Nothing

`MultiBD`

is an `R`

package for direct likelihood-based inference of multivariate birth-death processes.

- Install (if necessary) package dependencies and helpers:

```
install.packages(c("Rcpp", "RcppParallel", "BH", "devtools"))
```

- Install
`MultiBD`

from`github`

(until package becomes available via`CRAN`

):

```
devtools::install_github("msuchard/MultiBD")
```

```
library(MultiBD)
data(Eyam)
loglik_sir <- function(param, data) {
alpha <- exp(param[1]) # Rates must be non-negative
beta <- exp(param[2])
# 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
```

`MultiBD`

is licensed under Apache License 2.0

Beta

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

- Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA.
Birth(death)/birth-death processes and their computable transition probabilities with statistical applications.
*arXiv preprint arXiv*:1603.03819, 2016.

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