Cannot re-level strata of a snpclone object about poppr HOT 1 OPEN

Hi @Neato-Nick,

Sorry for the late reply. This is more of an adegenet, issue, but I will still tackle it here.

There are two solutions for this issue depending on the problem you are trying to solve:

1. To adjust how the strata are plotted in the legend for the MSN, rearrange them in the MSN object
2. if you want to re-level the strata for the data set itself so you don't have to constantly rearrange the levels, then the best method is to use the x@strata$year to set it directly (yes, I cringe at this because I spent years telling people to not use the slot directly, but this is literally the only way [see below])

Note: be careful because levels(x) <- sort(levels(x)) does not rearrange the levels like you want it to do, it re-assigns the levels, so your data will all be mis-labeled:

x <- factor(c("b", "a", "c"), levels = c("b", "a", "c"))
x
#> [1] b a c
#> Levels: b a c
levels(x) <- sort(levels(x))
x
#> [1] a b c
#> Levels: a b c

^{Created on 2021-07-24 by the reprex package (v2.0.0)}

What you want is to recreate the factor all together:

x <- factor(c("b", "a", "c"), levels = c("b", "a", "c"))
x
#> [1] b a c
#> Levels: b a c
x <- factor(x, sort(levels(x)))
x
#> [1] b a c
#> Levels: a b c

^{Created on 2021-07-24 by the reprex package (v2.0.0)}

Why does adegenet force the strata to be in the order of observation?

Honestly, I'm not sure. If you look at the code that controls strata()<-, you can see that it will force-reorder the data: https://github.com/thibautjombart/adegenet/blob/e03d87382117a5fcaa914928f8ec37dc72d267cd/R/strataMethods.R#L29-L44

You'll have to ask 2015 Zhian for why he thought that was a good idea, but I think the idea was that people would have prepared their data in a specific order before reading it into R, so we wanted to respect that ordering.

from poppr.