Tag Archives: boxplot

Comparing quantiles for two samples

Recently, for a research paper, I got some samples, and I wanted to compare them. Not to compare their means (by construction, all of them were centered) but there dispersion. And not their variance, but more their quantiles. Consider the following boxplot type function, where everything here is quantile related (which is not the case for standard boxplot, see http://freakonometrics.hypotheses.org/4138, in French)

> boxplotqbased=function(x){
+ q=quantile(x[is.na(x)==FALSE],c(.05,.25,.5,.75,.95))
+ plot(1,1,col="white",axes=FALSE,xlab="",ylab="",
+ xlim=range(X),ylim=c(1-.6,1+.6))
+ polygon(c(q[2],q[2],q[4],q[4]),1+c(-.4,.4,.4,-.4))
+ segments(q[1],1-.4,q[1],1+.4)
+ segments(q[5],1,q[4],1)
+ segments(q[5],1-.4,q[5],1+.4)
+ segments(q[1],1,q[2],1)
+ segments(q[3],1-.4,q[3],1+.4,lwd=2)
+ xt=x[(x<q[1])|(x>q[5])]
+ points(xt,rep(1,length(xt)))
+ axis(1)
+ }

(one can easily adapt the code for lists, e.g.). Consider for instance temperature, when the (linear) trend is removed (see http://freakonometrics.hypotheses.org/1016 for a discussion on that series, in Paris),

from January 1st till December 31st. Let us remove now the seasonal cycle, i.e. we do have here the difference with the average seasonal temperature (with here upper and lower quantiles),

Seasonal boxplots are here (with Autumn on top, then Summer, Spring and Winter, below),

If we zoom in, we do have (where upper and lower segments are 95% and 5% quantiles, while classically, boxes are related to the 75% and the 25% quantiles)

Is there a (standard) test to compare quantiles – some of them perhaps ? Can we compare easily quantiles when have two (or more) samples ?

Note that this example on temperature could be related to other old posts (see e.g. http://freakonometrics.hypotheses.org/2190), but the research paper was on a very different topic.

Consider two (i.i.d.) samples https://latex.codecogs.com/gif.latex?\{x_1,\cdots,x_m\} and https://latex.codecogs.com/gif.latex?\{y_1,\cdots,y_n\}, considered as realizations of random variables https://latex.codecogs.com/gif.latex?X and https://latex.codecogs.com/gif.latex?Y. In all statistical courses, tests on the average are always considered, i.e.




Usually, the idea in courses is to start with a one sample test, and to test something like




The idea is to assume that samples are from Gaussian variables,

Under https://latex.codecogs.com/gif.latex?H_0https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20T has a Student t distribution. All that can be found in any Statistics 101 course. We can derive https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20pvalue, computing probabilities that https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20T exceeds the observed values (for two sided tests, the probability that the absolute value of https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20T exceed the absolute value of the observed statistics). This test is closely related to the construction of confidence intervals for https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20\mu. If https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20\mu_\star belongs to the confidence interval, then it might be a suitable value. The graphical representation of this test is related to the following graph

Here the observed value was 1,96, i.e. the https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20pvalue (the area in red above) is exactly 5%.

To compare means, the standard test is based on


which has – under https://latex.codecogs.com/gif.latex?H_0 – a Student-t distribution, with https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20\nu degrees of freedom, where


Here, the graphical representation is the following,

But tests on quantiles are rarely considered in statistical courses. In a general setting,define quantiles as


one might be interested to test
for some https://latex.codecogs.com/gif.latex?p\in(0,1). Note that we might be interested also to test if

for all https://latex.codecogs.com/gif.latex%20?%20%20k, for some vector of probabilities https://latex.codecogs.com/gif.latex?\boldsymbol{p}=(p_1,\cdots,p_d)\in(0,1)^d.
One can imagine that this multiple test will be more complex. But more interesting, e.g. a test on boxplots (are the four quantiles equal ?).  Let us start with something a bit more simple: a test on quantiles for one sameple, and the derivation of a confidence interval for quantiles.

  • Quantiles for one sample

The important idea here is that it should be extremely simple to get https://latex.codecogs.com/gif.latex?pvalues. Consider the following sample, and let us run a test to assess if the median can be zero.

