Some hypothesis testing procedures in R

This module demonstrates some of the many statistical tests that R can perform. It is impossible to give an exhaustive list of such testing functionality, but we hope not only to provide several examples but also to elucidate some of the logic of statistical hypothesis tests with these examples.


T tests, permutation-based and otherwise

In the exploratory data analysis and regression module, we used exploratory techniques to identify 92 stars from the Hipparcos data set that are associated with the Hyades. We did this based on the values of right ascension (between 50 and 100), principal motion of right ascension (between 90 and 130), and principal motion of declination (between -60 and -10). We then excluded two additional stars, one with an outlying value of declination and one with a large error of parallax measurement:

   hip = read.table("http://astrostatistics.psu.edu/datasets/HIP_star.dat",
      header=T,fill=T)
   attach(hip)
   x1=(RA>50 & RA<100)
   x2=(pmRA>90 & pmRA<130)
   x3=(pmDE>-60 & pmDE< -10) # Space in '< -' is necessary!
   x4=x1&x2&x3
   x5=x4 & (DE>0) & (e_Plx<5)
   sum(x5)

In this section of the tutorial, we will compare these Hyades stars with the remaining stars in the Hipparcos dataset on the basis of the B.V (B minus V) variable. That is, we are comparing the groups in the boxplot below:

   boxplot(B.V~x5,notch=T,ylab="B minus V")

For ease of notation, we define vectors H and nH (for "Hyades" and "not Hyades") that contain the data values for the two groups.

   H=B.V[x5]
   nH=B.V[!x5 & !is.na(B.V)]

In the definition of nH above, we needed to exclude the NA values (there are no NAs among the 92 Hyades stars here).

A two-sample t-test may be performed with a single line:

   t.test(H,nH)

Because it is instructive and quite easy, we may obtain the same results without resorting to the t.test function. First, we calculate the variances of the sample means for each group:

   v1=var(H)/92
   v2=var(nH)/2586

The t statistic is based on the standardized difference between the two sample means. Because the two samples are assumed independent, the variance of this difference equals the sum of the individual variances (i.e., v1+v2). Nearly always in a two-sample t-test, we wish to test the null hypothesis that the true difference in means equals zero. Thus, standardizing the difference in means involves subtracting zero and then dividing by the square root of the variance:

   tstat=(mean(H)-mean(nH))/sqrt(v1+v2)
   tstat

To test the null hypothesis, this t statistic is compared to a t distribution. In a Welch test, we assume that the variances of the two populations are not necessarily equal, and the degrees of freedom of the t distribution are computed using the so-called Satterthwaite approximation:

   (v1 + v2)^2 / (v1^2/91 + v2^2/2585)

The two-sided p-value may now be determined by using the cumulative distribution function of the t distribution, which is given by the pt function.

   2*pt(tstat,97)

Incidentally, one of the assumptions of the t-test, namely that each of the two underlying populations is normally distributed, is almost certainly not true in this example. However, because of the central limit theorem, the t-test is robust against violations of this assumption; even if the populations are not roughly normally distributed, the sample means are.

In this particular example, the Welch test is probably not necessary, since the sample variances are so close that an assumption of equal variances is warranted:

   c(var(H),var(nH))

Thus, we might conduct a slightly more restrictive t-test that assumes equal population variances. Without going into the details here, we merely present the R output:

   t.test(H,nH,var.equal=T)

For this latter type of test, there is an alternative method for computing a p-value associated with a t statistic called a permutation test. Understanding this method is conceptually very helpful in understanding the definition of p-value. Suppose we phrase the null hypothesis as follows: The distributions of the two populations are the same (here, "the two populations" refers to the populations from which the samples were drawn; in this case, we mean all Hyades-like stars, and all other stars). In that case, the particular split of our 2678 stars into one sample of 92 and one sample of 2586 is essentially arbitrary. Thus, we may repeatedly and randomly reassign these 2678 stars into two groups of 92 and 2586, calculating the t statistic in each case:

   tlist=NULL
   all=c(H,nH)
   for(i in 1:5000) {
      s=sample(2586,92) # choose a sample
      tlist=c(tlist, t.test(all[s],all[-s],
        var.eq=T)$stat) # add t-stat to list
   }

Note: The above code is not built for speed!

By definition, the p-value is the probability of obtaining a test statistic more extreme than the observed test statistic under the null hypothesis. Let's take a look at the null distribution of the t statistic we just calculated, along with the observed value:

   hist(tlist,xlim=c(-4.6,4))
   abline(v=-4.59,lty=2,col=2)

Thus, in 5000 random trials, we did not see a single instance of a test statistic at least as extreme as the observed test statistic (I write this with some confidence even though the random outcome is different each time). A true p-value for the permutation test would take into account all possible random reassignments, but as there are 3.78x10172 of these in this example, a random sample of reassignments will have to suffice.


