Study 1

• Original: http://journal.sjdm.org/16/16428/expt1.csv
• Cleaned https://dl.dropboxusercontent.com/u/7618380/Millar_study1.txt

Study 2

• Original: http://journal.sjdm.org/16/16428/expt2.csv
• Cleaned https://dl.dropboxusercontent.com/u/7618380/Millar_study2.txt

0. For this assignment, you’ll need both the yarrr package and the dplyr package. Install (if you don’t have them already) and load the packages using the following code:

# Install the dplyr and yarrr packages (if you don't have them already)
install.packages("dplyr")
install.packages("yarrr")

# Load the libraries for the the assignment
library("dplyr")
library("yarrr")

1. Open your R project from last week (I recommended calling it RCourse or something similar). There should be at least two folders in this working directory: data and R.

2. Open a new R script and save it as wpa5.R in the R folder in your project directory

3. The data are stored in two separate .csv files. Study 1 is at https://dl.dropboxusercontent.com/u/7618380/Millar_study1.txt and Study 2 is at https://dl.dropboxusercontent.com/u/7618380/Millar_study2.txt. Load the data into R by using read.table() (or the Import Dataset button in RStudio) into new objects called study1 and study2. Note: You can either read the tables directly from the web, or download the files to your computer, and then load them (Hint: Make sure to use the arguments sep = "\t" and header = TRUE)

4. Look at the structure of each data frame using str() and head() to make sure they were loaded correctly.

Histograms

10. Create a histogram of the acceptability scores from study 1. Add appropriate labels and colors as you see fit!

# FIX THE CODE BY REPLACING ZZZ WITH THE CORRECT ARGUMENTS
hist(x = ZZZ
     main = "ZZZ",
     xlab = "ZZZ",
     col = "ZZZ")

11. Now do the same for study 2. And for this plot, add a vertical line at the mean of the distribution with abline() (or segments())

# FIX THE CODE BY REPLACING ZZZ WITH THE CORRECT ARGUMENTS

hist(x = ZZZ
     main = "ZZZ",
     xlab = "ZZZ",
     col = "ZZZ")

# Add vertical line at mean of the distribution
abline(v = ZZZ,
       lty = 2)

Scatterplots

12. Create a scatterplot showing the relationship between age and acceptability score in study 1. Add appropriate labels!

# FIX THE CODE BY REPLACING ZZZ WITH THE CORRECT ARGUMENTS

plot(x = ZZZ,
     y = ZZZ,
     xlab = "ZZZ",
     ylab = "ZZZ",
     main = "ZZZ")

13. Now, make the plot look a bit nicer! Try changing the point types (e.g.; pch = 16), point colors (e.g.; col = gray(.0, .2), or col = transparent("blue", .5))

14. Now add grid lines with grid() (Hint: Just evaluate grid() after your plot!)

15. Now let’s add a regression line to the plot. Adding a regression line is easy. First, create a linear model object created with lm(). Then add the model to the plot with abline():

# JUST COPY, PASTE, AND RUN!

# Create a regression model
model <- lm(acceptability ~ age, 
            data = study1)

# Add the model to the plot!
abline(model,
       lwd = 2, 
       col = "red")

16. Now create the same scatterplot for the study 2 data. Be sure to include the gridlines and regression line

Barplot

The authors present the following barplot on page 328, let’s try to represent the same data with a barplot in R:

17. In order to create a stacked barplot with the barplot() function, we first need to create a matrix of values. Run the following code to calculate a matrix of mean acceptability scores as a function of Important and Direct with aggregate() and cbind():

# JUST COPY, PASTE, AND RUN!

# Create a matrix of group means
s1.as.means <- aggregate(acceptability ~ important + direct,
                      FUN = mean, 
                      data = study1)

s1.as.means.mtx <- cbind(s1.as.means[1:2, 3], s1.as.means[3:4, 3])
colnames(s1.as.means.mtx) <- c("Means", "Side Effect")
rownames(s1.as.means.mtx) <- c("Important", "Unimportant")

18. Now create a barplot from the study 1 data by entering the correct arguments in the following code

# FIX THE CODE BY REPLACING ZZZ WITH THE CORRECT ARGUMENTS

barplot(height = s1.as.means.mtx,
        beside = TRUE, 
        legend.text = TRUE, 
        ylim = c(ZZZ, ZZZ),
        ylab = "ZZZ")

19. Now, repeat the process to get the same plot from study 2:

pirateplot

20. Now create a pirateplot of the same data from study 1 (see the help menu by running ?pirateplot). Add appropriate labels and feel free to use your favorite theme (1, 2, or 3), and palette from the piratepal() function like "evildead" or "pony"! (run piratepal("all") to see all of the palettes!

pirateplot(formula = ZZZ ~ ZZZ,
           data = ZZZ,
           pal = ZZZ,
           theme = ZZZ)

21. Now do the same from study 2. Again, add appropriate labels and feel free to use your favorite palette or theme.

21b. Turn your pirateplot from question 21 into a boring barplot by setting theme = 4, point.o = 0

