Linear Trend Analysis with R and SPSS

This is an introduction to contrast analysis for estimating the  linear trend among condition means with R and SPSS . The tutorial focuses on obtaining point and confidence intervals.  The contents of this introduction is based on Maxwell, Delaney, and Kelley (2017) and Rosenthal, Rosnow, and Rubin (2000). I have taken the (invented) data from Haans (2018). The estimation perspective to statistical analysis is aimed at obtaining point and interval estimates of effect sizes. Here, I will use the frequentist perspective of obtaining a point estimate and a 95% Confidence Interval of the relevant effect size. For linear trend analysis, the relevant effect size is the slope coefficient of the linear trend, so, the purpose of the analysis is to estimate the value of the slope and the 95% confidence interval of the estimate. We will use contrast analysis to obtain the relevant data.

[Note: A pdf-file that differs only slightly from this blogpost can be found on my Researchgate page: here; I suggest Haans (2018) for an easy to follow introduction to contrast analysis, which should really help understanding what is being said below].

The references cited above are clear about how to construct contrast coefficients (lambda coefficients) for linear trends (and non-linear trends for that matter) that can be used to perform a significance test for the null-hypothesis that the slope equals zero. Maxwell, Delaney, and Kelley (2017) describe how to obtain a confidence interval for the slope and make clear that to obtain interpretable results from the software we use, we should consider how the linear trend contrast values are scaled. That is, standard software (like SPSS) gives us a point estimate and a confidence interval for the contrast estimate, but depending on how the coefficients are scaled, these estimates are not necessarily interpretable in terms of the slope of the linear trend, as I will make clear
momentarily.

So our goal of the data-analysis is to obtain a point and interval estimate of the slope of the linear trend and the purpose of this contribution is to show how to obtain output that is interpretable as such.

Planning for Precise Contrast Estimates: Introduction and Tutorial (Preprint)

I just finished a preprint of an introduction and tutorial to sample size planning for precision of contrast estimates. The tutorial focuses on single factor between and within subjects designs, and mixed factorial designs with one within and one between factor. The tutorial contains R-code for sample size planning in these designs.

The preprint is availabe on researchgate: Click (but I am just as happy to send it to you if you like; just let me know).

Planning for precise contrast estimates in between subjects designs

Here I would like to explain the procedure for sample size planning for one-way and two-way (factorial) between subjects designs. We will consider examples based on and described in Haans (2018).

The first example: one-way design

The first example considers the effect of seating location  of students on their educational performance. Seating location is defined as distance from the teacher and operationalized in terms of the row the student is seated in, with first row being the closest to the teacher and the fourth row being the furthest away. 20 Students are randomly assigned to one of the four possible rows, so N = 20, n = 5. The dependent variable is the course grade of the student. (Note: the data and study are hypothetical).

As Haans (2018) explains, one psychological theory explaining the effect of seating position on educational performance is based on social influence. This theory posits that due to the social influence of the teacher, the students that are seated closest to the teacher find themselves in a state of undivided attention. This undivided attention causes their educational performance to be better than the students who are seated further away.

In operational terms, then, we may expect that first row students will have a better average grade than students seated on the other rows. So, the quantitative research question we are interested in is:

“How much do the average grades differ between students seated first row and the students seated on other rows?”

We can estimate this quantity with a Helmert Contrast, where we assign a contrast weight of 1 to mean of the first row grades and weights -1/3 to the means of the grades in the other rows.

Haans (2018) gives us the following results. The contrast estimate equals 2.00 , 95% CI [0.27, 3.73]. In order to interpret this more easily, we divide this estimate by the square root Mean Square Error, to obtain the standardized estimate and standardized confidence interval (not to be confused with the confidence interval of the standardized estimate, but that’s a different story. The result is: 1.26, 95% CI [0.17, 2.36].

To answer the research question, the estimated difference equals 1.26 standard deviations, which according to rule-of-thumbs frequently used in psychology is a large difference. The CI shows the enormous amount of uncertainty of this estimate: population values between 0.17 (small) and 2.36 (very large) are also consistent with the observed data and our statistical assumptions. So, it seems safe to conclude that it looks like there is a positive effect of seating position, but the wide range of the CI makes it clear that the data do not tell us enough about the size of the effect, the precision is simply too low.

The precision is f = 1.09, which according to my rules-of-thumb is very imprecise (I consider f = 0.65, to be barely tolerable).

So, let’s plan for a replication study with a reasonably precise estimate of  f = 0.40, with 80% assurance. (Note: for some advice on setting target Moe: Planning with assurance, with assurance. ) I’ve used the app: https://gmulder.shinyapps.io/PlanningFactorialContrasts/ with the default values for a single factor between subjects design with 4 conditions.  According to the app, we need n = 36 participants per condition (making a total of  N = 144).

