Learning Statistics with R - A tutorial for psychology students and other beginners, 2018a

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framework to be able to include multiple predictors. Perhaps some kind of multiple regression model wouldbeinorder? Multiple regression is conceptually very simple. All we do is add more terms to our regression equation. Let’s suppose that we’ve got two variables that we’re interested in; perhaps we want to use both dan.sleep and baby.sleep to predict the dan.grump variable. As before, we let Y i refer to my grumpiness on the i-th day. But now we have two X variables: the first corresponding to the amount of sleep I got and the second corresponding to the amount of sleep my son got. So we’ll let X i1 refer to the hours I slept on the i-th day, and X i2 refers to the hours that the baby slept on that day. If so, then we can write our regression model like this: Y i “ b 2 X i2 ` b 1 X i1 ` b 0 ` ɛ i As before, ɛ i is the residual associated with the i-th observation, ɛ i “ Y i ´ Ŷi. In this model, we now have three coefficients that need to be estimated: b 0 is the intercept, b 1 is the coefficient associated with my sleep, and b 2 is the coefficient associated with my son’s sleep. However, although the number of coefficients that need to be estimated has changed, the basic idea of how the estimation works is unchanged: our estimated coefficients ˆb 0 , ˆb 1 and ˆb 2 are those that minimise the sum squared residuals. 15.3.1 Doing it in R Multiple regression in R is no different to simple regression: all we have to do is specify a more complicated formula when using the lm() function. For example, if we want to use both dan.sleep and baby.sleep as predictors in our attempt to explain why I’m so grumpy, then the formula we need is this: dan.grump ~ dan.sleep + baby.sleep Notice that, just like last time, I haven’t explicitly included any reference to the intercept term in this formula; only the two predictor variables and the outcome. By default, the lm() function assumes that the model should include an intercept (though you can get rid of it if you want). In any case, I can create a new regression model – which I’ll call regression.2 – using the following command: > regression.2 print( regression.2 ) Call: lm(formula = dan.grump ~ dan.sleep + baby.sleep, data = parenthood) Coefficients: (Intercept) dan.sleep baby.sleep 125.96557 -8.95025 0.01052 The coefficient associated with dan.sleep is quite large, suggesting that every hour of sleep I lose makes me a lot grumpier. However, the coefficient for baby.sleep is very small, suggesting that it doesn’t really matter how much sleep my son gets; not really. What matters as far as my grumpiness goes is how much sleep I get. To get a sense of what this multiple regression model looks like, Figure 15.4 shows a 3D plot that plots all three variables, along with the regression model itself. - 462 -
Figure 15.4: A 3D visualisation of a multiple regression model. There are two predictors in the model, dan.sleep and baby.sleep; the outcome variable is dan.grump. Together, these three variables form a 3D space: each observation (blue dots) is a point in this space. In much the same way that a simple linear regression model forms a line in 2D space, this multiple regression model forms a plane in 3D space. When we estimate the regression coefficients, what we’re trying to do is find a plane that is as close to all the blue dots as possible. (This plot was drawn using the scatter3d() function in the car package, and it looked much nicer before it got butchered by the image conversion process that I used to get it into the book pdf) - 463 -
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Learning statistics with R: A tutor
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This book is published under a Crea
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Preface Table of Contents I Backgro
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8.6 Summary . . . . . . . . . . . .
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VI Endings, alternatives and prospe
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February 16, 2015 Preface to Versio
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and density is discussed. A detaile
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1. Why do we learn statistics? “T
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And finally, an invalid argument wi
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Admission rate (both genders) 0 20
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experiment, and they don’t get an
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2. A brief introduction to research
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different ways: the length of time
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that when I ask 100 people how they
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Table 2.1: The relationship between
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2.3 Assessing the reliability of a
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2.5.1 Experimental research The key
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things “inside” the study. Let
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they lack face validity, you’ll f
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that age is growing at an incredibl
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then it can be a big problem. 2.7.7
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2.7.10 Placebo effects The placebo
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it doesn’t, which one do you thin
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Part II. An introduction to R - 35
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go out into the real world. It’s
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download Rstudio. To understand why
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Most of this text is pretty uninter
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citation() To cite R in publication
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Table 3.1: Basic arithmetic operati
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Division / and Multiplication *, th
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sales * royalty [1] 2450 As far as
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x to the power of 0.5”. Personall
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As you can see, specifying the argu
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Figure 3.3: If you’ve typed the n
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sales.by.month sales.by.month [1]
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profit / days.per.month [1] 0.00000
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not true of R. R is not infinitely
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Table 3.3: Some more logical operat
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In other words, any.sales.this.mont
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and gotten exactly the same result.
