Diversity.jl

• Drop Julia pre-v1.0 compatibility
• Move to Phylo v0.4.0 API

New release for compatibility with updated EcoBase.

Full EcoJulia default implementation to allow cross-compatibility with other AbstractAssemblage-derived types. Moves EcoBase out of ext/ subfolder and uses released version directly. Resulting cross-compatibility allows diversity calculation of SpatialEcology Assemblage objects and plotting of Diversity Metacommunity objects.

Code now works with all of Julia v0.6, v0.7 and v1.0.
Also major speed up and reduction in memory use, and some preliminary code to adapt to EcoBase.

• Now validates using Julia v0.6.3 against R package rdiversity v1.2
• More minor Julia v0.7 fixes

• Fix iterator issues with Julia 0.7
• PackageEvaluator should no longer reject package tests

• Remove Nullable and replace with Union{T, Missing} for 0.7
• Base.Test -> Compat.Test
• Fix R igraph test errors for 0.6
• Update RCall to 0.10.0 with Missing

A major update to the codebase:

• Add general API for adding in new types of diversity, and interface for users to access it
  • Provides phylogenetic diversity measures through Diversity.Phylogenetics submodule
• Now Julia v0.6 (and mostly nightly) compliant, drop support for Julia v0.5
• Provides iterators for species and subcommunities
• Removes deprecated syntax from Diversity v0.2.x

This package is now in beta - it successfully validates against the R package boydorr/rdiversity.

• Update input format and deprecate old format
• Update output format to use DataFrames
• Remove deprecations for Julia v0.6 and drop v0.4