Archive for cross validated

generating from a failure rate function [X’ed]

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , on July 4, 2015 by xi'an

While I now try to abstain from participating to the Cross Validated forum, as it proves too much of a time-consuming activity with little added value (in the sense that answers are much too often treated as disposable napkins by users who cannot be bothered to open a textbook and who usually do not exhibit any long-term impact of the provided answer, while clogging the forum with so many questions that the individual entries seem to get so little traffic, when compared say with the stackoverflow forum, to the point of making the analogy with disposable wipes more appropriate!), I came across a truly interesting question the other night. Truly interesting for me in that I had never considered the issue before.

The question is essentially wondering at how to simulate from a distribution defined by its failure rate function, which is connected with the density f of the distribution by

\eta(t)=\frac{f(t)}{\int_t^\infty f(x)\,\text{d}x}=-\frac{\text{d}}{\text{d}t}\,\log \int_t^\infty f(x)\,\text{d}x

From a purely probabilistic perspective, defining the distribution through f or through η is equivalent, as shown by the relation

F(t)=1-\exp\left\{-\int_0^t\eta(x)\,\text{d}x\right\}

but, from a simulation point of view, it may provide a different entry. Indeed, all that is needed is the ability to solve (in X) the equation

\int_0^X\eta(x)\,\text{d}x=-\log(U)

when U is a Uniform (0,1) variable. Which may help in that it does not require a derivation of f. Obviously, this also begs the question as to why would a distribution be defined by its failure rate function.

dynamic mixtures [at NBBC15]

Posted in R, Statistics with tags , , , , , , , , , , , , on June 18, 2015 by xi'an

KleifarvatnA funny coincidence: as I was sitting next to Arnoldo Frigessi at the NBBC15 conference, I came upon a new question on Cross Validated about a dynamic mixture model he had developed in 2002 with Olga Haug and Håvård Rue [whom I also saw last week in Valencià]. The dynamic mixture model they proposed replaces the standard weights in the mixture with cumulative distribution functions, hence the term dynamic. Here is the version used in their paper (x>0)

(1-w_{\mu,\tau}(x))f_{\beta,\lambda}(x)+w_{\mu,\tau}(x)g_{\epsilon,\sigma}(x)

where f is a Weibull density, g a generalised Pareto density, and w is the cdf of a Cauchy distribution [all distributions being endowed with standard parameters]. While the above object is not a mixture of a generalised Pareto and of a Weibull distributions (instead, it is a mixture of two non-standard distributions with unknown weights), it is close to the Weibull when x is near zero and ends up with the Pareto tail (when x is large). The question was about simulating from this distribution and, while an answer was in the paper, I replied on Cross Validated with an alternative accept-reject proposal and with a somewhat (if mildly) non-standard MCMC implementation enjoying a much higher acceptance rate and the same fit.

arbitrary distributions with set correlation

Posted in Books, Kids, pictures, R, Statistics, University life with tags , , , , , , , , , , on May 11, 2015 by xi'an

A question recently posted on X Validated by Antoni Parrelada: given two arbitrary cdfs F and G, how can we simulate a pair (X,Y) with marginals  F and G, and with set correlation ρ? The answer posted by Antoni Parrelada was to reproduce the Gaussian copula solution: produce (X’,Y’) as a Gaussian bivariate vector with correlation ρ and then turn it into (X,Y)=(F⁻¹(Φ(X’)),G⁻¹(Φ(Y’))). Unfortunately, this does not work, because the correlation does not keep under the double transform. The graph above is part of my answer for a χ² and a log-Normal cdf for F amd G: while corr(X’,Y’)=ρ, corr(X,Y) drifts quite a  lot from the diagonal! Actually, by playing long enough with my function

tacor=function(rho=0,nsim=1e4,fx=qnorm,fy=qnorm)
{
  x1=rnorm(nsim);x2=rnorm(nsim)
  coeur=rho
  rho2=sqrt(1-rho^2)
  for (t in 1:length(rho)){
     y=pnorm(cbind(x1,rho[t]*x1+rho2[t]*x2))
     coeur[t]=cor(fx(y[,1]),fy(y[,2]))}
  return(coeur)
}

Playing further, I managed to get an almost flat correlation graph for the admittedly convoluted call

tacor(seq(-1,1,.01),
      fx=function(x) qchisq(x^59,df=.01),
      fy=function(x) qlogis(x^59))

zerocorNow, the most interesting question is how to produce correlated simulations. A pedestrian way is to start with a copula, e.g. the above Gaussian copula, and to twist the correlation coefficient ρ of the copula until the desired correlation is attained for the transformed pair. That is, to draw the above curve and invert it. (Note that, as clearly exhibited by the graph just above, all desired correlations cannot be achieved for arbitrary cdfs F and G.) This is however very pedestrian and I wonder whether or not there is a generic and somewhat automated solution…

the most patronizing start to an answer I have ever received

Posted in Books, Kids, R, Statistics, University life with tags , , , , , , on April 30, 2015 by xi'an

