Merge branch 'master' of https://github.com/BioDataScience-Course/BioDataScience

Author: phgrosjean

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioDataScience
 Type: Package
-Version: 2018.0.0
+Version: 2019.0.0
 Title: A Series of Learnr Documents for Biological Data Science
 Description: Interactive documents using learnr for studying biological data science.
 Authors@R: c(

NEWS.md

@@ -1,5 +1,9 @@
 # BioDataScience News
 
+## Changes in version 2019.0.0
+
+- Review of the all tutorials (00a - 13c) with the **svbox 2019**
+
 ## Changes in version 2018.0.0
 
 - `run()` modified to install latest release matching svbox year.

inst/tutorials/00a_jde_2019/jde2019.html

@@ -283,7 +283,7 @@ <h2>R, les assignations</h2>
 <h2>R, les fonctions</h2>
 <p>Les fonctions sont très importantes dans R. C’est elles qui effectuent tous vos calculs. Pour appeler une fonction, on utilise son nom suivi d’une parenthèse, et éventuellement un ou plusieurs arguments fournis à l’intérieur de la parenthèse et séparés par une virgule <code>fun_name(arg1, arg2, ...)</code>. Voici un exemple d’une fonction appelée sans argument :</p>
 <pre class="r"><code>Sys.Date()</code></pre>
-<pre><code>[1] &quot;2019-08-22&quot;</code></pre>
+<pre><code>[1] &quot;2019-08-23&quot;</code></pre>
 <p>Une autre fonction appelée avec un seul argument :</p>
 <pre class="r"><code>x &lt;- 1:4
 sum(x)</code></pre>
@@ -374,7 +374,7 @@ <h2>Imbrication et chaînage</h2>
 <p>Mais dans ce dernier cas, la lecture devient plus difficile. On peut aussi <strong>chaîner</strong> des instructions avec l’opérateur <code>%&gt;.%</code> dans la version <code>SciViews::R</code> qui charge des “packages” supplémentaires pour fournir des fonctions en plus de R de base :</p>
 <pre class="r"><code># Installer SciViews::R
 SciViews::R</code></pre>
-<pre><code>── Attaching packages ────────────────────────────────────────── SciViews::R 1.1.0 ──</code></pre>
+<pre><code>── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────── SciViews::R 1.1.0 ──</code></pre>
 <pre><code>✔ SciViews  1.1.0        ✔ purrr     0.3.2   
 ✔ chart     1.3.0        ✔ readr     1.3.1   
 ✔ flow      1.0.0        ✔ tidyr     0.8.3   
@@ -383,7 +383,7 @@ <h2>Imbrication et chaînage</h2>
 ✔ forcats   0.4.0        ✔ tidyverse 1.2.1   
 ✔ stringr   1.4.0        ✔ lattice   0.20.38 
 ✔ dplyr     0.8.0.1      ✔ MASS      7.3.51.3</code></pre>
-<pre><code>── Conflicts ─────────────────────────────────────────────── tidyverse_conflicts() ──
+<pre><code>── Conflicts ───────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
 ✖ dplyr::filter() masks stats::filter()
 ✖ dplyr::lag()    masks stats::lag()
 ✖ dplyr::select() masks MASS::select()</code></pre>
@@ -532,7 +532,7 @@ <h2>Conclusion</h2>
 <!--/html_preserve-->
 <!--html_preserve-->
 <script type="application/shiny-prerendered" data-context="execution_dependencies">
-{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages"]}},"value":[{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages","version"]},"class":{"type":"character","attributes":{},"value":["data.frame"]},"row.names":{"type":"integer","attributes":{},"value":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111]}},"value":[{"type":"character","attributes":{},"value":["acepack","assertthat","backports","base","base64enc","BioDataScience","broom","cellranger","chart","checkmate","cli","cluster","codetools","colorspace","compiler","cowplot","crayon","data.io","data.table","datasets","digest","dplyr","ellipse","evaluate","flow","forcats","foreign","Formula","generics","ggplot2","ggplotify","ggpubr","glue","graphics","grDevices","grid","gridExtra","gridGraphics","gtable","haven","Hmisc","hms","htmlTable","htmltools","htmlwidgets","httpuv","httr","igraph","inline","jsonlite","knitr","later","lattice","latticeExtra","lazyeval","learnr","lubridate","magrittr","markdown","MASS","