2 variable histogram

22. Create the following overlapping histogram showing the distribution of acceptability scores between the two studies:

# FIX THE CODE BY REPLACING ZZZ WITH THE CORRECT ARGUMENTS

# study1 acceptability scores
hist(x = ZZZ, 
     col = transparent("blue", .5),
     border = "white", 
     xlab = "ZZZ", 
     main = "ZZZ")

# study2 acceptability scores
hist(x = ZZZ, 
     col = transparent("red", .5),
     border = "white", 
     add = TRUE)

legend(x = 1,
       y = 100, 
       legend = c("ZZZ", "ZZZ"), 
       col = c("blue", "red"), 
       pch = c(15, 15), 
       bty = "n")

Scatterplot with reference lines

23. Add a new column to study2$income that shows income as a function of Age as follows:

# JUST COPY, PASTE, AND RUN!

# Add a new column to study 1 called Income
study1$income <- study1$age + rnorm(n = nrow(study1), mean = 10, sd = 15)

# Add a new column to study 1 called Income
study2$income <- 40 + rnorm(n = nrow(study2), mean = 10, sd = 15)

24. Now, create the following scatterplot using the following template:

# FIX THE CODE BY REPLACING ZZZ WITH THE CORRECT ARGUMENTS


#  Create a blank plot with labels
plot(x = 1, 
     y = 1,
     xlim = c(ZZZ, ZZZ),
     ylim = c(ZZZ, ZZZ),
     xlab = "ZZZ", 
     ylab = "ZZZ",
     main = "ZZZ",
     type = "n")

# Add points for study1
points(x = ZZZ, 
       y = ZZZ, 
       pch = 16, 
       col = transparent("red", .8))

# Add regression line for study 1
abline(lm(income ~ age, data = study1), 
       col = "red", lty = 2, lwd = 2)

# Add points for study2
points(x = ZZZ, 
       y = zzz, 
       pch = 16, 
       col = transparent("blue", .8))

# Add regression line for study2
abline(lm(income ~ age, data = study2), 
       col = "blue", lty = 2, lwd = 2)

# Add legend

legend(x = 70,
       y = 40,
       legend = c("ZZZ", "ZZZ"), 
       pch = 16, 
       col = c("blue", "red"),
       bty = "n")

grid()

Balloon plots

24. You can have a lot of fun with plots. Let’s make a new type of plot called a balloon plot. A balloon plot will be a customized scatterplot where points are shown as balloons. In the code below, I’ll create a new custom function (we’ll get to this later in the course) called balloonplot(). Look at the code to see how it generally works. Then, copy, paste, and run the code in your script.

# JUST COPY, PASTE, AND RUN!

# Create balloonplot(), a wrapper function for plot() that turns points into balloons!

balloonplot <- function(
                  x, y,    # x and y vectors
                  cex = 1, # point sizes
                  col = piratepal("basel"), # color 
                  ... # Other arguments passed to plot()
                  ) {
  
# Set up the plotting space
plot(1, 
     bty = "n",
     xlim = c(min(x), max(x)),
     ylim = c(min(y), max(y)),
     type = "n",
     ...
)

# Add Strings with segments()
segments(x0 = x + rnorm(length(x), mean = 0, sd = .3), 
         y0 = y - cex * diff(range(y)) / 25, 
         x1 = x, 
         y1 = y, 
         col = gray(.5, .5),
         lwd = cex / 4
         )

# Add balloons
points(x, 
       y, 
       cex = cex, # Size of the balloons
       pch = 21, 
       col = "white", # white border
       bg = col)

# Add gridlines
grid()
}

25. Now let’s try our new balloonplot() function on some data! Run the following to create a balloon plot of the relationship between pirate’s height and weight:

# JUST COPY, PASTE, AND RUN!

balloonplot(x = pirates$height, 
             y = pirates$weight, 
             cex = 1.5,
             col = piratepal("xmen", .3),
             xlab = "Height", 
             ylab = "Weight", 
             main = "Balloon plot of pirate data")

26. Now, create a balloon plot of the age and income data from study 1! Play around with col and the cex arguments to see how the plot changes.

You pick the plot

For the following exercises, make a plot that you think represents the data bast.

The movies dataframe in the yarrr package contains data about the top 5000 grossing movies of all time. You can learn more about the data using the help menu ?movies

27. Create a plot that shows the relationship between a movie’s release year and its running time. Customise it and make it look nice!

28. Create a plot that shows the relationship between a movie’s budget and its revenue. Customise it and make it look nice!

29. Create a plot that shows the relationship between genre and time. Customise it and make it look nice! (Hint: You may notice that many of the times are equal to 0, try creating the plot after excluding these values using subset.)

Submit!

Save and email your wpa_4_LastFirst.R file to me at nathaniel.phillips@unibas.ch. Then, go to https://goo.gl/forms/UblvQ6dvA76veEWu1 to complete the WPA submission form.