Merge branch 'NBISweden:master' into master

README.md

@@ -37,9 +37,33 @@ If you are using command line, you can install `vd` and open and edit the file `
 
 ### Docker
 
-A docker container is used in GitHub actions to build the website. The Dockerfile contains the image definition. To update the docker image, follow the steps below:
+R packages needed to build the website and run the labs are all contained in a Docker container. To run docker container locally, follow instructions below:
+
+:exclamation: Image is about 4.8 GB!
+
+```
+# pull the container
+docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-r:latest
+
+# render whole website
+docker run --platform=linux/amd64 --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest Rscript -e 'rmarkdown::render_site()'
+
+# render one file
+docker run --platform=linux/amd64 --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest Rscript -e 'rmarkdown::render("index.Rmd")'
+```
+
+To run RStudio server and develop in the browser, run;
+
+```
+docker run --platform=linux/amd64 --rm -e PASSWORD=rstudio -p 8788:8787 -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest
+```
+
+Go to [http://localhost:8788/](http://localhost:8788/) or [http://0.0.0.0:8788](http://0.0.0.0:8788). Username is `rstudio` and password is `rstudio`. Change to folder `/rmd` to see your files.
+
+To add new packages, you need to update `Dockerfile`, rebuild the container, test it and push it to repository. Make changes to the `Dockerfile` as needed. Then to rebuild and push the docker image, follow the steps below:
 
 :exclamation: Remember to update the version number
+:exclamation: Remember to render the whole website to make sure everything works
 
 ```
 # build container and add tags
@@ -50,12 +74,6 @@ docker tag ghcr.io/nbisweden/workshop-r:1.1.0 ghcr.io/nbisweden/workshop-r:lates
 docker login ghcr.io
 docker push ghcr.io/nbisweden/workshop-r:1.1.0
 docker push ghcr.io/nbisweden/workshop-r:latest
-
-# run container locally
-# render whole website
-docker run --platform=linux/amd64 --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest Rscript -e 'rmarkdown::render_site()'
-# render one file
-docker run --platform=linux/amd64 --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest Rscript -e 'rmarkdown::render("index.Rmd")'
 ```
 
 ---

home_content.Rmd

@@ -30,12 +30,13 @@ This page contains links to different lectures (slides) and practical exercises
 * [Intro to R (Slides)](slide_r_intro.html)  
 * [Intro to R environment (Slides)](slide_r_environment.html)
 * [Intro to programming in R (Slides)](slide_r_programming_1.html)  
-* [Variables and Operators (Slides)](slide_elements_1.pdf)  
+* [Variables and Operators (Slides)](slide_r_elements_1.html)  
 * [Data types (Lab)](lab_datatypes.html)  
-* [Vectors and Strings (Slides)](slide_elements_2.pdf)  
-* [Matrices, Lists and Dataframes (Slides)](slide_elements_3.pdf)  
+* [Vectors and Strings (Slides)](slide_r_elements_2.html)  
+* [Matrices, Lists and Dataframes (Slides)](slide_r_elements_3.html)  
 * [Working with Vectors (Lab)](lab_vectors.html)
 * [Dataframes (Lab)](lab_dataframes.html)
+* [Loops and functions (Slides)](slide_r_elements_4.html)
 
 **Data wrangling**
 

home_precourse.Rmd

@@ -65,21 +65,26 @@ RStudio provides you with tools like code editor with highlighting, project mana
 
 Extra R packages used in the workshop exercises (if any) are listed below. It is recommended that you install this in advance. Simply copy and paste the code into R.
 
-```{r,eval=TRUE,chunk.title=NULL,echo=FALSE,comment="",class.output="r"}
-# this code block reads package names from '_site.yml' and prints them as installation instruction.
+```{r include=FALSE}
+# this first chunk runs through the root directory, finds the installed packages across the files and prints them as installation instruction.
 
-pkg <- yaml::read_yaml("_site.yml")
+#Add to the pkg_discard object the packages you want to discard from the list
+
+pkg<-unique(renv::dependencies()$Package)
+
+pkg_discard<-c("mkteachr")
+
+pkg_list<-pkg[!pkg %in% pkg_discard]
+
+```
+
+```{r echo=FALSE, warning=FALSE, chunk.title=NULL, class.output="r", comment="", r,eval=TRUE}
 
-if(!is.null(pkg$packages$packages_cran_student)) {
  cat("# install from cran\n")
- cat(paste0("install.packages(c('",paste(pkg$packages$packages_cran_student,sep="",collapse="','"),"'))"))
+ cat(paste0("install.packages(c('",paste(pkg_list,sep="",collapse="','"),"'))"))
  cat("\n")
-}
 
