# Quiz

Get the quiz sheet for this module from the general Assessments page. Fill it in, then submit to the online grading system before the deadline.

# Exercise

This project asks you to write code to do a simple data analysis. This also involves group work, and of course GitHub.

The first part of the project is due by Wednesday, so your classmate can do their part before the Friday deadline.

Since this will be part of your portfolio site, and you already posted a link to that previously, you don’t need to post anything, I know where to find it. Therefore there is no exercise Slack channel for this module.

## Group setup

Assign each member in your group an (arbitrary) number (I’m calling them M1, M2, …). For this exercise, everyone will first work on their own and finish this part by Wednesday. Then M1 will contribute to M2’s repository, M2 will work on M3, etc. The last person (M3/M4/M5, based on the number of people in our group), will work on M1’s repository. This way, everyone will work on their own and one group member’s repository. Details are given below.

## Getting started

Open your portfolio website project in RStudio. Then open the file for the coding exercise, coding_exercise.qmd.

If you write R code, your comments will be lines that start with #. For QUarto or R Markdown files, you can either add comments as Markdown text above/below your code, and/or add comments inside your R code chunks. Both is ideal. R Studio allows you to quickly turn sections of a document into comments or un-comment them (In the Code section of the R Studio menu). That can be useful for turning on/off code during testing, or hiding some parts of text that’s just meant for you but not for the reader.

We’ll look at and play with some data from the dslabs package. Write a code chunk using the library() function that loads the package (install the dslabs package first if you don’t have it yet).

It is good practice to load all packages at the beginning of your code. So if you are using some R package, instead of loading it with library just before you use it, place all your library commands at the beginning of your R script or Quarto file. Also, add a short comment explaining why you are loading a certain package. For a complex project, it might even make sense to list all packages you use in a readme file. Even better is to use something like the renv package which keeps track of all your packages and makes sure someone running your project at a later time gets exactly the same packages you use. While I’m not requiring renv for the course, I encourage you to check it out and if you are up for it, use it for the class exercises and the project.

All the code you write for this (and any other) project should be written into an R or Quarto file, not in the R console. The reason for that is that you want a permanent record of what you did, and the ability to modify and re-run your analysis easily. For this exercise, you can either write the code directly into the Quarto document, or if you prefer the setup of a separate R script and pulling code into the Quarto document (see the data analysis template for an example), you can do it that way too.

We’ll look at the gapminder dataset from dslabs. Write a code chunk using the help() function that pulls up the help page for the data to see what it contains. Then use the str() and summary() functions to take a look at the data. Use the class() function to check what type of object gapminder is.

To illustrate how that should look, you should have these lines of code so far for this exercise.

#load dslabs package
library("dslabs")
#look at help file for gapminder data
help(gapminder)
#get an overview of data structure
str(gapminder)
#get a summary of data
summary(gapminder)
#determine the type of object gapminder is
class(gapminder)

## Processing data

You can accomplish the next steps (and pretty much anything) with just basic R commands and not using extra functionality from packages. However, things are often easier with packages. For data processing tasks, the packages from the tidyverse are very useful. You can do the following tasks with any commands/packages you like.

Write code that assigns only the African countries to a new object/variable called africadata. Run str and summary on the new object you created. You should now have 2907 observations, down from 10545. Depending on how you do this, you might also notice that all the different categories are still kept in the continent (and other) variables, but show 0. R does not automatically remove categories of what in R is called a factor variable (a categorical variable) even if they are empty. We don’t have to worry about that just now, but something to keep in mind, it can sometimes lead to strange behavior.

Take the africadata object and create two new objects (name them whatever you want), one that contains only infant_mortality and life_expectancy and one that contains only population and life_expectancy. You should have two new objects/variables with 2907 rows and two columns. Use the str, and summary commands to take a look at both.

I find it the least confusing to call things which store values in R objects (e.g., x is an object here: x <- 2 + 2) and reserve the word variable for a data variable, i.e., usually a column. However, it is common in programming to refer to an object as a variable as well. Because of that, I sometimes use that terminology (inadvertently) too. So if I talk about a variable, you need to determine from the context if I mean a certain variable in the data (e.g. height or weight), or a variable in R (e.g. x or result) that stores some content.

