adegenet

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Change tolerances to system-level tolerance?

1

One thing I've noticed is the use of 1e-30 or 1e-10 to account for computational tolerance: https://github.com/thibautjombart/adegenet/blob/762b9ca3c8dea3a0735fc3417da0236e4912c297/R/dapc.R#L308-L309 I'm wondering if instead we should use `.Machine$double.eps ^ 0.5`, which sets the...

zkamvar

This issue came up in #209, when I was trying to make a reprex, I noticed that I would get an error when I attempted to even up the number...

zkamvar

reorder passed info when setting new pop and strat

6

If `foo` is named in these operations: ``` pop(x)

thibautjombart

Replace sapply calls with vapply or lapply

1

as of 4d76f6529, there are a lot of sapply calls. We should probably convert these at some point. The following list is generated with: ``` $ grep -inr sapply R...

zkamvar

glSim with observed allele frequencies and linkage structure

2

We are interested in describing rates of migration among genetically similar populations. Given that they are genetically similar, we would expect to falsely identify some individuals as migrants. We are...

tjsmyser

Add procedure, and add an option to plot SNPs by chromosome. Relates to this post: --- Hi there, basically the workflow should be 1) split data by chromosome and 2)...

thibautjombart

glPca order of magnitude faster

4

For 'wide' data sets (~100 individuals, 100k NAs, `glPca` gets really slow - minutes to hours. The reason is twofold - it either uses cross product implementation with the 'hot...

libor-m

Global option for parallel processing

7

Right now for anything dealing with genlight objects, parallel processing is dependent on whether or not the package parallel is installed: ``` r glSim(..., parallel = require("parallel")) ``` It can...

zkamvar

Add method to check if hierarchy is hierarchical.

6

The hierarchy slot currently will store a formula defining what levels of the strata slot are hierarchical. One thing that we do not have implemented is a method to actually...

zkamvar

Branches - developers, read me! =D

4

### Permanent branches - [master](https://github.com/thibautjombart/adegenet/tree/master): functional devel version, meant to be used by people, so it should be relatively safe. Please do **not** push changes preventing the package from being...

thibautjombart