The practical today will be guided using a Qualtrics survey. The survey can be found here:
Below are instructions for today’s practical (also found at the beginning of the qualtrics survey)
2022 International Statistical Genetics Workshop
Assumptions and biases in biometrical models and extended twin family designs
Today you’ll be working together as a group to better understand CTD and NTFD models, their instantiation in openMx scripts, and biases in those models if assumptions are violated.
Everyone can open the Qualtrics survey, but only the group Scribe (more on that person below) should answer questions in the survey. I.e., one set of answers per group. This Qualtrics survey will guide you through the practical and help the tutors understand where groups are at and how they’re doing.
Throughout the practical, you will be asked to work out solutions to problems and to share your solutions using this survey. Some of these problems have exact numerical answers. Others are open-ended thought questions. Please discuss and debate your answers among yourselves before asking the Scribe to put down your group answer in Qualtrics. Everyone should try to participate. After you have collectively come up with your best answer, put that answer in the answer box.
You will also be working through an R script alongside the Qualtrics survey. Everyone should have the R script open on their computer and everyone should run it together at the same time. When prompted in the Qualtrics survey, run the relevant Section of the R script line by line (e.g., hitting Ctr + Enter, or Apple + Enter) or in small chunks of code. The R scripts are broken up into Sections. Please don’t skip ahead - keep pace with the Qualtrics survey.
Groups should ask one person (Group Leader; see below) to share their screen. This can be the same person as the Scribe but it might be better to have them be different people because the Scribe will be busy writing. The Leader should share their screen with the group, alternating between the Qualtrics survey window and the RStudio window. Everyone should work through the survey and script together. The Leader should read the Qualtrics questions and also read the parts of the R script denoted “NOTE:”
After everyone in the group has finished a particular Section of the R script, the group should pause to discuss it and any questions they have about it.
No cheating: Don’t skip ahead in the survey or run the whole R script to get answers. The point of all this isn’t to get a good “score” - it’s to learn!
Please spend a couple of minutes introducing yourselves. You will need to then choose two people who will serve two different roles in your group:
Group Scribe : This person will submit the groups’ answers in this Qualtrics survey.
Group Leader : The Leader doesn’t need to know more about the topic; they’re just the reader/screen sharer, but that doesn’t quite roll off the tongue like “Leader” does. The Leader will share their screen, alternating between the Qualtrics and RStudio windows. They will read aloud the Qualtrics questions as well as specific comments in the R script that begin with the word “NOTE”. The comments following the word “NOTE” are ones that I think are especially important for you to understand. Groups should discuss these comments among themselves to ensure that they’re understood.
People other than the group Leader are free to share screen if there are particular points to be made. Remember that anyone can also share code or instructions via chat.
As you’re going through this tutorial, we’ll call you back into the main room once or twice to check in and take a break.
There are hints built into some of the questionnaire. Also, answers to some questions come later on in the Qualtrics survey or the R script (remember, no cheating). If you need more help please click the ‘Ask for help’ button in Zoom and someone will be by.
To get started ssh into the workshop server. Use mkdir to make a working directory for today’s tutorial and copy the files from /faculty/matt/2022/CTD.NTFD/ to your working directory. So navigate to where your working directory is, and then type the following command (the period at the end is part of the code):
cp -r /faculty/matt/2022/CTD.NTFD/ .