In this lab, we’ll try to cover some of the basic ways of interacting with R and then pretty quickly switch to data wrangling and data visualization. I recommend using RStudio, https://support.rstudio.com, because they have lots of great resources (e.g., Help –> Cheatsheets).

Another great resource for many of the functions we’ll use: http://r4ds.had.co.nz/.

Calculator

First of all, R can be used as a calculator:

1 + 1
## [1] 2
2 * 3
## [1] 6
3 ^ 2
## [1] 9
5 %% 3
## [1] 2

It’s a good idea not to work directly in the console but to have a script where you will first write your commands and then execute them in the console. Once you open a new R script there are a few useful things to note:

Variables

Values can be stored as variables

a <- 2
a
## [1] 2
b <- 2 + 2
b
## [1] 4
c <- b + 3
c
## [1] 7

When you’re defining variables, try to use meaningful names like average_of_ratings rather than variable1.

Functions

A function is an object that takes some arguments and returns a value.

log(4)
## [1] 1.386294
print("hello world")
## [1] "hello world"
help(log)
?log

Vectors

If you want to store more than one thing in a variable you may want to make a vector.To do this you will use the function c() which combines values

v1 <- c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
v1
##  [1]  1  2  3  4  5  6  7  8  9 10

HINT: If you are ever unsure about how a function works or what arguments it takes. Typing ?[FUNCTION NAME GOES HERE] will open up a help file (e.g., ?c).

Now that we have some values stored in a vector, we may want to access those values and we can do this by using their position in the vector or index.

v1[1]
## [1] 1
v1[5]
## [1] 5
v1[-1]
## [1]  2  3  4  5  6  7  8  9 10
v1[c(2, 7)]
## [1] 2 7
v1[-c(2, 7)]
## [1]  1  3  4  5  6  8  9 10
v1[1:3]
## [1] 1 2 3
v1[-(1:3)]
## [1]  4  5  6  7  8  9 10

You may also want to get some overall information about the vector:

Earlier we created v1 by simply listing all the elements in it and usingc() but if you have lots of values, this is very tedious. There are some functions that can help make vectors more efficiently

v2 <- (1:10)
v2
##  [1]  1  2  3  4  5  6  7  8  9 10
v3 <- rep(x = 1, times = 10)
v3
##  [1] 1 1 1 1 1 1 1 1 1 1
v4 <- rep(1:2, 5)
v4
##  [1] 1 2 1 2 1 2 1 2 1 2
v5 <- seq(from = 1, to = 20, by = 2)
v5
##  [1]  1  3  5  7  9 11 13 15 17 19

Note that for v4, I didn’t include the names of the arguments but R figures out which is which by the order

You can also apply operations to all elements of the vector simultaneously.

v1 + 1
##  [1]  2  3  4  5  6  7  8  9 10 11
v1 * 100
##  [1]  100  200  300  400  500  600  700  800  900 1000

You can also do pair-wise operations on 2 vectors.

v1 + v2
##  [1]  2  4  6  8 10 12 14 16 18 20

Characters

So far we’ve looked at numeric variables and vectors, but they can also be strings

name <- "Rachel"
name
## [1] "Rachel"
friends <- c("Rachel", "Ross", "Joey", "Monica", "Chandler", "Phoebe")
friends
## [1] "Rachel"   "Ross"     "Joey"     "Monica"   "Chandler" "Phoebe"
str(friends)
##  chr [1:6] "Rachel" "Ross" "Joey" "Monica" "Chandler" "Phoebe"

You can even store numbers as strings (and sometimes data you load from a file will be stored this way so watch out for that)

some_numbers <- c("2", "3", "4")

…but you can’t manipulate them as numbers

some_numbers + 1

So you might want to convert the strings into numbers first using as.numeric()

some_numbers <- as.numeric(some_numbers)
some_numbers + 1
## [1] 3 4 5

NA

Another important datatype is NA. Say I’m storing people’s heights in inches in a dataframe, but I don’t have data on the third person.

heights <- c(72, 70, NA, 64)
str(heights)
##  num [1:4] 72 70 NA 64

Even though it’s composed of letters, NA is not a string, in this case it’s numeric, and represents a missing value, or an invalid value, or whatever. You can still perform operations on the height vector:

heights + 1
## [1] 73 71 NA 65
heights * 2
## [1] 144 140  NA 128

if you had an NA in a vector of strings, its datatype would be a character.

