details /tableflip

my_first_notebook.Rmd

@@ -32,15 +32,15 @@ If git is installed, R studio will download (aka 'pull') the code from the gitla
 
 R is a powerful software for statistical analysis. It allows for simple table manipulations, and graph plots. In addition to the basic software, it also comes with several dedicated packages which enhances specific aspects, such as plotting with ggplot2 (grammar of graphic), or linear mixed models with lme4. 
 
-Modern installments of R, through the graphical user interface R studio allow to keep R notebooks which combine text (and simple formatting rules => markdown), with traditional codes. This is was we are using now. This section is part of the text. Code examples will follow below. Interestingly, R notebook can integrate code from multiple languages into one notebook (one notebook to rule them all). For instance, it can run `bash` code, `python`, and of course, `r`. 
+Modern installments of R, through the graphical user interface R studio allow to keep R notebooks which combine text (and simple formatting rules => [markdown](https://en.wikipedia.org/wiki/Markdown)), with traditional codes. This is what we are using now. This section is part of the text. Code examples will follow below. Interestingly, R notebook can integrate code from multiple languages into one notebook (one notebook to rule them all). For instance, it can run `bash` code, `python`, and of course, `r`. 
 
-In this exercise, we will see how a R notebook is kept, how to do basic text formatting, how to integrate `r` code into the document, and how to output this into a document that can be shared (e.g. html or pdf). Finally we will see how Rstudio integrates `git` for version control, project management, and collaborative work. 
+In this exercise, we will see how a R notebook is kept, how to do basic text formatting, how to integrate `r` code into the document, and how to output this into a document that can be shared (e.g. html, pdf, md). Finally we will see how Rstudio integrates `git` for version control, project management, and collaborative work. 
 
 
 ### Lab journal introduction
 The idea being a lab journal is to keep track of protocols, analysis, results, and to provide a short interpretation of the results. This allows the supervisor to keep track of the progress, it also allows the student to have a track-record of previous experiments and what how protocols and analysis evolved over time. 
 
-The R notebook formats allows adding images to the notebook, text comments, but also, code. By using git, the student ensures that the lab journal is archived and accessible for later use (e.g. by future students, etc..)
+The R notebook format allows adding images to the notebook, text comments, but also, code. By using git, the student ensures that the lab journal is archived and accessible for later use (e.g. by future students, etc..)
 
 Fundamentally, your lab journal can be organized in two ways, either chronologically, or following a narrative. 
 
@@ -57,7 +57,7 @@ I've learnt that I can implement codes in my lab notebook. I've learn that the `
 
 #### Narrative lab journal
 ##### Intro
-This is the intro to my project
+I seek to learn how to use R and R notebooks
 
 ##### Results
 ```{r}
@@ -70,7 +70,7 @@ above are the results of my second line of code. I've learnt that I can put text
 I can present my lab notebook either chronologically or as a narrative. If I use a narrative format, I can anyway retrieve the older versions of the document on the git repository (if I've uploaded, i.e. pushed, the codes on a regular basis).
 
 #### previewing the text
-You are currently looking at the editor, which is used to write code, etc..  To get a previous of the document neatly organized, press the 'knit' button. A new window should open with the formatted document. 'Knitting' effectively assembles the document together, and applies different formatting options that you may have set. 
+If the document is opened in R, you are currently looking at the editor, which is used to write code, etc..  To get a previous of the document neatly organized, press the 'knit' button. A new window should open with the formatted document. 'Knitting' effectively assembles the document together, and applies different formatting options that you may have set. 
 
 #### How to format the text
 The text section of a R notebook is formatted using 'markdown'. You can find [cheat sheets](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) into markdown on the internet. 

my_first_notebook.md

@@ -41,15 +41,16 @@ mixed models with lme4.
 
 Modern installments of R, through the graphical user interface R studio
 allow to keep R notebooks which combine text (and simple formatting
-rules =\> markdown), with traditional codes. This is was we are using
-now. This section is part of the text. Code examples will follow below.
-Interestingly, R notebook can integrate code from multiple languages
-into one notebook (one notebook to rule them all). For instance, it can
-run `bash` code, `python`, and of course, `r`.
+rules =\> [markdown](https://en.wikipedia.org/wiki/Markdown)), with
+traditional codes. This is what we are using now. This section is part
+of the text. Code examples will follow below. Interestingly, R notebook
+can integrate code from multiple languages into one notebook (one
+notebook to rule them all). For instance, it can run `bash` code,
+`python`, and of course, `r`.
 
 In this exercise, we will see how a R notebook is kept, how to do basic
 text formatting, how to integrate `r` code into the document, and how to
-output this into a document that can be shared (e.g. html or pdf).
+output this into a document that can be shared (e.g. html, pdf, md).
 Finally we will see how Rstudio integrates `git` for version control,
 project management, and collaborative work.
 
@@ -61,7 +62,7 @@ allows the supervisor to keep track of the progress, it also allows the
 student to have a track-record of previous experiments and what how
 protocols and analysis evolved over time.
 
-The R notebook formats allows adding images to the notebook, text
+The R notebook format allows adding images to the notebook, text
 comments, but also, code. By using git, the student ensures that the lab
 journal is archived and accessible for later use (e.g. by future
 students, etc..)
@@ -95,7 +96,7 @@ can run the code above. A section of code within the text is known as a
 
 ##### Intro
 
-This is the intro to my project
+I seek to learn how to use R and R notebooks
 
 ##### Results
 
@@ -120,11 +121,12 @@ codes on a regular basis).
 
 #### previewing the text
 
-You are currently looking at the editor, which is used to write code,
-etc.. To get a previous of the document neatly organized, press the
-‘knit’ button. A new window should open with the formatted document.
-‘Knitting’ effectively assembles the document together, and applies
-different formatting options that you may have set.
+If the document is opened in R, you are currently looking at the editor,
+which is used to write code, etc.. To get a previous of the document
+neatly organized, press the ‘knit’ button. A new window should open with
+the formatted document. ‘Knitting’ effectively assembles the document
+together, and applies different formatting options that you may have
+set.
 
 #### How to format the text