ -34,17 +29,13 @@ cat( ' ', map, '', - file = "_site/sitemapindex.xml", + file = "sitemapindex.xml", sep = "\n", append = FALSE ) -``` -```{r} -#| label: search -#| echo: false ## Build search index -search_pkg <- search_ref <- list() +search_pkg <- list() for (i in seq_along(url_pkg)) { path <- url_pkg[[i]] tmp <- try( @@ -55,21 +46,22 @@ for (i in seq_along(url_pkg)) { for (j in seq_along(tmp)) { ## Add package name tmp[[j]]$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 +::: + +::: +::: + +::: {#gallery .column-page} +::: diff --git a/sitemap.xml b/sitemap.xml deleted file mode 100644 index 06c5253a2..000000000 --- a/sitemap.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - https://packages.tesselle.org/index.html - - diff --git a/style.css b/style.css new file mode 100644 index 000000000..38397705a --- /dev/null +++ b/style.css @@ -0,0 +1,70 @@ +/* css styles */ + .logo-institution { + height: 72px; + } + +html { + scroll-behavior: smooth; +} + +#hero-banner { +padding-top: 35px; +background-color: rgb(237,243,249); +} + +#quarto-content main { +margin-top: 0; +padding-top: 0; +} + +.headline { + font-size: 1.25em; + font-weight: 300; + padding-bottom: 1em; +} + +.headline p { + margin: 0; + padding-bottom: 0.5rem; +} + +/* Forms */ + form { + margin: 1em 0.5em; + } + +/* from https://github.com/r-lib/pkgdown/blob/51268b0d9cb0588d7a6404a2b8ef4ee19c435e89/inst/assets/BS4/pkgdown.css */ + .algolia-autocomplete { + width: 100%; + } +.algolia-autocomplete .aa-hint { + color: #999; +} +.algolia-autocomplete .aa-dropdown-menu { + width: max(100%, 20rem); + background-color: #fff; + border: 1px solid var(--gray); + border-radius: 0.2rem; + margin-top: 2px; + + max-height: 50vh; + overflow-y: auto; +} +.algolia-autocomplete .aa-dropdown-menu .aa-suggestion { + cursor: pointer; + padding: 5px 4px; + border-bottom: 1px #ddd solid; + /* font-size: 0.9rem; */ + color: #5E5E5E; + +} + +.search-details { + /* font-size: 0.9rem; */ + color: #0054AD; + display: inline; + font-weight: bolder; +} +.algolia-autocomplete .aa-dropdown-menu .aa-suggestion.aa-cursor { + background-color: #B2D7FF; +}