friends <- c("Rachel", NA, "Joey", "Monica", "Chandler", "Phoebe")
str(friends)
##  chr [1:6] "Rachel" NA "Joey" "Monica" "Chandler" "Phoebe"

If you have NA in your vector and want to use a function on it, this can complicate things

mean(heights)
## [1] NA

To avoid returning NA, you may want to just throw out the NA values using na.omit and work with what’s left.

heights_no_NA <- na.omit(heights)
mean(heights_no_NA)
## [1] 68.66667

Alternatively, many functions have a built-in argument na.rm that you can use to tell the function what to do about NA values. So you can do the previous step in 1 line:

mean(heights_no_NA, na.rm = TRUE)
## [1] 68.66667

It can also be useful to know if a vector contains NA ahead of time and where those values are:

is.na(heights)
## [1] FALSE FALSE  TRUE FALSE
which(is.na(heights))
## [1] 3

Booleans

This brings us to another important datatype: booleans. They are TRUE or FALSE, or T or F. Here are some expressions that return boolean values:

1 < 100
## [1] TRUE
500 == 500 # for equality testing, use double-equals!
## [1] TRUE
1 == 2 | 2 == 2 # OR
## [1] TRUE
1 == 1 & 100 == 100 # AND
## [1] TRUE
1 == 1 & 100 == 101 # AND
## [1] FALSE

Try it yourself…

  1. Make a vector, “tens” of all the multiples of 10 up to 200.

  2. Find the indices of the numbers divisible by 3

    tens <- seq(from = 10, to = 200, by = 10)
tens
    ##  [1]  10  20  30  40  50  60  70  80  90 100 110 120 130 140 150 160 170
## [18] 180 190 200
    which(tens %% 3 == 0)
    ## [1]  3  6  9 12 15 18

Dataframes

Most data you will work with in R will be in a dataframe format. Dataframes are basically tables where each column is a vector with a name. Dataframes can combine character vectors, numeric vectors, logical (boolean) vectors, etc. This is really useful for data from experiments where you may want one column to contain information about the name of the condition (a string) and another column to contain response times (a number).

Let’s read in some data!

But first a digression… One of the best things about R is that it is open-source and lots of R users who find that some functionality is missing from base R (which is what we’ve been using so far) will write their own functions and then share them with the R community. Often times they’ll write whole packages of functions to greatly enhance the capabilities of base R. In order for you to use those packages, they need to be installed on your computer and loaded up in your current session. For current purposes, you will need the tidyverse package and you can install it with this simple command:

install.packages("tidyverse")

When the installation is done, load up the library of functions in the package with the following command:

library(tidyverse)
library(stringr)

Okay, digression over.

Let’s read in your lexical decision data from earlier using a tidyverse function called read_csv().

data_source <- "http://web.mit.edu/psycholinglab/data/"
rt_data <- read_csv(file.path(data_source, "in_lab_rts_2018.csv"))

Our data is now stored as a dataframe. The output message tells us what datatype read_csv() assigned to every column. It usually does a pretty good job of guessing the appropriate datatype but on occasion you may have to correct using a function like as.numeric() or as.character().

Note that the path to the data can be any folder on your computer or online (a url). If you just put in the filename without the path, it will look for the file in the local folder.

Also note, that if you have column headers in your csv file, read_csv() will automatically name your columns accordingly and you won’t have to specify col_names=.

At this point, it’s a good idea to look at your data to make sure everything was correctly uploaded. In R Studio, you can open up a viewing pane with the command View(d) to see the data in spreadsheet form. You can also use summary(), str() and glimpse()

glimpse(rt_data)
## Observations: 264
## Variables: 5
## $ time    <dbl> 1.518185e+12, 1.518185e+12, 1.518185e+12, 1.518185e+12...
## $ subject <int> 9, 9, 7, 9, 7, 9, 8, 6, 3, 7, 9, 0, 8, 6, 3, 9, 7, 8, ...
## $ word    <chr> "book", "noosin", "book", "eat", "noosin", "goamboozle...
## $ trial   <int> 0, 1, 0, 2, 1, 3, 0, 0, 0, 2, 4, 0, 1, 1, 1, 5, 3, 2, ...
## $ rt      <dbl> 2.2346671, 0.8533659, 3.4355321, 0.5956440, 0.8158729,...

