https://github.com/nononoexe/setariaviridis
πΎ Field-collected data of green foxtail
https://github.com/nononoexe/setariaviridis
data data-science dataset rpackage
Last synced: 4 months ago
JSON representation
πΎ Field-collected data of green foxtail
- Host: GitHub
- URL: https://github.com/nononoexe/setariaviridis
- Owner: NONONOexe
- License: other
- Created: 2021-09-20T13:27:33.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2025-01-30T02:45:04.000Z (over 1 year ago)
- Last Synced: 2026-02-15T07:18:57.080Z (4 months ago)
- Topics: data, data-science, dataset, rpackage
- Language: R
- Homepage: https://nononoexe.github.io/setariaviridis/
- Size: 4.76 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "75%",
warning = FALSE,
message = FALSE,
fig.align = "center"
)
```
# setariaviridis 
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://CRAN.R-project.org/package=setariaviridis)
[](https://github.com/NONONOexe/setariaviridis/actions/workflows/R-CMD-check.yaml)
[](https://cran.r-project.org/package=setariaviridis)
## Overview
*Setaria viridis* (green foxtail, γγ³γΈγ£γ©γ·) is a common weed. This package contains measurements from individual branches of a wild *Setaria viridis* plant collected near the author's home.
The 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.
## Installation
You can install the setariaviridis using the following methods:
### CRAN version
```r
install.packages("setariaviridis")
```
### Development version
#### Using `install.packages()` (R-universe)
```r
# Enable the R-universe
options(repos = c(
nononoexe = "https://nononoexe.r-universe.dev",
cran = "https://cloud.r-project.org"
))
# Install the package
install.packages("setariaviridis")
```
#### Using `pak`
``` r
# install.packages("pak")
pak::pak("NONONOexe/setariaviridis")
```
## About the data
The data in this package comprises measurements of *Setaria viridis* collected by the author around their home in Aichi Prefecture, Japan.
```{r, echo = FALSE}
knitr::include_graphics("man/figures/collect-location.png", dpi = 300)
```
This 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.
```{r, echo = FALSE}
knitr::include_graphics("man/figures/collecting-data.png", dpi = 300)
```
The data can be accessed as follows:
```{r showdata}
library(setariaviridis)
data(package = "setariaviridis")
head(setaria_viridis)
```
If you want to see for more info: `?setaria_viridis`
The 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:
```{r, echo = FALSE}
knitr::include_graphics("man/figures/setariaviridis-part.png", dpi = 300)
```
Data 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:
```{r, echo = FALSE}
knitr::include_graphics("man/figures/setariaviridis-mesurement.png", dpi = 300)
```
## Example
Using setariaviridis, you can visualize like followings:
```{r culm-hist, echo = FALSE}
library(tidyverse)
# Calculate histogram parameters
hist_params <- lst(
data = setaria_viridis$culm_length,
bin_count = nclass.Sturges(data),
boundary = 16,
bin_width = round(diff(range(data)) / bin_count),
x_min = seq(boundary, max(data), by = bin_width),
x_max = x_min + bin_width,
center = (x_min + x_max) / 2,
labels = str_c(x_min, "-", x_max)
)
# Create histogram plot
culm_hist <-
ggplot(setaria_viridis, aes(x = culm_length)) +
# Add histogram layer with specified parameters
geom_histogram(
binwidth = hist_params$bin_width,
boundary = hist_params$boundary,
colour = "white",
fill = "darkolivegreen4"
) +
# Set plot labels
labs(
title = "Culm length distribution",
x = "Culm length (cm)",
y = "Frequency"
) +
# Customize x-axis scale
scale_x_continuous(
breaks = hist_params$center,
labels = hist_params$labels
) +
# Apply theme customizations
theme_bw() +
theme(
plot.title.position = "plot",
panel.grid = element_blank(),
panel.grid.major.y = element_line(
colour = "black",
linewidth = 0.2
),
axis.ticks.x = element_blank(),
axis.text.x = element_text(
angle = 45,
hjust = 1,
colour = "black",
margin = margin(t = 3, b = 3)
)
)
# Display the histogram
culm_hist
```
```{r panicle-size, echo = FALSE}
# Create scatter plot
panicle_size <-
ggplot(setaria_viridis, aes(x = panicle_width, y = panicle_length)) +
geom_point(colour = "darkolivegreen4") +
labs(
title = "Panicle size",
x = "Panicle width (cm)",
y = "Panicle length (cm)"
) +
theme_bw() +
theme(
plot.title.position = "plot",
panel.grid = element_blank(),
panel.grid.major = element_line(
colour = "black",
linewidth = 0.2,
linetype = "dashed"
)
)
panicle_size
```
## Code of conduct
Please note that this project is released with a [Contributor Code of Conduct](https://nononoexe.github.io/setariaviridis/CODE_OF_CONDUCT.html).
By participating in this project you agree to abide by its terms.