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# msuchard / MultiBD

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# MultiBD `MultiBD` is an `R` package for direct likelihood-based inference of multivariate birth-death processes.

## Installation

1. Install `CRAN` release version:
``````install.packages("MultiBD")
``````
1. Install the bleeding-edge version of `MultiBD` from `github`:
``````devtools::install_github("msuchard/MultiBD")
``````

## Short example

``````library(MultiBD)
data(Eyam)

loglik_sir <- function(param, data) {
alpha <- exp(param) # Rates must be non-negative
beta  <- exp(param)

# Set-up SIR model
drates1 <- function(a, b) { 0 }
brates2 <- function(a, b) { 0 }
drates2 <- function(a, b) { alpha * b     }
trans12 <- function(a, b) { beta  * a * b }

sum(sapply(1:(nrow(data) - 1), # Sum across all time steps k
function(k) {
log(
dbd_prob(  # Compute the transition probability matrix
t  = data\$time[k + 1] - data\$time[k], # Time increment
a0 = data\$S[k], b0 = data\$I[k],       # From: S(t_k), I(t_k)
drates1, brates2, drates2, trans12,
a = data\$S[k + 1], B = data\$S[k] + data\$I[k] - data\$S[k + 1],
computeMode = 4, nblocks = 80         # Compute using 4 threads
)[1, data\$I[k + 1] + 1]                 # To: S(t_(k+1)), I(t_(k+1))
)
}))
}

loglik_sir(log(c(3.204, 0.019)), Eyam) # Evaluate at mode
``````

## Vignettes

`MultiBD` is licensed under Apache License 2.0

## Development status Beta

## Acknowledgements

• This project is supported in part through the National Science Foundation grant DMS 1264153 and National Institutes of Health grant R01 AI107034.

## References

1. Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA (2018). Birth/birth-death processes and their computable transition probabilities with biological applications. Journal of Mathematical Biology 76(4) 911-944.
2. Ho LST, Crawford FW, Suchard MA (2018). Direct likelihood-based inference for discretely observed stochastic compartmental models of infectious disease. Annals of Applied Statistics. In press.

No description, website, or topics provided.

## Releases 1

CRAN acceptance Latest
Jul 29, 2016

## Packages 0

No packages published

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