SIMPLEGEN 0.2.0

Get started
- Installation
- Simulating malaria transmission
- TODO - A simple model
- TODO - Sampling from the population
- Overlaying genetics
- TODO - Pruning the transmission record
- TODO - Pedigrees and relatedness
The pipeline
- What is the SIMPLEGEN pipeline?
- The transmission record
Models and calibration
- Overall approach
- Model development and calibration
- Transmission models
- The inbuilt transmission model
- Calibration
- Genetic models
- TODO - Description
- Calibration
  - TODO - Genetic calibration
Data
- Epidemiological data
- Prevalence, incidence and EIR
- Diagnostic sensitivity
- Age-incidence
- Genetic data
- TODO - Complexity of infection
Misc
- Integrating with SLiM
Functions

A series of internally-used colours

Source: R/plot.R

simplegen_cols.Rd

These colours are purely used to make plots look consistent.

simplegen_cols()

Contents

Developed by Bob Verity, Shazia Ruybal, Isobel Routledge, Sophie Berube, Daniel Larremore.

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