lgatto / 2017-04-03-adv-r-progr-embl

Advanced R programming course at EMBL, 3-4 April 2017

• 📉️ Professor of Bioinformatics at the de Duve Institute, UCLouvain in Brussels, Belgium
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2017-04-03-adv-r-progr-embl's Issues

Update the S4 objects used in Sequences?

I've made a few changes in the ROO teaching material:

• use sequence() instead of seq()
• changed id() into name()
• don't re-declare S4 generics when S3 exists (this is now done automatically by R)

We should probably update the sequences package to reflect these changes at some point?

Package dependencies

Here is a list of all required packages:

assertthat
Biobase
covr
datasets
devtools
dplyr
formatR
ggplot2
ggvis
hexbin
log4r
magrittr
microbenchmark
msdata
MSnbase
mypackage
profvis
pRolocdata
pryr
readr
reshape2
roxygen2
RUnit
sequences
shiny
testthat
tidyverse

To install all of them, please run

pkgs <- c("assertthat", "Biobase", "covr", "datasets", "devtools",
          "devtools", "dplyr", "formatR", "ggplot2", "ggvis",
          "hexbin", "log4r", "magrittr", "microbenchmark", "msdata",
          "MSnbase", "mypackage", "profvis", "pRolocdata", "pryr",
          "readr", "reshape2", "roxygen2", "RUnit", "sequences",
          "shiny", "testthat", "tidyverse")
if (!require("BiocInstaller")) {
    ## try http:// if https:// URLs are not supported
    source("https://bioconductor.org/biocLite.R")
}  
library("BiocInstaller")
biocLite(pkgs)

Material in the intro

The material in the introduction contains (so far)

• style (from the defensive programming section)
• writing a function (small part from functional programming)
• apply (small part from functional programming)

My suggestion would be to remove the style section from defensive programming (maybe just add a sentence to remind that this is important in the frame of good programming) and leave the two other topics, as they are short and part of more related content.

Cc: @rstojnic

Javadoc in R?

First at all: Very nice course! You have done a great job!
For the next courses it would be nice to have an example of an "good practice" function example. You showed a lot of nice examples, but is there a common way?
I missed the in java called Javadoc (if this exists). Is there a common way in R for function documentation (functions which are not part of a package. For this you can use roxygen2 as you mentioned).

Testing material

Quite a bit of content from debug (defensive programming) material overlaps with the
testing section. As the second morning is already quite busy, I suggest to just keep bullet points as reminder in the debugging part.

Cc: @rstojnic