Closed zkamvar closed 8 years ago
Yes, this is a long list, BUT, many of these are small changes. I believe it would be best to create branches for each major point and do pull requests. @hlapp, does that sound reasonable?
Yes, and awesome list! :+1:
I need @smanel's input for the Differentiation SNP vignette. What does this phrase mean?
Five groups were finally detected and represented by the discriminant analysis. The 11 states are not the good level for population analysis. But we need to remember that we used only 20 SNPs to conduct the analysis.
I suggest to replace by:
With a subset of 20 SNPs, five groups were finally detected and represented by the discriminant analysis.
With a subset of 20 SNPs, five groups were finally detected and represented by the discriminant analysis.
My concern with this is that the analysis shows that the groups are not well represented since there is a significant level of overlap: http://nescent.github.io/popgenInfo/DifferentiationSNP.html#unsupervised-clustering
Perhaps something like:
It's clear that a subset of 20 SNPs does not have a strong enough signal to separate the samples into distinct groups. What would happen if we used more SNPs?
Oh sorry. I do not check it again. Yes of course. This is really better.
All done, so closing this out.
Before publication, all vignettes and content should be ship shape. I will list issues here, no matter how small. critical issues are bold
Vignettes
Mydata
is not necessary ashw.test()
works on genind objects.set.seed()
needs to be called beforefind.clusters()
If it's not, the cluster assignment could be 5 or 6 clusters, making the statement in the text inaccurate.distgen()
in text should readdist.gene()
apex::read.multiFASTA()
Package Developement
Other