update tests, doc, description

DESCRIPTION

@@ -1,15 +1,17 @@
 Package: archeofrag
 Type: Package
-Title: Refitting and Spatial Analysis in Archaeology
-Version: 0.9.3
-Date: 2024-12-08
+Title: Spatial Analysis in Archaeology from Refitting Fragments
+Version: 1.0.0
+Date: 2024-12-12
 Authors@R: person("Sebastien", "Plutniak", email = "sebastien.plutniak@posteo.net", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6674-3806"))
 Author: Sebastien Plutniak [aut, cre] (<https://orcid.org/0000-0002-6674-3806>)
 Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
 Description: Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. Empirical datasets are provided as examples. Documentation about 'archeofrag' is provided by the vignette included in this package, by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by a companion GUI application available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/>.
 License: GPL-3
 Repository: CRAN
 Encoding: UTF-8
+LazyData: true
+Depends:   R (>= 3.5.0)
 Imports:
 	igraph,
     graphics,

NEWS.md

@@ -10,9 +10,8 @@ Fourth major release.
 * Values returned by `frag.layers.admixture()` and `frag.layers.cohesion()` are now rounded to four digits (to avoid negative admixture values).
 * Fix the sorting of the the pairs of layers returned by `frag.layers.admixture()` to correspond to the same order returned by `frag.layers.cohesion()`.
 * Revising and optimising `frag.edges.weighting()`.
-* Add verbose parameter to `frag.edges.weighting()` and `frag.get.layers.pair()`, frag.layers.admixture(), frag.layers.cohesion().
-* TODO : link the R Shiny application.
-* TODO : add a function (or parameter in `frag.layers.admixture()`) to handle similarity relationships, return result as a distance object
+* Add verbose parameter to `frag.edges.weighting()`, `frag.get.layers.pair()`, `frag.get.parameters()`, `frag.layers.admixture()`, `frag.layers.cohesion()`.
+* Add dependency to R (>= 3.5.0) to use serialized datasets 
 
 # archeofrag 0.8.3
 Released: 2022-11-16

README.Rmd

@@ -25,14 +25,14 @@ An R package for refitting and spatial analysis in archeology.
 [![R build status](https://github.com/sebastien-plutniak/archeofrag/workflows/R-CMD-check/badge.svg)](https://github.com/sebastien-plutniak/archeofrag/actions)
 [![codecov](https://codecov.io/gh/sebastien-plutniak/archeofrag/branch/master/graph/badge.svg)](https://app.codecov.io/gh/sebastien-plutniak/archeofrag)
 [![CRAN Version](http://www.r-pkg.org/badges/version/archeofrag)](https://cran.r-project.org/package=archeofrag)
-[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/archeofrag)](https://cran.r-project.org/package=archeofrag)
+[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/grand-total/archeofrag?color=brightgreen&.svg)](https://cran.r-project.org/package=archeofrag)
 [![r-universe](https://sebastien-plutniak.r-universe.dev/badges/archeofrag)](https://sebastien-plutniak.r-universe.dev/ui#package:archeofrag)
+[![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/cran/archeofrag/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/cran/archeofrag)
 [![license](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.r-project.org/Licenses/GPL-3)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4271900.svg)](https://doi.org/10.5281/zenodo.4271900)
 [![status](https://joss.theoj.org/papers/ff2007d87bd4c8460b265c69dc403316/status.svg)](https://joss.theoj.org/papers/ff2007d87bd4c8460b265c69dc403316)
 
 
-
 - [**References**](#references)
 - [**Installation**](#installation)
 - [**Community guidelines**](#community-guidelines)
@@ -70,8 +70,8 @@ install.packages("archeofrag")
 The development version is available on GitHub and can be installed with:
 
 ```r
-# install.packages("devtools")
-devtools::install_github("sebastien-plutniak/archeofrag")
+# install.packages("remotes")
+remotes::install_github("sebastien-plutniak/archeofrag")
 ```
 
 Some optional functionalities of *Archeofrag* requires the *RBGL* package available through *Bioconductor*:
@@ -110,8 +110,7 @@ The `make_cr_graph` function takes a frag object and generates an `igraph` graph
 
 ```{r make-empirical-graph,  message=F}
 library(archeofrag)
-data(LiangAbu)
-abu.frag <- make_frag_object(cr=df.cr, fragments=fragments.info)
+abu.frag <- make_frag_object(cr=liangabu.connection, fragments=liangabu.fragments)
 abu.g <- make_cr_graph(abu.frag)
 ```
 
@@ -386,7 +385,7 @@ The `make_sr_graph` function takes a “frag” object and  generates an `igraph
 
 ```{r make-similarity}
 # make a frag object and generate a similarity graph:
-abu.frag <- make_frag_object(sr=df.sr, fragments=fragments.info)
+abu.frag <- make_frag_object(sr=liangabu.similarity, fragments=liangabu.fragments)
 abu.sr <- make_sr_graph(abu.frag)
 ```