Matrix","methods","mime","modelr","mongolite","munsell","nlme","nnet","pillar","pkgconfig","plyr","promises","proto","pryr","purrr","R6","RColorBrewer","Rcpp","readr","readxl","remotes","rlang","rmarkdown","rpart","rprojroot","rstudioapi","rvcheck","rvest","scales","SciViews","shiny","splines","stats","stringi","stringr","survival","svMisc","tibble","tidyr","tidyselect","tidyverse","tools","tsibble","utils","viridis","viridisLite","withr","xfun","xml2","xtable","yaml"]},{"type":"character","attributes":{},"value":["1.4.1","0.2.1","1.1.3","3.5.3","0.1-3","0.23.1","0.5.2","1.1.0","1.3.0","1.9.1","1.1.0","2.0.8","0.2-16","1.4-1","3.5.3","0.9.4","1.3.4","1.2.2","1.12.2","3.5.3","0.6.18","0.8.0.1","0.4.1","0.13","1.0.0","0.4.0","0.8-71","1.2-3","0.0.2","3.1.1","0.0.3","0.2","1.3.1","3.5.3","3.5.3","3.5.3","2.3","0.3-0","0.3.0","2.1.0","4.2-0","0.4.2","1.13.1","0.3.6","1.3","1.5.1","1.4.0","1.2.4","0.3.15","1.6","1.22","0.8.0","0.20-38","0.6-28","0.2.2","0.9.2.1","1.7.4","1.5","0.9","7.3-51.3","1.2-17","3.5.3","0.6","0.1.4","2.0.1","0.5.0","3.1-138","7.3-12","1.3.1","2.0.2","1.8.4","1.0.1","1.0.0","0.1.4","0.3.2","2.4.0","1.1-2","1.0.1","1.3.1","1.3.1","2.0.2","0.3.4","1.12","4.1-13","1.3-2","0.10","0.1.3","0.3.2","1.0.0","1.1.0","1.3.0","3.5.3","3.5.3","1.4.3","1.4.0","2.44-1.1","1.1.0","2.1.1","0.8.3","0.2.5","1.2.1","3.5.3","0.7.0","3.5.3","0.5.1","0.3.0","2.1.2","0.6","1.2.0","1.8-3","2.2.0"]}]}]}
+{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages"]}},"value":[{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages","version"]},"class":{"type":"character","attributes":{},"value":["data.frame"]},"row.names":{"type":"integer","attributes":{},"value":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111]}},"value":[{"type":"character","attributes":{},"value":["acepack","assertthat","backports","base","base64enc","BioDataScience","broom","cellranger","chart","checkmate","cli","cluster","codetools","colorspace","compiler","cowplot","crayon","data.io","data.table","datasets","digest","dplyr","ellipse","evaluate","flow","forcats","foreign","Formula","generics","ggplot2","ggplotify","ggpubr","glue","graphics","grDevices","grid","gridExtra","gridGraphics","gtable","haven","Hmisc","hms","htmlTable","htmltools","htmlwidgets","httpuv","httr","igraph","inline","jsonlite","knitr","later","lattice","latticeExtra","lazyeval","learnr","lubridate","magrittr","markdown","MASS","Matrix","methods","mime","modelr","mongolite","munsell","nlme","nnet","pillar","pkgconfig","plyr","promises","proto","pryr","purrr","R6","RColorBrewer","Rcpp","readr","readxl","remotes","rlang","rmarkdown","rpart","rprojroot","rstudioapi","rvcheck","rvest","scales","SciViews","shiny","splines","stats","stringi","stringr","survival","svMisc","tibble","tidyr","tidyselect","tidyverse","tools","tsibble","utils","viridis","viridisLite","withr","xfun","xml2","xtable","yaml"]},{"type":"character","attributes":{},"value":["1.4.1","0.2.1","1.1.3","3.5.3","0.1-3","0.25.0","0.5.2","1.1.0","1.3.0","1.9.1","1.1.0","2.0.8","0.2-16","1.4-1","3.5.3","0.9.4","1.3.4","1.2.2","1.12.2","3.5.3","0.6.18","0.8.0.1","0.4.1","0.13","1.0.0","0.4.0","0.8-71","1.2-3","0.0.2","3.1.1","0.0.3","0.2","1.3.1","3.5.3","3.5.3","3.5.3","2.3","0.3-0","0.3.0","2.1.0","4.2-0","0.4.2","1.13.1","0.3.6","1.3","1.5.1","1.4.0","1.2.4","0.3.15","1.6","1.22","0.8.0","0.20-38","0.6-28","0.2.2","0.9.2.1","1.7.4","1.5","0.9","7.3-51.3","1.2-17","3.5.3","0.6","0.1.4","2.0.1","0.5.0","3.1-138","7.3-12","1.3.1","2.0.2","1.8.4","1.0.1","1.0.0","0.1.4","0.3.2","2.4.0","1.1-2","1.0.1","1.3.1","1.3.1","2.0.2","0.3.4","1.12","4.1-13","1.3-2","0.10","0.1.3","0.3.2","1.0.0","1.1.0","1.3.0","3.5.3","3.5.3","1.4.3","1.4.0","2.44-1.1","1.1.0","2.1.1","0.8.3","0.2.5","1.2.1","3.5.3","0.7.0","3.5.3","0.5.1","0.3.0","2.1.2","0.6","1.2.0","1.8-3","2.2.0"]}]}]}
 </script>
 <!--/html_preserve--></li>
 </ul>