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Figure 3.6: The options window in R
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- 72 -
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print( keeper ) [1] 8.539539 So, fr
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to import an SPSS data file into R,
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The output here is telling you that
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Figure 4.3: The Rstudio dialog box
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Figure 4.5: The Rstudio “Environm
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this should be obvious already. But
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Figure 4.6: The “file panel” is
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from this file into my workspace. T
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2 February 28 100 high 3 March 31 2
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Figure 4.9: The Rstudio window for
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4.6.1 Special values The first thin
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x y x * y Error in x * y : non-nu
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4.7.1 Introducing factors Suppose,
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factors in 7.11.2, but for now you
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An alternative method is to use the
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4.11 Generic functions There’s on
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load (base) R Documentation The R D
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Warning Saved R objects are binary
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5. Descriptive statistics Any time
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mean of these observations is just:
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mean( afl.margins[1:5] ) [1] 36.6 A
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the median rises only to $62,500. I
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Next, let’s calculate means and m
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5.2 Measures of variability The sta
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English: which game value deviation
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and you get the same... no, wait...
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Mean − SD Mean Mean + SD Figure 5
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Negative Skew No Skew Positive Skew
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Platykurtic ("too flat") Mesokurtic
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e useful, let’s try this for a ne
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argument specifies the grouping var
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grumpiness score. 13 If the mean is
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Frequency 0 5 10 15 20 Frequency 0
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My grumpiness 40 50 60 70 80 90 4 6
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following extract illustrates the b
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Y1 4 5 6 7 8 9 10 Y2 3 4 5 6 7 8 9
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Okay, so let’s have a look at our
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pay 0.760 0.720 . 0.137 . 0.196 . d
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5 6.68 9.75 NA 5 6 5.99 5.04 72 6 B
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• Measures of variability. In con
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6. Drawing graphs Above all else sh
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delete the plot and then type a new
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Fibonacci 2 4 6 8 10 12 1 2 3 4 5 6
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high-level functions all rely on th
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type = ’p’ type = ’o’ type
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Fibonacci 2 4 6 8 10 12 1 2 3 4 5 6
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Figure 6.8: Altering the scale and
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y the height of the leftmost bar in
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6.3.1 Visual style of your histogra
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0 20 40 60 80 100 120 (a) (b) Figur
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0 20 40 60 80 100 120 Winning Margi
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0 50 100 150 200 250 300 Winning Ma
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6.5.3 Drawing multiple boxplots One
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Winning Margin 0 50 100 150 1987 19
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The second way do to it is to use a
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cor( x = parenthood ) # calculate c
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0 10 20 30 0 10 20 30 Adelaide Fitz
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value for mar is c(5.1, 4.1, 4.1, 2
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This takes the “active” figure
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7. Pragmatic matters The garden of
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in the command above I didn’t nam
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speaker ee onk oo pip makka-pakka 0
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2 7 3 3 1 3 3 -1 1 -1 BLAH BLAH BLA
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seen it before. In any case, those
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Table 7.2: Two more arithmetic oper
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fact R does provide a function for
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But suppose, on the other hand, tha
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is select several different variabl
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column number. So, if we want to pi
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case.2 upsy-daisy pip 2 case.4 makk
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Note that R will only allow you to
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7.6.2 Sorting a factor You can also
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Two other methods that I want to br
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At this point you should have two q
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(alcohol, caffeine or no drug). Bec
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3 3 female 4.6 643 7.4 226 7.3 412
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discuss melt() and cast() in a fair
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paste( hw, ng, sep = ".", collapse
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Table 7.3: The ordering of various
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Table 7.4: Standard escape characte
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sub( pattern = "a", replacement = "
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Figure 7.1: The booksales2.csv data
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note that if you don’t have the R
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etween the two. However, there are
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a third variable to the cross-tabs
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today print(today) # display the d
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encode numbers in binary, 29 0.1 is
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environment. And so when you type i
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8. Basic programming Machine dreams
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for ages, you figure out some reall
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Figure 8.2: A screenshot showing th
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8.1.5 Differences between scripts a
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to the second value in vector; and
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crunching, we tell R (on line 21) t
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What this does is create a function
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hundreds of other things besides. H
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Part IV. Statistical theory - 269 -
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me: I guess I don’t see that. Sur
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discussion of probability theory is
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In this case 11 of these 20 coin fl
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frequentists do this sometimes. And
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Probability of event 0.0 0.1 0.2 0.