> set.seed(1)
> X=rnorm(20)
> sort(X)
[1] -2.21469989 -0.83562861 -0.82046838 -0.62645381 -0.62124058 -0.30538839
[7] -0.04493361 -0.01619026  0.18364332  0.32950777  0.38984324  0.48742905
[13]  0.57578135  0.59390132  0.73832471  0.82122120  0.94383621  1.12493092
[19]  1.51178117  1.59528080
> sum(X<=0)
[1] 8

Here, 8 observations (out of 20, i.e. 40%) were below zero. But we do know the distribution of https://latex.codecogs.com/gif.latex%20?%20%20N the number of observation below the target


It is a binomial distribution. Under https://latex.codecogs.com/gif.latex?H_0, it is a binomial distribution https://latex.codecogs.com/gif.latex?\mathcal{B}(n,p_\star) where https://latex.codecogs.com/gif.latex?p_\star is the probability target (here 50% since the test is on the median). Thus, one can easily compute the https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20p-value,

> plot(n,dbinom(n,size=20,prob=0.50),type="s",xlab="",ylab="",col="white")
> abline(v=sum(X<=0),col="red")
> for(i in 1:sum(X<=0)){
+ polygon(c(n[i],n[i],n[i+1],n[i+1]),
+ c(0,rep(dbinom(n[i],size=20,prob=0.50),2),0),col="red",border=NA)
+ polygon(21-c(n[i],n[i],n[i+1],n[i+1]),
+ c(0,rep(dbinom(n[i],size=20,prob=0.50),2),0),col="red",border=NA)
+ }
> lines(n,dbinom(n,size=20,prob=0.50),type="s")

which yields

Here, the https://latex.codecogs.com/gif.latex%20?%20%20%20%20%20p-value is

> 2*pbinom(sum(X<=0),20,.5)
[1] 0.5034447

Here the probability is easy to compute. But one can observe that there is some kind of disymmetry here. Actually, if the observed value was not 8, but 12, some minor changes should be done (to keep some symmetry),

> plot(n,dbinom(n,size=20,prob=0.50),type="s",xlab="",ylab="",col="grey")
> abline(v=20-sum(X<=0),col="red")
> for(i in 1:sum(X<=0)){
+ polygon(c(n[i],n[i],n[i+1],n[i+1])-1,
+ c(0,rep(dbinom(n[i],size=20,prob=0.50),2),0),col="red",border=NA)
+ polygon(21-c(n[i],n[i],n[i+1],n[i+1])-1,
+ c(0,rep(dbinom(n[i],size=20,prob=0.50),2),0),col="red",border=NA)
+ }
> lines(n-1,dbinom(n,size=20,prob=0.50),type="s")

Based on those observations, one can easily write a code to test if the https://latex.codecogs.com/gif.latex?p_\star-quantile of a sample is https://latex.codecogs.com/gif.latex?x_\star. Or not. For a two sided test, consider

> quantile.test=function(x,xstar=0,pstar=.5){
+ n=length(x)
+ T1=sum(x<=xstar)
+ T2=sum(x< xstar)
+ p.value=2*min(1-pbinom(T2-1,n,pstar),pbinom(T1,n,pstar))
+ return(p.value)}

Here, we have

> quantile.test(X)
[1] 0.5034447

Now, based on that idea, due to the duality between confidence intervals and tests, one can easily write a function that computes confidence interval for quantiles,

> quantile.interval=function(x,pstar=.5,conf.level=.95){
+ n=length(x)
+ alpha=1-conf.level
+ r=qbinom(alpha/2,n,pstar)
+ alpha1=pbinom(r-1,n,pstar)
+ s=qbinom(1-alpha/2,n,pstar)+1
+ alpha2=1-pbinom(s-1,n,pstar)
+ c.lower=sort(x)[r]
+ c.upper=sort(x)[s]
+ conf.level=1-alpha1-alpha2
+ return(list(interval=c(c.lower,c.upper),confidence=conf.level))}
> quantile.interval(X,.50,.95)
[1] -0.3053884  0.7383247

[1] 0.9586105

Because of the use of non-asymptotic distributions, we can not get exactly a 95% confidence interval. But it is not that bad, here.

  • Comparing quantiles for two samples

Now, to compare quantiles for two samples… it is more complicated. Exact tests are discussed in Kosorok (1999) (see http://bios.unc.edu/~kosorok/…) or in Li, Tiwari and Wells (1996) (see http://jstor.org/…). For the computational aspects, as mentioned in a post published almost one year ago on http://nicebread.de/… there is a function to compare quantiles for two samples.

> install.packages("WRS")
> library("WRS")

Some multiple tests on quantiles can be performed here. For instance, on the temperature, if we compare quantiles for Winter and Summer (on only 1,000 observations since it can be long to run that function), i.e. 5%, 25%, 75% and 95%,