## Plotting

Using the new variables you created, plot life expectancy as a function of infant mortality and as a function of population size. Make two separate plots. Plot the data as points. For the plot with population size on the x-axis, set the x-axis to a log scale.

You should see a negative correlation between infant mortality and life expectancy, which makes sense. You should also see a positive correlation between population size and life expectancy. In both plots, especially the second one, you will see ‘streaks’ of data that seem to go together. Can you figure out what is going on here? Take another look at the africadata data we generated, which should give you a hint of what’s happening.

## More data processing

I’m sure you realized that the pattern we see in the data is due to the fact that we have different years for individual countries, and that over time these countries increase in population size and also life expectancy. Let’s pick only one year and see what patterns we find. We want a year for which we have the most data. You might have noticed that in africadata, there are 226 NA (i.e., missing values) for infant mortality. Write code that figures out which years have missing data for infant mortality. You should find that there is missing up to 1981 and then again for 2016. So we’ll avoid those years and go with 2000 instead. Create a new object by extracting only the data for the year 2000 from the africadata object. You should end up with 51 observations and 9 variables. Check it with str and summary.

## More plotting

Let’s make the same plots as above again, this time only for the year 2000. Based on those plots, there seems to still be a negative correlation between infant mortality and life expectancy, and no noticeable correlation between population size and life expectancy. Let’s apply some statistics to this data.

## A simple fit

Use the lm function and fit life expectancy as the outcome, and infant mortality as the predictor. Then use the population size as the predictor. (Use the data from 2000 only.) Save the result from the two fits into two objects (e.g. fit1 and fit2) and apply the summary command to both, which will print various fit results to the screen. Based on the p-values for each fit, what do you conclude?

Once you are done with your exercise, re-build your website. Make sure no error messages show up. A preview should show up, check that the page for this exercise looks the way you want it to. Once you are happy with how everything looks, close RStudio. Go to GitKraken, commit your changes, and push to the remote repository. Check your portfolio website online to make sure you can now see the newly created R exercise document (in addition to your previously created About page). Of course, at any point, feel free to make further enhancements to your portfolio website.

## Improving each other’s work

Once everyone has done their part (by Wednesday at the latest), you’ll contribute to another group member’s project.

Earlier, we did collaborative work by having individuals added as collaborators for a repository. There are other ways, we’ll try a different one here, called the Fork and pull-request workflow. You’ll be using that multiple times throughout this class.

The basic idea is as follows. First, you make a copy of someone’s GitHub repository. In GitHub terminology, that is called doing a fork of their repository. You can do that for any public repository, even if you are not a collaborator on the repository.

Then you implement your improvements in the forked repository. Once you are done, you ask the owner of the original repository to incorporate the updates you made in the fork into their main repository. This last part is called issuing a pull request. You are requesting that the other person pull your changes into their repository, hence the at times confusing (at least for me) terminology. I prefer to think of them as merge requests or sync requests, i.e. you are requesting that they merge or sync your changes into their repository. You’ll find the terminology merge request is used at times. If the person who controls the main repository likes your changes, they will merge your fork into the main branch. And just like that, you have contributed to some project becoming better! We will practice this fork and pull flow now.

Find the repository of the team member you will contribute to and Fork their repository. You can find links to everyone’s portfolio repository in the Introductions Slack channel. Then clone it to your local machine, as you have done previously with your own repositories. In fact, this fork is now your own repository, you have it forever, even if the person who owns the original repository deletes theirs.

Open the file that contains the coding exercise. It should look fairly similar to yours, though probably somewhat different since there are many ways to do things in R, and their comments might be different.

Start a new section below the part your classmate did. Add a sentence to indicate where your section starts and also add your name. E.g., you can write something like “this section added by YOURNAME”.

Write some more code to do some more analysis of the dataset. This is fairly open-ended. I want you to create a few more plots of the data, and fit another model to some parts of data and display the fitting results in a table. You can e.g. use the broom package to convert output from lm into a data frame you can show as a table. What exactly you explore, plot and fit is up to you.

Once you wrote your code, confirm that it runs without problems and errors, and produces the expected results. Once everything is good, commit and push your changes to the remote. Note that this pushes to your fork (i.e. copy) of the repository. Now it’s time to offer your contribution to your classmate to integrate into their repository.

