[Rd] unstable corner of parameter space for qbeta?
Martin Maechler
m@ech|er @end|ng |rom @t@t@m@th@ethz@ch
Thu Mar 26 09:02:18 CET 2020
>>>>> Ben Bolker
>>>>> on Wed, 25 Mar 2020 21:09:16 -0400 writes:
> I've discovered an infelicity (I guess) in qbeta(): it's not a bug,
> since there's a clear warning about lack of convergence of the numerical
> algorithm ("full precision may not have been achieved"). I can work
> around this, but I'm curious why it happens and whether there's a better
> workaround -- it doesn't seem to be in a particularly extreme corner of
> parameter space. It happens, e.g., for these parameters:
> phi <- 1.1
> i <- 0.01
> t <- 0.001
> shape1 = i/phi ## 0.009090909
> shape2 = (1-i)/phi ## 0.9
> qbeta(t,shape1,shape2) ## 5.562685e-309
> ## brute-force uniroot() version, see below
> Qbeta0(t,shape1,shape2) ## 0.9262824
> The qbeta code is pretty scary to read: the warning "full precision
> may not have been achieved" is triggered here:
> https://github.com/wch/r-source/blob/f8d4d7d48051860cc695b99db9be9cf439aee743/src/nmath/qbeta.c#L530
> Any thoughts?
Well, qbeta() is mostly based on inverting pbeta() and pbeta()
has *several* "dangerous" corners in its parameter spaces
{in some cases, it makes sense to look at the 4 different cases
log.p = TRUE/FALSE // lower.tail = TRUE/FALSE separately ..}
pbeta() itself is based on the most complex numerical code in
all of base R, i.e., src/nmath/toms708.c and that algorithm
(TOMS 708) had been sophisticated already when it was published,
and it has been improved and tweaked several times since being
part of R, notably for the log.p=TRUE case which had not been in
the focus of the publication and its algorithm.
[[ NB: part of this you can read when reading help(pbeta) to the end ! ]]
I've spent many "man weeks", or even "man months" on pbeta() and
qbeta(), already and have dreamed to get a good student do a
master's thesis about the problem and potential solutions I've
looked into in the mean time.
My current gut feeling is that in some cases, new approximations
are necessary (i.e. tweaking of current approximations is not
going to help sufficiently).
Also not (in the R sources) tests/p-qbeta-strict-tst.R
a whole file of "regression tests" about pbeta() and qbeta()
{where part of the true values have been computed with my CRAN
package Rmpfr (for high precision computation) with the
Rmpfr::pbetaI() function which gives arbitrarily precise pbeta()
values but only when (a,b) are integers -- that's the "I" in pbetaI().
Yes, it's intriguing ... and I'll look into your special
findings a bit later today.
> Should I report this on the bug list?
Yes, please. Not all problem of pbeta() / qbeta() are part yet,
of R's bugzilla data base, and maybe this will help to draw
more good applied mathematicians look into it.
Martin Maechler
ETH Zurich and R Core team
(I'd call myself the "dpq-hacker" within R core -- related to
my CRAN package 'DPQ')
> A more general illustration:
> http://www.math.mcmaster.ca/bolker/misc/qbeta.png
> ===
> fun <- function(phi,i=0.01,t=0.001, f=qbeta) {
> f(t,shape1=i/phi,shape2=(1-i)/phi, lower.tail=FALSE)
> }
> ## brute-force beta quantile function
> Qbeta0 <- function(t,shape1,shape2,lower.tail=FALSE) {
> fn <- function(x) {pbeta(x,shape1,shape2,lower.tail=lower.tail)-t}
> uniroot(fn,interval=c(0,1))$root
> }
> Qbeta <- Vectorize(Qbeta0,c("t","shape1","shape2"))
> curve(fun,from=1,to=4)
> curve(fun(x,f=Qbeta),add=TRUE,col=2)
> ______________________________________________
> R-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
More information about the R-devel
mailing list