You can also extract just the names of the columns:

names(rt_data)
## [1] "time"    "subject" "word"    "trial"   "rt"

Or just the first (or last) few rows of the dataframe:

head(rt_data)
## # A tibble: 6 x 5
##           time subject       word trial        rt
##          <dbl>   <int>      <chr> <int>     <dbl>
## 1 1.518185e+12       9       book     0 2.2346671
## 2 1.518185e+12       9     noosin     1 0.8533659
## 3 1.518185e+12       7       book     0 3.4355321
## 4 1.518185e+12       9        eat     2 0.5956440
## 5 1.518185e+12       7     noosin     1 0.8158729
## 6 1.518185e+12       9 goamboozle     3 0.6285422
tail(rt_data)
## # A tibble: 6 x 5
##           time subject           word trial        rt
##          <dbl>   <int>          <chr> <int>     <dbl>
## 1 1.518185e+12      14         seefer    18 0.7138901
## 2 1.518185e+12      14            sqw    19 0.6964531
## 3 1.518185e+12      13   encyclopedia    20 1.5294392
## 4 1.518185e+12      14   encyclopedia    20 0.9169972
## 5 1.518185e+12      13 understandable    21 1.0834951
## 6 1.518185e+12      14 understandable    21 0.5998409

Or look at the dimensions of your dataframe

dim(rt_data)
## [1] 264   5
nrow(rt_data)
## [1] 264
ncol(rt_data)
## [1] 5

To access a specific column, row, or cell you can use indexing in much the same way you can with vectors (just now with 2 dimensions)

rt_data[1, 2] # what's in the 1st row, 2nd column
## # A tibble: 1 x 1
##   subject
##     <int>
## 1       9
rt_data[1, ] # the 1st row for all columns
## # A tibble: 1 x 5
##           time subject  word trial       rt
##          <dbl>   <int> <chr> <int>    <dbl>
## 1 1.518185e+12       9  book     0 2.234667
rt_data[, 2] # all rows for the 2nd column
## # A tibble: 264 x 1
##    subject
##      <int>
##  1       9
##  2       9
##  3       7
##  4       9
##  5       7
##  6       9
##  7       8
##  8       6
##  9       3
## 10       7
## # ... with 254 more rows
rt_data[, c(2, 5)] # all rows for columns 2 and 5
## # A tibble: 264 x 2
##    subject        rt
##      <int>     <dbl>
##  1       9 2.2346671
##  2       9 0.8533659
##  3       7 3.4355321
##  4       9 0.5956440
##  5       7 0.8158729
##  6       9 0.6285422
##  7       8 0.7227321
##  8       6 1.2849419
##  9       3 1.0876911
## 10       7 0.6137280
## # ... with 254 more rows
rt_data[, c("subject", "rt")]
## # A tibble: 264 x 2
##    subject        rt
##      <int>     <dbl>
##  1       9 2.2346671
##  2       9 0.8533659
##  3       7 3.4355321
##  4       9 0.5956440
##  5       7 0.8158729
##  6       9 0.6285422
##  7       8 0.7227321
##  8       6 1.2849419
##  9       3 1.0876911
## 10       7 0.6137280
## # ... with 254 more rows

Another easy way to extract a dataframe column is by using the $ operator and the column name

head(rt_data$rt)
## [1] 2.2346671 0.8533659 3.4355321 0.5956440 0.8158729 0.6285422

rt_data$rt is a (numeric) vector so you can perform various operations on it (as we saw earlier)

head(rt_data$rt * 2)
## [1] 4.469334 1.706732 6.871064 1.191288 1.631746 1.257084
mean(rt_data$rt)
## [1] 0.866832

Data manipulation (dplyr)

Often when you upload data it’s not yet in a convenient, “tidy” form so data wrangling refers to the various cleaning and re-arranging steps between uploading data and being able to visualize or analyze it. I’ll start out by showing you a few of the most common things you might want to do with your data.

For example, in this dataset, we want to know about how response times on the lexical decision task might differ depending on whether it’s a real word or a non-word but this information is missing from our data.