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proceed to roll all 20 dice, what
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(a) Probability 0.00 0.05 0.10 0.15
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In other words, there is a 76.9% ch
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Probability Density 0.0 0.1 0.2 0.3
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Shaded Area = 68.3% Shaded Area = 9
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Probability Density 0.0 0.1 0.2 0.3
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• The χ 2 distribution is anothe
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work rather than rchisq() - the obs
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10.1.1 Defining a population A samp
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Figure 10.2: Biased sampling withou
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a stratified sampling technique you
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10.2 The law of large numbers In th
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Table 10.1: Ten replications of the
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Sample Size = 1 Sample Size = 2 Sam
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Sample Size = 1 Sample Size = 2 0.0
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efer to them. For instance, if true
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Average Sample Mean 96 98 100 102 1
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10.5 Estimating a confidence interv
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sense idea of what it means to say
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Average Attendance 0 10000 30000 19
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Here’s how to plot the means and
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Let’s suppose that this glorious
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Dan’s research hypothesis: “ESP
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the type I error rate. As Blackston
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Critical Regions for a Two−Sided
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Critical Region for a One−Sided T
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one based on Neyman’s approach to
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alternative hypothesis is a near ce
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Sampling Distribution for X if θ=.
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Table 11.2: A crude guide to unders
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ureaucratic process. It’s not par
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(binomial test was non significant)
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12. Categorical data analysis Now t
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observations that fall within the i
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it is when it predicts too many (wh
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df = 3 df = 4 df = 5 0 2 4 6 8 10 V
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That’s why I told R to use the up
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clubs 35 40 0.2 diamonds 51 60 0.3
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only one of many (albeit one of the
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That’s more or less what we’re
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Well, since these probabilities hav
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Chapek 9 has an unfortunate tendenc
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12.5 Assumptions of the test(s) All
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To get the test of independence, al
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This is a bit more output than we g
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subj.1 : 1 no :70 no :90 subj.10 :
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13. Comparing two means In the prev
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40 50 60 70 80 90 Grades Figure 13.
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Two Sided Test One Sided Test −1.
