Thanks, Emmanuel. I was not familiar with .Random.seed objects until R
CHECK started complaining about such elements in saved workspaces
within .rdata files within packages (requiring rm to remove them), and
then was mainly familiar with them regarding set.seed() (and so I
thought ace must be setting a seed, not just initializing one). It
makes sense that any random number generation would incur a seed, and
apparently fresh R sessions do not immediately initialize a seed.
Thanks to everyone who helped me see my confusion! Just me missing a
basic comp sci concept.
-Dave
On Fri, Oct 20, 2017 at 4:26 AM, Emmanuel Paradis
<emmanuel.para...@ird.fr> wrote:
> Hi Dave,
>
> The seed is created every time you generate random data (see details in
> ?.Random.seed):
>
> R> exists(".Random.seed")
> [1] FALSE
> R> sample(1)
> [1] 1
> R> exists(".Random.seed")
> [1] TRUE
>
> So in your code below the seed is created by calling rtree(). Indeed, with
> ape 4.1:
>
> R> rm(".Random.seed")
> R> data(bird.orders)
> R> x <- 1:23
> R> exists(".Random.seed")
> [1] FALSE
> R> o <- ace(x, bird.orders)
> R> exists(".Random.seed")
> [1] FALSE
>
> However, with the new "soon-to-be-on-CRAN" version, a seed is created by the
> same code. The "culprit" is actually Rcpp: the new ape has C++ code linked
> to Rcpp. For a reason I ignore, it seems that a random seed is initialized
> when calling a function linked to Rcpp. Here is an example:
>
> R> rm(".Random.seed")
> R> library(RcppEigen)
> R> exists(".Random.seed")
> [1] FALSE
> R> o <- fastLm(1, 1)
> R> exists(".Random.seed")
> [1] TRUE
>
> The new C++ code in ape is called by reorder(phy, "postorder") which is used
> by many functions in ape (ace, pic, plot.phylo, vcv, ...).
>
> Best,
>
> Emmanuel
>
>
> Le 19/10/2017 à 21:00, David Bapst a écrit :
>>
>> Emmanuel, all-
>>
>> I noticed today that a workspace I was working with had a random
>> number seed set in it, but didn't remember setting one. Finally, I
>> discovered the culprit was ace. Here's a reproducible example,
>> demonstrating that a seed exists after running ace:
>>
>> library(ape)
>> tree<-rtree(10)
>> ace(1:10,tree)
>> .Random.seed
>>
>> I am using ape 4.1, and it doesn't seem to be addressed in the
>> forthcoming version, given my reading of the changes log (but I might
>> have missed it). What's going? Why is a random number seed being set?
>>
>> Cheers,
>> -Dave
>>
>
--
David W. Bapst, PhD
Postdoc, Ecology & Evolutionary Biology, Univ of Tenn Knoxville
Lecturer, Geology & Geophysics, Texas A & M University
https://github.com/dwbapst/paleotree
Google Calender: https://goo.gl/EpiM4J
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