Sublaunching SLiM in R

[Yujean Kim]

Hi,

Currently I am trying to understand how to sublaunch SLiM into R. To understand this, I tried to follow the following recipe:

https://github.com/MesserLab/SLiM-Extras/blob/master/sublaunching/basic_r_usage_aggregateLocalAncestry.R

Even when I copy-pasted the same code and changed the file directory, I keep getting an error, as illustrated in the image I have attached. What would be the problem?

Kind regards,

Yujean Kim

[Ben Haller]

Hi Yujean.  My first guess would be that the SLiM model you're running is halting with an error, and that R is reporting that an error occurred.  You can check the file where you told system2() to direct error output; or you could rewrite the call to system2() to have the running process (i.e., SLiM) send its error output to R's console instead of to a file; or you could log out all of the parameters that are being sent to SLiM through system2(), and run slim the same way with the same parameters at the command line.  I can't really provide additional help on those topics, since this is an R issue, not a SLiM issue, but perhaps Sam will notice this thread and reply with further advice.

In general, because getting error messages indirectly after system2() calls is annoying, it is best to completely debug your model before you start trying to run it through an automated script like this.  :->

Cheers,

-B.

Benjamin C. Haller

Messer Lab

Cornell University

[Sam Champer]

I must admit that I run SLiM from python much more often than I do from R!

As Ben mentioned, the error could indeed be happening in the underlying SLiM file itself, so that would be the first place I'd check!

That said, if you want to look at a slightly different R workflow, you could take a look at https://github.com/MesserLab/SLiM-Extras/blob/master/sublaunching/sublaunching_tutorial/running_slim_using_r.r along with the SLiM file run by that script (https://github.com/MesserLab/SLiM-Extras/blob/master/sublaunching/sublaunching_tutorial/minimal_gene_drive.slim).

On Wednesday, August 4, 2021 at 11:36:25 AM UTC-4 yujean...@gmail.com wrote: