fst_WC84

fst_WC84: is now a separate and very fast function that can compute: the overall and pairwise Weir and Cockerham 1984 Theta/Fst. Bootstrap resampling of markers is avalaible to build Confidence Intervals (For Louis Bernatchez and his students;). The estimates are available as a data frame and a matrix with upper diagonal filled with Fst values and lower diagonal filled with the confidence intervals.

but fix

v.0.2.5

• cleaner code for strata section
• bug fix restricted to assignment_ngs + assignment.analysis = "adegenet" + sampling.method = "ranked".
  A line at the beginning of a gsi_sim code section was deleted makig the assignment with adegenet go through that chunk of code and causing 100% assignment! if (assignment.analysis = "gsi_sim") {code} prevent this problem...

introducing a new function `import_subsamples_fst`

introducing a new function import_subsamples_fst to import the fst ranking
results from all the subsample runs inside an assignment folder.

bug fix

bug fix in the compilation results section

consistency in output files naming in assignment_ngs

consistency in output files naming in assignment_ngs

assignment of mixture data

v.0.2.1

• updated the function assignment_mixture with sampling.method = "ranked" and
  assignment.analysis = "adegenet".

easier gsi_sim install

To install assigner and gsi_sim:

install_github("thierrygosselin/assigner") # to install
library(assigner) # to load
install_gsi_sim(fromSource = TRUE) # to install gsi_sim from source

assignment with gsi_sim or adegenet

You can now opt between gsi_sim or adegenet, a R package developed by Thibaul Jombart, to conduct the assignment analysis

new input file

v.0.1.7

• New input file: Re-introduced the haplotype data frame file from stacks.
• Argument name change: imputations is now impute.method.
• New argument: impute with 2 options: impute = "genotype" or impute = "allele".

v.0.1.6

PLINK tped/tfam can be used to import large number of markers for assignment analysis