Population Graphs - Swift

So this spring, I’m going to make a large push at porting over the population graphs analyses Dyer & Nason 2004 that I have in R to a version that runs as a native app on iOS/MacOS. The long-term goals here are to leverage the upcoming advances in Augmented Reality and LiDAR at the phone/glasses level that I suspect will be more mainstream by 2023 or so.

Big Picture

So, in the long run, I’m looking to have a set of software that can do the following:

  • Estimate a population graph from genotype data.

  • Write custom SVD routines linked with [Accelerate](https://developer.apple.com/documentation/accelerate).

  • Wrap in [GeneticStudio](craftdocs://open?blockId=D1B89492-9912-42FC-A789-D957E1FEF4C9&spaceId=07b940d2-163d-ebd5-c7c7-647f9d1cfbd1) interface for Genotype & Project CRUD.

  • Visualize the graph in either 2D SpriteKit 3D SceneKit, and ARKit.

  • Force directed estimation of location in 2-space

  • Expand to 3-space

  • Develop individual physics models for dynamical system in SpriteKit & SceneKit

  • Comprehensive set of network-based analytical output for local (node- and edge- centric) as well as global parameters.

  • Overlay spatial network on GeoTiff for prevalence/avoidance of features.

  • Chromosome walking - Use engine to analyze how population covariance changes along stretches of chromosomes from SNP-like data.

  • Population Simulation - Develop stochastic simulation background that is visualized using dynamical population graphs for hypothesis testing, where we specify a model and