02-probability.qmd

```{r setup, include=FALSE}
source("R_setup.R")
```

# Probability Models {#sec-probmodels}

> How Do I Get a Sampling Distribution?

> Key concepts: bootstrapping/bootstrap sample, sampling with replacement, exact approach, approximation with a theoretical probability distribution, binomial distribution, (standard) normal distribution, (Student) _t_ distribution, _F_ distribution, chi-squared distribution, condition checks for theoretical probability distributions, sample size, equal population variances, independent samples, dependent/paired samples.

Watch the micro lecture @vid-intro-prob-models on probability models for an overview of the chapter.

::: {#vid-intro-prob-models}

{{< video https://www.youtube.com/embed/zA6_9Mbg8d0
    width="100%"
    height="360" 
>}}

Introduction to probability models.
:::

### Summary {-}

::: {.callout-important appearance="simple"}
How do we get a sampling distribution without drawing many samples ourselves?

:::

In the previous chapter, we drew a large number of samples from a population to obtain the sampling distribution of a sample statistic, for instance, the proportion of yellow candies or average candy weight in the sample. The procedure is quite simple: Draw a sample, calculate the desired sample statistic, add the sample statistic value to the sampling distribution, and repeat this thousands of times.  

Although this procedure is simple, it is not practical. In a research project, we would have to draw thousands of samples and administer a survey to each sample or collect data on the sample in some other way. This requires too much time and money to be of any practical value. So how do we create a sampling distribution, if we only collect data for a single sample? This chapter presents three ways of doing this: exact approaches, theoretical approximations, and bootstrapping.

After studying this chapter, you should know the limitations of the three methods of creating a sampling distribution, when to use which method, and how to check the conditions for using a method.

## Exact Approaches to the Sampling Distribution

The first approach we will discuss to constructing a sampling distribution has implicitly been demonstrated in the section on probability distributions (@sec-probdistribution). In this section, we calculated the true sampling distribution of the proportion of yellow candies in a sample from the probabilities of the colours. If we know or think we know the proportion of yellow candies in the population, we can exactly calculate the probability that a sample of ten candies includes one, two, three, or ten yellow candies. See the section on discrete random variables for details (@sec-discreterandomvariable).  

```{r}
#| label: tbl-exact-approach
#| tbl-cap: "Number of heads for a toss of three coins."
#| echo: false
#| warning: false


# Several scenarios (choice list) for discrete probability distributions (dice, coin flips) ; display a table with all outcomes sampling space), all possible combinations for each oucome , and calculated probabilities.
# Scenarios: number of heads per toss if we toss 1, 2, 3 unbiased coins; sum of the number of eyes per throw if we throw 1 or 2 unbiased dice.
# If feasible: Don't show probabilities but let user enter probabilities if a scenario is used for the second (or later) time within a session.
d <- data.frame(Outcome = c(0,1,1,1,2,2,2,3,"Total"), 
                Combinations = c("tail-tail-tail", "tail-tail-head", "head-tail-tail", "tail-head-tail", "head-head-tail", "head-tail-head", "tail-head-head", "head-head-head", "8"),
                Probability_of_combination = c("1/2 * 1/2 * 1/2 = 1/8 =  .125", "1/2 * 1/2 * 1/2 = 1/8 =  .125","1/2 * 1/2 * 1/2 = 1/8 =  .125","1/2 * 1/2 * 1/2 = 1/8 =  .125","1/2 * 1/2 * 1/2 = 1/8 =  .125","1/2 * 1/2 * 1/2 = 1/8 =  .125","1/2 * 1/2 * 1/2 = 1/8 =  .125","1/2 * 1/2 * 1/2 = 1/8 =  .125", ""),
                Probability_of_outcome = c("1/8 =  .125", "", "", "3/8 =  .375", "", "", "3/8 =  .375", "1/8 =  .125", "1.000"))
knitr::kable(d, 
             booktabs  = TRUE, 
             col.names = c("Outcome", "Combination", "Probability: Combination", "Probability: Outcome"), 
             align     = c("l", "l", "l", "r")) %>%
  kable_styling(font_size = 12, full_width = F, latex_options = c("HOLD_position", "scale_down")) 
# %>%
#   row_spec(c(2:4, 8), color = "black", background = "#EEEEEE") %>%
#   row_spec(c(1, 5:7), color = "black", background = "white")
```


> Examine @tbl-exact-approach, and try to determine why the probability of throwing 2 times head out of 3 is .375.


The calculated probabilities of all possible sample statistic outcomes give us an exact approach to the sampling distribution. Note that I use the word _approach_ instead of _approximation_ here because the obtained sampling distribution is no longer an approximation, that is, more or less similar to the true sampling distribution. No, it is the true sampling distribution itself.  

### Exact approaches for categorical data
An exact approach lists and counts all possible combinations. This can only be done if we work with discrete or categorical variables. For an unlimited number of categories (continues variables), we cannot list all possible combinations.

A proportion is based on frequencies and frequencies are discrete (integer values), so we can use an exact approach to create a sampling distribution for one proportion such as the proportion of yellow candies in the example above. The exact approach uses the [binomial probability](https://en.wikipedia.org/wiki/Binomial_distribution) formula to calculate probabilities. Consult the internet if you want to know this formula; we are not going to use it in this course.

