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

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Sample Size = 1 Sample Size = 2 Sample Size = 10 60 80 100 120 140 IQ Score 60 80 100 120 140 IQ Score 60 80 100 120 140 IQ Score (a) (b) (c) Figure 10.7: An illustration of the how sampling distribution of the mean depends on sample size. In each panel, I generated 10,000 samples of IQ data, and calculated the mean IQ observed within each of these data sets. The histograms in these plots show the distribution of these means (i.e., the sampling distribution of the mean). Each individual IQ score was drawn from a normal distribution with mean 100 and standard deviation 15, which is shown as the solid black line). In panel a, each data set contained only a single observation, so the mean of each sample is just one person’s IQ score. As a consequence, the sampling distribution of the mean is of course identical to the population distribution of IQ scores. However, when we raise the sample size to 2, the mean of any one sample tends to be closer to the population mean than a one person’s IQ score, and so the histogram (i.e., the sampling distribution) is a bit narrower than the population distribution. By the time we raise the sample size to 10 (panel c), we can see that the distribution of sample means tend to be fairly tightly clustered around the true population mean. ....................................................................................................... Doing this over and over again would give me a very different sampling distribution, namely the sampling distribution of the maximum. The sampling distribution of the maximum of 5 IQ scores is shown in Figure 10.6. Not surprisingly, if you pick 5 people at random and then find the person with the highest IQ score, they’re going to have an above average IQ. Most of the time you’ll end up with someone whose IQ is measured in the 100 to 140 range. 10.3.3 The central limit theorem At this point I hope you have a pretty good sense of what sampling distributions are, and in particular what the sampling distribution of the mean is. In this section I want to talk about how the sampling distribution of the mean changes as a function of sample size. Intuitively, you already know part of the answer: if you only have a few observations, the sample mean is likely to be quite inaccurate: if you replicate a small experiment and recalculate the mean you’ll get a very different answer. In other words, the sampling distribution is quite wide. If you replicate a large experiment and recalculate the sample mean you’ll probably get the same answer you got last time, so the sampling distribution will be very narrow. You can see this visually in Figure 10.7: the bigger the sample size, the narrower the sampling distribution gets. We can quantify this effect by calculating the standard deviation of the sampling distribution, which is referred to as the standard error. The standard error of a statistic is often denoted SE, and since we’re usually interested in the standard error of the sample mean, weoften use the acronym SEM. As you can see just by looking at the picture, as the sample size N increases, the - 312 -
SEM decreases. Okay, so that’s one part of the story. However, there’s something I’ve been glossing over so far. All my examples up to this point have been based on the “IQ scores” experiments, and because IQ scores are roughly normally distributed, I’ve assumed that the population distribution is normal. What if it isn’t normal? What happens to the sampling distribution of the mean? The remarkable thing is this: no matter what shape your population distribution is, as N increases the sampling distribution of the mean starts to look more like a normal distribution. To give you a sense of this, I ran some simulations using R. To do this, I started with the “ramped” distribution shown in the histogram in Figure 10.8. As you can see by comparing the triangular shaped histogram to the bell curve plotted by the black line, the population distribution doesn’t look very much like a normal distribution at all. Next, I used R to simulate the results of a large number of experiments. In each experiment I took N “ 2 samples from this distribution, and then calculated the sample mean. Figure 10.8b plots the histogram of these sample means (i.e., the sampling distribution of the mean for N “ 2). This time, the histogram produces a X-shaped distribution: it’s still not normal, but it’s a lot closer to the black line than the population distribution in Figure 10.8a. When I increase the sample size to N “ 4, the sampling distribution of the mean is very close to normal (Figure 10.8c),andbythetimewereachasamplesizeofN “ 8 it’s almost perfectly normal. In other words, as long as your sample size isn’t tiny, the sampling distribution of the mean will be approximately normal no matter what your population distribution looks like! On the basis of these figures, it seems like we have evidence for all of the following claims about the sampling distribution of the mean: • The mean of the sampling distribution is the same as the mean of the population • The standard deviation of the sampling distribution (i.e., the standard error) gets smaller as the sample size increases • The shape of the sampling distribution becomes normal as the sample size increases As it happens, not only are all of these statements true, there is a very famous theorem in statistics that proves all three of them, known as the central limit theorem. Among other things, the central limit theorem tells us that if the population distribution has mean μ and standard deviation σ, then the sampling distribution of the mean also has mean μ, and the standard error of the mean is SEM “ Because we divide the population standard devation σ by the square root of the sample size N, the SEM gets smaller as the sample size increases. It also tells us that the shape of the sampling distribution becomes normal. 4 This result is useful for all sorts of things. It tells us why large experiments are more reliable than small ones, and because it gives us an explicit formula for the standard error it tells us how much more reliable a large experiment is. It tells us why the normal distribution is, well, normal. In real experiments, many of the things that we want to measure are actually averages of lots of different quantities (e.g., arguably, “general” intelligence as measured by IQ is an average of a large number of “specific” skills and abilities), and when that happens, the averaged quantity should follow a normal distribution. Because of this mathematical law, the normal distribution pops up over and over again in real data. 4 As usual, I’m being a bit sloppy here. The central limit theorem is a bit more general than this section implies. Like most introductory stats texts, I’ve discussed one situation where the central limit theorem holds: when you’re taking an average across lots of independent events drawn from the same distribution. However, the central limit theorem is much broader than this. There’s a whole class of things called “U-statistics” for instance, all of which satisfy the central limit theorem and therefore become normally distributed for large sample sizes. The mean is one such statistic, but it’s not the only one. σ ? N - 313 -
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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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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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Page 290 and 291: discussion of probability theory is
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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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