1.5 R Commander basics

Main window of `R Commander`, with the plug-ins `RcmdrPlugin.FactoMineR`, `RcmdrPlugin.KMggplot2` and `RcmdrPlugin.Demos` loaded.

Figure 1.2: Main window of R Commander, with the plug-ins RcmdrPlugin.FactoMineR, RcmdrPlugin.KMggplot2 and RcmdrPlugin.Demos loaded.

When you start R Commander you will see a window similar to Figure 1.2. This GUI has the following items:

  1. Drop-down menus. They are pretty self-explanatory. A quick summary:
    • 'File'. Saving options for different files (.R, .Rmd, .txt output and .RData). The latter corresponds to saving the workspace of the session.
    • 'Edit'. Basic edition within the GUI text boxes ('Copy', 'Paste', 'Undo', …).
    • 'Data'. Import, manage and manipulate datasets.
    • 'Statistics'. Perform statistical analyses, such as 'Summaries' and 'Fit models'.
    • 'Graphs'. Compute the available graphs (depending on the kind of variables) for the active dataset.
    • 'Models'. Graphical, numerical and inferential analyses for the active model.
    • 'Distributions'. Operations for continuous/discrete distributions: sampling, computation of probabilities and quantiles, and plotting of density and distribution functions.
    • 'Tools'. Options for R Commander. Here you can 'Load Rcmdr plug-in(s)...', which enables to expand the number of menus available via plug-ins1. R Commander will need to restart prior to loading a plug-in2.
    • 'Help'. Several help resources.
  2. Dataset manipulation. Select the active dataset among the list of loaded datasets. Edit (very basic) and view the active dataset.
  3. Model selector. Select an active model among the available ones to work with.
  4. Switch to script or report mode. Switch between the generated R code and the associated R Markdown code.
  5. Input panel. The R code generated by the drop-down menus appears here and is passed to the output console. You can type code here and run it without using the drop-down menus.
  6. Submit/Generate report buttom. Allows to pass and run selected R code to the output console (keyboard shortcut: 'Control' + 'R').
  7. Output console. Shows the commands that were run (red) and their visible result (blue), if any.
  8. Messages. Displays possible error messages, warnings and notes.

When you close R Commander you will be asked on what files to save: 'script file' and 'R Markdown file' (contents in the two tabs of panel 5, respectively), and 'output file' (panel 7). If you want to save the workspace, you have to do it through the 'File’ menu.

Focus on understanding the purpose of each element in the GUI. When performing the real-case studies we will take care of explaining the many features of R Commander step by step.

  1. The standardization of X1, …, Xn is Z1, …, Zn, with \(Z_i=\frac{X_i-\bar X}{s_x}\), where sx is the standard deviation of X1, …, Xn