Exact approaches are also available for the association between two categorical (nominal or ordinal) variables in a contingency table: Do some combinations of values for the two variables occur relatively frequently? For example, are yellow candies more often sticky than red candies? If candies are either sticky or not sticky and they have one out of a limited set of colours, we have two categorical variables. We can create an exact probability distribution for the combination of colour and stickiness. The _Fisher-exact test_ is an example of an exact approach to the sampling distribution of the association between two categorical variables.

### Computer-intensive {#sec-comp-int}
The exact approach can be applied to discrete variables because they have a limited number of values. Discrete variables are usually measured at the nominal or ordinal level. If the number of categories becomes large, a lot of computing time can be needed to calculate the probabilities of all possible sample statistic outcomes. Exact approaches are said to be _computer-intensive_. 

It is usually wise to set a limit to the time you allow your computer to work on an exact sampling distribution because otherwise the problem may keep your computer occupied for hours or days. In this course, we will set the time limit in SPSS on 5 minutes (@sec-SPSS-exact) 





## Exact Approaches in SPSS {#sec-SPSS-exact}

### Introduction {#sec-exact-intro}

To perform an exact approach in SPSS, let us walk through a research example. Let's say you are having some friends over and put some candy out on the table. During the night you and your friends notice some candies being way stickier than other candies. One of your friends makes the observation that it seems to differ by candy colour. You are sceptical and want to investigate this. 

Your research question is: _Are yellow candies more often sticky than red candies_? It concerns two variables. The first variable is candy colour (yellow versus red) and the second variable is stickiness (sticky versus not sticky). These two variables are both categorical (with two categories).

Thus, we can create an exact probability distribution for the combination of colour and stickiness. 

If SPSS offers an exact approach of the sampling distribution, the test dialog window contains an `Exact` button. We can find this in the dialog window for creating a contingency table (`Analyze > descriptive statistics > crosstab`) and in several legacy dialogs for non-parametric tests (`Analyze > nonparametric tests > legacy dialogs`). In the Exact dialog, we check the `Exact` option and SPSS automatically sets an upper limit of five minutes to the execution of the command. We can leave this at five minutes (see @sec-comp-int for why we have to do this).

As established, we have two categorical variables with two categories. To correct statistical test for these variables is a Chi Square test. Don't worry - we will discuss this in more detail later, but you can already have a brief look at the test selection table (@sec-test-selection). Within the dialog window `crosstabs` we open the `Statistics` dialog to select Chi-square and we open the `Exact` dialog to select the option `Exact`.

_Note_. A Fisher's exact test is automatically run when there is a 2x2 contingency table. When we perform this test on larger contingency tables we need to select the `Exact` option, which is why we teach it to you here.

### Instructions

In the video below you can see how to perform an Exact test in SPSS using our example of the relationship between candy colour and stickiness from the previous @sec-exact-intro. Specifically, we perform an exact test on a 2 (colour: red vs. yellow) x 2 (stickiness: sticky vs. not sticky) contingency table. 

First we show you the approach via the `analyze > nonparametric tests > legacy dialogs > chi-square test`, where you only have to select the `Exact` option and the time limit of five minutes. 

Then we show how how to do an Exact test while testing a proportion. This is done via `analyze > nonparametric tests > legacy dialogs > binomial test`. Again, you select the `Exact` option with a five minute time limit. 

Lastly, the crosstabs option is shown. This is the method you will probably use the most. Here we select the _Exact_ option with the five minute time limit, but we also select `Chi-Square` in the `Statistics` dialog. In the `Statistics` dialog we also select an effect size, you usually use four. For at least one nominal variable in your research, we use Cramer's V for a symmetrical association and Lambda for an asymmetrical association. For all ordinal variables in your research, we use Gamma (van Goodman en Kruskal) for a symmetrical association and Somer's d for an asymmetrical association. Thus, for this example (two nominal variables and a symmetrical association) we use `Phi and Cramer's V`. Under the `Cells...` dialog, we select the `observed counts` and the `column` percentages. Then you can run the analysis. Do not forget to click `paste` instead of `OK` in order to save your syntax. With a syntax you can always check your work.

Watch the video for step by step instructions on how to perform the exact approach in SPSS and some additional information.

::: {#vid-SPSSExact1}

{{< video https://www.youtube.com/embed/SrfZeLvsHwg
    width="100%"
    height="315" 
>}}

Perform an exact test in SPSS.
:::

In the video below, we will interpret the results of an Exact test in SPSS.

The video shows you the different tables that yield from the analysis. Output from an analysis often starts with a type of summary. Here you can check things similar to descriptive analyses (e.g., case numbers, means, etc.). In the case of an exact test, we see the numbers of cases in the first table _case processing summary_.

The second table shows us the crosstabulation with the added percentages for all columns. The percentages alone can already give you a good idea about the nature of your results and can help you interpret the test statistics. 

In the third table, _chi square tests_, we can see our test statistics and values like the p-value. In the third row you can find Fisher's Exact Test. Here, you find the numbers you need to report the results of your statistical test. The p-value tells us whether an effect is significant or not based on this sample. A p-value that is smaller than .05 is commonly considered to indicate significance. There is more to this, but we will elaborate in Chapter 4. If you find a significant results, like shown in the video, the percentages (in the crosstabulation or second table) can help you interpret which groups differ from each other and in which way. 