> qcomhd(Z1[1:1000],Z2[1:1000],q=c(.05,.25,.75,.95))
q   n1   n2      est.1      est.2 est.1_minus_est.2     ci.low     ci.up     p_crit p.value signif
1 0.05 1000 1000 -6.9414084 -6.3312131       -0.61019530 -1.6061097 0.3599339 0.01250000   0.220     NO
2 0.25 1000 1000 -3.3893867 -3.1629541       -0.22643261 -0.6123292 0.2085305 0.01666667   0.322     NO
3 0.75 1000 1000  0.5832394  0.7324498       -0.14921041 -0.4606231 0.1689775 0.02500000   0.338     NO
4 0.95 1000 1000  3.7026388  3.6669997        0.03563914 -0.5078507 0.6067754 0.05000000   0.881     NO

or if we compare quantiles for Winter and Summer

> qcomhd(Z1[1:1000],Z3[1:1000],q=c(.05,.25,.75,.95))
q   n1  n2      est.1     est.2 est.1_minus_est.2     ci.low       ci.up     p_crit p.value signif
1 0.05 1000 984 -6.9414084 -6.438318        -0.5030906 -1.3748624  0.39391035 0.02500000   0.278     NO
2 0.25 1000 984 -3.3893867 -3.073818        -0.3155683 -0.7359727  0.06766466 0.01666667   0.103     NO
3 0.75 1000 984  0.5832394  1.010454        -0.4272150 -0.7222362 -0.11997409 0.01250000   0.012    YES
4 0.95 1000 984  3.7026388  3.873347        -0.1707078 -0.7726564  0.37160846 0.05000000   0.539     NO

(the following graphs are then plotted)

Those tests are based on the procedure proposed in Wilcox, Erceg-Hurn,  Clark and Carlson (2013), online on http://tandfonline.com/…. They rely on the use of bootstrap samples. The idea is quite simple actually (even if, in the paper, they use Harrell–Davis estimator to estimate quantiles, i.e. a weighted sum of ordered statistics – as described in http://freakonometrics.hypotheses.org/1755 – but the idea can be understood with any estimator): we generate several bootstrap samples, and compute the median for all of them (since our interest was initially on the median)

>  Q=rep(NA,10000)
>  for(b in 1:10000){
+  Q[b]=quantile(sample(X,size=20,replace=TRUE),.50)
+  }

Then, to derive a confidence interval (with, say, 95% confidence), we compute quantiles of those median estimates,

> quantile(Q,c(.025,.975))
     2.5%     97.5% 
-0.175161  0.666113

We can actually visualize the distribution of that bootstrap median,

> hist(Q)

Now, if we want to compare medians from two independent samples, the strategy is rather similar: we bootstrap the two samples – independently – then compute the median, and keep in mind the difference. Then, we will look if the difference is significantly different from 0. E.g.

> set.seed(2)
> Y=rnorm(50,.6)
> QX=QY=D=rep(NA,10000)
> for(b in 1:10000){
+ QX[b]=quantile(sample(X,size=length(X),replace=TRUE),.50)
+ QY[b]=quantile(sample(Y,size=length(Y),replace=TRUE),.50)
+ D[b]=QY[b]-QX[b]
+ }

The 95% confidence interval obtained from the bootstrap difference is

> quantile(D,c(.025,.975))
      2.5%      97.5% 
-0.2248471  0.9204888

which is rather close to was can be obtained with the R function

> qcomhd(X,Y,q=.5)
    q n1 n2    est.1     est.2 est.1_minus_est.2    ci.low     ci.up p_crit p.value signif
1 0.5 20 50 0.318022 0.5958735        -0.2778515 -0.923871 0.1843839   0.05    0.27     NO

(where the difference is here the oppositive of mine). And when testing for 2 (or more) quantiles, Bonferroni method can be used to take into account that those tests cannot be considered as independent.

More climate extremes, or simply global warming ?

In the paper on the heat wave in Paris (mentioned here) I discussed changes in the distribution of temperature (and autocorrelation of the time series).

During the workshop on Statistical Methods for Meteorology and Climate Change today (here) I observed that it was still an important question: is climate change affecting only averages, or does it have an impact on extremes ? And since I’ve seen nice slides to illustrate that question, I decided to play again with my dataset to see what could be said about temperature in Paris.
Recall that data can be downloaded here (daily temperature of the XXth century).


On the plot below, the dots in red are the annual maximum temperatures, while the dots in blue are the annual minimum temperature. The plain line is the regression line (based on the annual max/min), and the dotted lines represent the average maximum/minimum daily temperature (to illustrate the global tendency),

It is also possible to look at annual boxplot, and to focus either on minimas, or on maximas.


Plain dots are average temperature below the 5% quantile for minima, or over the 95% quantile for maxima (again with the regression line),

We can observe an increasing trend on the minimas, but not on the maximas !
Finally, an alternative is to remember that we focus on annual maximas and minimas. Thus, Fisher and Tippett theory (mentioned here) can be used. Here, we fit a GEV distribution on a blog of 10 consecutive years. Recall that the GEV distribution is

for(s in 1:10){

The location parameter http://freakonometrics.blog.free.fr/public/perso/gev4.png is the following, with on the left the minimas and on the right the maximas,

while the scale parameter http://freakonometrics.blog.free.fr/public/perso/gev3.png is

and finally the shape parameter http://freakonometrics.blog.free.fr/public/perso/gev2.png is

On those graphs, it is very difficult to say anything regarding changes in temperature extremes… And I guess this is a reason why there is still active research on that area…