inst/tutorials/02a_base/base.html

@@ -1191,7 +1191,7 @@ <h2>Conclusion</h2>
 <!--/html_preserve-->
 <!--html_preserve-->
 <script type="application/shiny-prerendered" data-context="execution_dependencies">
-{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages"]}},"value":[{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages","version"]},"class":{"type":"character","attributes":{},"value":["data.frame"]},"row.names":{"type":"integer","attributes":{},"value":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113]}},"value":[{"type":"character","attributes":{},"value":["acepack","assertthat","backports","base","base64enc","BioDataScience","broom","cellranger","chart","checkmate","cli","cluster","codetools","colorspace","compiler","cowplot","crayon","data.io","data.table","datasets","digest","dplyr","ellipse","evaluate","flow","forcats","foreign","Formula","generics","ggplot2","ggplotify","ggpubr","glue","graphics","grDevices","grid","gridExtra","gridGraphics","gtable","haven","highr","Hmisc","hms","htmlTable","htmltools","htmlwidgets","httpuv","httr","igraph","inline","jsonlite","knitr","labeling","later","lattice","latticeExtra","lazyeval","learnr","lubridate","magrittr","markdown","MASS","Matrix","methods","mime","modelr","mongolite","munsell","nlme","nnet","pillar","pkgconfig","plyr","promises","proto","pryr","purrr","R6","RColorBrewer","Rcpp","readr","readxl","remotes","rlang","rmarkdown","rpart","rprojroot","rstudioapi","rvcheck","rvest","scales","SciViews","shiny","splines","stats","stringi","stringr","survival","svMisc","tibble","tidyr","tidyselect","tidyverse","tools","tsibble","utils","viridis","viridisLite","withr","xfun","xml2","xtable","yaml"]},{"type":"character","attributes":{},"value":["1.4.1","0.2.1","1.1.3","3.5.3","0.1-3","0.23.1","0.5.2","1.1.0","1.3.0","1.9.1","1.1.0","2.0.8","0.2-16","1.4-1","3.5.3","0.9.4","1.3.4","1.2.2","1.12.2","3.5.3","0.6.18","0.8.0.1","0.4.1","0.13","1.0.0","0.4.0","0.8-71","1.2-3","0.0.2","3.1.1","0.0.3","0.2","1.3.1","3.5.3","3.5.3","3.5.3","2.3","0.3-0","0.3.0","2.1.0","0.8","4.2-0","0.4.2","1.13.1","0.3.6","1.3","1.5.1","1.4.0","1.2.4","0.3.15","1.6","1.22","0.3","0.8.0","0.20-38","0.6-28","0.2.2","0.9.2.1","1.7.4","1.5","0.9","7.3-51.3","1.2-17","3.5.3","0.6","0.1.4","2.0.1","0.5.0","3.1-138","7.3-12","1.3.1","2.0.2","1.8.4","1.0.1","1.0.0","0.1.4","0.3.2","2.4.0","1.1-2","1.0.1","1.3.1","1.3.1","2.0.2","0.3.4","1.12","4.1-13","1.3-2","0.10","0.1.3","0.3.2","1.0.0","1.1.0","1.3.0","3.5.3","3.5.3","1.4.3","1.4.0","2.44-1.1","1.1.0","2.1.1","0.8.3","0.2.5","1.2.1","3.5.3","0.7.0","3.5.3","0.5.1","0.3.0","2.1.2","0.6","1.2.0","1.8-3","2.2.0"]}]}]}