(For more detailed information considering sample size planning for contrast analysis see: http://small-s.science/?p=10 and for some guidelines for setting target MoE: http://small-s.science/?p=14)

The second example: factorial design

Our second example is also taken from Haans (2018). It considered the same phenomenon, the effect of students’ seating distance from the teacher and the educational performance of the students.

A second theory explaining the effect is that the effect is mainly caused by the teacher having decreased levels of eye contact with the students sitting farther to the back in the lecture hall.

To test that theory, a experiment was conducted with N = 72 participants attending a lecture. The lecture was given to two independent groups of 36 pariticpant. The first group attended the lecture while the teacher was wearing dark sunglasses, the second group attented the lecture while the teacher was not wearing sunglasses,. Again, all participants were randomly assigned to 1 of 4 possible rows. The dependent variable was the score on a 10-item questionnaire about the contents of the lecture.

Now, if the eyecontact of the teachter is the causal variable, we may expect that in this experimental setup the difference between the average score of the persons seated on the first row and the averages of the other rows will be smaller for the condition where the teacher wears sunglasses than for the condition in which the teacher does not wear these glasses, as wearing sunglasses prevents eye-contact between the teacher and the students. Our quantitative question is therefore:

“How much does the contrast between the first row and the others rows differ between the conditions with and without sunglasses?”

In other words, we are interested in the size of the interaction effect.

I’ve downloaded the dataset from http://pareonline.net/sup/v23n9.zip (between2by4data.sav) and specified the following syntax in SPSS:

UNIANOVA retention BY sunglasses location
/LMATRIX = “Interaction contrast” sunglasses*location 1 -1/3 -1/3 – 1/3 -1 1/3 1/3 1/3 intercept 0
/DESIGN= sunglasses*location.

The result of the analysis is that the contrast estimate equals 1.0, 95% CI [-0.33, 2.33]. If we standardize this with the within condition variance (the condition being the combination of the levels of the two factors), we get 0.82, 95% CI [-0.27, 1.90].

So, it appears that the difference between the means of the first row and that of the other rows is on average 1.0 points larger in the condition without sunglasses than in the condition with sunglasses. This corresponds to a large difference (dwith = .82). However, the CI also contains negative population difference (albeit that they are smallish), so even though the results are promising for the theory (eyecontact), these negative effects will not persuade a critical reviewer of the study. Indeed, these negative effects contradict the substantive hypothesis.

Again, the confidence interval is so wide, that effects ranging from small negative effects to huge positive effects are considered plausible. Since the results are promising for the theory, a replication study with more precision may be needed to persuade the critics. Let’s plan for a precision of f = .25 with 95% assurance.

I’ve used the app: https://gmulder.shinyapps.io/PlanningFactorialContrasts/ specifying that we have a factorial design with a = 2 levels and b = 4 levels. The result is that for the interaction contrast  with f = .25 and assurance = .95, we need 175 participants per combination of the two factors. This means, that a total of N = 1400 must be recruited.

I’ve taken this from the following output.

 Figure 1: Output of sample size planning

I’ve looked at the  “Contrast Summary Tab” to check that interaction A1B1 is the correct one (see Figure 2).

 Figure 2. Summary of contrast weights.

What’s important in the above figure is that the set of weights for A1B1 matches the set of weights used to get the contrast estimate in SPSS (In the LMATRIX-subcommand), so that’s how we know that A1B1 is the contrast we want.  (Note: if you switch the number of levels in the app, that is, use 4 levels for A and 2 for B, the interaction weights will match perfectly).

Reference
Haans, Antal (2018). Contrast Analysis: A Tutorial. Practical Assessment, Research, & Education, 23(9). Available online: http://pareonline.net/getvn.asp?v=23&n=9

Planning for a precise interaction contrast estimate

In my previous post (here),  I wrote about obtaining a confidence interval for the estimate of an interaction contrast. I demonstrated, for a simple two-way independent factorial design, how to obtain a confidence interval by making use of the information in an ANOVA source table and estimates of the marginal means and how a custom contrast estimate can be obtained with SPSS.

One of the results of the analysis in the previous post was that the 95% confidence interval for the interaction was very wide. The estimate was .77, 95% CI [0.04, 1.49]. Suppose that it is theoretically or practically important to know the value of the contrast to a more precise degree.  (I.e. some researchers will be content that the CI allows for a directional qualitative interpretation: there seems to exist a positive interaction effect, but others, more interested in the quantitative questions may not be so easily satisfied).  Let’s see how we can plan the research to obtain a more precise estimate. In other words, let’s plan for precision.

