archaeophases

Post-processing MCMC Simulations for Chronological Modelling

https://github.com/archaeostat/archaeophases

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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Found .zenodo.json file
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Found 6 DOI reference(s) in README
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Links to: zenodo.org
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3 of 7 committers (42.9%) from academic institutions
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Low similarity (17.0%) to scientific vocabulary

Keywords

archaeological-science archaeology bayesian-statistics geochronology markov-chain r-package radiocarbon-dates

Last synced: 6 months ago · JSON representation

Repository

Post-processing MCMC Simulations for Chronological Modelling

Basic Info

Host: GitHub
Owner: ArchaeoStat
License: gpl-3.0
Language: R
Default Branch: master
Homepage: https://archaeostat.github.io/ArchaeoPhases/
Size: 57.5 MB

Statistics

Stars: 10
Watchers: 4
Forks: 2
Open Issues: 1
Releases: 2

Topics

archaeological-science archaeology bayesian-statistics geochronology markov-chain r-package radiocarbon-dates

Created over 8 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta Zenodo

README.Rmd

---
output: github_document
bibliography: vignettes/bibliography.bib
nocite: '@*'
---



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  fig.path = "man/figures/README-",
  fig.width = 7,
  out.width = NULL
)
Sys.setenv(LANGUAGE = "en") # Force locale
```

# ArchaeoPhases


[![R-CMD-check](https://github.com/ArchaeoStat/ArchaeoPhases/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ArchaeoStat/ArchaeoPhases/actions/workflows/R-CMD-check.yaml)
[![codecov](https://codecov.io/gh/ArchaeoStat/ArchaeoPhases/graph/badge.svg)](https://app.codecov.io/gh/ArchaeoStat/ArchaeoPhases)
[![Dependencies](https://tinyverse.netlify.app/badge/ArchaeoPhases)](https://cran.r-project.org/package=ArchaeoPhases)

[![r-universe](https://ArchaeoStat.r-universe.dev/badges/ArchaeoPhases)](https://ArchaeoStat.r-universe.dev/ArchaeoPhases){.pkgdown-devel}
[![CRAN Version](https://www.r-pkg.org/badges/version/ArchaeoPhases)](https://cran.r-project.org/package=ArchaeoPhases){.pkgdown-release}
[![CRAN checks](https://badges.cranchecks.info/worst/ArchaeoPhases.svg)](https://cran.r-project.org/web/checks/check_results_ArchaeoPhases.html){.pkgdown-release}
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/ArchaeoPhases)](https://cran.r-project.org/package=ArchaeoPhases){.pkgdown-release}

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8087121.svg)](https://doi.org/10.5281/zenodo.8087121)
[![DOI JSS](https://img.shields.io/badge/JSS-10.18637/jss.v093.c01-brightgreen)](https://doi.org/10.18637/jss.v093.c01)


## Overview

Statistical analysis of archaeological dates and groups of dates. **ArchaeoPhases** allows to post-process Markov Chain Monte Carlo (MCMC) simulations from [ChronoModel](https://chronomodel.com) [@lanos2020], [Oxcal](https://c14.arch.ox.ac.uk/oxcal.html) [@bronkramsey2009] or [BCal](https://bcal.shef.ac.uk) [@buck1999]. This package provides functions for the study of rhythms of the long term from the posterior distribution of a series of dates (tempo and activity plot). It also allows the estimation and visualization of time ranges from the posterior distribution of groups of dates (e.g. duration, transition and hiatus between successive phases).

**ArchaeoPhases v2.0 brings a comprehensive package rewrite, resulting in the renaming of nearly all functions. For more information, please refer to `news(Version >= "2.0", package = "ArchaeoPhases")`.**

```{r citation, echo=FALSE, comment=''}
cite <- utils::citation("ArchaeoPhases")
print(cite, bibtex = FALSE)
```

## Installation

You can install the released version of **ArchaeoPhases** from [CRAN](https://CRAN.R-project.org) with:

```{r cran-installation, eval=FALSE}
install.packages("ArchaeoPhases")
```

And the development version from [GitHub](https://github.com/) with:

```{r gh-installation, eval=FALSE}
# install.packages("remotes")
remotes::install_github("ArchaeoStat/ArchaeoPhases")
```

You can install the 1.x releases from the CRAN archives:

```{r archive-installation, eval=FALSE}
# install.packages("remotes")
remotes::install_version("ArchaeoPhases", version = "1.8")
```

## Usage

**ArchaeoPhases** v2.0 uses [**aion**](https://packages.tesselle.org/aion/) for internal date representation. Look at `vignette("aion", package = "aion")` before you start.

These examples use data available through the [**ArchaeoData**](https://github.com/ArchaeoStat/ArchaeoData) package which is available in a [separate repository](https://archaeostat.r-universe.dev). **ArchaeoData** provides MCMC outputs from ChronoModel, OxCal and BCal.