The fourth table, _symmetric measures_, shows us the effect size. In this case we conclude there is a moderate association between candy stickiness and colour.

In other words, the significant result in this video combined with the percentages can tell us that according to this data it seems that blue, green and orange candies tend to be stickier than red and yellow candies. Good to know when you are hosting the next birthday party!

Watch the video for the step by step instructions on how to interpret the exact approach in SPSS and some additional information.


```{r, echo=FALSE, eval=FALSE}
# Perform an exact test in SPSS.
# Example: exact test on crosstab of candy colour and candy stickiness.
# If SPSS offers an exact approach of the sampling distribution, the test dialog window contains an _Exact_ button. You will find it in the dialog for contingency tables (_Analyze>Descriptive Statistics>Crosstabs_) and in several legacy dialogs for non-parametric tests (_Analyze>Nonparametric Tests>Legacy Dialogs_). 
# 
# In the _Exact_ dialog, you only need to check the _Exact_ option. SPSS sets an upper limit of five minutes to the execution of the command. If this happens to be too short, increase it and run the test again.  
# 
# Are some candy colours more sticky? An exact approach calculates and reports only a p value. We need a contingency table of the two categorical variables and a Fisher-exact test. This test is obtained if both the option _Chi-square_ is selected in the _Statistics..._ dialog and the option _Exact_ is selected in the _Exact..._ dialog. 
# 
# Note that SPSS automatically executes a Fisher-exact test on a 2x2 table, that is, a table containing two rows and two columns. For larger tables, the _Exact_ option must be selected to get the exact test.
```

::: {#vid-SPSSExact2}

{{< video https://www.youtube.com/embed/PlT28wfc6K4
    width="100%"
    height="315" 
>}}

Interpret exact test results in SPSS.
:::


```{r, echo=FALSE, eval=FALSE}
# Interpret exact test results in SPSS.
# Example: exact test on crosstab of candy colour and candy stickiness.
# The output of a Fisher-exact test on the relation between candy colour and candy stickiness is shown below. We included column percentages in the cells and a symmetric measure of association (Phi and Cramer's V). 
# 
# For the test result, you should interpret the p value reported in the table __Chi-Square Tests__. This value is clearly below .05 so we conclude that the test is statistically significant. It is unlikely that all colours are equally sticky in the population (_p_ = .010). According to the percentages in the contingency table, blue, red, and yellow candies are more often sticky than orange and green candies and the association is strong (Phi = .52). 
```











## Theoretical Approximations of the Sampling Distribution {#sec-theoretical-approx}

You have learned that the exact approach requires a lot of computer power, which was a big problem in the not so very distant pre-computer age. In those days, mathematicians and statisticians discovered that many sampling distributions look a lot like known mathematical functions. For example, the sampling distribution of the sample mean can be quite similar to the well-known bell-shape of the _normal distribution_ or the closely related _(Student) t distribution_. The mathematical functions are called _theoretical probability distributions_. Most statistical tests use a theoretical probability distribution as approximation of the sampling distribution.

::: {#fig-normal-approximation}

```{=html}
<iframe src="https://sharon-klinkenberg.shinyapps.io/normal-approximation/" width="100%" height="300px" style="border:none;">
</iframe>
``` 
Normal curve as theoretical approximation of a sampling distribution.
:::



The [normal distribution](https://en.wikipedia.org/wiki/Normal_distribution) is a mathematical function linking continuous scores, e.g., a sample statistic such as the average weight in the sample, to right-hand and left-hand probabilities, that is, to the probability of finding at least, or at most, this score. Such a function is called a _probability density function_ (@sec-cont-random-var).  

We like to use a theoretical probability distribution as an approximation of the sampling distribution because it is convenient. A computer can calculate probabilities from the mathematical function very quickly. We also like theoretical probability distributions because they usually offer plausible arguments about chance and probabilities.  

### Reasons for a bell-shaped probability distribution

Let's consider the example of average candy weight as our sample statistic of interest. What would the sample distribution look like if we sampled thousands of candy bags and plotted their average weight? The bell shape of the normal distribution makes sense. Each sample of candies is just as likely to be heavier than the true population average, as it is to be lighter. Thus, we expect the sampling distribution of the sample mean to be symmetrical around the expected value. A normal distribution is symmetrical.

In addition, it is more likely that each sample bag of candies has an average weight that is near the true average candy weight in the population than an average weight that is much larger or much smaller than the true average. Bags with an extremely high or low average weight may occur, but they are extremely rare. From these intuitions we would expect a bell shape for the sampling distribution. 

From this argumentation, we conclude that the normal distribution is a reasonable model for the probability distribution of sample means. Actually, it has been proven that the normal distribution exactly represents the sampling distribution in particular cases, for instance the sampling distribution of the mean of a very large sample.

### Conditions for the use of theoretical probability distributions {#sec-cond-probdistr}

Theoretical probability distributions, then, are plausible models for sampling distributions. They are known or likely to have the same shape as the true sampling distributions under particular circumstances or conditions. 

If we use a theoretical probability distribution, we must assume that the conditions for its use are met. We have to check the conditions and decide whether they are close enough to the ideal conditions. _Close enough_ is of course a matter of judgement. In practice, rules of thumb have been developed to decide if the theoretical probability distribution can be used.

