A system for statistical analysis. Instructions for installing software. R, R-studio and the R-commander
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1 Instructions for installing software R, R-studio and the R-commander Manchester Institute of Education, University of Manchester This course uses the following software... R, which performs statistical analyses, the R-studio, which provides a sophisticated interface for R, and the Rcmdr, which provides a convenient way for using and learning R. These programmes are used in combination to provide a simple and sophisticated analytical system... It is easy to install the software in the following order install R 2. install the R-studio 3. install the Rcmdr
2 1. Install R R is available for all major operating systems (Linux, MacOS X, Windows) and can be downloaded from CRAN (Comprehensive R Archive Network), which can be accessed from the R home page... Follow this link
3 Choose an appropriate mirror site, select an operating system and then follow the instructions... Select your operating system... Please note... Linux: select your operating system (Ubuntu, Debian, Suse) and then follow the instructions for installation. Mac OS X: In addition to R-x.y.z.pkg you need to also install gfortran (gfortran-x.y.z.pkg) and tcltk (tcltk-x.y.x.pkg). Windows: install the base system. Once R has been installed, install the R-studio...
4 2. Install the R-studio R-studio is available for all major operating systems (Linux, MacOS X, Windows). The programme can be installed directly from the R-studio website. R-studio is very easy to install - just follow the instructions given on the R-studio home page... Running R-studio If you have installed R-studio to a USB drive, change to the directory RStudio\bin and double click rstudio.exe. If you have installed directly to your lap-top, simply click the icon on your desktop. The R-studio should load and automatically load the default version of R that is installed on your computer.
5 R-studio interface load and write R code, show data, use mark-down scripts... import datasets and record history the R console File, plots and package manager; Help system 3. Install the Rcmdr Use the R-studio to install the Rcmdr. The Rcmdr provides a point-and-click interface to R and can be installed from the Packages, Install Packages tab in the lower-right window of the R-studio (you can also use the R-studio menu options Tools, Install Packages...). Simply enter Rcmdr into the packages text window and press Install...
6 Once installed, the Rcmdr is added to the list of packages on your system and can be run by ticking the appropriate box in the R-studio Packages list... Note: clicking on the Rcmdr name will provide access to the help files...
7 The Rcmdr should load, giving the following interface... You now have a fully-integrated analysis system... Using R There are many ways of using R. One of the simplest is use the Rcmdr to select and run your analysis and then use R-notebooks to edit and document these...
8 Using R-notebooks One of the easiest ways of working with R is to use an R-notebook to save, edit and document your analyses. Before you start this example, make sure you have closed all versions of R-studio you currently have running on your computer. Open up an R-notebook in R-studio Start the R-studio and open up an R-notebook using the menu commands... File, New File, R Notebook... This will open a default R Notebook file...
9 A default notebook The default notebook contains useful information about using notebooks and how to run R commands. For example, to run the plot(cars) command on line 11, select the green triangle on the right. The plot will appear below...
10 It is easy to make changes to this graph by simply editing the command. For example, the plotting characters (pch) and colour can be changed... The graph can also be changed to a boxplot...
11 Boxplots also allow changes to be made to the plotting characters (pch) and colour and also allow a main title to be added... It is also easy to add new commands using the insert button. Try inserting the command summary(cars) to get some summary statistics for the cars dataset...
12 Using the Rcmdr This course uses the Rcmdr to run many of the analyses. The following short exercise shows how the Rcmdr can be used in conjunction with the R-notebook to analyse data... Start a new R-notebook and delete the example text (everything from line 6). Give your notebook a title and a description... Load the Rcmdr from the list of packages available in the R-studio (see above on how to do this...).
13 The R console shows the command to load the Rcmdr (for my computer it is library(rcmdr); this command may be different for other computer systems). Copy this command (library(rcmdr)) into your R-notebook. We will use the Rcmdr to load some data. Select the SLID dataset from the cardata package using the Rcmdr menu options Data, Data in packages, Read data set from an attached package...
14 The data file is loaded into memory and the command used to achieve this is shown in the Rcmdr script window... Copy and paste this command into your R-notebook (don t forget to insert an R-chunk)... {r} data(slid, package= cardata ) There are many ways to view your data in R. Two useful methods to view the dataset SLID are to use tail(slid) which shows the last few lines of the dataset, or View(SLID) which opens up the dataset in a spreadsheet. Both of these commands can be entered in to your R-notebook...
15 Any analysis run in the Rcmdr can be copied to the R-notebook. For example, a histogram of wages can be plotted using the Rcmdr... copying the code for the histogram allows you to plot the graph in your R-notebook...
16 and edit the graph, if desired... Saving, viewing and printing documents
17 Your R-notebook can be viewed using the Preview tab and can also be saved to an html, pdf or Word document using the knit function, which runs all R-commands in your notebook and outputs to the desired format... There is a lot you can do with R-markdown. Look at the R-studio help menu for the cheatsheets (Help, Cheatsheets) and the markdown quick reference (Help, Markdown Quick Reference). Your R-notebook file is saved as a *.Rmd file and can be opened using the R-studio File, Open File... menu. A copy of all the analyses used in this presentation is available in an R-command file from... (simply copy and paste the text into a new R-notebook).
18 Exercise Using the SLID data and the Rcmdr, draw a scatterplot Matrix of age, education and wages plotted by Sex. Copy and paste this command into an R-notebook. Produce the graph from within the notebook. Look at the help pages for scatterplotmatrix in the R-studio and see what options are available for editing the graphic. You might like to experiment with changing the colours... col=c(2,4) or col=c(3,6) the plotting characters... pch=7 or pch=19 the size of the legend... cex=2 or cex=0.6 the size of the axis text... cex.axis=2 or cex.axis=0.6 or what appears on the diagonal panels... diagonal= histogram or diagonal= boxplot Dont forget to save your notebook so that you can revisit this analysis at a later date!
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