Let’s see what words were included in the experiment.

words <- unique(rt_data$word)
words
##  [1] "book"             "noosin"           "eat"             
##  [4] "goamboozle"       "condition"        "xdqww"           
##  [7] "word"             "retire"           "feffer"          
## [10] "fly"              "qqqwqw"           "coat"            
## [13] "condensationatee" "sporm"            "art"             
## [16] "goam"             "gold"             "three"           
## [19] "seefer"           "sqw"              "encyclopedia"    
## [22] "understandable"

Now let’s make a vector containing only the real words:

real_words <- words[c(1, 3, 5, 7, 8, 10, 12, 15, 17, 18, 21, 22)]
real_words
##  [1] "book"           "eat"            "condition"      "word"          
##  [5] "retire"         "fly"            "coat"           "art"           
##  [9] "gold"           "three"          "encyclopedia"   "understandable"

We can check if a value is represented in an array using the operator %in%.

"cat" %in% c("cat", "dog", "horse")
## [1] TRUE
c("cat", "ocelot") %in% c("cat", "dog", "horse")
## [1]  TRUE FALSE

mutate

Now we can add a column to our dataframe, rt_data, that contains that condition information. We’re going to do this using the mutate() function.

rt_data <- mutate(rt_data, is_real = word %in% real_words)
head(rt_data)
## # A tibble: 6 x 6
##           time subject       word trial        rt is_real
##          <dbl>   <int>      <chr> <int>     <dbl>   <lgl>
## 1 1.518185e+12       9       book     0 2.2346671    TRUE
## 2 1.518185e+12       9     noosin     1 0.8533659   FALSE
## 3 1.518185e+12       7       book     0 3.4355321    TRUE
## 4 1.518185e+12       9        eat     2 0.5956440    TRUE
## 5 1.518185e+12       7     noosin     1 0.8158729   FALSE
## 6 1.518185e+12       9 goamboozle     3 0.6285422   FALSE

mutate() is extremely useful anytime you want to add information to your data. For instance, the reaction times here appear to be in seconds but maybe we want to look at them in milliseconds. Maybe we also want to code if the word starts with the letter “b” and code which words are longer than 6 letters long. This can be done all at once.

mutate(rt_data,
       rt_ms = rt * 1000,
       starts_d = str_sub(word, 1, 1) == "b",
       longer_than_6 = if_else(str_length(word) > 6, "long", "short"))
## # A tibble: 264 x 9
##            time subject       word trial        rt is_real     rt_ms
##           <dbl>   <int>      <chr> <int>     <dbl>   <lgl>     <dbl>
##  1 1.518185e+12       9       book     0 2.2346671    TRUE 2234.6671
##  2 1.518185e+12       9     noosin     1 0.8533659   FALSE  853.3659
##  3 1.518185e+12       7       book     0 3.4355321    TRUE 3435.5321
##  4 1.518185e+12       9        eat     2 0.5956440    TRUE  595.6440
##  5 1.518185e+12       7     noosin     1 0.8158729   FALSE  815.8729
##  6 1.518185e+12       9 goamboozle     3 0.6285422   FALSE  628.5422
##  7 1.518185e+12       8       book     0 0.7227321    TRUE  722.7321
##  8 1.518185e+12       6       book     0 1.2849419    TRUE 1284.9419
##  9 1.518185e+12       3       book     0 1.0876911    TRUE 1087.6911
## 10 1.518185e+12       7        eat     2 0.6137280    TRUE  613.7280
## # ... with 254 more rows, and 2 more variables: starts_d <lgl>,
## #   longer_than_6 <chr>

Note: + str_sub() extracts a subset of word starting at position 1 and ending at position 1 (i.e., just the first letter). + if_else() is a useful function which takes a logical comparison as a first argument and then what to do if it is TRUE as the second argument and what to do if it is FALSE as the third.

filter

Now let’s say we want to look at only a subset of the data, we can filter() it:

filter(rt_data, str_length(word) > 6)
## # A tibble: 60 x 6
##            time subject       word trial        rt is_real
##           <dbl>   <int>      <chr> <int>     <dbl>   <lgl>
##  1 1.518185e+12       9 goamboozle     3 0.6285422   FALSE
##  2 1.518185e+12       9  condition     4 0.6441879    TRUE
##  3 1.518185e+12       7 goamboozle     3 1.2371540   FALSE
##  4 1.518185e+12       7  condition     4 0.7699041    TRUE
##  5 1.518185e+12       8 goamboozle     3 0.6066039   FALSE
##  6 1.518185e+12       6 goamboozle     3 0.6936800   FALSE
##  7 1.518185e+12       3 goamboozle     3 0.7247601   FALSE
##  8 1.518185e+12       8  condition     4 0.7711821    TRUE
##  9 1.518185e+12       6  condition     4 0.5985160    TRUE
## 10 1.518185e+12       0 goamboozle     3 0.8194630   FALSE
## # ... with 50 more rows