@fig-normal-approx-proportion shows an example in which the normal distribution is a good approximation for the sampling distribution of a proportion in some situations, but not in all situations.

::: {#fig-normal-approx-proportion .column-page-inset-right}

```{=html}
<iframe src="https://sharon-klinkenberg.shinyapps.io/normal-approx-proportion/" width="100%" height="315px" style="border:none;">
</iframe>
``` 
How does the shape of the sampling distribution of sample proportions change with sample size and proportion value?
:::

Do theoretical probability distributions fit the true sampling distribution? As you may have noticed while playing with @fig-normal-approx-proportion, this is not always the case. In general, theoretical probability distributions fit sampling distributions better if the sample is larger. In addition, the population value may be relevant to the fit of the theoretical probability distribution. The sampling distribution of a sample proportion is more symmetrical, like the normal distribution, if the proportion in the population is closer to .5.

This illustrates that we often have several conditions for a theoretical probability distribution to fit the sampling distribution. We should evaluate all of them at the same time. In the example of proportions, a large sample is less important if the true proportion is closer to .5 but it is more important for true proportions that are more distant from .5.

The rule of thumb for using the normal distribution as the sampling distribution of a sample proportion combines the two aspects by multiplying them and requiring the resulting product to be larger than five.  If the probability of drawing a yellow candy is .2 and our sample size is 30, the product is .2 * 30 = 6, which is larger than five. So we may use the normal distribution as approximation of the sampling distribution.

Note that this rule of thumb uses one minus the probability, if the probability is larger than .5. In other words, it uses the smaller of two probabilities: the probability that an observation has the characteristic and the probability that it has not. For example, if we want to test the probability of drawing a candy that is not yellow, the probability is .8 and we use 1 - 0.8 = 0.2, which is then multiplied by the sample size.

Apart from the [normal distribution](https://en.wikipedia.org/wiki/Normal_distribution), there are several other theoretical probability distributions. We have the [_binomial distribution_](https://en.wikipedia.org/wiki/Binomial_distribution) for a proportion, the [_t distribution_](https://en.wikipedia.org/wiki/Student%27s_t-distribution) for one or two sample means, regression coefficients, and correlation coefficients, the [_F distribution_](https://en.wikipedia.org/wiki/F-distribution) for comparison of variances and comparing means for three or more groups (analysis of variance, ANOVA), and the [_chi-squared distribution_](https://en.wikipedia.org/wiki/Chi-squared_distribution) for frequency tables and contingency tables.

For most of these theoretical probability distributions, sample size is important. The larger the sample, the better. There are additional conditions that must be satisfied such as the distribution of the variable in the population. The rules of thumb are summarized in @tbl-thumb. Bootstrapping and exact tests can be used if conditions for theoretical probability distributions have not been met. Special conditions apply to regression analysis (see @sec-moderationcat, @sec-regr-inference).

```{r}
#| label: tbl-thumb
#| tbl-cap: "Rules of thumb for using theoretical probability distributions."
#| echo: false
#| warning: false

knitr::kable(rbind(c("Binomial distribution", "proportion", "-", "-"), c("(Standard) normal distribution", "proportion", "times test proportion (<= .5) >= 5", "-"), c("(Standard) normal distribution", "one or two means", "> 100", "OR variable is normally distributed in the population and population standard deviation is known (for each group)"), c("t distribution", "one or two means", "each group > 30", "OR variable is normally distributed in each group's population"), c("t distribution", "(Pearson) correlation coefficient", "-", "variables are normally distributed in the population"), c("t distribution", "(Spearman) rank correlation coefficient", "> 30", "-"), c("t distribution", "regression coefficient", "20+ per independent variable", "See Chapter 8."), c("F distribution", "3+ means", " all groups are more or less of equal size", "OR all groups have the same population variance"), c("F distribution", "two variances", "-", "no conditions for Levene's F test"), c("chi-squared distribution", "row or cell frequencies", "expected frequency >= 1 and 80% >= 5", "contingency table: 3+ rows or 3+ columns")), booktabs = TRUE, col.names = c("Distribution", "Sample statistic", "Minimum sample size", "Other requirements")) %>%
  kable_styling(font_size = 12, latex_options = c("HOLD_position", "scale_down"))
```

@tbl-thumb shows the conditions that must be satisfied if we want to use a theoretical probability distribution to approximate a sampling distribution. Only if the conditions are met, the theoretical probability distribution resembles the sampling distribution sufficiently.

In @tbl-thumb the minimal required sample sizes for using theoretical approximation of  sampling distributions are presented. If you plan to do a *t* test, each group should contain more than thirty cases. So if you intend to apply *t* tests, recruit more than thirty participants for each experimental group or more than thirty respondents for each group in your survey. If you expect non-response, that is, sampled participants or respondents unwilling to participate in your research, you should recruit more participants or respondents to have more than thirty observations in the end.

Chi-squared tests require a minimum of five expected frequencies per category in a frequency distribution or cell in a contingency table. Your sample size should be at least the number of categories or cells times five to come even near this requirement. Regression analysis requires at least 20 cases per independent variable in the regression model.

The variation of sample size across groups is important in analysis of variance (ANOVA), which uses the *F* distribution. If the number of cases is more or less the same across all groups, we do not have to worry about the variances of the dependent variable for the groups in the population. To be on the safe side, then, it is recommended to design your sampling strategy in such a way that you end up with more or less equal group sizes if you plan to use analysis of variance.