Another occurrence [out of many!] of a question on X validated where the originator (primitivus petitor) was trying to get an explanation without the proper background. On either Bayesian statistics or simulation. The introductory sentence to the question was about “trying to understand how the choice of priors affects a Bayesian model estimated using MCMC” but the bulk of the question was in fact failing to understand an R code for a random-walk Metropolis-Hastings algorithm for a simple regression model provided in a introductory blog by Florian Hartig. And even more precisely about confusing the R code dnorm(b, sd = 5, log = T) in the prior with rnorm(1,mean=b, sd = 5, log = T) in the proposal…

“You should definitely invest some time in learning the bases of Bayesian statistics and MCMC methods from textbooks or on-line courses.” X

So I started my answer with the above warning. Which sums up my feelings about many of those X validated questions, namely that primitivi petitores lack the most basic background to consider such questions. Obviously, I should not have bothered with an answer, but it was late at night after a long day, a good meal at the pub in Kenilworth, and a broken toe still bothering me. So I got this reply from the primitivus petitor that it was a patronizing piece of advice and he prefers to learn from R code than from textbooks and on-line courses, having “looked through a number of textbooks”. Good luck with this endeavour then!

simulating correlated Binomials [another Bernoulli factory]

Posted in Books, Kids, pictures, R, Running, Statistics, University life with tags , , , , , , , on April 21, 2015 by xi'an

This early morning, just before going out for my daily run around The Parc, I checked X validated for new questions and came upon that one. Namely, how to simulate X a Bin(8,2/3) variate and Y a Bin(18,2/3) such that corr(X,Y)=0.5. (No reason or motivation provided for this constraint.) And I thought the following (presumably well-known) resolution, namely to break the two binomials as sums of 8 and 18 Bernoulli variates, respectively, and to use some of those Bernoulli variates as being common to both sums. For this specific set of values (8,18,0.5), since 8×18=12², the solution is 0.5×12=6 common variates. (The probability of success does not matter.) While running, I first thought this was a very artificial problem because of this occurrence of 8×18 being a perfect square, 12², and cor(X,Y)x12 an integer. A wee bit later I realised that all positive values of cor(X,Y) could be achieved by randomisation, i.e., by deciding the identity of a Bernoulli variate in X with a Bernoulli variate in Y with a certain probability ϖ. For negative correlations, one can use the (U,1-U) trick, namely to write both Bernoulli variates as

X_1=\mathbb{I}(U\le p)\quad Y_1=\mathbb{I}(U\ge 1-p)

in order to minimise the probability they coincide.

I also checked this result with an R simulation

> z=rbinom(10^8,6,.66)
> y=z+rbinom(10^8,12,.66)
> x=z+rbinom(10^8,2,.66)
cor(x,y)
> cor(x,y)
[1] 0.5000539

Searching on Google gave me immediately a link to Stack Overflow with an earlier solution with the same idea. And a smarter R code.

intuition beyond a Beta property

Posted in Books, Kids, R, Statistics, University life with tags , , , on March 30, 2015 by xi'an

betas

A self-study question on X validated exposed an interesting property of the Beta distribution:

If x is B(n,m) and y is B(n+½,m) then √xy is B(2n,2m)

While this can presumably be established by a mere change of variables, I could not carry the derivation till the end and used instead the moment generating function E[(XY)s/2] since it naturally leads to ratios of B(a,b) functions and to nice cancellations thanks to the ½ in some Gamma functions [and this was the solution proposed on X validated]. However, I wonder at a more fundamental derivation of the property that would stem from a statistical reasoning… Trying with the ratio of Gamma random variables did not work. And the connection with order statistics does not apply because of the ½. Any idea?

Is Jeffreys’ prior unique?

Posted in Books, Statistics, University life with tags , , , , , on March 3, 2015 by xi'an

“A striking characterisation showing the central importance of Fisher’s information in a differential framework is due to Cencov (1972), who shows that it is the only invariant Riemannian metric under symmetry conditions.” N. Polson, PhD Thesis, University of Nottingham, 1988

Following a discussion on Cross Validated, I wonder whether or not the affirmation that Jeffreys’ prior was the only prior construction rule that remains invariant under arbitrary (if smooth enough) reparameterisation. In the discussion, Paulo Marques mentioned Nikolaj Nikolaevič Čencov’s book, Statistical Decision Rules and Optimal Inference, Russian book from 1972, of which I had not heard previously and which seems too theoretical [from Paulo’s comments] to explain why this rule would be the sole one. As I kept looking for Čencov’s references on the Web, I found Nick Polson’s thesis and the above quote. So maybe Nick could tell us more!

However, my uncertainty about the uniqueness of Jeffreys’ rule stems from the fact that, f I decide on a favourite or reference parametrisation—as Jeffreys indirectly does when selecting the parametrisation associated with a constant Fisher information—and on a prior derivation from the sampling distribution for this parametrisation, I have derived a parametrisation invariant principle. Possibly silly and uninteresting from a Bayesian viewpoint but nonetheless invariant.

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