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Open Source Science

https://github.com/4ment/skyplotr

https://github.com/4ment/skyplotr

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.1%) to scientific vocabulary

Keywords

beast coalescent ggplot2 mcmc visualization
Last synced: 5 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: 4ment
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 715 KB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
beast coalescent ggplot2 mcmc visualization
Created almost 2 years ago · Last pushed 12 months ago
Metadata Files
Readme License

README.md

skyplotr

License: GPL v3

Overview

skyplotr is an R package providing functions for plotting the population size trajectory across time. The plots created by skyplotr are ggplot objects, which means that after a plot is created it can be further customized using various functions from the ggplot2 package.

Installation

  • Install the latest development version from GitHub (requires devtools package):

r devtools::install_github("4ment/skyplotr")

Example

HCV.tsv contains 1000 MCMC samples obtained from BEAST. This analysis involves a nucleotide alignment of Hepatitis C Virus (HCV), utilizing the piecewise-constant coalescent model (aka skygrid). This model comprises 75 epochs with a cutoff set at 400.

```r library(dplyr) library(ggplot2) library(skyplotr)

samples <- read.csv("data-raw/HCV-skygrid.tsv", sep = "\t")

rootheight <- samples$treeModel.rootHeight logpopsize <- select(samples, startswith("skygrid.logPopSize")) cutoff <- samples$skygrid.cutOff[1] skygrid <- prepareskygrid(rootheight, logpopsize, cutoff, ageofyoungest=1994) skygrid <- mutate(skygrid, across(allof(c("trajectory", "trajectorylow", "trajectory_high")), exp))

plot_title <- ggtitle("Population size trajectory", "with median and 95% intervals")

skyplot(skygrid, fill="darkcyan") + plot_title + ylab("Effective population size") ```

HCV-skygrid

Owner

  • Name: Mathieu Fourment
  • Login: 4ment
  • Kind: user
  • Location: Australia
  • Company: University of Technology Sydney

GitHub Events

Total
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 1
  • Push event: 1
Last Year
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 1
  • Push event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 4
  • Total Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
4ment m****t@g****m 4

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: about 6 hours
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: about 6 hours
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • Dx-wmc (1)
Pull Request Authors
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bug (1)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • ggplot2 * imports
  • rlang * imports
  • scales * imports
  • knitr * suggests
  • rmarkdown * suggests