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SIMPLEGEN
0.2.0
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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
Calibrating the in-built transmission model
Prevalence, incidence and EIR
Diagnostics
Age-incidence
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
Pipe operator
Source:
R/utils.R
pipe.Rd
See
magrittr::%>%
for details.
lhs
%>%
rhs
Contents