{"id":32206390,"url":"https://github.com/nononoexe/setariaviridis","last_synced_at":"2026-02-27T03:02:22.484Z","repository":{"id":161909019,"uuid":"408453920","full_name":"NONONOexe/setariaviridis","owner":"NONONOexe","description":"🌾 Field-collected data of green foxtail","archived":false,"fork":false,"pushed_at":"2025-01-30T02:45:04.000Z","size":4993,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-02-15T07:18:57.080Z","etag":null,"topics":["data","data-science","dataset","rpackage"],"latest_commit_sha":null,"homepage":"https://nononoexe.github.io/setariaviridis/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NONONOexe.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-09-20T13:27:33.000Z","updated_at":"2026-02-05T00:51:56.000Z","dependencies_parsed_at":null,"dependency_job_id":"fa19335f-caba-429e-ac0c-a5f8de312cf5","html_url":"https://github.com/NONONOexe/setariaviridis","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/NONONOexe/setariaviridis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NONONOexe%2Fsetariaviridis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NONONOexe%2Fsetariaviridis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NONONOexe%2Fsetariaviridis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NONONOexe%2Fsetariaviridis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NONONOexe","download_url":"https://codeload.github.com/NONONOexe/setariaviridis/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NONONOexe%2Fsetariaviridis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29883111,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-26T23:51:21.483Z","status":"online","status_checked_at":"2026-02-27T02:00:06.759Z","response_time":57,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["data","data-science","dataset","rpackage"],"created_at":"2025-10-22T05:24:04.225Z","updated_at":"2026-02-27T03:02:22.478Z","avatar_url":"https://github.com/NONONOexe.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"75%\",\n  warning = FALSE,\n  message = FALSE,\n  fig.align = \"center\"\n)\n```\n\n# setariaviridis \u003ca href=\"https://nononoexe.github.io/setariaviridis/\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"138\" alt=\"setariaviridis website\" /\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![CRAN status](https://www.r-pkg.org/badges/version/setariaviridis)](https://CRAN.R-project.org/package=setariaviridis)\n[![R-CMD-check](https://github.com/NONONOexe/setariaviridis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/NONONOexe/setariaviridis/actions/workflows/R-CMD-check.yaml)\n[![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/setariaviridis)](https://cran.r-project.org/package=setariaviridis)\n\u003c!-- badges: end --\u003e\n\n## Overview\n\n*Setaria viridis* (green foxtail, ネコジャラシ) is a common weed. This package contains measurements from individual branches of a wild *Setaria viridis* plant collected near the author's home.\n\nThe dataset is intended for practicing basic data analysis techniques. It's ideal for learning how to calculate basic descriptive statics, create visualizations such as histograms and scatter plots, and gain experience with data manipulation and exploration using R. Its relatively small size and straightforward structure make this dataset easy to work with for beginners in data analysis.\n\n## Installation\n\nYou can install the setariaviridis using the following methods:\n\n### CRAN version\n\n```r\ninstall.packages(\"setariaviridis\")\n```\n\n### Development version\n\n#### Using `install.packages()` (R-universe)\n\n```r\n# Enable the R-universe\noptions(repos = c(\n  nononoexe = \"https://nononoexe.r-universe.dev\",\n  cran = \"https://cloud.r-project.org\"\n))\n\n# Install the package\ninstall.packages(\"setariaviridis\")\n```\n\n#### Using `pak`\n\n``` r\n# install.packages(\"pak\")\npak::pak(\"NONONOexe/setariaviridis\")\n```\n\n## About the data\n\nThe data in this package comprises measurements of *Setaria viridis* collected by the author around their home in Aichi Prefecture, Japan.