qnbinom with small size is slow
?? I can reproduce this on R Under development (unstable) (2020-07-24 r78910) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Pop!_OS 18.04 LTS ? In my opinion this is worth reporting, but discussing it here first was a good idea.? Many more people read this list than watch the bug tracker, so it will get more attention here; once the excitement has died down here (which might be almost immediately!), if no-one has already volunteered to post it to the bug tracker, request an account (as specified at https://www.r-project.org/bugs.html ) ? Thanks! ?? Ben Bolker For what it's worth it doesn't seem to be a threshold effect: approximately log10(time[seconds]) ~ -8 - log10(-size) over the range from 1e-6 to 1e-9 ff <- function(x) { ?? system.time(qnbinom(0.5, mu=3, size=10^x))[["elapsed"]] } svec <- seq(-5,-9,by=-0.2) res <- lapply(svec, function(x) { ??? cat(x,"\n") ??? replicate(10,ff(x)) ??? }) dd <- data.frame(size=rep(svec,each=10), ???????????????? time=unlist(res)) boxplot(log10(time)~size, dd) summary(lm(log10(time)~size, data=dd, subset=time>0))
On 8/7/20 2:01 PM, Constantin Ahlmann-Eltze via R-devel wrote:
Hi all,
I recently noticed that `qnbinom()` can take a long time to calculate
a result if the `size` argument is very small.
For example
qnbinom(0.5, mu = 3, size = 1e-10)
takes ~30 seconds on my computer.
I used gdb to step through the qnbinom.c implementation and noticed
that in line 106
(https://github.com/wch/r-source/blob/f8d4d7d48051860cc695b99db9be9cf439aee743/src/nmath/qnbinom.c#L106)
`y` becomes a very large negative number. Later in the function `y` is
(as far as I can see) only used as input for `pnbinom()` which is why
I would assume that it should be a non-negative integer.
I was wondering if this behavior could be considered a bug and should
be reported on the bugzilla? I read the instructions at
https://www.r-project.org/bugs.html and wasn't quite sure, so I
decided to ask here first :)
Best,
Constantin
PS: I tested the code with R 4.0.0 on macOS and the latest unstable
version using docker (https://github.com/wch/r-debug). The session
info is
sessionInfo()
R Under development (unstable) (2020-08-06 r78973) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04 LTS Matrix products: default BLAS: /usr/local/RD/lib/R/lib/libRblas.so LAPACK: /usr/local/RD/lib/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.1.0
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