gl.recode.pop bug
Berry, Olly (NCMI, IOMRC Crawley)
Hi,
I’m having trouble renaming my sites in my genlight file with the gl.recode.pop function, and wonder if there is a bug? I get the same error for both my data and also bandicoot.gl or testset.gl.
I can create a draft recode table via the gl.make.recode.pop function and edit it in excel, or even RStudio. However, when I use it to run gl.recode.pop my pops are labelled as numbers. The function seems to be treating them as factors. I even get the error if I don’t edit the recode table.
I can repeat the whole process, but recoding individuals with the very similar gl.recode.ind function and have no problem.
Delving inexpertly into some of the code for these two functions, one difference I see is that @ line 83 gl.recode.ind sets stringsAsFactors=FALSE, whereas gl.recode.pop has stringsAsFactors = TRUE @ line 87. If I edit that code to be stringsAsFactors = TRUE and rerun using my edited version of the function, I seem to be able to get it to work properly.
What do you think Arthur/Bernd?
Cheers,
Olly
My code is as follows:
gl.make.recode.pop(working.gl, out.recode.file = "testpop.csv", outpath = getwd())
working.gl <- gl.recode.pop(working.gl, pop.recode = "testpop.csv", recalc = FALSE, mono.rm = FALSE, verbose = 5)
levels(working.gl$pop)
Bernd.Gruber
Hi Olly,
This seems to be an error that came in with R 4. Because here the default is stringsAsFactors = FALSE when using read.csv, which is not what you want in most cases from our point of view. Here I think we made a mistake and it needs be set to FALSE as you suggested.
Will be in the next update (Luis is starting the coming week 😊)
Cheers, Bernd
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