diff --git a/session_1/HTML_tuto.Rmd b/session_1/HTML_tuto.Rmd
index 37409a574e2e2ea1c20d27e44da859da3124427d..e93b6dc426fd02beddd1c058b0eb4ebce405d3b3 100644
--- a/session_1/HTML_tuto.Rmd
+++ b/session_1/HTML_tuto.Rmd
@@ -50,36 +50,34 @@ The objectives of this session will be to:
### Acknowledgments
<div id='pencadre'>
- <img src="./img/software_carpentry_logo.svg" alt="" width="300"/>
+
+ {width=300px}
+
https://software-carpentry.org/
</div>
<div id='pencadre'>
- <img src="./img/r_for_data_science.png" alt="" width="100"/>
-
+ {width=100px}
+
http://swcarpentry.github.io/r-novice-gapminder/
</div>
+
# Some R background
-\includegraphics[width=40pt]{img/Rlogo.png}
+{width=40px}
is a programming language and free software environment for statistical
computing and graphics supported by the *R Foundation for Statistical Computing*.
-# Some R background
-
-\includegraphics[width=40pt]{img/Rlogo.png}
-
- Created by **Ross Ihaka** and **Robert Gentleman**
- initial version released in 1995
- free and open-source implementation the S programming language
- currently developed by the **R Development Core Team**.
-# Some R background
-Reasons to use \includegraphics[width=40pt]{img/Rlogo.png}
+Reasons to use it:
- It’s free, well documented, and runs almost everywhere
- it has a large (and growing) user base among scientists
@@ -89,27 +87,25 @@ Reasons to use \includegraphics[width=40pt]{img/Rlogo.png}
- **3,087** available packages on http://www.bioconductor.org
- **122,720** available repository on https://github.com/
-# Some R background
+
-\includegraphics[width=\textwidth]{img/R_terminal.png}
-# RStudio, the R IDE
+# RStudio, the R Integrated development environment (IDE)
-\begin{block}{IDR: Integrated development environment}
-application that provides {\bf comprehensive facilities} to computer programmers for
+IDR application that provides **comprehensive facilities** to computer programmers for
software development
-\end{block}
+
- free
- open source
-## An interface
+### An interface
-\includegraphics[width=\textwidth]{img/RStudio.png}
+
-## The same console as before
+### The same console as before
-\includegraphics[width=\textwidth]{img/RStudio_console.png}
+
# R as a calculator
@@ -120,34 +116,57 @@ software development
- Exponents: `^` or `**`
- Parentheses: `(`, `)`
-# R as a calculator
+<div id='pencadre'>
+**Write the commands in the grey box in the terminal.**
-```R
+**The expected results will always be printed in a white box here.**
+
+**You can "copy-paste" but I advise you to practice writing directly in the terminal. To validate the line at the end of your command: press 'Enter'.**
+</div>
+
+
+### First commands
+
+```{r calculatorstep1, include=TRUE}
1 + 100
-1 +
```
-\pause
+ \
+```R
+1 +
+```
+The console displays '+'.
+It is waiting for the next command. Write juste '100' :
```R
+100
+```
+```{r calculatorstep2, echo=FALSE}
+1 + 100
+```
+
+
+### R keeps to the mathematical order
+```{r calculatorstep3, include=TRUE}
3 + 5 * 2
```
-```R
+```{r calculatorstep4, include=TRUE}
(3 + 5) * 2
```
-\pause
+ \
-```R
+```{r calculatorstep5, include=TRUE}
(3 + (5 * (2 ^ 2))) # hard to read
3 + 5 * 2 ^ 2 # clear, if you remember the rules
3 + 5 * (2 ^ 2) # if you forget some rules, this might help
```
+ \
+ **Note :** The text following a '#' is a comment. It will not be interpreted by R. In the future, I advise you to use comments a lot to explain in your own words what the command means.
-\pause
-
-```R
+### Scientific notation
+```{r calculatorstep6, include=TRUE}
2/10000
```
@@ -155,70 +174,73 @@ software development
`2e-4` is shorthand for `2 * 10^(-4)`
-```R
+```{r calculatorstep7, include=TRUE}
5e3
```
-## Mathematical functions
+### Mathematical functions
-```R
+```{r calculatorstep8, include=TRUE}
log(1) # natural logarithm
```
-\pause
-
-```R
+```{r calculatorstep9, include=TRUE}
log10(10) # base-10 logarithm
```
-\pause
-
-```R
+```{r calculatorstep10, include=TRUE}
exp(0.5)
```
-\pause
+\
-Compute the factorial of `9`
+Compute the factorial of `9` (9!)
-\pause
+```{r calculatorstep11, include=TRUE}
+9 * 8 * 7 * 6 * 5 * 4 * 3 * 2 * 1
+```
-```R
+ \
+**or**
+```{r calculatorstep12, include=TRUE}
factorial(9)
```
-## Comparing things
+### Comparing things
+
+Comparisons can be made with R. The result will return a TRUE or FALSE value.
+
equality (note two equal signs read as "is equal to")
-```R
+```{r calculatorstep13, include=TRUE}
1 == 1
```
-\pause
+
inequality (read as "is not equal to")
-```R
+```{r calculatorstep14, include=TRUE}
1 != 2
```
-\pause
+
less than
-```R
+```{r calculatorstep15, include=TRUE}
1 < 2
```
-\pause
+
less than or equal to
-```R
+```{r calculatorstep16, include=TRUE}
1 <= 1
```
-\pause
+
greater than
-```R
+```{r calculatorstep17, include=TRUE}
1 > 0
```
-## Variables and assignment
+# Variables and assignment
`<-` is the assignment operator in R. (read as left member take right member value)
@@ -234,7 +256,7 @@ x
\includegraphics[width=\textwidth]{img/RStudio_environment.png}
-## Variables and assignment
+### Variables and assignment
```R
log(x)