{"id":15633,"date":"2020-04-05T21:24:35","date_gmt":"2020-04-05T20:24:35","guid":{"rendered":"https:\/\/www.datanovia.com\/en\/?p=15633"},"modified":"2020-04-05T21:24:35","modified_gmt":"2020-04-05T20:24:35","slug":"publish-reproducible-examples-from-r-to-datanovia-website","status":"publish","type":"post","link":"https:\/\/www.datanovia.com\/en\/blog\/publish-reproducible-examples-from-r-to-datanovia-website\/","title":{"rendered":"Publish Reproducible Examples from R to Datanovia Website"},"content":{"rendered":"<div id=\"rdoc\">\n<p>This article describes how to publish a <strong>reproducible example from R to the datanovia website<\/strong> using the <code>pubr<\/code> package.<\/p>\n<p>The goal of <code>pubr<\/code> R package is to convert reproducible R scripts and Rmd contents into a publishable HTML block. It makes it easy to share reproducible R code in (wordpress) website comments and blog posts.<\/p>\n<p>You will learn many examples for publishing reproducible R scripts.<\/p>\n<p>Contents:<\/p>\n<div id=\"TOC\">\n<ul>\n<li><a href=\"#prerequisites\">Prerequisites<\/a><\/li>\n<li><a href=\"#main-requirements\">Main requirements<\/a><\/li>\n<li><a href=\"#example-1-reproducible-r-script-using-r-built-in-data\">Example 1: Reproducible R script using R built-in data<\/a><\/li>\n<li><a href=\"#example-2-reproducible-r-script-using-data-from-clipboard\">Example 2: Reproducible R script using data from clipboard<\/a><\/li>\n<li><a href=\"#example-3-reproducible-r-script-using-external-data-file\">Example 3: Reproducible R script using external data file<\/a><\/li>\n<li><a href=\"#example-4-render-a-reproducible-rmd\">Example 4: Render a reproducible Rmd<\/a><\/li>\n<\/ul>\n<\/div>\n<div id=\"prerequisites\" class=\"section level2\">\n<h2>Prerequisites<\/h2>\n<p>Install the <code>pubr<\/code> package:<\/p>\n<pre class=\"r\"><code>if(require(devtools)) install.packages(\"devtools\")\r\ndevtools::install_github(\"kassambara\/pubr\")<\/code><\/pre>\n<p>Load the package:<\/p>\n<pre class=\"r\"><code>library(\"pubr\")<\/code><\/pre>\n<p>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: <code>xclip<\/code> or <code>xsel<\/code>. This can be installed using for example <code>apt-get install xclip<\/code> in bash terminal.<\/p>\n<\/div>\n<div id=\"main-requirements\" class=\"section level2\">\n<h2>Main requirements<\/h2>\n<ol style=\"list-style-type: decimal;\">\n<li><strong>Include a demo data<\/strong>, which can be <a href=\"https:\/\/stat.ethz.ch\/R-manual\/R-patched\/library\/datasets\/html\/00Index.html\">built-in data<\/a> or a sample of your own data. Examples of built-in R datasets are: <code>ToothGrowth<\/code>, <code>PlantGrowth<\/code>, <code>mtcars<\/code> and <code>iris<\/code><\/li>\n<li><strong>Include commands on a strict \u201cneed to run\u201d basis<\/strong><\/li>\n<li><strong>Include the so-called \u201csession info\u201d<\/strong>: <code>pubr::render_r(session_info = TRUE)<\/code><\/li>\n<li>Use <a href=\"https:\/\/www.datanovia.com\/en\/blog\/r-coding-style-best-practices\/\">good R coding style<\/a><\/li>\n<\/ol>\n<div class=\"success\">\n<p>Yes, creating a great reproducible example (<code>reprex<\/code>) requires work. You are asking other people to do work too. It\u2019s a partnership.<\/p>\n<p>80% of the time you will solve your own problem in the course of writing an excellent reprex.<\/p>\n<p>The remaining 20% of the time, you will create a reprex that is more likely to elicit the desired behavior in others.<\/p>\n<\/div>\n<\/div>\n<div id=\"example-1-reproducible-r-script-using-r-built-in-data\" class=\"section level2\">\n<h2>Example 1: Reproducible R script using R built-in data<\/h2>\n<ol style=\"list-style-type: decimal;\">\n<li>Write a pure R script in Rstudio<\/li>\n<li>Select and copy the script<\/li>\n<li>Run <code>pubr::render_r()<\/code>. The output of the rendered R script is a HTML block, which is automatically copied into the clipboard.