From 0e22ab653ad18d17f7b0692637050cf1e31ebed8 Mon Sep 17 00:00:00 2001
From: Ghislain Durif <gd.dev@libertymail.net>
Date: Thu, 5 Oct 2023 17:11:06 +0200
Subject: [PATCH] remove Rmd metadata regarding output, useless copy-paste code
 management and add conflicted package management when necessary

---
 session_1/session_1.Rmd | 25 -------------------------
 session_2/session_2.Rmd | 20 ++++----------------
 session_3/session_3.Rmd | 16 ----------------
 session_4/session_4.Rmd | 19 +++----------------
 session_5/session_5.Rmd | 21 ++++-----------------
 session_6/session_6.Rmd | 17 -----------------
 session_7/session_7.Rmd | 20 +++-----------------
 session_8/session_8.Rmd | 20 +++-----------------
 8 files changed, 17 insertions(+), 141 deletions(-)

diff --git a/session_1/session_1.Rmd b/session_1/session_1.Rmd
index 5706d04..4586fd4 100644
--- a/session_1/session_1.Rmd
+++ b/session_1/session_1.Rmd
@@ -2,43 +2,18 @@
 title: 'R.1: Introduction to R and RStudio'
 author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr);\n Hélène Polvèche [hpolveche@istem.fr](mailto:hpolveche@istem.fr)"
 date: "2022"
-output:
-  rmdformats::downcute:
-    self_contain: true
-    use_bookdown: true
-    default_style: "light"
-    lightbox: true
-    css: "../www/style_Rmd.css"
 ---
 
 ```{r include=FALSE}
 library(fontawesome)
 ``` 
 
-&ensp;`r fa(name = "fas fa-house", fill = "grey", height = "1em")` &ensp;https://can.gitbiopages.ens-lyon.fr/R_basis/
-
 ```{r setup, include=FALSE , echo=FALSE}
 rm(list=ls())
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(comment = NA)
 ```
 
-```{r klippy_install, echo=FALSE, include=FALSE}
-if (! require("klippy")) {
-  install.packages("remotes")
-  remotes::install_github("rlesur/klippy")
-}
-```
-
-
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
-  position = c('top', 'right'),
-  color = "white",
-  tooltip_message = 'Click to copy',
-  tooltip_success = 'Copied !')
-```
-
 
 # Introduction
 
diff --git a/session_2/session_2.Rmd b/session_2/session_2.Rmd
index f1f1ae3..3957e32 100644
--- a/session_2/session_2.Rmd
+++ b/session_2/session_2.Rmd
@@ -2,33 +2,21 @@
 title: "R.2: introduction to Tidyverse"
 author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr);\nHélène Polvèche [hpolveche@istem.fr](mailto:hpolveche@istem.fr)"
 date: "2022"
-output:
-  rmdformats::downcute:
-    self_contain: true
-    use_bookdown: true
-    default_style: "light"
-    lightbox: true
-    css: "../www/style_Rmd.css"
 ---
 
 ```{r include=FALSE}
 library(fontawesome)
-``` 
 
-&ensp;`r fa(name = "fas fa-house", fill = "grey", height = "1em")` &ensp;https://can.gitbiopages.ens-lyon.fr/R_basis/
+if("conflicted" %in% .packages())
+    conflicted::conflicts_prefer(dplyr::filter)
+``` 
 
 ```{r setup, include=FALSE}
 rm(list=ls())
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(comment = NA)
 ```
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
-  position = c('top', 'right'),
-  color = "white",
-  tooltip_message = 'Click to copy',
-  tooltip_success = 'Copied !')
-```
+
 ```{r download_data, include=FALSE, eval=T}
 library("tidyverse")
 tmp <- tempfile(fileext = ".zip")
diff --git a/session_3/session_3.Rmd b/session_3/session_3.Rmd
index d13d3d6..8e07389 100644
--- a/session_3/session_3.Rmd
+++ b/session_3/session_3.Rmd
@@ -2,33 +2,17 @@
 title: 'R.3: Transformations with ggplot2'
 author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr), Hélène Polvèche [hpolveche@istem.fr](mailto:hpolveche@istem.fr)"
 date: "2022"
-output:
-  rmdformats::downcute:
-    self_contain: true
-    use_bookdown: true
-    default_style: "light"
-    lightbox: true
-    css: "../www/style_Rmd.css"
 ---
 
 ```{r include=FALSE}
 library(fontawesome)
 ``` 
 
-&ensp;`r fa(name = "fas fa-house", fill = "grey", height = "1em")` &ensp;https://can.gitbiopages.ens-lyon.fr/R_basis/
-
 ```{r setup, include=FALSE}
 rm(list=ls())
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(comment = NA)
 ```
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
-  position = c('top', 'right'),
-  color = "white",
-  tooltip_message = 'Click to copy',
-  tooltip_success = 'Copied !')
-```
 
 # Introduction
 
diff --git a/session_4/session_4.Rmd b/session_4/session_4.Rmd
index 1839c1a..d22517b 100644
--- a/session_4/session_4.Rmd
+++ b/session_4/session_4.Rmd
@@ -2,33 +2,20 @@
 title: "R.4: data transformation"
 author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr), Hélène Polvèche [hpolveche@istem.fr](mailto:hpolveche@istem.fr)"
 date: "2022"
-output:
-  rmdformats::downcute:
-    self_contain: true
-    use_bookdown: true
-    default_style: "light"
-    lightbox: true
-    css: "../www/style_Rmd.css"
 ---
 
 ```{r include=FALSE}
 library(fontawesome)
-``` 
 
-&ensp;`r fa(name = "fas fa-house", fill = "grey", height = "1em")` &ensp;https://can.gitbiopages.ens-lyon.fr/R_basis/
+if("conflicted" %in% .packages())
+    conflicted::conflicts_prefer(dplyr::filter)
+``` 
 
