approaches.md: A quick summary document of progress

JR_NegBinom_Result.md (.pdf): The main background and proceeding document for current MSV random network. RZ is working on summarize recent progress to update this document.

• Compiled as html here: https://dushoff.github.io/phenHet/JR_NegBinom_Result.html (Hyperlink in .html version not working due to folder issue)

NoteForR_i.md(.pdf): Details of $\mathcal{R}_i$ results

NoteForR_c.md(.pdf): Details of $\mathcal{R}_c$ and $\mathcal{R}^*_c$ results

NoteForMu.md: Discussion of expression of $\mu$ in $\mathcal{R}_c$ (need to update JD&TP's discussion email)

Rc.tex(.pdf): Todd version note for ODE of $p(t)$ and $\mathcal{R}_c$ and IV problem for $p(0)$

• Rc_SIR.tex(.pdf) simpler idea for shooting methods
• p0Note.md(.pdf): Richard's attempt on $p(0)$ problem

Initial_Values.md(.pdf): Eigen-direction idea for initial values of $R(0)$ and $\mathcal{R}_c(0)$

Simulation.md: Summary notes of simulation results.

/Manuscript/main.tex: Main .tex file for the manuscript. Just templates now.

• Paper.md: Structure skeleton of the paper
• resources.md: Summary notes for related literatures and previous investigations:
• literature.md: Summary of literature reviews

todo: Todo list, not being maintained for now

simulator info

• NetSimulator.cpp is a vertex-based simulator
• edgelist.cpp is an edge-based simulator
• scaleExamples.R is set up to use either machinery, based on what's in the Makefile: compare scaleEdges.Rout with scaleExamples.Rout. compareSims.R (not yet plumbed) is the beginning of machinery to compare the two approaches.

Other code files

JD's R file: see Makefile

• NetworkODE.R: MSV style ODE numeric solving machine
• NetworkRun.R: Working file for comparing vertex-based simulations and results. Need to update with new edge-based machinery
• NetworkSimulator.R: Vertex-based network transmission simulator in R based on Gillespie Algorithm
• simMSV.R compares the $\mathcal{R}_i$ and $\mathcal{R}_c$ result with the edge-based simulations.
• JD_RZ_curves generate Zhao1 result curves for primary investigation of Zhao1 result