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

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• A theoretical construct. This is the thing that you’re trying to take a measurement of, like “age”, “gender” or an “opinion”. A theoretical construct can’t be directly observed, and often they’re actually a bit vague. • A measure. The measure refers to the method or the tool that you use to make your observations. A question in a survey, a behavioural observation or a brain scan could all count as a measure. • An operationalisation. The term “operationalisation” refers to the logical connection between the measure and the theoretical construct, or to the process by which we try to derive a measure from a theoretical construct. • A variable. Finally, a new term. A variable is what we end up with when we apply our measure to something in the world. That is, variables are the actual “data” that we end up with in our data sets. In practice, even scientists tend to blur the distinction between these things, but it’s very helpful to try to understand the differences. 2.2 Scales of measurement As the previous section indicates, the outcome of a psychological measurement is called a variable. But not all variables are of the same qualitative type, and it’s very useful to understand what types there are. A very useful concept for distinguishing between different types of variables is what’s known as scales of measurement. 2.2.1 Nominal scale A nominal scale variable (also referred to as a categorical variable) is one in which there is no particular relationship between the different possibilities: for these kinds of variables it doesn’t make any sense to say that one of them is “bigger’ or “better” than any other one, and it absolutely doesn’t make any sense to average them. The classic example for this is “eye colour”. Eyes can be blue, green and brown, among other possibilities, but none of them is any “better” than any other one. As a result, it would feel really weird to talk about an “average eye colour”. Similarly, gender is nominal too: male isn’t better or worse than female, neither does it make sense to try to talk about an “average gender”. In short, nominal scale variables are those for which the only thing you can say about the different possibilities is that they are different. That’s it. Let’s take a slightly closer look at this. Suppose I was doing research on how people commute to and from work. One variable I would have to measure would be what kind of transportation people use to get to work. This “transport type” variable could have quite a few possible values, including: “train”, “bus”, “car”, “bicycle”, etc. For now, let’s suppose that these four are the only possibilities, and suppose - 14 -
that when I ask 100 people how they got to work today, and I get this: Transportation Number of people (1) Train 12 (2) Bus 30 (3) Car 48 (4) Bicycle 10 So, what’s the average transportation type? Obviously, the answer here is that there isn’t one. It’s a silly question to ask. You can say that travel by car is the most popular method, and travel by train is the least popular method, but that’s about all. Similarly, notice that the order in which I list the options isn’t very interesting. I could have chosen to display the data like this Transportation Number of people (3) Car 48 (1) Train 12 (4) Bicycle 10 (2) Bus 30 and nothing really changes. 2.2.2 Ordinal scale Ordinal scale variables have a bit more structure than nominal scale variables, but not by a lot. An ordinal scale variable is one in which there is a natural, meaningful way to order the different possibilities, but you can’t do anything else. The usual example given of an ordinal variable is “finishing position in a race”. You can say that the person who finished first was faster than the person who finished second, but you don’t know how much faster. As a consequence we know that 1st ą 2nd, and we know that 2nd ą 3rd, but the difference between 1st and 2nd might be much larger than the difference between 2nd and 3rd. Here’s an more psychologically interesting example. Suppose I’m interested in people’s attitudes to climate change, and I ask them to pick one of these four statements that most closely matches their beliefs: (1) Temperatures are rising, because of human activity (2) Temperatures are rising, but we don’t know why (3) Temperatures are rising, but not because of humans (4) Temperatures are not rising Notice that these four statements actually do have a natural ordering, in terms of “the extent to which they agree with the current science”. Statement 1 is a close match, statement 2 is a reasonable match, statement 3 isn’t a very good match, and statement 4 is in strong opposition to the science. So, in terms of the thing I’m interested in (the extent to which people endorse the science), I can order the items as 1 ą 2 ą 3 ą 4. Since this ordering exists, it would be very weird to list the options like this. . . (3) Temperatures are rising, but not because of humans (1) Temperatures are rising, because of human activity (4) Temperatures are not rising (2) Temperatures are rising, but we don’t know why . . . because it seems to violate the natural “structure” to the question. - 15 -
Page 2 and 3: Learning statistics with R: A tutor
Page 4 and 5: This book is published under a Crea
Page 6 and 7: Preface Table of Contents I Backgro
Page 8 and 9: 8.6 Summary . . . . . . . . . . . .