-if(!is.null(pkg$packages$packages_bioc_student)) {
- cat("# install from bioconductor\n")
- cat(paste0("BiocManager::install(c('",paste(pkg$packages$packages_bioc_student,sep="",collapse="','"),"'))"))
-}
+
 ```
 
 `r fa1("chevron-circle-right")` &nbsp; **Install Docker**

slide_r_elements_4.Rmd

@@ -1,7 +1,7 @@
 ---
 title: "Replication, Control Structures & Functions"
 subtitle: "Elements of the R language"
-author: "Marcin Kierczak and Nima Rafati"
+author: "Marcin Kierczak, Nima Rafati, Miguel Redondo"
 keywords: bioinformatics, course, scilifelab, nbis, R
 output:
   xaringan::moon_reader:
@@ -55,7 +55,7 @@ name: repeating_actions_1
 
 # Repeating actions
 
-Somtimes you want to repeat certain action several times.  
+Sometimes you want to repeat certain action several times.  
 
 There are few alternatives in R, for example:  
 - `for` loop 
@@ -66,13 +66,19 @@ name: for_loop_0
 
 # Repeating actions — for loop
 
-One way to repeat an action is to use the **for-loop**
+One way to repeat an action is to use the **for-loop**. 
+
+This is the general syntax:
 
 ```{r for.loop.general, eval=FALSE, echo=TRUE}
 for (var in seq) {
   expr
 }
 ```
+Where:
+- var = variable that will take values from the sequence
+- seq= sequence of values
+- expr = expression to be executed
 
 ---
 name: for_loop_1
@@ -82,17 +88,17 @@ Example.
 
 ```{r for.loop, echo=T}
 for (i in 1:5) {
-  cat(paste('Performing operation no.', i), '\n')
+  cat(paste('Performing operation on no.', i), '\n')
 }
 ```
 
 --
 
-A slight modification of the above example will skip odd indices.
+A slight modification of the above example.
 
 ```{r for.loop2, echo=T}
 for (i in c(2,4,6,8,10)) {
-  cat(paste('Performing operation no.', i), '\n')
+  cat(paste('Performing operation on no.', i), '\n')
 }
 ```
 
@@ -106,9 +112,10 @@ Sometimes, we also want an external counter:
 ```{r for.loop.cnt, echo=T}
 cnt <- 1
 for (i in c(2,4,6,8,10)) {
-  cat(paste('Performing operation no.', cnt,
-            'on element', i), '\n')
+  cat(paste('Iteration', cnt,
+            'Performing operation on no.', i), '\n')
   cnt <- cnt + 1
+  
 }
 ```
 
@@ -122,6 +129,11 @@ Say, we want to add 1 to every element of a vector:
 ```{r for.loop.ex1, echo=T}
 vec <- c(1:5)
 vec
+
+```
+
+```{r for.loop.ex2, echo=T}
+
 for (i in vec) {
   vec[i] <- vec[i] + 1
 }
@@ -165,6 +177,37 @@ for (i in vec) {
 proc.time() - ptm # for-loop
 ```
 
+
+---
+name: loops_avoid_growing
+
+# Loops &mdash; avoid growing data
+
+Avoid changing dimensions of an object inside the loop:
+
+```{r avoid.growing, echo=T}
+v <- c() # Initialize
+for (i in 1:100) {
+  v <- c(v, i)
+}
+```
+
+--
+
+It is much better to do it like this:
+
+```{r avoid.growing2, echo=T}
+v <- rep(NA, 100) # Initialize with length
+for (i in 1:100) {
+  v[i] <- i
+}
+```
+
+--
+
+Always try to know the size of the object you are going to create!
+
+
 ---
 name: while_loop
 
@@ -174,14 +217,15 @@ There is also another type of loop in R, the **while loop** which is executed as
 ```{r loop.while, echo=T}
 x <- 1
 while (x < 5) {
-  cat(x, " ... ")
+  cat("x equals",x, "\n")
   x <- x + 1
 }
 ```
 
 ---
 name: recursion
-
+exclude: true
+# Any questions so far?
 <!-- # Recursion
 
 When we explicitely repeat an action using a loop, we talk about **iteration**. We can also repeat actions by means of **recursion**, i.e. when a function calls itself. Let us implement a factorial $!$:
@@ -231,35 +275,7 @@ proc.time() - ptm
 -->
 
 ---
-name: loops_avoid_growing
-
-# Loops &mdash; avoid growing data
-
-Avoid changing dimensions of an object inside the loop:
-
-```{r avoid.growing, echo=T}
-v <- c() # Initialize
-for (i in 1:100) {
-  v <- c(v, i)
-}
-```
 
---
-
-It is much better to do it like this:
-
-```{r avoid.growing2, echo=T}
-v <- rep(NA, 100) # Initialize with length
-for (i in 1:100) {
-  v[i] <- i
-}
-```
-
---
-
-Always try to know the size of the object you are going to create!
-
----
 name: if_clause
 
 # Decisions, an if-clause

slide_r_intro.Rmd

@@ -216,15 +216,22 @@ e.g. an agent-based simulation is a challenge
 name: num_packages
 
 # Ecosystem of R packages
-
 <br>
 
-```{r num_pkgs, echo=FALSE, fig.align='center', fig.height=7, fig.width=9, cache=TRUE, message=FALSE}
+
+```{r num_pkgs, eval=FALSE, fig.align='center', fig.height=7, fig.width=9, message=FALSE, cache=TRUE, include=FALSE}
+#I mute this chunk because it gives a readLines error in the 2024 course
+#I add the figure instead below the chunk
+#Maybe modify in the future
 data <- mkteachr::update_repos_data()
 gg <- mkteachr::plot_repos_data(data)
 gg
 ```
 
+<div style="text-align: center;">
+    <img src="data/slide_intro/num_pkgs.jpg" style="width:80%;">
+</div>
+
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