v.0.4.6 `write_colony` replace `haplo2colony` and `stackr` now likes PCs!

v.0.4.6

• I'm pleased to announce that stackr parallel mode now works with Windows!
  Nothing to install, just need to choose the number of CPU,
  the rest is done automatically.
• haplo2colony is deprecated. Use the new function called write_colony!
• write_colony: works similarly to the deprecated function haplo2colony,
  • with the major advantage that it's no longer restricted to STACKS
    haplotypes file.
  • The function is using the tidy_genomic_data module
    to import files. So you can choose one of the 10 input file formats supported
    by stackr!
  • other benefits also include the possibility to efficiently test MAF,
    snp.ld, haplotypes/snp approach, whitelist of markes,
    blacklist of individuals, blacklist of genotypes, etc. with the buit-it
    arguments.
  • the function only keeps markers in common between populations/groups
    and is removing monomorphic markers.
  • Note: there are several defaults in the function and
    it's a complicated file format, so make sure to read the function
    documentation, please, and COLONY manual.

**v.0.4.5**

v.0.4.5

• temporary fix to tidy_genomic_data to read unconventional Tassel VCF

• new function ibdg_fh computes the FH measure that was previously
  computed in summary_haplotypes.
  It now works with biallelic and multiallelic data.

  The FH measure is based on the excess in the observed number of homozygous
  genotypes within an individual relative to the mean number of homozygous
  genotypes expected under random mating (see function for details). The IBDg in
  the name is because the measure is a proxy of the realized proportion of the genome
  that is identical by descent by reference to the current population
  under hypothetical random mating.

• missing_visualization now computes the FH measure and look for correlation
  with average missingness per individual.

• tidy_stacks_haplotypes_vcf is now deprecated in favor of using tidy_genomic_data
  that will import haplotypic vcf files.

**v.0.4.4**

v.0.4.4

• several updates to make function faster.
• stackr_imputations_module no longer imputes globally after imputations
  by populations. Instead, use common.markers or not to test impacts.
• bug fix with ref_alt_alleles that was not working properly inside
  the imputation module.
• snp_ld is not a separate module available for users. Check documentation.
• missing_visualization now show the proportion of variance with plot axis text.

v.0.4.3

v.0.4.3

• bug fix in summary_haplotypes stemming from a new readr version
• artifacts replace paralogs in summary_haplotypes

**v.0.4.2**

v.0.4.2

• gtypes object from strataG package
  can now be read/write in/out of Stackr using the tidy_genomic_data and
  genomic_converter functions.

v.0.3.9

v.0.3.9

• several performance update
• couple of bug fix for detecting file formats

v.0.3.8

v.0.3.8

• fixed a bug in filter_genotype_likelihood, since the updated function to the
  interactive mode, some old code where still present in if/else sentences, breaking
  the code. Thanks to Jaromir Guzinski for the bug report.

v.0.3.7

• fixed a bug in write_vcf, the function was using REF/ALT coding in integer
  not character format. This function is used inside vcf_imputation and
  sometimes inside genomic_converter.
  Thanks to @jeansebastienmoore for
  highlighting the problem.

v.0.3.6. bug fix

v.0.3.6

• fixed a bug in vcf_imputation, the function now calls genomic_converter
  with all the bells and whistles of that function (updated vcf import and imputations modules)

update

v.0.3.4

• updated documentation
• bug fix in summary_haplotypes introduced by the new version of dplyr::distinct (v.0.5.0)
• calculations of Pi is done in parallel inside summary_haplotypes