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BIOL710AdvBiometry

learnR labs for advanced biometry

adapted from Sara Stoudt and labs for Open Intro ISRS by Jenna Ekwealor

For instructors: the overview blog post from Sara Stoudt that taught me how to use learnR labs can be found here.

Course Lab Manual can be found here

To install this Pre-Lab package:

  1. One time only (may need to reinstall for updates throughout the semester):

install.packages("remotes")

remove.packages("learnr") ## might not need this if you do not have learnr pre-installed

remotes::install_github("rstudio/learnr")

remotes::install_github("rstudio-education/gradethis")

remotes::install_github("jenna-tb-ekwealor/BIOL710AdvBiometry")

  1. After install is complete (I know this seems weird, but go with it):

remove.packages("htmltools")

install.packages("htmltools")

Exit RStudio and then open it again.

Launch a lesson:

  1. In the console (bottom left) type: learnr::run_tutorial("PreLab_Week1", "BIOL710AdvBiometry")

Stop a lesson

  1. Click stop sign on the left.

Submission Instructions

There will be a pre-lab and a lab report for each lab. The pre-lab will be completed individually via learnR and graded for completion. This is due by the start of class on MONDAYS, except for Week 1, which is due Wednesday January 31. Then during lab you will work in a team of three (or so) to complete a lab report in R. Both pre-labs and lab reports are submitted on Canvas (see below). The lab report is due each class day by 11:59 pm.

How to Submit Pre-Lab

How to Submit Lab Report

Download our custom "Lab Report" template or from Canvas and save it somewhere handy on your computer. This copy will serve as your template for each Lab this semester. Then, open it and File -> Save As with a useful name in your working_directory folder for that week, with a .Rmd file extension. This is the copy you can work with for that day's Lab Activity. Knit to a PDF using the triangle next to the Knit button in the top of RStudio. Save your PDF and submit to the appropriate assignment in Canvas.

Troubleshooting

  • General RStudio issues: -- Stop saving RData. In RStudio go to Tools -> Global Options, and under Workspace uncheck the box for "Save .RData ...". Also change the dropdown box to "Never" so that it never asks you if you want to do this. There are few cases, in my opinion, where you'd want to automatically save RData, and definitely not for this class. 

-- Possibly, it might be necessary to update to the newest version of R, and to install RTools (on Windows machines.)

Troubleshooting Pre-Labs

  • These packages have more recent versions available. Which would you like to update? --> If the list only includes htmltools say No.

  • Do you want to install from sources the package which needs compilation? (in reference to dplyr 1.0.3 instead of dplyr 1.0.4) --> No

  • If you get some kind of error having to do with "parse" when you try to run a tutorial:

Click "Session" --> "Restart R" and try to run the tutorial again.

  • The tutorial will often pop up in a new browser tab automatically. If you have a popup blocker, you might need to turn it off or update the settings.

  • If you can't seem to get installations to install with remotes::install_github(), you can try another package that helps install from GitHub. First, install.packages("devtools"), then replace "remotes" with "devtools" in the above code and try again, such as: devtools::install_github(...).

Troubleshooting Lab Reports

  • If the Knit to PDF option is not showing up for you when you click the triangle next to the Knit button, you should try 2 things. First, make sure you are using the BIOL710 Lab Report Template which includes output: pdf_document: default in the YAML header (at the top). If that is done, you can try installing a package to help knit to PDF such as TinyTeX with tinytex::install_tinytex()

Run into any problems not listed above? Let me know and when we figure it out we'll add to the list.