<\/li>\n<li>Paste into a website comment areas or into a blog post<\/li>\n<\/ol>\n<pre class=\"r\"><code># Load required package\r\nsuppressPackageStartupMessages(library(ggpubr))\r\n\r\n# Data preparation\r\ndata(\"ToothGrowth\")\r\ndf &lt;- ToothGrowth\r\ndf$dose &lt;-as.factor(df)\r\n\r\n# Create a boxplot\r\nggboxplot(df, x = \"dose\", y = \"len\")<\/code><\/pre>\n<p><img decoding=\"async\" src=\"https:\/\/www.datanovia.com\/en\/wp-content\/uploads\/dn-tutorials\/r-tutorial\/images\/render-r-script-using-built-in-r-data.gif\" alt=\"Render R script using built-in data\" \/><\/p>\n<\/div>\n<div id=\"example-2-reproducible-r-script-using-data-from-clipboard\" class=\"section level2\">\n<h2>Example 2: Reproducible R script using data from clipboard<\/h2>\n<ol style=\"list-style-type: decimal;\">\n<li>Write a pure R script in Rstudio<\/li>\n<li>Copy the data from an Excel spreadsheet and paste it into R using the function <code>pubr::paste_data()<\/code><\/li>\n<li>Select and copy the script<\/li>\n<li>Run <code>pubr::render_r()<\/code>. The output of the rendered R script is a HTML block, which is automatically copied into the clipboard.<\/li>\n<li>Paste into a website comment area or into a blog post<\/li>\n<\/ol>\n<pre class=\"r\"><code># Data preparation\r\ndf &lt;- pubr::paste_data()\r\n\r\n# Summary statistics\r\nsummary(df)<\/code><\/pre>\n<p><img decoding=\"async\" src=\"https:\/\/www.datanovia.com\/en\/wp-content\/uploads\/dn-tutorials\/r-tutorial\/images\/render-r-script-using-data-from-clipboard.gif\" alt=\"Render R script using data from clipboard\" \/><\/p>\n<\/div>\n<div id=\"example-3-reproducible-r-script-using-external-data-file\" class=\"section level2\">\n<h2>Example 3: Reproducible R script using external data file<\/h2>\n<ol style=\"list-style-type: decimal;\">\n<li>Write a pure R script in Rstudio<\/li>\n<li>Paste your data into R using the function <code>pubr::paste_data(data_file)<\/code><\/li>\n<li>Select and copy the script<\/li>\n<li>Run <code>pubr::render_r()<\/code>. The output of the rendered R script is a HTML block, which is automatically copied into the clipboard.<\/li>\n<li>Paste into a website comment area or into a blog post<\/li>\n<\/ol>\n<pre class=\"r\"><code># Data preparation\r\ndata_file &lt;-system.file(\"demo_data\", \"toothgrowth.txt\", package = \"pubr\")\r\ndf &lt;- pubr::paste_data(data_file)\r\n\r\n# Create a boxplot\r\nsummary(df)<\/code><\/pre>\n<\/div>\n<div id=\"example-4-render-a-reproducible-rmd\" class=\"section level2\">\n<h2>Example 4: Render a reproducible Rmd<\/h2>\n<ol style=\"list-style-type: decimal;\">\n<li>Write an Rmd (without yaml header) from Rstudio<\/li>\n<li>Select and copy the Rmd content<\/li>\n<li>Run <code>pubr::render_rmd()<\/code>. The output of the rendered Rmd content is a HTML block, which is automatically copied into the clipboard.<\/li>\n<li>Paste into a website comment area or into a blog post<\/li>\n<\/ol>\n<p><img decoding=\"async\" src=\"https:\/\/www.datanovia.com\/en\/wp-content\/uploads\/dn-tutorials\/r-tutorial\/images\/render-rmd-contents-web.gif\" alt=\"Render Rmd contents\" \/><\/p>\n<\/div>\n<\/div>\n<p><!--end rdoc--><\/p>\n","protected":false},"excerpt":{"rendered":"<p>This article describes how to publish a reproducible example from R to the datanovia website using the pubr package. The goal of pubr R package is to convert reproducible R [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":15634,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"rating_form_position":"","rating_results_position":"","mr_structured_data_type":"","footnotes":""},"categories":[138],"tags":[],"class_list":["post-15633","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-r-programming"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v25.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Publish Reproducible Examples from R to Datanovia Website - Datanovia<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.datanovia.com\/en\/blog\/publish-reproducible-examples-from-r-to-datanovia-website\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publish Reproducible Examples from R to Datanovia Website - Datanovia\" \/>\n<meta property=\"og:description\" content=\"This article describes how to publish a reproducible example from R to the datanovia website using the pubr package. 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