slides.Rmd: add R introduction

session_1/slides.Rmd

 ---
 title: "R#1: Introduction to R and RStudio"
 author: Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)
-date: 6 Jun 2018
+date: 10 Oct 2019
 output:
   beamer_presentation:
     theme: "metropolis"
     slide_level: 3
+    fig_caption: false
+    df_print: tibble
+    highlight: tango
+    latex_engine: xelatex
 ---
 
 The goal of this practical is to familiarize yourself with R and the RStudio
 environment.
 
+The objectives of this session will be to:
+
+- Understand the purpose of each pane in RStudio
+- Do basic computation with R
+- Define variables and assign data to variables
+- Manage a workspace in R
+- Call functions
+- Manage packages
+
+---
+
+\begin{columns}
+  \begin{column}{0.5\textwidth}
+    \includegraphics[width=\textwidth]{img/software_carpentry_logo}
+    {\bf https://software-carpentry.org/}
+  \end{column}
+  \begin{column}{0.5\textwidth}
+    \includegraphics[width=\textwidth]{img/r_for_data_science.png}
+  \end{column}
+\end{columns}
+
 # Some R background
 
-```{r, out.width = "40px",echo=FALSE}
-knitr::include_graphics("img/Rlogo.png")
-```
+\includegraphics[width=40pt]{img/Rlogo.png}
 is a programming language and free software environment for statistical
 computing and graphics supported by the *R Foundation for Statistical Computing*.
 
 ---
 
 
-```{r, out.width = "40px",echo=FALSE}
-knitr::include_graphics("img/Rlogo.png")
-```
+\includegraphics[width=40pt]{img/Rlogo.png}
 
 - created by **Ross Ihaka** and **Robert Gentleman**
-- free and opensource implementation the S programming language
 - initial version released in 1995
-- at the University of Auckland, New Zealand
+- free and open source implementation the S programming language
 - currently developed by the **R Development Core Team**.
 
 ---
 
-```{r, out.width = "100%",echo=FALSE}
-knitr::include_graphics("img/R_terminal.png")
-```
+
+Reasons to use \includegraphics[width=40pt]{img/Rlogo.png}
+
+- it’s free, well-documented, and runs almost everywhere
+- it has a large (and growing) user base among scientists
+- it has a large library of external packages available for performing diverse tasks. 
+
+- 15,068 available packages on https://cran.r-project.org/
+- 3,087available packages on http://www.bioconductor.org
+- 122,720 available repository on https://github.com/
+
+---
+
+\includegraphics[width=\textwidth]{img/R_terminal.png}
 
 # RStudio, the R IDE
 
@@ -45,22 +76,36 @@ application that provides {\bf comprehensive facilities} to computer programmers
 software development
 \end{block}
 
+- free
+- open source
+
 ## An interface
 
-![RStudio](img/RStudio.png)
+\includegraphics[width=\textwidth]{img/RStudio.png}
 
 ## The same console as before
 
-![R console](img/RStudio_console.png)
+\includegraphics[width=\textwidth]{img/RStudio_console.png}
 
 ## A code editor
 
-![R editor](img/RStudio_editor.png)
+\includegraphics[width=\textwidth]{img/RStudio_editor.png}
 
-## Various outpus
+---
+
+RStudio offers you great flexibility in running code from within the editor window. There are buttons, menu choices, and keyboard shortcuts. To run the current line, you can
 
-![R outputs](img/RStudio_outputs.png)
+- click on the Run button above the editor panel, or
+- select “Run Lines” from the “Code” menu, or
+- hit Ctrl+Return in Windows or Linux or ⌘+Return on OS X. To run a block of code, select it and then Run. 
+
+If you have modified a line of code within a block of code you have just run, there is no need to reselect the section and Run, you can use the next button along, Re-run the previous region. This will run the previous code block including the modifications you have made.
 
 ## The environment
 
-![R environment](img/RStudio_environment.png)
+\includegraphics[width=\textwidth]{img/RStudio_environment.png}
+
+## Various outpus
+
+\includegraphics[width=\textwidth]{img/RStudio_outputs.png}
+