Nothing
`fitSPVAR` <-
function(bt, init = c(2, .2, 0.1))
{
STIMES <- getSpeciationtimes(bt);
TMAX <- max(bt);
getLam0.SPVAR <- function(x)
{
k <- x[2];
mu0 <- x[3];
lam0 <- (x[1] + mu0) * exp(TMAX* k);
return(lam0);
}
#the likelihood function, constrained version
optimLH.SPVAR <- function(init) #c(r, k, mu0)
{
k <- init[2];
mu0 <- init[3];
lam0 <- (init[1] + mu0) * exp(TMAX* k);
LH <- getLikelihood.SPVAR(lam0, k, mu0, STIMES, TMAX);
return(-LH);
}
low <- c(0.001, 0.001, 0.001);
up <- c(Inf, Inf, Inf);
temp <- optim(init, optimLH.SPVAR, method='L-BFGS-B', lower= low, upper=up );
res <- list(model = 'SPVAR', LH = -temp$value, aic=(2*temp$value)+6, lam0 = getLam0.SPVAR(temp$par), k=temp$par[2], mu0 = temp$par[3]);
return(res);
}
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