Publish Reproducible Examples from R to Datanovia Website

Prerequisites

Install the pubr package:

if(require(devtools)) install.packages("devtools")
devtools::install_github("kassambara/pubr")

Load the package:

library("pubr")

Note that, if you are using Rstudio on linux, make sure you have installed the following system dependencies that make it easy to interact with clipboard: xclip or xsel. This can be installed using for example apt-get install xclip in bash terminal.

Main requirements

1. Include a demo data, which can be built-in data or a sample of your own data. Examples of built-in R datasets are: ToothGrowth, PlantGrowth, mtcars and iris
2. Include commands on a strict “need to run” basis
3. Include the so-called “session info”: pubr::render_r(session_info = TRUE)
4. Use good R coding style

Example 1: Reproducible R script using R built-in data

1. Write a pure R script in Rstudio
2. Select and copy the script
3. Run pubr::render_r(). The output of the rendered R script is a HTML block, which is automatically copied into the clipboard.
4. Paste into a website comment areas or into a blog post

# Load required package
suppressPackageStartupMessages(library(ggpubr))

# Data preparation
data("ToothGrowth")
df <- ToothGrowth
df$dose <-as.factor(df)

# Create a boxplot
ggboxplot(df, x = "dose", y = "len")

Example 2: Reproducible R script using data from clipboard

1. Write a pure R script in Rstudio
2. Copy the data from an Excel spreadsheet and paste it into R using the function pubr::paste_data()
3. Select and copy the script
4. Run pubr::render_r(). The output of the rendered R script is a HTML block, which is automatically copied into the clipboard.
5. Paste into a website comment area or into a blog post

# Data preparation
df <- pubr::paste_data()

# Summary statistics
summary(df)

Example 3: Reproducible R script using external data file

1. Write a pure R script in Rstudio
2. Paste your data into R using the function pubr::paste_data(data_file)
3. Select and copy the script
4. Run pubr::render_r(). The output of the rendered R script is a HTML block, which is automatically copied into the clipboard.
5. Paste into a website comment area or into a blog post

# Data preparation
data_file <-system.file("demo_data", "toothgrowth.txt", package = "pubr")
df <- pubr::paste_data(data_file)

# Create a boxplot
summary(df)

Example 4: Render a reproducible Rmd

1. Write an Rmd (without yaml header) from Rstudio
2. Select and copy the Rmd content
3. Run pubr::render_rmd(). The output of the rendered Rmd content is a HTML block, which is automatically copied into the clipboard.
4. Paste into a website comment area or into a blog post