# 15.6.1 Hypothesis tests for a single correlation

I don’t want to spend too much time on this, but it’s worth very briefly returning to the point I made earlier, that Pearson correlations are basically the same thing as linear regressions with only a single predictor added to the model. What this means is that the hypothesis tests that I just described in a regression context can also be applied to correlation coefficients. To see this, let’s take a summary() of the regression.1 model:

summary( regression.1 )
##
## Call:
## lm(formula = dan.grump ~ dan.sleep, data = parenthood)
##
## Residuals:
##     Min      1Q  Median      3Q     Max
## -11.025  -2.213  -0.399   2.681  11.750
##
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)
## (Intercept) 125.9563     3.0161   41.76   <2e-16 ***
## dan.sleep    -8.9368     0.4285  -20.85   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 4.332 on 98 degrees of freedom
## Multiple R-squared:  0.8161, Adjusted R-squared:  0.8142
## F-statistic: 434.9 on 1 and 98 DF,  p-value: < 2.2e-16

The important thing to note here is the t test associated with the predictor, in which we get a result of t(98)=−20.85, p<.001. Now let’s compare this to the output of a different function, which goes by the name of cor.test(). As you might expect, this function runs a hypothesis test to see if the observed correlation between two variables is significantly different from 0. Let’s have a look:

cor.test( x = parenthood$dan.sleep, y = parenthood$dan.grump )
##
##  Pearson's product-moment correlation
##
## data:  parenthood$dan.sleep and parenthood$dan.grump
## t = -20.854, df = 98, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  -0.9340614 -0.8594714
## sample estimates:
##       cor
## -0.903384

Again, the key thing to note is the line that reports the hypothesis test itself, which seems to be saying that t(98)=−20.85, p<.001. Hm. Looks like it’s exactly the same test, doesn’t it? And that’s exactly what it is. The test for the significance of a correlation is identical to the t test that we run on a coefficient in a regression model.

# 15.6.2 Hypothesis tests for all pairwise correlations

Okay, one more digression before I return to regression properly. In the previous section I talked about the cor.test() function, which lets you run a hypothesis test on a single correlation. The cor.test() function is (obviously) an extension of the cor() function, which we talked about in Section 5.7. However, the cor() function isn’t restricted to computing a single correlation: you can use it to compute all pairwise correlations among the variables in your data set. This leads people to the natural question: can the cor.test() function do the same thing? Can we use cor.test() to run hypothesis tests for all possible parwise correlations among the variables in a data frame?

The answer is no, and there’s a very good reason for this. Testing a single correlation is fine: if you’ve got some reason to be asking “is A related to B?”, then you should absolutely run a test to see if there’s a significant correlation. But if you’ve got variables A, B, C, D and E and you’re thinking about testing the correlations among all possible pairs of these, a statistician would want to ask: what’s your hypothesis? If you’re in the position of wanting to test all possible pairs of variables, then you’re pretty clearly on a fishing expedition, hunting around in search of significant effects when you don’t actually have a clear research hypothesis in mind. This is dangerous, and the authors of cor.test() obviously felt that they didn’t want to support that kind of behaviour.

On the other hand… a somewhat less hardline view might be to argue we’ve encountered this situation before, back in Section 14.5 when we talked about post hoc tests in ANOVA. When running post hoc tests, we didn’t have any specific comparisons in mind, so what we did was apply a correction (e.g., Bonferroni, Holm, etc) in order to avoid the possibility of an inflated Type I error rate. From this perspective, it’s okay to run hypothesis tests on all your pairwise correlations, but you must treat them as post hoc analyses, and if so you need to apply a correction for multiple comparisons. That’s what the correlate() function in the lsr package does. When we use the correlate() function in Section 5.7 all it did was print out the correlation matrix. But you can get it to output the results of all the pairwise tests as well by specifying test=TRUE. Here’s what happens with the parenthood data:

library(lsr)
## Warning: package 'lsr' was built under R version 3.5.2
correlate(parenthood, test=TRUE)
##
## CORRELATIONS
## ============
## - correlation type:  pearson
## - correlations shown only when both variables are numeric
##
##            dan.sleep    baby.sleep    dan.grump       day
## dan.sleep          .         0.628***    -0.903*** -0.098
## baby.sleep     0.628***          .       -0.566*** -0.010
## dan.grump     -0.903***     -0.566***         .     0.076
## day           -0.098        -0.010        0.076         .
##
## ---
## Signif. codes: . = p < .1, * = p<.05, ** = p<.01, *** = p<.001
##
##
## p-VALUES
## ========
## - total number of tests run:  6
## - correction for multiple testing:  holm
##
##            dan.sleep baby.sleep dan.grump   day
## dan.sleep          .      0.000     0.000 0.990
## baby.sleep     0.000          .     0.000 0.990
## dan.grump      0.000      0.000         . 0.990
## day            0.990      0.990     0.990     .
##
##
## SAMPLE SIZES
## ============
##
##            dan.sleep baby.sleep dan.grump day
## dan.sleep        100        100       100 100
## baby.sleep       100        100       100 100
## dan.grump        100        100       100 100
## day              100        100       100 100

The output here contains three matrices. First it prints out the correlation matrix. Second it prints out a matrix of p-values, using the Holm method218 to correct for multiple comparisons. Finally, it prints out a matrix indicating the sample size (number of pairwise complete cases) that contributed to each correlation.

So there you have it. If you really desperately want to do pairwise hypothesis tests on your correlations, the correlate() function will let you do it. But please, please be careful. I can’t count the number of times I’ve had a student panicking in my office because they’ve run these pairwise correlation tests, and they get one or two significant results that don’t make any sense. For some reason, the moment people see those little significance stars appear, they feel compelled to throw away all common sense and assume that the results must correspond to something real that requires an explanation. In most such cases, my experience has been that the right answer is “it’s a Type I error”.