### Checking conditions {#sec-cond-check} 

Rules of thumb about sample size are easy to check once we have collected our sample. By contrast, rules of thumb that concern the scores in the population cannot be easily checked, because we do not have information on the population. If we already know what we want to know about the population, why would we draw a sample and do the research in the first place?  

We can only use the data in our sample to make an educated guess about the distribution of a variable in the population. For example, if the scores in our sample are clearly normally distributed, it is plausible that the scores in the population are normally distributed. 

In this situation, we do not _know_ that the population distribution is normal but we _assume_ it is. If the sample distribution is clearly not normally distributed, we had better not assume that the population is normally distributed. In short, we sometimes have to make assumptions when we decide on using a theoretical probability distribution.

We could use a histogram of the scores in our sample with a normal distribution curve added to evaluate whether a normal distribution applies. Sometimes, we have statistical tests to draw inferences about the population from a sample that we can use to check the conditions. We discuss these tests in a later chapter.  

### More complicated sample statistics: differences {#sec-complicatedsampling}

Up to this point, we have focused on rather simple sample statistics such as the proportion of yellow candies or the average weight of candies in a sample. @tbl-thumb, however, contains more complicated sample statistics. 

If we compare two groups, for instance, the average weight of yellow and red candies, the sample statistic for which we want to have a sampling distribution must take into account both the average weight of yellow candies and the average weight of red candies. The sample statistic that we are interested in is the difference between the averages of the two samples.

::: {#fig-mean-independent}

```{=html}
<iframe src="https://sharon-klinkenberg.shinyapps.io/mean-independent/" width="100%" height="580px" style="border:none;">
</iframe>
``` 
How do we obtain a sampling distribution for the mean difference of two independent samples?
:::

If we draw a sample from both the red and yellow candies in the population, we may calculate the means for both samples and the difference between the two means. For example, the average weight of red candies in the sample bag is 2.76 grams and the average for yellow candies is 2.82 grams. For this pair of samples, the statistic of interest is 2.76 - 2.82 = -0.06, that is, the difference in average weight. If we repeat this many, many times and collect all differences between means in a distribution, we obtain the sampling distribution that we need.

The sampling distribution of the difference between two means is similar to a _t_-distribution, so we may use the latter to approximate the former. Of course, the conditions for using the _t_-distribution must be met.  

It is important to note that we do not create separate sampling distributions for the average weight of yellow candies and for the average weight of red candies and then look at the difference between the two sampling distributions. Instead, we create _one sampling distribution for the statistic of interest_, namely the difference between means. We cannot combine different sampling distributions into a new sampling distribution. We will see the importance of this when we discuss mediation (@sec-mediation).

### Independent samples  

If we compare two means, there are two fundamentally different situations that are sometimes difficult to distinguish. When comparing the average weight of yellow candies to the average weight of red candies, we are comparing two samples that are _statistically independent_ (see @fig-mean-independent), which means that we could have drawn the samples separately.  

In principle, we could distinguish between a population of yellow candies and a population of red candies, and sample yellow candies from the first population and separately sample red candies from the other population. Whether we sampled the colours separately or not does not matter. The fact that we could have done so implies that the sample of red candies is not affected by the sample of yellow candies or the other way around. The samples are statistically independent.

This is important for the way in which probabilities are calculated. Just think of the simple example of flipping two coins. The probability of having heads twice in a row is .5 times .5, that is .25, if the coins are fair and the result of the second coin does not depend on the result of the first coin. The second flip is not affected by the first flip. 

Imagine that a magnetic field is activated if the first coin lands with heads up and that this magnetic field increases the odds that the second coin will also be heads. Now, the second toss is not independent of the first toss and the probability of getting heads twice is larger than .25.  

### Dependent samples {#sec-dependentsamples}

The example of a manipulated second toss is applicable to repeated measurements. If we want to know how quickly the yellow colour fades when yellow candies are exposed to sun light, we may draw a sample of yellow candies once and measure the colourfulness of each candy at least twice: at the start and end of some time interval. We compare the colourfulness of a candy at the second measurement to its colourfulness at the first measurement.  

::: {#fig-mean-dependent}

```{=html}
<iframe src="https://sharon-klinkenberg.shinyapps.io/mean-dependent/" width="100%" height="580px" style="border:none;">
</iframe>
``` 
Dependent samples.
:::





In this example, we are comparing two means, just like the yellow versus red candy weight example, but now the samples for both measurements are the same. It is impossible to draw the sample for the second measurement independently from the sample for the first measurement if we want to compare repeated measurements. Here, the second sample is fixed once we have drawn the first sample. The samples are _statistically dependent_; they are _paired samples_.

With dependent samples, probabilities have to be calculated in a different way, so we need a special sampling distribution. In the interactive content above, you may have noticed a relatively simple solution for two repeated measurements. We just calculate the difference between the two measurements for each candy in the sample and use the mean of this new difference variable as the sample statistic that we are interested in. The _t_-distribution, again, offers a good approximation of the sampling distribution of dependent samples if the samples are not too small. 

For other applications, the actual sampling distributions can become quite complicated but we do not have to worry about that. If we choose the right technique, our statistical software will take care of this.   



















