You should have R and RStudio installed (that was homework zero). If you have never used R before, the following swirl tutorial will get you started. If you have used some R before, it is likely a good idea to work through the tutorial to make sure you have the required background for this course. More experienced users can help newer users get started.
In R or RStudio, type install.packages("swirl") to download the swirl tutorial package from the internet. Every line of code must be followed by the [ENTER] key, but usually we don’t mention that. The [ENTER] key is sometimes called [RETURN].
Now swirl is installed on your computer, you can type library("swirl") to load the package into your R session.
Finally, swirl() starts the tutorial program. Select 1: R Programming by typing 1 [ENTER] and then, again, hit 1 [ENTER] to start Lesson 1: Basic Building Blocks.
Repeat this with Lesson 3: Sequences of Numbers and Lesson 4: Vectors. We will not need the material in Lesson 2: Workspace and Files but you can do this tutorial too if you have time.
The lessons are designed to take 10-20 minutes each. In addition to introducing some knowledge, they give your fingers a chance to start practicing coding in R. You will have a chance to ask swirl questions during lab. If possible, bring your laptop to lab.
For your homework report, write a brief paragraph on what you did with swirl and the techical or conceptual obstacles (if any) that you encountered and (hopefully) overcame.
Here we will test some of the basics of R data manipulation which you should know or should have learned by following the tutorials above. We will look at the data in the file femaleMiceWeights.csv taken from a study of diabetes. The body weight of mice (in grams) was measured after around two weeks on one of two diets (chow or high fat). These data are in comma separated variable (csv) format. You can read the data into R with
mice <- read.csv("https://ionides.github.io/401w18/hw/hw01/femaleMiceWeights.csv")Report the body weight of the first mouse and the exact name of the column containing the weights.
The [ and ] symbols can be used to extract specific rows and specific columns of the table. What is the entry in the 12th row and second column?
You should have learned how to use the $ character to extract a column from a table and return it as a vector. Use $ to extract the weight column and report the weight of the mouse in the 11th row.
The length function returns the number of elements in a vector. How many mice are included in our dataset?
To create a vector with the numbers 3 to 7, we can use seq(3,7) or, because they are consecutive, 3:7. View the data and determine what rows are associated with the high fat or hf diet. Then use the mean function to compute the average weight of these mice.
For your homework report, give answers to the questions above and the code used to generate them. If you already know Rmarkdown, this is a great tool for statistical writing and data analysis, and you can write your homework by editing the Rmarkdown document at https://ionides.github.io/401w18/hw/hw01/hw01.Rmd. If you don’t know Rmarkdown yet, working it out may be too much for this homework; you can simply cut and paste from the homework document and an R session.
License: This material is provided under an MIT license
Acknowledgement: This homework is derived from https://genomicsclass.github.io/book