Here is an illustration of my problem:

I have two stimuli (A and B) given to a number of subjects. Each subject is sequentially subjected to each stimulus 5 times (AAAAABBBBB or BBBBBAAAAA, but not both). I have randomized the presentation order of these stimuli to each subject. The data might look like:

enter image description here

My question is how can I statistically show:

  1. Did stimulus presentation order affect the "Responded" outcome?
  2. Did one stimulus induce response more than the other?

First question addresses this comparison:

enter image description here

Second question addresses this comparison:

enter image description here

I don't remember learning how to deal with data like this. THANK YOU!

DATA: Here's some data for this question for replication purposes

  • 3
    $\begingroup$ (1) "Stimuli" is plural, "stimulus" is singular ... so "Did one stimulus...". (2) when comparing A first vs A second, are you just interested in a difference in the average or are you interested in any difference in pattern? [Either way, for data like this you're probably looking at some form of binomial model - a GLM or GLMM.] $\endgroup$
    – Glen_b
    May 20, 2015 at 9:31
  • $\begingroup$ (1) Thanks Glen_b, I've adjusted the spelling where possible. Can't redo the graphs at the moment. (2) I am interested in the patterns. For that objective, I'd like to show that each stimulus exhibits the same decay in response frequency regardless of whether that stimulus was presented first or second. $\endgroup$
    – suchafool
    Jun 9, 2015 at 4:51
  • 1
    $\begingroup$ Sorry, Glen_b. I should have said I was interested in the patterns and the means. I want to know if there is a difference in the average at each trial number (1 vs 6; 2 vs 7;etc) and also if there is a comparable decay rate in the response frequency between the two presentation order groups (trials 1-5 pattern/rate vs. 6-10 pattern/rate). If there is no difference in both cases, I'd like to lump all the data for each stimulus regardless of presentation order and then perform the same analysis, but I'd be comparing the two stimuli. $\endgroup$
    – suchafool
    Jun 9, 2015 at 5:19

2 Answers 2


Assuming that you are interested in the mean responses by subject and since you treat them as two separate question I will suggest two distinct and simple ways of dealing with this which I am sure are not the only ones.

For your first question you could create a new variable and code as 0 and 1 the type of presentations (e.g. 0=AAABBB, 1=BBBAAA), and perform an independent sample t-test (or the non-parametric equivalent as you are not giving out any information about the distribution of the responses) using the sum of the responses as the dependent variable.

For the second one you could create two variables (you 'd also have to change your dataset from long to wide format after computing the sum of the responses), one representing the responses for subjects when they were presented with stimulus A and a second one for subjects when they were presented with stimulus B and run a related-samples t-test (or non-parametric equivalent) using as the dependent variable the sum of responses.

Note: If your interest is in modelling the binary outcome though, then a GLM or GLMM would be suitable as Glen_b has already pointed out

  • $\begingroup$ Thank you, StevenP. I am interested in the mean response over time ("response decay rate") by subject for my 2nd objective, but I am hoping to ignore the stimulus presentation order by showing that it had no significant effect on the mean and response decay rate of response frequency (1st objective). $\endgroup$
    – suchafool
    Jun 9, 2015 at 5:11

Unfortunately, this answer is more of a comment, but I think that your question is too complex to be answered properly here without actually seeing your data. I would like to offer pointers that I consider important for you:

  1. Decide what your outcome should be. Your example and your data suggest that a person responds to a stimuli for some time and then stops and doesn`t respond again. In this case your outcome might be whether and when an individual stops responding. If the subjects can switch back and forth between responding and not, I would also go with some sort of binomial model.
  2. Consider whether your goal is to construct a model (explorative) or to do significance testing (confirmatory). When doing hypothesis testing you do not want to bias your p-values, so you should stick with a pre-decided model to answer these questions. If you want to construct a model, you probably would not go for hypothesis testing, but instead look at how well your model can simulate data that looks like your input. I think in Bayesian Data Analysis by Andrew Gelman there is a model for data very much like this. Unfortunately, I do not have my copy at hand.
  • $\begingroup$ Erik, thanks for the response. (1) Typically, you are correct that a person responds and then stops and does not begin responding again. However, this is not always the case and would need to be included. (2) I think I am only interested in doing significance testing. The point of my 1st objective is to rule out any effect of presentation order so that I can lump data from the same stimulus while ignoring presentation order for my 2nd objective. Perhaps presentation order would be better included as a term in some form of model? I'll look into Gelman's book. Thanks for the reference. $\endgroup$
    – suchafool
    Jun 9, 2015 at 4:58

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