 




## SPSS and Theoretical Approximation of the Sampling Distribution

By default, SPSS uses a theoretical probability distribution to approximate the sampling distribution. It chooses the correct theoretical distribution but you yourself should check if the conditions for using this distribution are met. For example, is the sample large enough or is it plausible that the variable is normally distributed in the population?

In one case, SPSS automatically selects an exact approach if the conditions for a theoretical approximation are not met. If you apply a chi-squared test to a contingency table in SPSS, SPSS will automatically apply Fisher's exact test if the table has two rows and two columns. In all other cases, you have to select bootstrapping or an exact approach yourself if the conditions for a theoretical approximation are not met.

We are not going to practice with theoretical approximations in SPSS, now. Because theoretical approximation is the default approach in SPSS, we will encounter it in the exercises in later chapters. The default approach in SPSS means that if we conduct an analysis in SPSS without changing the settings to include an exact approach or bootstrapping (which you will learn in the next paragraph), we are using a theoertical approximation on our data.

## The Bootstrap Approximation of the Sampling Distribution {#sec-boot-approx}

The third way to obtain a sampling distribution is still based on the idea of drawing a large number of samples. However, we only draw one sample from the population for which we collect data. As a next step, we draw a large number of samples from our initial sample. The samples drawn in the second step are called _bootstrap samples_. The technique was developed by Bradley Efron [-@RefWorks:3956; -@RefWorks:3957]. For each bootstrap sample, we calculate the sample statistic of interest and we collect these as our sampling distribution. We usually want about 5,000 bootstrap samples for our sampling distribution.  

::: {#fig-bootstrapping .column-page-inset-right}

```{=html}
<iframe src="https://sharon-klinkenberg.shinyapps.io/bootstrapping/" width="100%" height="462px" style="border:none;">
</iframe>
``` 
How do we create a sampling distribution with bootstrapping?
:::

In @fig-bootstrapping, an initial sample (left panel) has been drawn from a population containing five candy colours in equal proportions.









```{block2, type='rmdmunchhausen'}
The _bootstrap_ concept refers to the story in which Baron von M&uuml;nchhausen saves himself by pulling himself and his horse by his bootstraps (or hair) out of a swamp. In a similar miraculous way, bootstrap samples resemble the sampling distribution even though they are drawn from a sample instead of the population. This miracle requires some explanation and it does not work always, as we will discuss in the remainder of this section. 

[Picture: Baron von M&uuml;nchhausen pulls himself and his horse out of a swamp. Theodor Hosemann (1807-1875), public domain, via Wikimedia Commons](https://commons.wikimedia.org/wiki/File:M%C3%BCnchhausen-Sumpf-Hosemann.png)
```

### Sampling with and without replacement  

As we will see in @sec-param-estim, for example @sec-precisionsesamplesize, the size of a sample is very important to the shape of the sampling distribution. The sampling distribution of samples with twenty-five cases can be very different from the sampling distribution of samples with fifty cases. To construct a sampling distribution from bootstrap samples, the bootstrap samples must be exactly as large as the original sample.  

How can we draw many different bootstrap samples from the original sample if each bootstrap sample must contain the same number of cases as the original sample?

::: {#fig-replacement .column-page-inset-right}

```{=html}
<iframe src="https://sharon-klinkenberg.shinyapps.io/bootstrapping-replacement/" width="100%" height="448px" style="border:none;">
</iframe>
``` 
Sampling with and without replacement.
:::



If we allow every case in the original sample to be sampled only once, each bootstrap sample contains all cases of the original sample, so it is an exact copy of the original sample. Thus, we cannot create different bootstrap samples. 

By the way, we often use the type of sampling described above, which is called _sampling without replacement_. If a person is (randomly) chosen for our sample, we do not put this person back into the population so she or he can be chosen again. We want our respondents to fill out our questionnaire only once or participate in our experiment only once.  

If we do allow the same person to be chosen more than once, we sample _with replacement_. The same person can occur more than once in a sample. Bootstrap samples are sampled with replacement from the original sample, so one bootstrap sample may differ from another. Some cases in the original sample may not be sampled for a bootstrap sample while other cases are sampled several times. You probably have noticed this in @fig-replacement. Sampling with replacement allows us to obtain different bootstrap samples from the original sample, and still have bootstrap samples of the same size as the original sample.  

In conclusion, we sample bootstrap samples in a different way (with replacement) than participants for our research (without replacement).

### Limitations to bootstrapping  

Does the bootstrapped sampling distribution always reflect the true sampling distribution?

::: {#fig-bootstrap-lim}

```{=html}
<iframe src="https://sharon-klinkenberg.shinyapps.io/bootstrap-lim/" width="100%" height="560px" style="border:none;">
</iframe>
``` 
How is bootstrapping influenced by sample size? In the population, twenty per cent of the candies are yellow.
:::







We can create a sampling distribution by sampling from our original sample with replacement. It is hardly a miracle that we obtain different samples with different sample statistics if we sample with replacement. Much more miraculous, however, is that this bootstrap distribution resembles the true sampling distribution that we would get if we draw lots of samples directly from the population.  

Does this miracle always happen? No. The original sample that we have drawn from the population must be more or less representative of the population. The variables of interest in the sample should be distributed more or less the same as in the population. If this is not the case, the sampling distribution may give a distorted view of the true sampling distribution. This is the main limitation to the bootstrap approach to sampling distributions.  