\n\n```{r, echo = FALSE}\nknitr::include_graphics(\"man/figures/collect-location.png\", dpi = 300)\n```\n\nThis data was obtained in August 2021 by hand-harvesting Setaria viridis plants, root and all, from a dense population. Measurements of each plant part were taken manually using a tape measure and a ruler.\n\n```{r, echo = FALSE}\nknitr::include_graphics(\"man/figures/collecting-data.png\", dpi = 300)\n```\n\nThe data can be accessed as follows:\n\n```{r showdata}\nlibrary(setariaviridis)\ndata(package = \"setariaviridis\")\nhead(setaria_viridis)\n```\n\nIf you want to see for more info: `?setaria_viridis`\n\nThe data contains of 54 branches across 10 *Setaria viridis* plants. *Setaria viridis* consists of 4 parts: panicle, leaf, culm, and root, as illustrated in the figure below:\n\n```{r, echo = FALSE}\nknitr::include_graphics(\"man/figures/setariaviridis-part.png\", dpi = 300)\n```\n\nData sharing the same roots can be identified by the `root_number`. For all other measurement items, please refer to the following figure to understand which parts were measured:\n\n```{r, echo = FALSE}\nknitr::include_graphics(\"man/figures/setariaviridis-mesurement.png\", dpi = 300)\n```\n\n## Example\n\nUsing setariaviridis, you can visualize like followings:\n\n```{r culm-hist, echo = FALSE}\nlibrary(tidyverse)\n\n# Calculate histogram parameters\nhist_params \u003c- lst(\n  data      = setaria_viridis$culm_length,\n  bin_count = nclass.Sturges(data),\n  boundary  = 16,\n  bin_width = round(diff(range(data)) / bin_count),\n  x_min     = seq(boundary, max(data), by = bin_width),\n  x_max     = x_min + bin_width,\n  center    = (x_min + x_max) / 2,\n  labels    = str_c(x_min, \"-\", x_max)\n)\n\n# Create histogram plot\nculm_hist \u003c-\n  ggplot(setaria_viridis, aes(x = culm_length)) +\n  # Add histogram layer with specified parameters\n  geom_histogram(\n    binwidth = hist_params$bin_width,\n    boundary = hist_params$boundary,\n    colour   = \"white\",\n    fill     = \"darkolivegreen4\"\n  ) +\n  # Set plot labels\n  labs(\n    title = \"Culm length distribution\",\n    x     = \"Culm length (cm)\",\n    y     = \"Frequency\"\n  ) +\n  # Customize x-axis scale\n  scale_x_continuous(\n    breaks = hist_params$center,\n    labels = hist_params$labels\n  ) +\n  # Apply theme customizations\n  theme_bw() +\n  theme(\n    plot.title.position = \"plot\",\n    panel.grid          = element_blank(),\n    panel.grid.major.y  = element_line(\n      colour    = \"black\",\n      linewidth = 0.2\n    ),\n    axis.ticks.x        = element_blank(),\n    axis.text.x         = element_text(\n      angle  = 45,\n      hjust  = 1,\n      colour = \"black\",\n      margin = margin(t = 3, b = 3)\n    )\n  )\n\n# Display the histogram\nculm_hist\n```\n\n```{r panicle-size, echo = FALSE}\n# Create scatter plot\npanicle_size \u003c-\n  ggplot(setaria_viridis, aes(x = panicle_width, y = panicle_length)) +\n  geom_point(colour = \"darkolivegreen4\") +\n  labs(\n    title = \"Panicle size\",\n    x     = \"Panicle width (cm)\",\n    y     = \"Panicle length (cm)\"\n  ) +\n  theme_bw() +\n  theme(\n    plot.title.position = \"plot\",\n    panel.grid          = element_blank(),\n    panel.grid.major    = element_line(\n      colour    = \"black\",\n      linewidth = 0.2,\n      linetype  = \"dashed\"\n    )\n  )\n\npanicle_size\n```\n\n## Code of conduct\n\nPlease note that this project is released with a [Contributor Code of Conduct](https://nononoexe.github.io/setariaviridis/CODE_OF_CONDUCT.html).\nBy participating in this project you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnononoexe%2Fsetariaviridis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnononoexe%2Fsetariaviridis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnononoexe%2Fsetariaviridis/lists"}