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lower.area print( lower.area ) [1]
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df = 2 df = 10 −4 −2 0 2 4 valu
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than I’ve done here. For instance
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Anastasia’s students Bernadette
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null hypothesis μ alternative hypo
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ut once again I’m going to start
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for the difference “(mean 1) minu
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null hypothesis μ alternative hypo
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13.5.1 The data The data set that w
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ciMean( x = chico$improvement ) 2.5
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Paired samples t-test Variables: gr
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Grouping variable: ID variable: tim
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In a one-sided confidence interval,
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Page 429 and 430: ut you no longer believe that the c
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Page 433 and 434: Sampling distribution of W (for nor
Page 435 and 436: We then count up the number of chec
Page 437 and 438: • A paired samples t-test is used
Page 439 and 440: 14. Comparing several means (one-wa
Page 441 and 442: Mood Gain 0.5 1.0 1.5 placebo anxif
Page 443 and 444: This formula looks pretty much iden
Page 445 and 446: is true, then you’d expect all th
Page 447 and 448: mean square, MS w , can be viewed a
Page 449 and 450: 3 placebo 0.1 0.45 -0.350 0.1225 4
Page 451 and 452: is choose an α level (i.e., accept
Page 453 and 454: names( my.anova ) [1] "coefficients
Page 455 and 456: etaSquared( x = my.anova ) eta.sq e
Page 457 and 458: One thing that bugs me slightly abo
Page 459 and 460: If we compare these three p-values
Page 461 and 462: • Homogeneity of variance. Notice
Page 463 and 464: Secondly, I did mention that it’s
Page 465 and 466: Frequency 0 1 2 3 4 5 6 7 Sample Qu
Page 467 and 468: Looking at this table, notice that
Page 469 and 470: • Post hoc analysis and correctio
Page 471 and 472: 15. Linear regression The goal in t
Page 473 and 474: The Best Fitting Regression Line No
Page 475: • data. The data frame containing
Page 479 and 480: Wonderful. A big number that doesn
Page 481 and 482: If our regression model has K predi
Page 483 and 484: You can see why this is handy, sinc
Page 485 and 486: what it is. The test for the signif
Page 487 and 488: Fortunately, confidence intervals f
Page 489 and 490: • Uncorrelated predictors. The id
Page 491 and 492: Outlier Outcome Predictor Figure 15
Page 493 and 494: Outcome High influence Predictor Fi
Page 495 and 496: Cook’s distance 0.00 0.02 0.04 0.
Page 497 and 498: Standardized residuals −2 −1 0
Page 499 and 500: 78 Residuals vs Fitted Residuals
Page 501 and 502: In a lot of cases, the solution to
Page 503 and 504: Signif. codes: 0 *** 0.001 ** 0.01
Page 505 and 506: 15.10.1 Backward elimination Okay,
Page 507 and 508: + day 1 1.55760 1837.2 297.08 + bab
Page 509 and 510: etween those two SS values as a sum
Page 511 and 512: 16. Factorial ANOVA Over the course
Page 513 and 514: At this point we have 12 different
Page 515 and 516: drug 2 3.45 1.727 18.6 8.6e-05 ***
Page 517 and 518: means can be organised into the sam
Page 519 and 520: attributable to the “ANOVA model
Page 521 and 522: Only Factor A has an effect Only Fa
Page 523 and 524: The effect of CBT (difference betwe
Page 525 and 526: Now, if you go back to the formulas
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Here’s what I mean. Again, let’
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Speaking of interaction effects, he
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16.4 Assumption checking As with on
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16.5.1 The F test comparing two mod
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the degrees of freedom here is 15.
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tfm.2 grade attend reading 1 90 yes
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line, we obtain the following: Ŷ 7
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Estimate Std. Error t value Pr(>|t|
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that contains the same data as clin
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What about the case when there does
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R comes with a variety of functions
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enlightening read. There are a lot
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16.8 Post hoc tests Time to switch
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diff lwr upr p adj anxifree:no.ther
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1 yes none 3.700 2 no none 5.550 3
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Analysis of Variance Table Response
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III tests (which are simple) before
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sugar 2.13 2 4.0446 0.045426 * milk
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even simpler. The main effect of su
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However, when we do the same thing
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Part VI. Endings, alternatives and
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first I want to work through a simp
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This is a very useful table, so it
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P pd|hqP phq P ph|dq “ P pdq And
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Bayesian approach relative to the o
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hardly unusual: in my experience, m
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Cumulative Probability of Type I Er
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are wrong. Worse yet, because we do
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library( BayesFactor ) # ...because
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make sense to people who already un
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-------------- [1] Non-indep. (a=1)
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Before moving on, it’s worth high
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17.6.2 The Bayesian version Okay, s
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[2] day : 0.2724027 ˘0% [3] baby.s
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therapy 0.4672 1 8.5816 0.01262 * d
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command that I use when I want to g
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- 586 -
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• Other types of correlations. In
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measurements mean that independence
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the list that I’ve given above is
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So if you were forced to guess my w
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to be able to do more than ANOVA, m
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Fisher, R. A. (1922a). On the inter
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