```{r ArchaeoData, eval=FALSE}
## Install the data package
install.packages("ArchaeoData", repos = "https://archaeostat.r-universe.dev")
```

```{r packages-load, message=FALSE}
## Load
library(ArchaeoPhases)
```

Import a CSV file containing a sample from the posterior distribution:

```{r read-chronomodel}
## Construct the paths to the data
path <- file.path("chronomodel", "ksarakil")
path_event <- system.file(path, "Chain_all_Events.csv", package = "ArchaeoData")
path_phase <- system.file(path, "Chain_all_Phases.csv", package = "ArchaeoData")

## Read events from ChronoModel
(chrono_events <- read_chronomodel_events(path_event))

## Read phases from ChronoModel
(chrono_phases <- read_chronomodel_phases(path_phase))
```

### Analysis of a series of dates

```{r events-plot, fig.width=5, fig.align='default', fig.height=5, out.width='50%', fig.show='hold'}
## Plot the first event
plot(chrono_events[, 1], interval = "hdr")

## Plot all events
plot(chrono_events)
```

```{r tempo-plot, fig.width=5, fig.align='default', fig.height=5, out.width='50%', fig.show='hold'}
## Tempo plot
tp <- tempo(chrono_events, level = 0.95)
plot(tp)

## Activity plot
ac <- activity(chrono_events)
plot(ac)
```

### Analysis of a group of dates (phase)

```{r phases-boundaries}
bound <- boundaries(chrono_phases, level = 0.95)
as.data.frame(bound)
```

```{r phases-plot}
## Plot all phases
plot(chrono_phases)
```

```{r succession-plot}
plot(chrono_phases[, c("UP", "EPI"), ], succession = "hiatus")
plot(chrono_phases[, c("UP", "EPI"), ], succession = "transition")
```

## Translation

This package provides translations of user-facing communications, like messages, warnings and errors, and graphical elements (axis labels). The preferred language is by default taken from the locale. This can be overridden by setting of the environment variable `LANGUAGE` (you only need to do this once per session):

``` r
Sys.setenv(LANGUAGE = "")
```

Languages currently available are English (`en`) and French (`fr`).

## References

Owner

Name: ArchaeoStat
Login: ArchaeoStat
Kind: organization

Repositories: 2
Profile: https://github.com/ArchaeoStat

CodeMeta (codemeta.json)

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GitHub Events

Total

Commit comment event: 2
Release event: 1
Issues event: 1
Watch event: 1
Issue comment event: 8
Push event: 26

Last Year

Commit comment event: 2
Release event: 1
Issues event: 1
Watch event: 1
Issue comment event: 8
Push event: 26

Committers

Last synced: over 2 years ago

All Time

Total Commits: 245
Total Committers: 7
Avg Commits per committer: 35.0
Development Distribution Score (DDS): 0.461

Past Year

Commits: 43
Committers: 1
Avg Commits per committer: 43.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
nfrerebeau	n**u@u**r	132
Thomas S. Dye	t**d@t**e	66
philippe-a	a**e@u**r	34
vibet	v**t@M**l	8
Marie-Anne Vibet	m**t@u**r	3
Thomas S. Dye	t**d@t**m	1
vibet	v**t@m**e	1

Committer Domains (Top 20 + Academic)

univ-nantes.fr: 2 macbook-air-de-vibet-1.home: 1 tsdye.com: 1 tsdye.online: 1 u-bordeaux-montaigne.fr: 1

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Last synced: 6 months ago

All Time

Total issues: 3
Total pull requests: 21
Average time to close issues: 3 days
Average time to close pull requests: 30 days
Total issue authors: 2
Total pull request authors: 3
Average comments per issue: 6.0
Average comments per pull request: 0.1
Merged pull requests: 20
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 8.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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tsdye (2)
rdinapoli (1)

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tsdye (17)
philippe-a (3)
nfrerebeau (1)

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Total packages: 1
Total downloads:
- cran 677 last-month

Total dependent packages: 2
Total dependent repositories: 2
Total versions: 10
Total maintainers: 1

cran.r-project.org: ArchaeoPhases

Post-Processing of Markov Chain Monte Carlo Simulations for Chronological Modelling

Homepage: https://ArchaeoStat.github.io/ArchaeoPhases/
Documentation: http://cran.r-project.org/web/packages/ArchaeoPhases/ArchaeoPhases.pdf
License: GPL (≥ 3)
Latest release: 1.4.5
published over 5 years ago

Versions: 10
Dependent Packages: 2
Dependent Repositories: 2
Downloads: 677 Last month

Rankings

Dependent packages count: 13.7%

Forks count: 17.0%

Stargazers count: 18.3%

Dependent repos count: 19.2%

Average: 19.7%

Downloads: 30.5%

Maintainers (1)

anne.philippe@univ-nantes.fr

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
coda * depends
hdrcde * depends
digest * imports
dplyr * imports
ggalt * imports
ggplot2 * imports
ggraph * imports
gplots * imports
grDevices * imports
graphics * imports
gtools * imports
magrittr * imports
readr * imports
reshape2 * imports
shiny * imports
stats * imports
toOrdinal * imports
utils * imports
ArchaeoPhases.dataset >= 0.1.0 suggests
knitr * suggests
rmarkdown * suggests
testthat >= 2.1.0 suggests

ecosyste.ms

Data

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Indexes

Applications

Experiments

Open Source Science

archaeophases

Science Score: 59.0%

Keywords

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Basic Info

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README.Rmd

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