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Setup / Prerequisites Suggestions -- Remedial Links or Assessments? #438

NikVetr opened this issue Jul 2, 2019 · 3 comments


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NikVetr commented Jul 2, 2019

This is related to an issue raised and closed here, but I didn't quite find its resolution entirely satisfactory and so am opening this issue now. This all relates to the setup instructions here and the prerequisites box here.

Specifically, I think it would be helpful to 1) include a link to remedial material in case prospective students have trouble installing R / RStudio or are not sure whether they "understand the concepts of files and directories", and 2) provide a quick self-check of whether R has been successful installed and of their understanding of directory structure / syntax. A link in 1) can be unobtrusive (but inside should be as painfully explicit as possible), and then 2) can potentially get some of the opening troubleshooting out of the way, as well as potentially filter out students for whom the material would be inappropriate. Possibly also a third suggestion, 3) might be to sneak a bit of new-ish material in when you're doing 2).

(I've never taught a carpentries course, but I have taught both undergrad-level and grad-level labs / workshops on intro computational statistics type stuff, and without fail the first big chunk is spent just getting everyone on board with navigating a directory system, changing working directories, specifying file paths, etc.)

I think 1) can be accomplished by linking to something like this video, which is already SWC-associated, or else maybe one of many similar videos up on youtube. Not sure of a good resource for the latter, but I imagine something with lots of pictures of nested folders in Finder / Explorer alongside corresponding paths would serve well.

For 2) then, I think it would be good for them to 'do' something in R in order to confirm that it's been installed correctly and that they understand the concepts of files and directories. Maybe having them call something like print("hello world") or 1+1 and confirm the screen output is as expected. You could also maybe have that setwd("~/Desktop/r-novice-inflammation/") box from the first part go into the setup, and then have them list.files(path = "data") to confirm everything's been unzipped correctly (also, it might be helpful to break down the path and clarify that the tilde conventionally points to the home directory... except I think in Windows it sometimes points to the Documents folder by default?). Also, before setwd()'ing it up I think it would be better to call getwd() to see where you're starting from.

Finally, for 3), why not use R itself to make the folder, download the data, and unzip it? (also -- I've also had student struggle to understand what 'unzipping' means, dunno if that's an issue in SWC courses. I think most OSes come prepackaged with something that can do this nowadays, but linking to a picture showing how to extract file contents could be nice?). Having them run something like:

#check your current working directory

#change working directory to somewhere appropriate, with path specified relative to home directory
setwd("~/SWC_Workshop") #relative to home directory
setwd(dir = "/Volumes/macOS/Users/nikolai/SWC_Workshop") #absolute path

#create a new directory to hold the data for this tutorial, and change the current working directory to it

#download the data to your new folder, naming it "r-novice-inflammation-data"
download.file(url = "", destfile = "r-novice-inflammation-data")

#check to make sure it is there

#the downloaded file is zipped, so unzip it
unzip(zipfile = "r-novice-inflammation-data")

#check to make sure that the files have unzipped

#make sure the first one can be read in
read.csv(file = "data/inflammation-01.csv", header = FALSE)

#...start the lesson here

could be helpful in making sure everyone's on the same page coming into the workshop.

Anyway, those are just some thoughts, and I'm happy to discuss on elaborate upon them further. :]


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We could also include an .Rproj file in our download, so that people don't get into the habit of setwd manually.

I tend towards agreeing with your download.file suggestion, instead of doing it manually and checking it in the Unix shell. I'll be happy to review a PR that updates /setup :-)

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The idea of adding a SWC video link can be very helpful as many novices get stuck when installing the required software such as R Studio. Also as a prerequisite, the student can also be encouraged to play around with the graphical interface of R studio and familiarize themselves with the key icons and features.

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diyadas commented Aug 11, 2019

Would be happy to review a PR on this issue!

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