## Making a pull request

Let’s contribute your code to your classmate’s project. Go to the GitHub.com website for your (forked) repository. In the top left, you should see the New Pull Request button. (Underneath, it should say something like this branch is N commits ahead of NNN). Click the New Pull Request button. A page comes up showing what you want to do, which is to send your changes to the original repository. You are requesting that the other person pull your changes into their repository. Hopefully, you’ll see a green check-mark that says able to merge. If your classmate made changes to the same files you did, it could have created a merge conflict. Hopefully, this won’t be the case. In either case (merge conflict or not), you can click the green button and Create a pull request. You are presented with a box in which you want to add a meaningful title, so the other person knows what you changed and some more explanation in the box. Then click Create pull request.

## Checking and merging pull requests

Once your classmate who has worked on your repository creates a pull request, you should receive a notification that a pull request was created. Go to the GitHub site and to your online portfolio repository. Click on Pull requests, then click on the request (there should only be one). Take a look. On the first page, it shows you their message and if there are conflicts with your version of the repository. Hopefully, you didn’t change things around while they did, so there shouldn’t be any conflicts. Click on the Files changed button, which will show you an overview of the code they changed. Removals are red, and additions are green.

On the main pull request site, you can do various things. If you don’t like the suggested edits, you can write a comment and close the pull request without merging their changes into your repository. If you like most of what they did, but there is something they need to adjust, write a comment and let them know. Still, close the pull request and ask them to send a new one. If you are ok with their changes (hopefully, this is the case here), you can merge the pull request and close it. Their updates are now part of your repository.

Important: To check that everything is ok, pull the updated repository to your local computer. Rebuild the website, make sure the preview looks ok and all the updates show. Since the website rebuilt on your local machine likely changed some files, commit your updates, push to the remote. If you now go to your portfolio website, you should see the changes from your classmates showing underneath what you wrote originally.

Since this will be part of your portfolio site, and you already posted a link to that previously, you don’t need to post anything, I know where to find it.

I mentioned this before, but it doesn’t hurt repeating. At times, you will get merge conflicts. At that stage, it gets a bit tricky. GitKraken has a good tool to help you resolve conflicts, and it works well for text files (code, Rmd, md, etc.). It doesn’t work well for other files (word, Excel, etc.). Sometimes you have to temporarily move one of the conflicting files out of the repository, then do the merge, then manually see how the files changed and do the merge yourself. To minimize conflicts, it is good practice to make multiple pull requests with small changes instead of a single large pull request. If you changed 20 files and 2 of them create a conflict, the person has to reject your complete pull request if they don’t want those conflicts. It is better to change a few files and work on just one topic, then issue a pull request. After that, start the next set, and issue another pull request. By breaking them up, it is more likely that conflicts are avoided or localized.

Some more information on forks and pulls and what to do if things don’t go right can be found in happygitwithR. Note that a lot of the commands described for use on the command line (e.g. stash) can be applied graphically through GitKraken.

Github also has branches. Those are similar to forks but meant for more internal use. For instance, if you have a project and want to implement something new, but it might not work, you can create a branch, work in that branch, and once everything is ok, you can merge the branch into the main/master. This is useful if you write software that others are using, and you don’t want to break the whole thing. It is also helpful if you work with collaborators on a project. To be able to use branches, you need to be an owner or member of a repository. In contrast, you can fork any public repository.

## Another fork and pull exercise

This is optional. You can do it at any time during this course (and more than once) 😁.

Help improve the course with your contributions! Find something wrong/unclear/worth improving with this course (e.g. a typo, something confusing, a broken link, a suggestion for a new reference, or anything else). Go to the Github repository for this course. Follow the steps outlined above: Fork the course to your personal account, clone it to your local computer, implement your updates, push it back to GitHub, then initiate a pull request. I will get a notification of your pull request. If things look ok and no conflicts exist, I will merge your improvements into the course. And just like that, you have contributed to improving this course! (And of course, you will be listed in the Acknowledgments section of the main course page.)

Another option for helping to improve the course website is to file a GitHub Issue. Feel free to do so any time during the course to let me know of anything that needs fixing.

# Discussion

Describe one thing you learned in this module about R that you find rather annoying or confusing or dumb, and one thing about R that you find interesting or cool or awesome.