Pkg3 compatibility

Merge pull request #26 from kescobo/pkg3

Update for Pkg3

Some new functions

• Add present() and prevalence() functions
• Last release before switching to Pkg3 compatible structure

Support for julia 1.0

Tests pass on Julia 1.0

Support for julia-0.7

Major changes:

• Dropped support for julia-0.6, moved on to julia-0.7
• Moved Plotting and BioBakery utilities out to separate packages to reduce dependencies
  • These two new packages will be released shortly
• I'm keeping DataFrames dependency for now, though I'd like to move to IterableTables soonish (though constructors might be more sense in EcoBase)

Final support for julia v0.6

Changes since v0.2.0

• New BioJulia contributing documentation
  • Issue templates
  • PR templates
  • CoC and Contributing docs
• Switch to FileIO/CSVFiles dependency for reading tables
• New functions for calculating alpha diversity
• Some lingering deprecation fixes.

After this, I'm switching to julia-v0.7, and dropping support for julia-v0.6. Any julia-v0.6 bug fixes should be released on microbiome-v0.2.x tags, while the julia-v0.7 and 1.0 releases will be microbiome-v0.3+.

Update to SpatialEcology Backend

Now using types from SpatialEcology.jl. Also:

• Better docs
• More tests
• Plotting functions that actually work!

Minor Documenter fix

Also, hopefully METADATA now that it knows the correct address.

v0.1.1 Documentation

• Added Documenter.jl docs.
• Switched repo to BioJulia Ownership

Initial Release

Initial release

Types

• AbundanceTable
• DistanceMatrix
• PCoA

Functions

• pcoa()
• various plotting functions using StatPlots
• relativeabundance() to normalize AbundanceTable
• topabund() to get the n most abundant bugs across many samples