 ```{r setup, include=FALSE}
 rm(list=ls())
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(comment = NA)
 ```
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
-  position = c('top', 'right'),
-  color = "white",
-  tooltip_message = 'Click to copy',
-  tooltip_success = 'Copied !')
-```
 
 # Introduction
 
diff --git a/session_5/session_5.Rmd b/session_5/session_5.Rmd
index 16aed13..33d98c5 100644
--- a/session_5/session_5.Rmd
+++ b/session_5/session_5.Rmd
@@ -1,34 +1,21 @@
 ---
-title: "R#5: Pipping and grouping"
+title: "R.5: Pipping and grouping"
 author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)"
 date: "2022"
-output:
-  rmdformats::downcute:
-    self_contain: true
-    use_bookdown: true
-    default_style: "light"
-    lightbox: true
-    css: "../www/style_Rmd.css"
 ---
 
 ```{r include=FALSE}
 library(fontawesome)
-``` 
 
-&ensp;`r fa(name = "fas fa-house", fill = "grey", height = "1em")` &ensp;https://can.gitbiopages.ens-lyon.fr/R_basis/
+if("conflicted" %in% .packages())
+    conflicted::conflicts_prefer(dplyr::filter)
+```
 
 ```{r setup, include=FALSE}
 rm(list=ls())
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(comment = NA)
 ```
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
-  position = c('top', 'right'),
-  color = "white",
-  tooltip_message = 'Click to copy',
-  tooltip_success = 'Copied !')
-```
 
 # Introduction
 
diff --git a/session_6/session_6.Rmd b/session_6/session_6.Rmd
index f159cc7..5188b93 100644
--- a/session_6/session_6.Rmd
+++ b/session_6/session_6.Rmd
@@ -2,34 +2,17 @@
 title: "R.6: tidydata"
 author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr);\nCarine Rey [carine.rey@ens-lyon.fr](mailto:carine.rey@ens-lyon.fr)"
 date: "2022"
-output:
-  rmdformats::downcute:
-    self_contain: true
-    use_bookdown: true
-    default_style: "light"
-    lightbox: true
-    css: "../www/style_Rmd.css"
 ---
 
 ```{r include=FALSE}
 library(fontawesome)
 ``` 
 
-&ensp;`r fa(name = "fas fa-house", fill = "grey", height = "1em")` &ensp;https://can.gitbiopages.ens-lyon.fr/R_basis/
-
-
 ```{r setup, include=FALSE}
 rm(list=ls())
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(comment = NA)
 ```
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
-  position = c('top', 'right'),
-  color = "white",
-  tooltip_message = 'Click to copy',
-  tooltip_success = 'Copied !')
-```
 
 # Introduction
 
diff --git a/session_7/session_7.Rmd b/session_7/session_7.Rmd
index e26c559..7ada9ea 100644
--- a/session_7/session_7.Rmd
+++ b/session_7/session_7.Rmd
@@ -2,34 +2,20 @@
 title: "R.7: String & RegExp"
 author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)"
 date: "2022"
-output:
-  rmdformats::downcute:
-    self_contain: true
-    use_bookdown: true
-    default_style: "light"
-    lightbox: true
-    css: "../www/style_Rmd.css"
 ---
 
 ```{r include=FALSE}
 library(fontawesome)
-``` 
-
-&ensp;`r fa(name = "fas fa-house", fill = "grey", height = "1em")` &ensp;https://can.gitbiopages.ens-lyon.fr/R_basis/
 
+if("conflicted" %in% .packages())
+    conflicted::conflicts_prefer(dplyr::filter)
+```
 
 ```{r setup, include=FALSE}
 rm(list=ls())
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(comment = NA)
 ```
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
-  position = c('top', 'right'),
-  color = "white",
-  tooltip_message = 'Click to copy',
-  tooltip_success = 'Copied !')
-```
 
 # Introduction
 
diff --git a/session_8/session_8.Rmd b/session_8/session_8.Rmd
index 35045b1..3437826 100644
--- a/session_8/session_8.Rmd
+++ b/session_8/session_8.Rmd
@@ -2,34 +2,20 @@
 title: "R.8: Factors"
 author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)"
 date: "2022"
-output:
-  rmdformats::downcute:
-    self_contain: true
-    use_bookdown: true
-    default_style: "light"
-    lightbox: true
-    css: "../www/style_Rmd.css"
 ---
 
 ```{r include=FALSE}
 library(fontawesome)
-``` 
-
-&ensp;`r fa(name = "fas fa-house", fill = "grey", height = "1em")` &ensp;https://can.gitbiopages.ens-lyon.fr/R_basis/
 
+if("conflicted" %in% .packages())
+    conflicted::conflicts_prefer(dplyr::filter)
+```
 
 ```{r setup, include=FALSE}
 rm(list=ls())
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(comment = NA)
 ```
-```{r klippy, echo=FALSE, include=TRUE}
-klippy::klippy(
-  position = c('top', 'right'),
-  color = "white",
-  tooltip_message = 'Click to copy',
-  tooltip_success = 'Copied !')
-```
 
 # Introduction
 
-- 
GitLab