To follow (tangently) on Klaus' message, I've released a book last year on some
advanced topics in R programming and development:
https://hal.ird.fr/ird-03850685
Chapter 9 is on parallelization and HPC. There are a few (detailed) examples
showing when multi-core is benefitial and when it is
Hello, Emmanuel,
I overlooked that repo, sorry. OK, so I opened
https://github.com/emmanuelparadis/ape/issues/72
and https://github.com/emmanuelparadis/ape/pull/71
Sincerely,
V.
Dne úterý 7. března 2023 12:13:49 CET, Emmanuel Paradis napsal(a):
> Hi Vojtěch,
> The GH repos for ape is:
>
Thank You, dear Martin,
I wasn't aware about TreeDist, going to explore. :-)
Yes, RF has some limits, e.g. single difference close to root...
Sincerely,
V.
Dne úterý 7. března 2023 12:23:07 CET, Martin R. Smith napsal(a):
> Dear Vojtěch,
> The performance of calculating Robinson-Foulds
Hello,
thank You for Your comments, dear Klaus.
Dne úterý 7. března 2023 13:01:07 CET, Klaus Schliep napsal(a):
> Dear Vojtěch,
> nice work. Just a few random comments:
> Parallelization is often not straightforward as it
> depends on the hardware and the operating system.
Yes. E.g. it typically
Dear Vojtěch,
nice work. Just a few random comments:
Parallelization is often not straightforward as it depends on the hardware
and the operating system. My preference is using the future package for
parallelization as it does some nice abstraction for the different R
packages, so you can try
Dear Vojtěch,
The performance of calculating Robinson-Foulds topological distances can be
improved using the algorithm of Day (1985), which is implemented in the R
package TreeDist:
https://ms609.github.io/TreeDist/reference/Robinson-Foulds.html
This will often be faster than dist.topo.
(As
Hi Vojtěch,
The GH repos for ape is:
https://github.com/emmanuelparadis/ape
I had a quick look at your code and these are interesting improvements. It
seems also possible to improve the basic code of dist.topo() (e.g., using
bitsplits) so it is worth opening an issue.
Cheers,
Emmanuel
