Basic Phylodynamic ILMs

[codecov[bot]]

Codecov Report

Merging #27 into master will decrease coverage by 6.65%. The diff coverage is 64.21%.

@@            Coverage Diff             @@
##           master      #27      +/-   ##
==========================================
- Coverage   63.02%   56.36%   -6.66%     
==========================================
  Files          41       55      +14     
  Lines        1044     1586     +542     
==========================================
+ Hits          658      894     +236     
- Misses        386      692     +306     

Impacted Files	Coverage Δ
src/core/Risks/RiskFunctions.jl	66.66% <0.00%> (-13.34%)	:arrow_down:
src/core/Transmissions/TransmissionRateCache.jl	0.00% <0.00%> (ø)
src/core/Transmissions/TransmissionRates.jl	20.00% <0.00%> (+7.50%)	:arrow_up:
src/inference/RiskPriors.jl	66.66% <0.00%> (-13.34%)	:arrow_down:
src/inference/start!.jl	19.04% <0.00%> (-75.96%)	:arrow_down:
src/visualization/observations.jl	0.00% <0.00%> (ø)
src/visualization/out_degree.jl	0.00% <0.00%> (ø)
src/visualization/population.jl	0.00% <0.00%> (ø)
src/visualization/trace.jl	0.00% <0.00%> (ø)
src/visualization/transmission_network.jl	0.00% <ø> (ø)
... and 78 more

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[jangevaare]

v0.4.x port progress

Utilities

• [x] summary() for TNILM
• [ ] summary() for PhyloILM
• [x] mode() for TNDistributions

Visualization

• [x] Out-degree
• [x] EventObservations

Extended functionality

• [ ] TNPrior support in inference
• [ ] EventExtents extension

Performance

• [ ] EventRateCache