https://github.com/mrc-ide/scott

Structured COalescent Transmission Tree simulation
https://github.com/mrc-ide/scott

Last synced: about 2 months ago
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Structured COalescent Transmission Tree simulation

• Host: GitHub
• URL: https://github.com/mrc-ide/scott
• Owner: mrc-ide
• License: mit
• Created: 2022-08-17T10:08:24.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-12-15T02:46:11.000Z (about 1 year ago)
• Last Synced: 2023-12-15T03:55:00.591Z (about 1 year ago)
• Language: R
• Size: 10.7 KB
• Stars: 3
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# `scott`: Structured Coalescent Transmission Tree simulation 

Example usage: 

```

# Simulate epidemic under exponential growth 

set.seed( 1111 ) 

library(phydynR)

births <- c(I = 'parms$beta * I' )

deaths <- c(I = 'parms$gamma * I' )

dm <- build.demographic.process(births=births

  , deaths = deaths

  , parameterNames=c('beta', 'gamma') 

  , rcpp=FALSE

  , sde = TRUE)

tfgy = dm( theta = list( beta = 1.5, gamma = 1 ), x0 = c(I = 1 ) , t0 = 0, t1 = 10  )

# Simulate transmission tree

library(scott)

n <- 75 # sample size

s <- rep(10, n ) # sample times 

X <- matrix( c(rep(1, n), rep(0,n)), byrow=FALSE , ncol = 2) # sample states

min_dt = 10 / 1e4 # controls precision of simulation 

o = scott(

  tfgy

  , s

  , X 

  , min_dt

  , event_tol = .1 

)

# Here is the table of transmission events within the sample 

(w <- o$waifw)

```

# Roadmap 2022-08-17

- Convenient subroutines for faster analysis 

	- scott which takes Ne(t) instead of tfgy 

	- scott which takes independent estimate of incidence and prevalence 

- Improve documentation and examples 

- Fast Rcpp version