Empirical distribution functions

Suppose we are curious about whether a given sample comes from a particular distribution. For instance, how normal is the random sample 'tlist' of t statistics obtained under the null hypothesis in the previous example? How normal (say) are 'H' and 'nH'?

A simple yet very powerful graphical device is called a Q-Q plot, in which some quantiles of the sample are plotted against the same quantiles of whatever distribution we have in mind. If a roughly straight line results, this suggests that the fit is good. Roughly, a pth quantile of a distribution is a value such that a proportion p of the distribution lies below that value.

A test against normality is so common that there is a separate function, qqnorm, that implements it. (Remember, normality is common in statistics not merely because many common populations are normally distributed -- which is not true in astronomy -- but because the central limit theorem guarantees the approximate normality of sample means.)

   par(mfrow=c(2,2))
   qqnorm(tlist,main="Null t statistics")
   abline(0,1,col=2)
   qqnorm(H,main="B-V (Hyades)")
   qqnorm(nH,main="B-V (non-Hyades)")

Not surprisingly, the tlist variable appears extremely nearly normally distributed (more precisely, it is nearly standard normal, as evidenced by the proximity of the Q-Q plot to the line x=y, shown in red). As for H and nH, the distribution of B minus V exhibits moderate non-normality in each case.

In the bottom right corner of the plotting window, let's reconstruct the Q-Q plot from scratch for tlist. This is instructive because the same technique may be applied to any comparison distribution, not just normal. If we consider the 5000 entries of tlist in increasing order, let's call the ith value the ((2i-1)/10000)th quantile for all i from 1 to 5000. We merely graph this point against the corresponding quantile of standard normal:

   plot(qnorm((2*(1:5000)-1)/10000),sort(tlist))
   par(mfrow=c(1,1)) # reset plotting window

Related to the Q-Q plot is a distribution function called the empirical distribution function, or EDF. (In fact, the EDF is almost the same as a Q-Q plot against a uniform distribution.) The EDF is, by definition, the cumulative distribution function for the discrete distribution represented by the sample itself -- that is, the distribution that puts mass 1/n on each of the n sample points. We may graph the EDF using the ecdf function:

   plot(ecdf(H))

While it is generally very difficult to interpret the EDF directly, it is possible to compare an EDF to a theoretical cumulative distribution function or two another EDF. Among the statistical tests that implement such a comparison is the Kolmogorov-Smirnov test, which is implemented by the R function ks.test.

   ks.test(tlist,"pnorm")
   ks.test(H,nH)

Whereas the first result above can be somewhat surprising (a small p-value means a statistically significant difference), the second result should not be; we already saw that H and nH have statistically significantly different means. However, if we center each, we obtain

   ks.test(H-mean(H),nH-mean(nH))

In other words, the Kolmogorov-Smirnov test finds no statistically significant evidence that the distribution of B.V for the Hyades stars is anything other than a shifted version of the distribution of B.V for the other stars.


Chi-squared tests for categorical data

We begin with a plot very similar to one seen in the exploratory data analysis and regression module:

   bvcat=cut(B.V, breaks=c(-Inf,.5,.75,1,Inf))
   boxplot(Vmag~bvcat, varwidth=T,
      ylim=c(max(Vmag),min(Vmag)),
      xlab=expression("B minus V"),
      ylab=expression("V magnitude"),
      cex.lab=1.4, cex.axis=.8)

The cut values for bvcat are based roughly on the quartiles of the B.V variable. We have created, albeit artificially, a second categorical variable (x5, the Hyades indicator, is the first). Here is a summary of the dataset based only on these two variables:

   table(bvcat,x5)

Note that the Vmag variable is irrelevant in the table above.

To perform a chi-squared test of the null hypothesis that the true population proportions falling in the four categories are the same for both the Hyades and non-Hyades stars, use the chisq.test function:

   chisq.test(bvcat,x5)

Since we already know these two groups differ with respect to the B.V variable, the result of this test is not too surprising. But it does give a qualitatively different way to compare these two distributions than simply comparing their means.

The p-value produced above is based on the fact that the chi-squared statistic is approximately distributed like a true chi-squared distribution (on 3 degrees of freedom, in this case) if the null hypothesis is true. However, it is possible to obtain exact p-values, if one wishes to calculate the chi-squared statistic for all possible tables of counts with the same row and column sums as the given table. Since this is rarely practical computationally, the exact p-value may be approximated using a Monte Carlo method. Such a method is implemented in the chisq.test function:

   chisq.test(bvcat,x5,sim=T,B=50000)

Thus, the first method produces the exact value of an approximate p-value, whereas the second method produces an approximation to the exact p-value!

The test above is usually called a chi-squared test of homogeneity. If we observe only one sample, but we wish to test whether the categories occur in some pre-specified proportions, a similar test (and the same R function) may be applied. In this case, the test is usually called a chi-squared test of goodness-of-fit.