A sample is more likely to be representative of the population if the sample is drawn in a truly random fashion and if the sample is large. But we can never be sure. There always is a chance that we have drawn a sample that does not reflect the population well. 

### Any sample statistic can be bootstrapped

The big advantage of the bootstrap approach (_bootstrapping_) is that we can get a sampling distribution for any sample statistic that we are interested in. Every statistic that we can calculate for our original sample can also be calculated for each bootstrap sample. The sampling distribution is just the collection of the sample statistics calculated for all bootstrap samples.  

Bootstrapping is more or less the only way to get a sampling distribution for the sample median, for example, the median weight of candies in a sample bag. We may create sampling distributions for the wildest and weirdest sample statistics, for instance the difference between sample mean and sample median squared. I would not know why you would be interested in the squared difference of sample mean and median, but there are very interesting statistics that we can only get at through bootstrapping. A case in point is the strength of an indirect effect in a mediation model (@sec-mediation).  

















## Bootstrapping in SPSS {#sec-boot-spss}

### Instructions

The last approach we will show you in SPSS is bootstrapping. In the video below you will see several analyses to which we add bootstrapping. 

Remember your birthday party with a lot of candy that sparks new questions every couple of minutes? This time one friend is getting a bit nauseous from the candy and another friend is doing just fine. They conclude they both have been eating the same amount of candy but one has a preference for strawberry flavoured and the other for lemon flavoured. Could it be that the friend who is constantly eating red candies has been eating more cnady than the friend that has been eating yellow candies? According to your friends, that could only be true if the red candies weigh more than the yellow candies.

In this case, we are investigating whether yellow and red candies weigh the same amount. Thus, we have two variables: candy colour (red and yellow; two categories) and candy weight (continuous). As you can see in @sec-test-selection, we can investigate these variables with an independent t-test. This independent t-test is shown in the video.

As you might remember from the exact approach, this data set contains more candy colours than red and yellow. It is important that we define the groups so that this analysis only includes red and yellow candies. Otherwise we will not find an answer to the question we have proposed above.

You might also remember from the theoretical approach that there are certain conditions we need to meet in order to be able to execute an independent samples t-test. Let's say your friends have been eating quite some candy and therefore we do not have 30 yellow and 30 red candies left. Consequently, we do not meet the conditions. This leads us to resort to bootstrapping to still be able to use the independent sample t-test. Via the  `bootstrap` button, we can check `perform bootstrapping`. Usually, we use 5000 bootstrap samples and 95% bias corrected confidence intervals. Please note that bootstrapping is random and therefore bootstrap results can always differ a little bit from each other, you might see this when working together with a friend or checking your answers on the preparatory assignments. Numbers can differ a little bit, this will not happen when we use the same seed - but we do not use that option in this course.

Watch the video for the step by step on how to perform an independent t-test with bootstrapping, the details and some additional information.

::: {#vid-SPSSbootstrap1}

{{< video https://www.youtube.com/embed/-6nQsBK4-E8
    width="100%"
    height="315" 
>}}

Perform bootstrapping in SPSS.
:::

Now that we have run the analysis in SPSS, we want to show you how to interpret this results. And thus, how to answer the question whether yellow and red candies weigh the same amount. 

As with the Fisher's exact test, the output starts - after a table with some bootstrap specifications - with a summary type table including descriptive like results. The _group statistics_, here we can find the number of cases (candies), means, standard deviations, etc. The means can already give you a sense of and a grip on your results, which can help with interpretation later on.

The table below, _independent samples test_, shows us the results of the independent samples t-test, including Leven's F-test, the test statistic, p-value and bootstrapped confidence interval. Levene's F-test is above .05 which leads us to conclude that equal variances are assumed (we will talk more about this during ANOVA, in chapter 5). This means we look at the upper row for our results. The t-value has a corresponding p-value that is also above .05 which menas that the effect of candy colour on candy weight is not significant. 

The second part of the _independent samples test_ shows us the mean difference which is very small, this makes sense given the fact that we found a not significant result. The bootstrapped confidence intervals show that the zero falls in the 95% interval. This means that there is a likelihood that the mean difference could be zero. Thus, looking at the intervals we would also conclude that the effect is not significant. 

In conclusion, the results show us that we could conclude that the hypothesis made by your friends gets no support from our data. Red and yellow candies seem to weigh approximately the same. We could have already seen this coming after looking at the mean values.

