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What's New

v0.8​

v0.8.0​

⚠️⚠️ Breaking Changes​

  • dropped support for Julia <v1.6
    • new count methods we use aren't supported by previous versions

✨✨ New Things​

  • k-means clustering using Kmeans++ via kmeans()
  • Principcal Component Analysis via pca()
  • Jason and Pavel both completed their doctorates!

⚡⚡ Improvements​

  • allele matrix creation methods (internal) have >50% fewer LOC and are >2x faster!

🐛🐛 Bug fixes​

  • none, I think

v0.7​

v0.7.0​

⚠️⚠️ Breaking Changes​

  • all PopData functionality moved to separate package PopGenCore.jl
  • PopGen.jl reexports functions from PopGenCore.jl for familiar functionality
  • .meta and .loci have been renamed .metadata and .genodata
  • .metadata is no longer a DataFrame and instead a new PopDataInfo type
  • latitude and longitude columns no longer mandatory and omitted in cases where not used

⚡⚡ Improvements​

  • PopData can be indexed like a DataFrame and it will return a brand new PopData!
  • PopDataInfo is self-updating (in most cases)
  • preliminary plink .bed file importing (not writing, yet)
  • show for PopData is now smaller and cleaner
  • INFO text for data importing now elides abs paths longer than the terminal width
  • VCF/BCF support no longer lazy loaded
  • VCF/BCF uses VariantCallFormat.jl now (instead of GeneticVariations.jl)
  • VCF/BCF uses different GZ library for decompression
  • try...catch blocks used in file io for faster file reading and fewer lines of code

🐛🐛 Bug fixes​

  • super slow structure io on larger files

v.0.6​

v.0.6.5​

Summary of changes from 0.6.2-5

⚡⚡ Improvements​

  • Bumped compat for DataFrames.jl to 1.0
  • VCF/BCF importing now naturally sorts the loci names
    • includes new NaturalSort.jl dep
  • file import INFO text consolidated somewhat
  • PopData show method information consolidated somehwat

🐛🐛 Bug fixes​

  • Hudson fst works as expected
  • isbiallelic returns correct answer when used on PopData object
  • [internal] conditional functions moved to Conditionals.jl file
  • keep and keep! are exported

v.0.6.1​

✨✨ New Features​

  • Hudson pairwise FST & Permutation
    • adds the Hudson et al. 1992 method
  • isbiallelic
    • adds boolean test if a PopData object has only biallelic loci
    • adds boolean test if a GenoArray is biallelic
  • drop_multiallelic
    • mutating and non-mutating methods to remove non-biallelic loci from a PopData object

⚡⚡ Improvements​

  • drop_monomorphic now uses the same logic as drop_multiallelic, which should make it faster and leaner

🐛🐛 Bug fixes​

  • vcf and bcf kwarg rename_loci now consistent in functions and docstrings
  • generate_meta now uses a comprehension rather than deprecated map(fn, groupeddataframe) method

v.0.5​

v.0.5.2​

⚡⚡ Improvements​

  • a rewrite of nei and weir-cockerham fst methods to be matrix-based (faster!)

✨✨ New Features​

  • fully implements permutation testing for both pairwise fst methods
  • adds method for avg_allele_freq to accommodate new pairwise_nei
  • extends pairwise_fst to include iterations keyword to activate permutation testing

v.0.5.1​

✨✨ New features​

  • pairwise_fst is now available for Weir & Cockerham (1984) and Nei (1987) methods
  • added skipinf, skipnan, and skipinfnan methods (unexported) to Utils.jl
  • dropped safemean because the skip___ methods are a lot faster and slimmer

v.0.5.0​

This release fixes a critical bug in all the file importing functions that returned nothing when dropping monomorphic loci. Other changes include

  • Dropping JLD2.jl suport due to its version-to-version instability. Two fewer dependencies!
    • As a result, datasets() now reads nancycats and gulfsharks directly from their source data files
    • To maintain all of the information, gulfsharks reads from a delimited file rather than a genepop file
  • populations type signature and behavior has been changed:
    • the default returns an array of the unique population names
    • the keyword listall::Bool has been replaced with counts::Bool, which now returns a dataframe of the number of samples per population

v.0.4​

v0.4.5​

This release builds off of 0.4.3 and does a better job with the VCF loading logic. Along with that, vcf and bcf exist in the namespace before loading in GeneticVariation.jl, meaning you can always view the docstrings. These stripped-down methods in the namespace will give helpful errors to remind you to load in GeneticVariation.jl and/or GZip.jl.

v0.4.3​

This release fixes and simplifies the under-the-hood allele_freq, geno_freq, and geno_count_xxx functions. The are faster now, and they infer types, making the output have expected type behavior.

Changes​

  • You no longer need to import both GeneticVariations.jl and GZip.jl to have the vcf and bcf functions work. The reason is that if your file isn't gzipped, then why load in an unnecessary library? Therefore, if your file is gzipped, then you'll need to load in GZip.jl too, otherwise you just need GeneticVariation.jl. 🆒
  • avg_allele_freq now has a different method, where the second positional argument is power, which will raise the calculated frequencies to the given value (default = 1). This simplifies having to do things like square the values of the resulting Dict.

v0.4.0​

This release adds a slew of relatedness estimators, which can be bootstrapped and are performed in parallel. Paired with release of PopGenSims.jl v0.0.2.

⚠️⚠️ Breaking changes​

  • CategoricalArrays replaced with PooledArrays
  • VCF/BCF now lazy load and require GeneticVariations.jl and GZip.jl separately

✨✨ New features​

  • relatedness estimators (see blog for tutorial)
  • internal functions:
    • loci_dataframe
    • loci_matrix
    • nonmissings
    • pairwise_pairs
  • pairwiseidentical() to compare percent identical loci
  • phase() method
  • Structure/fastStructure file IO

⚡⚡ Improvements​

  • some internal function locations moved around (housekeeping)
  • nancycats() and gulfsharks() are being phased out in favor of @nancycats and @gulfsharks. (You will see deprecation warning)
  • documentation (Docusaurus) upgrades
    • edit button now correctly works on blog posts
  • B/VCF reader rewritten (see docs)