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APP_README.md

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Project Name: Viral SpaceTime

Team Leaders: Ryan McMinds, Jesper Madsen

Team Members: Ann Mathew, Sofia Bhatia, Samuel Coleman, Omkar Dokur, Janelle Donglasan

GVN/USF mentors: Dr. Alash'le G. Abimiku

Objectives

Linking geospatial datasets with viral evolution rates

Methods and Implementation

1st pass:

  • download NextStrain US subset phylogenies, including time-scaled and divergence-scaled branch lengths, and geographic locations of tips.

  • impute mean geographic location of edges.

  • first impute ancestral nodes as a point on the shortest great-circle arc between the direct descendant nodes/tips. start at tips and iterate toward root of tree. The point for each ancestor corresponds to the location proportional to time-scaled branch lengths (e.g. if one descendant edge has length 2, and the other has length 1, the point is 1/3 the distance from descendant 1 to descendant 2.

  • then impute mean location for edges as midpoint between the ancestor and descendant

  • input imputed locations/distances into gaussian process or inla model

  • inla/gp model conditioned on geographic dataset, with imputed values at locations corresponding to the estimated location of phylogenetic edges

Results