Watch the video for the step by step on how to interpret an independent t-test with bootstrapping, the details and some additional information.

```{r, echo=FALSE, eval=FALSE}
# Perform bootstrapping in SPSS.
# Example: candies.sav, independent-samples t test, average weight of red (colour = 4) and yellow (colour = 4) candies.
# 
# In SPSS, several statistics can be bootstrapped. If so, the SPSS dialog for the statistic contains a button labelled _Bootstrap..._. A new menu opens, where you can select the bootstrapping option _Perform bootstrapping_ and set the number of bootstraps. It is recommended to use 5,000 bootstraps but you might try a lower number first to check computing time if your computer is not too fast. 
# 
# You can set some more bootstrapping options. The Mersenne Twister seed is a number that starts the randomizer used to draw random sample. If run the bootstrap with  the same seed number (any number will do) as the previous time, SPSS will yield exactly the same results as the preceding time. If this number is not set, applying bootstrap at different times will produce slightly different results because different random bootstrap samples are drawn. These differences, however, are usually too small to be of importance. Only set the seed number if you want to replicate your exact results when you rerun the bootstrap.
# 
# The confidence level of the confidence interval can be changed. We will discuss confidence levels in @sec-conf-interval. For now, never mind this option because the default (95%) is most widely used. There are two ways of calculating the confidence interval from the bootstraps. _Bias corrected accelerated (BCa)_ is the better option. It corrects for bias (difference between the sample result and the mean of the bootstrapped sampling distribution) and for skewness in the bootstrapped sampling distribution (which is more likely with a skewed sampling distribution?).
#
# Finally, it is possible to stratify the bootstrap sample. If you select a variable here, for example, candy colour, each bootstrap sample with have the same distribution of colours as the original sample. Usually, this is not necessary.
#
# BCa bootstrap does not work for data with more than a few hundred cases? In tests with SPSS V25, the median is sometimes not bootstrapped with 550 cases (and sometimes it is).
```

::: {#vid-SPSSbootstrap2}

{{< video https://www.youtube.com/embed/6E2LgeMtkL4
    width="100%"
    height="315" 
>}}

Interpret bootstrap results in SPSS. 
:::



```{r, echo=FALSE, eval=FALSE}
# Interpret bootstrap results in SPSS. 
# SPSS generates the sampling distribution in the background, so you cannot see it. SPSS just provides new p values ( _Sig._ ) and confidence intervals marked as _Bootstrap_. Report these values instead of the "ordinary" p value and confidence interval. For example, a bootstrapped independent-samples t test on the difference between the average weight of yellow and red candies produces the following output in SPSS.
# 
# The first table in the output merely tells us the options we selected for bootstrapping. The table __Group Statistics__ gives us the group means, standard deviations, and standard error of the mean (to be discussed in @sec-standard-error). Each of these has a bootstrap confidence interval, illustrating that we can bootstrap any sample statistic. 
# 
# Then we get the usual summary of the t test without bootstrapping in the __Independent Samples Test__ table and, finally, the bootstrap results for the t test. If we compare test significance (p value) and confidence intervals between the regular t test and the bootstrapped t test, we see very similar results. The bootstrap confidence interval is slightly narrower than the regular confidence interval. Both confidence intervals suggest that the weight difference between yellow and red candies can be both positive (red candies are on average heavier) and negative (yellow candies are heavier), so we best conclude that there is no difference in average weight.
# 
# The tables with bootstrap results include a column headed __Bias__. This is the difference between the value of the statistic in the original sample and its average value over all bootstrap samples. Bias should be small, as it is here. We do not care about small bias values because we use a bias-corrected bootstrapping method.
#
# In SPSS version 24 and earlier, bootstrapping remains active until you disable it. (example with paired t test as next test). There is one thing you should be aware of. If you select the _Perform bootstrapping_ option, all subsequent analyses in SPSS that allow for bootstrapping will be bootstrapped as well. This is usually not what you want and it can be very time-consuming to the computer. Don't forget to deselect this option if you run a new analysis that can be bootstrapped.
```

In principle, any sample statistic can be bootstrapped. SPSS, however, does not bootstrap sample statistics that we had better not use because they give bad (biased) results. For example, SPSS does not bootstrap the minimum value, maximum value or the range between minimum and maximum value of a variable. 

SPSS reports bootstrapping results as confidence intervals. We will discuss confidence intervals in detail in the next chapter.

## When Do We Use Which Approach to the Sampling Distribution?

```{r decisionscheme, echo=FALSE, fig.pos='H', fig.align='center', fig.cap="Diagram for selecting the type of sampling distribution.", out.width="775px"}
knitr::include_graphics("figures/decision.png")
```

By default, SPSS uses a theoretical approximation of the sampling distribution. Select the right test in SPSS and SPSS ensures that an appropriate theoretical probability distribution is used. You, however, must check whether the sample meets the conditions for using this theoretical probability distribution, see @tbl-thumb.

If the conditions for using a theoretical probability distribution are not met or if we do not have a theoretical approximation to the sampling distribution, we use bootstrapping or an exact approach. We can always use bootstrapping but an exact approach is available only if the variables are categorical. An exact approach is more accurate than bootstrapping and approximation with a theoretical probability distribution, for example, the chi-squared distribution, so we prefer the exact approach over bootstrapping if we are dealing with categorical variables.

## Take-Home Points  

* We may create an exact sampling distribution or simulate a bootstrap sampling distribution in simple situations or if we have a lot of computing power.  

* For a bootstrap sampling distribution, we need about 5,000 bootstrap samples from our original sample.  

* An exact sampling distribution can only be used with categorical variables.

* We can often approximate the sampling distribution of a sample statistic with a known theoretical probability distribution.  

* Approximations only work well under conditions, which we have to check.

* Conditions usually involve the size of the sample, sample type (independent vs. dependent/paired), and the shape or variance of the population distribution.

* If these conditions are not met or we do not have a theoretical approximation to the sampling distribution, we use bootstrapping or exact tests.

* Samples are independent if, in principle, we can draw a sample for one group without taking into account the sample for another group of cases. Otherwise, the samples are dependent or paired.