select

If your dataframe is getting unruly, you can focus on a few key columns with select()

select(rt_data, subject, word, rt)
## # A tibble: 264 x 3
##    subject       word        rt
##      <int>      <chr>     <dbl>
##  1       9       book 2.2346671
##  2       9     noosin 0.8533659
##  3       7       book 3.4355321
##  4       9        eat 0.5956440
##  5       7     noosin 0.8158729
##  6       9 goamboozle 0.6285422
##  7       8       book 0.7227321
##  8       6       book 1.2849419
##  9       3       book 1.0876911
## 10       7        eat 0.6137280
## # ... with 254 more rows

arrange

You can also sort the dataframe by one of the columns:

arrange(rt_data, rt)
## # A tibble: 264 x 6
##            time subject             word trial           rt is_real
##           <dbl>   <int>            <chr> <int>        <dbl>   <lgl>
##  1 1.518185e+12       1           retire     7 0.0003647804    TRUE
##  2 1.518185e+12       1 condensationatee    12 0.0007541180   FALSE
##  3 1.518185e+12      13            three    17 0.3730161190    TRUE
##  4 1.518185e+12      13              art    14 0.4536800385    TRUE
##  5 1.518185e+12       8             word     6 0.4927048683    TRUE
##  6 1.518185e+12      13              sqw    19 0.4932930470   FALSE
##  7 1.518185e+12      14             coat    11 0.4945719242    TRUE
##  8 1.518185e+12      14            three    17 0.5010519028    TRUE
##  9 1.518185e+12       9            xdqww     5 0.5207970142   FALSE
## 10 1.518185e+12       0             word     6 0.5246582031    TRUE
## # ... with 254 more rows

group_by and summarise

Most of the time when you have data, the ultimate goal is to summarize it in some way. For example, you may want to know the mean response time for each subject by type of word (real vs. fake).

summarise(group_by(rt_data, subject, is_real), mean_rt = mean(rt))
## # A tibble: 24 x 3
## # Groups:   subject [?]
##    subject is_real   mean_rt
##      <int>   <lgl>     <dbl>
##  1       0   FALSE 0.8384297
##  2       0    TRUE 0.8294404
##  3       1   FALSE 0.7580644
##  4       1    TRUE 0.8128119
##  5       3   FALSE 0.9057278
##  6       3    TRUE 0.8010959
##  7       4   FALSE 0.8137079
##  8       4    TRUE 0.6964481
##  9       6   FALSE 0.8390218
## 10       6    TRUE 0.7740091
## # ... with 14 more rows

As you can see, we often want to string tidyverse functions together which can get difficult to read. The solution to this is…

%>%

We can create a pipeline where the dataframe undergoes various transformations one after the other with the same functions, mutate(), filter(), etc. without having to repeat the name of the dataframe over and over and much more intuitive syntax.

