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{"name":"Reproducible-r","tagline":"Course - Introduction to R and reproducible research in R","body":"# Reproducible Research in R \r\n\r\n[](https://gitter.im/mrccsc/Reproducible-R?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)\r\n\r\n##The Course\r\n\r\nThis course introduces R and statistical programming as well as best practices for reproducible research using R's dynamic reporting and version capture tools.\r\n\r\nThe course consists of 3 sections, 2 on basic R and 1 on reproducibility in R. \r\nEach section is presented as both HTMl and Rpres markdown ( to allow for intergration of the presentation in the RStudion enviroment itself). Exercises and answer sheets are included after all subsections to practice techniques and provide future reference examples. \r\n\r\nCourse material and exercises are available to view as rendered HTML at http://mrccsc.github.io/reproducibleR. \r\nAll material is available to download under GPL v2 license.\r\n\r\nFor information on other courses run by our team see our [github IO page](http://mrccsc.github.io/training/).\r\n\r\n\r\n## The Team\r\nThis course was created and conducted by the MRC Clinical Sciences Centre Bioinformatics Team at Imperial College London, Hammersmith Hospital. \r\nFor more information on the team see our [github IO page](http://mrccsc.github.io/).\r\n\r\n\r\nThis course is free for MRC CSC and Imperial staff and students. If you would like to attend a future course contact [email protected].\r\n\r\n## Setting up.\r\n\r\n\r\n#### Install R.\r\n\r\nR can be installed from the R-project website. \r\nR 3.1.0 or higher is required for this course.\r\n\r\nhttp://www.r-project.org/\r\n\r\n#### Install RStudio.\r\n\r\nRStudio can be installed from the R-project website. \r\n\r\nhttp://www.rstudio.com/\r\n\r\n#### Install required packages.\r\n\r\nHaving downloaded R and RStudio, some additional packages are required (rmarkdown and ggplot2). \r\nTo install these,\r\n* First launch RStudio\r\n* Install the packages in the R console\r\n<pre>\r\ninstall.packages(\"ggplot2\",dependencies=TRUE)\r\ninstall.packages(\"rmarkdown\",dependencies=TRUE)\r\n</pre>\r\n\r\n#### Download the material\r\nThe material can either be downloaded as a [zip](https://github.com/ThomasCarroll/Reproducible-R/archive/master.zip)\r\n<pre>\r\nwget https://github.com/ThomasCarroll/Reproducible-R/archive/master.zip ./\r\n</pre>\r\nor checked out from our Github repository\r\nhttps://github.com/ThomasCarroll/Reproducible-R/\r\n\r\n\r\n<h2>\r\n<a id=\"the-r-sessions\" class=\"anchor\" href=\"#the-r-sessions\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"></span></a>The R Sessions</h2>\r\n\r\n<h4>\r\n<a id=\"Session1\" class=\"anchor\" href=\"#session1\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"></span></a>Introduction to R, Session 1</h4>\r\n\r\n<p>This section focuses on R basics such as simple data types, data IO, plotting and statistics.<br>\r\nSession sections:\r\n <ul>\r\n <li>Introduction to R</li>\r\n <li>Data Types</li>\r\n <li>Reading and Writing Data</li>\r\n <li>Plotting</li>\r\n <li>Statistics</li>\r\n </ul>\r\nLink to HTML presentation - <a href=\"http://mrccsc.github.io/r_course/introToR_Session1.html\">Session 1</a><br>\r\nLink to printable PDF - <br>\r\nLink to single page, printable HTML - <br>\r\n\r\n</p>\r\n\r\n\r\n<iframe src=\"http://mrccsc.github.io/r_course/introToR_Session1.html\" width=\"100%\" height=\"400\"></iframe>\r\n</span>\r\n<h4>\r\n<a id=\"Session2\" class=\"anchor\" href=\"#session2\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"></span></a>Introduction to R, Session 2</h4>\r\n\r\n<p>In session 2, programmatic techniques such as looping and use defined functions are introduced<br>\r\nThe session includes longer exercises and shorter slide decks and so more time should be allocated to exercises in this session.<br>\r\nSession sections:\r\n <ul>\r\n <li>Looping Conditional Branching</li>\r\n <li>Data Types</li>\r\n <li>Loading libraries</li>\r\n <li>Writing Scripts</li>\r\n <li>Getting</li>\r\n </ul>\r\nLink to HTML presentation - <a href=\"http://mrccsc.github.io/r_course/introToR_Session2.html\">Session 2</a><br>\r\nLink to printable PDF - <br>\r\nLink to single page, printable HTML - <br>\r\n \r\n</p>\r\n<iframe src=\"http://mrccsc.github.io/r_course/introToR_Session2.html\" width=\"100%\" height=\"400\"></iframe>\r\n</span>\r\n\r\n<h4>\r\n<a id=\"reproducible-r\" class=\"anchor\" href=\"#reproducible-r\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"></span></a>Introduction to R, Session 2</h4>\r\n\r\n<p>In the Reproducible R session, the use of dynamic documents is introduced with topics such as Markdown syntax, YAML headers and rmarkdown/knitr documen rendering functions<br>\r\nSession sections:\r\n <ul>\r\n <li>Creating reports from R scripts</li>\r\n <li>Markdown Syntax</li>\r\n <li>Markdown in R</li>\r\n </ul>\r\nLink to HTML presentation - <a href=\"http://mrccsc.github.io/r_course/reproducibleR.html\">Reproducible R</a><br>\r\nLink to printable PDF - <br>\r\nLink to single page, printable HTML - <br>\r\n","google":"","note":"Don't delete this file! It's used internally to help with page regeneration."}