+{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages"]}},"value":[{"type":"list","attributes":{"names":{"type":"character","attributes":{},"value":["packages","version"]},"class":{"type":"character","attributes":{},"value":["data.frame"]},"row.names":{"type":"integer","attributes":{},"value":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113]}},"value":[{"type":"character","attributes":{},"value":["acepack","assertthat","backports","base","base64enc","BioDataScience","broom","cellranger","chart","checkmate","cli","cluster","codetools","colorspace","compiler","cowplot","crayon","data.io","data.table","datasets","digest","dplyr","ellipse","evaluate","flow","forcats","foreign","Formula","generics","ggplot2","ggplotify","ggpubr","glue","graphics","grDevices","grid","gridExtra","gridGraphics","gtable","haven","highr","Hmisc","hms","htmlTable","htmltools","htmlwidgets","httpuv","httr","igraph","inline","jsonlite","knitr","labeling","later","lattice","latticeExtra","lazyeval","learnr","lubridate","magrittr","markdown","MASS","Matrix","methods","mime","modelr","mongolite","munsell","nlme","nnet","pillar","pkgconfig","plyr","promises","proto","pryr","purrr","R6","RColorBrewer","Rcpp","readr","readxl","remotes","rlang","rmarkdown","rpart","rprojroot","rstudioapi","rvcheck","rvest","scales","SciViews","shiny","splines","stats","stringi","stringr","survival","svMisc","tibble","tidyr","tidyselect","tidyverse","tools","tsibble","utils","viridis","viridisLite","withr","xfun","xml2","xtable","yaml"]},{"type":"character","attributes":{},"value":["1.4.1","0.2.1","1.1.3","3.5.3","0.1-3","0.25.0","0.5.2","1.1.0","1.3.0","1.9.1","1.1.0","2.0.8","0.2-16","1.4-1","3.5.3","0.9.4","1.3.4","1.2.2","1.12.2","3.5.3","0.6.18","0.8.0.1","0.4.1","0.13","1.0.0","0.4.0","0.8-71","1.2-3","0.0.2","3.1.1","0.0.3","0.2","1.3.1","3.5.3","3.5.3","3.5.3","2.3","0.3-0","0.3.0","2.1.0","0.8","4.2-0","0.4.2","1.13.1","0.3.6","1.3","1.5.1","1.4.0","1.2.4","0.3.15","1.6","1.22","0.3","0.8.0","0.20-38","0.6-28","0.2.2","0.9.2.1","1.7.4","1.5","0.9","7.3-51.3","1.2-17","3.5.3","0.6","0.1.4","2.0.1","0.5.0","3.1-138","7.3-12","1.3.1","2.0.2","1.8.4","1.0.1","1.0.0","0.1.4","0.3.2","2.4.0","1.1-2","1.0.1","1.3.1","1.3.1","2.0.2","0.3.4","1.12","4.1-13","1.3-2","0.10","0.1.3","0.3.2","1.0.0","1.1.0","1.3.0","3.5.3","3.5.3","1.4.3","1.4.0","2.44-1.1","1.1.0","2.1.1","0.8.3","0.2.5","1.2.1","3.5.3","0.7.0","3.5.3","0.5.1","0.3.0","2.1.2","0.6","1.2.0","1.8-3","2.2.0"]}]}]}
 </script>
 <!--/html_preserve-->
 </div>