# this is the previous syntax
mutate(rt_data,
       "rt_ms" = rt * 1000,
       "starts_d" = str_sub(word, 1, 1) == "b",
       "longer_than_6" = if_else(str_length(word) > 6, "long", "short"))
## # A tibble: 264 x 9
##            time subject       word trial        rt is_real     rt_ms
##           <dbl>   <int>      <chr> <int>     <dbl>   <lgl>     <dbl>
##  1 1.518185e+12       9       book     0 2.2346671    TRUE 2234.6671
##  2 1.518185e+12       9     noosin     1 0.8533659   FALSE  853.3659
##  3 1.518185e+12       7       book     0 3.4355321    TRUE 3435.5321
##  4 1.518185e+12       9        eat     2 0.5956440    TRUE  595.6440
##  5 1.518185e+12       7     noosin     1 0.8158729   FALSE  815.8729
##  6 1.518185e+12       9 goamboozle     3 0.6285422   FALSE  628.5422
##  7 1.518185e+12       8       book     0 0.7227321    TRUE  722.7321
##  8 1.518185e+12       6       book     0 1.2849419    TRUE 1284.9419
##  9 1.518185e+12       3       book     0 1.0876911    TRUE 1087.6911
## 10 1.518185e+12       7        eat     2 0.6137280    TRUE  613.7280
## # ... with 254 more rows, and 2 more variables: starts_d <lgl>,
## #   longer_than_6 <chr>
# this is the piping syntax
rt_data %>%
  mutate("rt_ms" = rt * 1000,
         "starts_d" = str_sub(word, 1, 1) == "b",
         "longer_than_6" = if_else(str_length(word) > 6, "long", "short"))
## # A tibble: 264 x 9
##            time subject       word trial        rt is_real     rt_ms
##           <dbl>   <int>      <chr> <int>     <dbl>   <lgl>     <dbl>
##  1 1.518185e+12       9       book     0 2.2346671    TRUE 2234.6671
##  2 1.518185e+12       9     noosin     1 0.8533659   FALSE  853.3659
##  3 1.518185e+12       7       book     0 3.4355321    TRUE 3435.5321
##  4 1.518185e+12       9        eat     2 0.5956440    TRUE  595.6440
##  5 1.518185e+12       7     noosin     1 0.8158729   FALSE  815.8729
##  6 1.518185e+12       9 goamboozle     3 0.6285422   FALSE  628.5422
##  7 1.518185e+12       8       book     0 0.7227321    TRUE  722.7321
##  8 1.518185e+12       6       book     0 1.2849419    TRUE 1284.9419
##  9 1.518185e+12       3       book     0 1.0876911    TRUE 1087.6911
## 10 1.518185e+12       7        eat     2 0.6137280    TRUE  613.7280
## # ... with 254 more rows, and 2 more variables: starts_d <lgl>,
## #   longer_than_6 <chr>

And we can keep adding functions to the pipeline very easily…

rt_data %>%
  mutate("rt_ms" = rt * 1000,
         "starts_d" = str_sub(word, 1, 1) == "b",
         "longer_than_6" = if_else(str_length(word) > 6, "long", "short")) %>%
  filter(rt > 0.002)
## # A tibble: 262 x 9
##            time subject       word trial        rt is_real     rt_ms
##           <dbl>   <int>      <chr> <int>     <dbl>   <lgl>     <dbl>
##  1 1.518185e+12       9       book     0 2.2346671    TRUE 2234.6671
##  2 1.518185e+12       9     noosin     1 0.8533659   FALSE  853.3659
##  3 1.518185e+12       7       book     0 3.4355321    TRUE 3435.5321
##  4 1.518185e+12       9        eat     2 0.5956440    TRUE  595.6440
##  5 1.518185e+12       7     noosin     1 0.8158729   FALSE  815.8729
##  6 1.518185e+12       9 goamboozle     3 0.6285422   FALSE  628.5422
##  7 1.518185e+12       8       book     0 0.7227321    TRUE  722.7321
##  8 1.518185e+12       6       book     0 1.2849419    TRUE 1284.9419
##  9 1.518185e+12       3       book     0 1.0876911    TRUE 1087.6911
## 10 1.518185e+12       7        eat     2 0.6137280    TRUE  613.7280
## # ... with 252 more rows, and 2 more variables: starts_d <lgl>,
## #   longer_than_6 <chr>
rt_data %>%
  mutate("rt_ms" = rt * 1000,
         "starts_d" = str_sub(word, 1, 1) == "b",
         "longer_than_6" = if_else(str_length(word) > 6, "long", "short")) %>%
  filter(rt > 0.002) %>%
  group_by(subject, is_real) %>%
  summarise(mean_rt = mean(rt))
## # A tibble: 24 x 3
## # Groups:   subject [?]
##    subject is_real   mean_rt
##      <int>   <lgl>     <dbl>
##  1       0   FALSE 0.8384297
##  2       0    TRUE 0.8294404
##  3       1   FALSE 0.8422099
##  4       1    TRUE 0.8866708
##  5       3   FALSE 0.9057278
##  6       3    TRUE 0.8010959
##  7       4   FALSE 0.8137079
##  8       4    TRUE 0.6964481
##  9       6   FALSE 0.8390218
## 10       6    TRUE 0.7740091
## # ... with 14 more rows

We can look just at conditions and add some summary stats

rt_data %>%
  group_by(is_real) %>%
  summarise(mean_rt = mean(rt),
            median_rt = median(rt),
            sd_rt = sd(rt))
## # A tibble: 2 x 4
##   is_real   mean_rt median_rt     sd_rt
##     <lgl>     <dbl>     <dbl>     <dbl>
## 1   FALSE 0.9442195 0.8029714 0.4748030
## 2    TRUE 0.8023425 0.7043273 0.3776124

It looks like average response time was longer for fake words.