Of course, there are several ways in which the precision of the estimate can be increased. For instance, by using measurement procedures that are designed to obtain reliable data, we could change the experimental design, for example switching to a repeated measures (crossed) design, and/or increase the number of observations. An example of the latter would be to increase the number of participants and/or the number of observations per participant.  We will only consider the option of increasing the number of participants, and keep the independent factorial design, although in reality we would of course also strive for a measurement instrument that generally gives us highly reliable data. (By the way, it is possible to use my Precision application to investigate the effects of changing the experimental design on the expected precision of contrast estimates in studies with 1 fixed factor and 2 random factors).

The plan for the rest of this post is as follows. We will focus on getting a short confidence interval for our interaction estimate, and we will do that by considering the half-width of the interval, the Margin of Error (MOE). First we will try to find a sample size that gives us an expected MOE (in repeated replication of the experiment with new random samples) no more than a target MOE. Second, we will try to find a sample size that gives a MOE smaller than or equal to our target MOE in a specifiable percentage (say, 80% or 90%) of replication experiments. The latter approach is called planning with assurance.

Let us get back to some of the SPSS output we considered in the previous post to get the ingredients we need for sample size planning. First, the ANOVA table.

 Table 1. ANOVA source table

We are interested in estimating and optimizing the precision of an interaction contrast estimate. The first things we need are an expression of the error variance needed to calculate the standard error of the estimate and the degrees of freedom that were used in estimating the error variance. In general, the error variance needed is the same error variance you would use in performing an F-test for the specific effect, in this case the interaction effect.

Thus, we note the error variance used to test the interaction effect, i.e. mean square error, and the degrees of freedom. The value of mean square error is 3.324, and the degrees of freedom are 389. Note that this value is the total sample sizes minus the number of conditions (393 – 4 = 389), or, equivalently, the total sample sizes minus the degrees of freedom of the intercept, the main effects, and the interaction (393 – (1 + 1 + 1 + 1) = 389).  I will call these degrees of freedom the error degrees of freedom, dfe.

MOE can be obtained by multiplying a critical t-value with the same degrees of freedom as the error degrees of freedom with the standard error of the estimate.

The standard error of the contrast estimate is

where is the contrast weight for the i-th condition mean, and the number of observations (in our example participants) in treatment condition i.  Note that is the variance of  treatment mean i, the square root of which gives the familiar standard error of the mean.

The contrast weights we used to estimate the 2 x 2 interaction were {-1, 1, 1, -1}. So, the expression for MOE becomes

Thus, suppose we have the independent 2×2 factorial design, , and the true value of Mean Square Error is 3.324, then MOE for the contrast estimate equals

.
Note that this is the value of MOE we obtain on average in repeated replications with new samples, if we use sample sizes of 100 (total number of participants is 400) and if the true value of the error variance is 3.324.  The value is close to the value we obtained in the previous post (MOE = 0.72) because the sample sizes were very close to 100 per group.

Now, we found the original confidence interval too wide, and we have just seen how 100 participants per group does not really help. MOE is only slightly smaller than our originally obtained MOE. We need to set a target MOE and then figure out how many participants we need to get that target MOE.

Intermezzo: Rules of thumb for target MOE

(Here are some updated rules of thumb: https://the-small-s-scientist.blogspot.com/2018/11/contrast-tutorial.html)

In the absence of theoretical or practical considerations about the precision we want, we may want to use rules of thumb. My (very first proposal for) rules of thumb are based on the default interpretations of Cohen’s d. Considering the absolute values of d ≤ .10 to be negligible d = .20 small, d = .50 medium and d = .80 large. (I really do not like rules-of-thumb, because using them is a sign that you are not thinking).

Now, suppose that we interpret the confidence interval as a range of plausible values for the true value of the effect size. It is not at all clear to me what such a supposition entails, but let’s simply take it for granted right now (please don’t). Then, I think it is reasonable to say that being able to distinguish between small and negligible effects sizes is relatively precise. Thus a MOE of .05 (pooled) standard deviations  can be considered precise because (on average) the 95% CI for the small effect sizes is [.15, .25], assuming we know the value of the standard deviation, so negligible effects will not be deemed plausible values on average, since effect sizes smaller than .10 are outside the interval.

By essentially the same reasoning. if we cannot distinguish between large and negligible effects, we are not estimating things very precisely. Therefore, a MOE of .80 standard deviations can be considered to be not very precise. On average, the CI for an existing large effect, will be [0,  1.60], so it includes both negligible and very large effects as plausible values.