Page 10 and 11: VI Endings, alternatives and prospe
Page 12 and 13: February 16, 2015 Preface to Versio
Page 14 and 15: and density is discussed. A detaile
Page 17 and 18: 1. Why do we learn statistics? “T
Page 19 and 20: And finally, an invalid argument wi
Page 21 and 22: Admission rate (both genders) 0 20
Page 23 and 24: experiment, and they don’t get an
Page 25 and 26: 2. A brief introduction to research
Page 27: different ways: the length of time
Page 31 and 32: Table 2.1: The relationship between
Page 33 and 34: 2.3 Assessing the reliability of a
Page 35 and 36: 2.5.1 Experimental research The key
Page 37 and 38: things “inside” the study. Let
Page 39 and 40: they lack face validity, you’ll f
Page 41 and 42: that age is growing at an incredibl
Page 43 and 44: then it can be a big problem. 2.7.7
Page 45 and 46: 2.7.10 Placebo effects The placebo
Page 47 and 48: it doesn’t, which one do you thin
Page 49: Part II. An introduction to R - 35
Page 52 and 53: go out into the real world. It’s
Page 54 and 55: download Rstudio. To understand why
Page 56 and 57: Most of this text is pretty uninter
Page 58 and 59: citation() To cite R in publication
Page 60 and 61: Table 3.1: Basic arithmetic operati
Page 62 and 63: Division / and Multiplication *, th
Page 64 and 65: sales * royalty [1] 2450 As far as
Page 66 and 67: x to the power of 0.5”. Personall
Page 68 and 69: As you can see, specifying the argu
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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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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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- 300 -
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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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are different tests. Secondly, I wa
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Table 13.1: A (very) rough guide to
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ut you no longer believe that the c
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Frequency 0 5 10 15 20 Normally Dis
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Sampling distribution of W (for nor
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We then count up the number of chec
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• A paired samples t-test is used
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14. Comparing several means (one-wa
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Mood Gain 0.5 1.0 1.5 placebo anxif
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This formula looks pretty much iden
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is true, then you’d expect all th
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mean square, MS w , can be viewed a
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3 placebo 0.1 0.45 -0.350 0.1225 4
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is choose an α level (i.e., accept
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names( my.anova ) [1] "coefficients
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etaSquared( x = my.anova ) eta.sq e
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One thing that bugs me slightly abo
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If we compare these three p-values
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• Homogeneity of variance. Notice
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Secondly, I did mention that it’s
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Frequency 0 1 2 3 4 5 6 7 Sample Qu
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Looking at this table, notice that
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• Post hoc analysis and correctio
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15. Linear regression The goal in t
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The Best Fitting Regression Line No
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• data. The data frame containing
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Figure 15.4: A 3D visualisation of
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Wonderful. A big number that doesn
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If our regression model has K predi
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You can see why this is handy, sinc
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what it is. The test for the signif
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Fortunately, confidence intervals f
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• Uncorrelated predictors. The id
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Outlier Outcome Predictor Figure 15
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Outcome High influence Predictor Fi
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Cook’s distance 0.00 0.02 0.04 0.
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Standardized residuals −2 −1 0
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78 Residuals vs Fitted Residuals
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In a lot of cases, the solution to
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Signif. codes: 0 *** 0.001 ** 0.01
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15.10.1 Backward elimination Okay,
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+ day 1 1.55760 1837.2 297.08 + bab
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etween those two SS values as a sum
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16. Factorial ANOVA Over the course
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At this point we have 12 different
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drug 2 3.45 1.727 18.6 8.6e-05 ***
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means can be organised into the sam
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attributable to the “ANOVA model
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Only Factor A has an effect Only Fa
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The effect of CBT (difference betwe
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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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