Try it yourself…

  1. Add a new column to rt_data that codes whether the word ends with “n”

  2. Get the means and counts for real and fake words split by whether they end in “n” or not

    rt_data_n <- rt_data %>%
  mutate("ends_with_n" = str_sub(word, -1, -1) == "n") %>%
  group_by(is_real, ends_with_n) %>%
  summarize(mean_rt = mean(rt),
            n_rt = n())
rt_data_n
    ## # A tibble: 4 x 4
## # Groups:   is_real [?]
##   is_real ends_with_n   mean_rt  n_rt
##     <lgl>       <lgl>     <dbl> <int>
## 1   FALSE       FALSE 0.9212505   108
## 2   FALSE        TRUE 1.1509408    12
## 3    TRUE       FALSE 0.7912822   132
## 4    TRUE        TRUE 0.9240052    12

Data visualization (ggplot2)

Looking at columns of numbers isn’t really the best way to do data analysis. You could be tripped up by placement of decimal points, you might accidentally miss a big number. It would be much better if we could PLOT these numbers so we can visually tell if anything stands out.

If you’ve taken an introductory Psych or Neuro course you might know that a huge proportion of human cortex is devoted to visual information processing; we have hugely powerful abilities to process visual data. By using plotting we can leverage that ability to get a fast sense of what is going on in our data.

Visualizing your data is an extremely important part of any data analysis. tidyverse contains a whole library of functions for plotting: ggplot2. I’ll be showing you how to use these functions but also I’ll be trying to give you some intuitions about how researchers use visualization to get a better understanding of their data.

The first thing you might want to know is what your dependent variable, in this case the response time, looks like. In other words, how is it distributed?

Histograms

ggplot(data = rt_data) +
  geom_histogram(mapping = aes(x = rt))

ggplot syntax might seem a little unusual. You can think of it as first creating a plot coordinate system with ggplot() and the you can add layers of information with +.

ggplot(data = rt_data) would create an empty plot because you haven’t told it anything about what variables you’re interested in or how you want to look at them. This is where geometric objects, or “geoms”, come in.

geom_histogram() is going to make this plot a histogram. A histogram has values of whatever variable you choose on the x axis and counts of those values on the y. The aesthetic mapping, aes(), arguments let us specify which variable, in this case rt, we want to know the distribution of. We can also change visual aspects of the geom, like the width of the bins, depending on what will make the graph more clear and informative.

ggplot(rt_data) +
  geom_histogram(aes(x = rt), bins = 60)

What can we learn from this histogram?

In this histogram we can see that there are a lot of response times around 1 second and a few longer outlier response times. This is important to know for when we analyze the response times because certain descriptive statistics like the mean are very sensitive to outliers.

Scatterplots

Let’s say we are curious to see if people speed up or slow down over the course of doing the lexical decision task. So, we want to plot trial number and compare it with mean rt. Let’s put trial number on the x axis, mean rt on the y axis, and make a scatterplot. For this we’re going to use a different geom, geom_point(). Contrary to geom_histogram() this takes a minimum of 2 arguments, x and y.

ggplot(rt_data) +
  geom_point(aes(x = trial, y = rt))

This is a fair number of data points so it’s a little difficult to see what’s going on. It might be useful to also show what the average across participants looks like at every timepoint. We can just add another layer to this same graph with the +, in this case we’ll use geom_line().

rt_by_trials <- rt_data %>%
  group_by(trial) %>%
  summarise(mean_rt = mean(rt))

ggplot() +
  geom_point(data = rt_data, aes(x = trial, y = rt), alpha = 0.2) +
  geom_line(data = rt_by_trials, aes(x = trial, y = mean_rt), color = "blue")

  • Because there were so many points and it was difficult to see, I made each point less opaque using alpha = 0.2 as an argument for geom_point() and I made the line connecting averages stand out by making it blue with color = "blue" as an argument to geom_line()

  • Note that I’m plotting 2 different datasets withing the same graph and this is easy to do because you can define data separately for each geom.

What can we learn from this scatterplot + line graph?

Is anything different happening in the first few trials? Does there seem to be a trend over the course of the trials?