For medium (does it make sense to speak of medium precision?) precision I would like to suggest .20-.25 standard deviations. On average, with this value for MOE, if there is a medium effect, small effects and large effects are relatively implausible.  In the case of small effects, medium precision entails that on average both effects in the opposite direction and medium effects are among the plausible values.

Of course, I am interpreting the d-values as strict boundaries, but the scale is not categorical, but continuous. So instead of small, large effect sizes, it’s better to speak of smallish and largish effect sizes. And as soon as I find a variant for medium effects sizes I will also include that term in the list.

Note: sample size planning may indicate that precision of MOE = .20-.25 standard deviations is unattainable. In that case, we will simply have to accept that our precision does not lead to confident conclusions about the population effect size. (Once I showed one of my colleagues my precision app, during which he said: “that amount of precision requires a very large sample. I do not like your ideas about sample size planning”).

(By the way, I am also considering rules-of-thumb for target MOE that include assurance. Something like: high precision is when repeated experiments have a high probability of distinguishing small and negligible effects; in that case the average MOE will be smaller than .05).

Planning for precision

Let’s plan for a precision of 0.25 standard deviation. In our case, that standard deviation is the pooled standard deviation: the square root of Mean Square Error. The (estimated) value of  Mean Square Error is 3.324 (see Table 1), so our value for the standard deviation is 1.8232.  Our target MOE is, therefore, 0.4558.
Let’s make things very clear. Here we are planning for a target MOE based on an estimate of the pooled standard deviation (and on assumptions about the population distribution). In order for our planning to be of practical value, we need some reassurance that that estimate is trustworthy. One way of doing that is to consider the CI for the standard deviation. I will not discuss that topic, and simply give you a CI: [2.90,  3.86].
Take a look at the expression for MOE.

where , since we are considering the 2×2 design.

Since our target MOE equals .4588, our goal becomes to solve the following equation for , since we want the sample size:

However, because determines both the standard error and the degrees of freedom (and thereby the critical value of t), the equation may be a little hard to solve.  So, I will create a function in R that enables me to quite easily get the required sample size. (It is relatively easy to create a more general function (see the Precision App), but here I will give an example tailored to the specific situation at hand).

First we create a function to calculate MOE:

MOE = function(n) {
MOE = 2*qt(.975, 4*(n - 1))*sqrt(3.324/n)
}


Next, we will define a loss function and use R’s built-in optimize function to determine the sample size. Note that the loss-function calculates the squared difference between MOE based on a sample size n and our target MOE. The optimize function minimizes that squared difference in terms of sample size n (starting with n = 100 and stopping at n = 1000).

loss <- function(n) {
(MOE(n) - 0.4558)^2
}

optimize(loss, c(100, 1000))

## $minimum ## [1] 246.4563 ## ##$objective
## [1] 8.591375e-18


Thus, according to the optimize function we need 247 participants (per group; total N = 988), to get an expected MOE equal to our target MOE. The expected MOE equals 0.4553, which you can confirm by using the MOE function we made above.

Planning with assurance

Although expected MOE is close to our target MOE, there is a probability 50% that the obtained MOE will be larger than our target MOE.  In other words, repeated sampling will lead to obtained MOEs larger than what we want. That is to say, we have 50% assurance that our obtained MOE will be at least as small as our target MOE.
Planning with assurance means that we aim for a certain specified assurance that our obtained MOE will not exceed our target MOE. For instance, we may want to have 80% assurance that our obtained MOE will not exceed our target MOE.
Basically, what we need to do is take the sampling distribution of the estimate of  Mean Square Error into account. We use the following formula (see also my post introducing the Precision App for the general formulae: https://the-small-s-scientist.blogspot.nl/2017/04/planning-for-precision.html).

where is the assurance expressed in a probability between 0 and 1.

Let’s do it in R. Again, the function that calculates assurance MOE is  tailored for the specific situation, but it is relatively easy to formulate these functions in a generally applicable way,
MOE.gamma = function(n) {
df = 4*(n-1)
MOE = 2*qt(.975, df)*sqrt(3.324/n*qchisq(.80, df)/df)
}
loss <- function(n) {
(MOE.gamma(n) - 0.4558)^2
}

optimize(loss, c(100, 1000))

## $minimum ## [1] 255.576 ## ##$objective
## [1] 2.900716e-18


Thus, according to the results, we need 256 persons per group (N = 1024 in total) to have a 80% probability of obtaining a MOE not larger than our target MOE. In that case, our expected MOE will be 0.4472.