Nothing
##
BDloglikelihood.PO.cov <- function(partialData,
coefs.LL, coefs.MM, beta.immig,
object.LL=NULL, data.LL=NULL,
object.MM=object.LL, data.MM=data.LL,
ZZ.LL=NULL, ZZ.MM=ZZ.LL,
delta=1e-4, r=4, n.fft=1024){ ##ctmcpo1 or ctmcpomany
##get ZZ design matrices
if (!is.null(object.LL) && !is.null(data.LL)){
ZZ.LL <- model.matrix(object.LL,data.LL)
ZZ.MM <- model.matrix(object.MM,data.MM)
} ## else use the passed-in ZZ.LL and ZZ.MM vals.
## compute birth,death,immig rates from coefficients&covariates
##pp.LL <- length(coefs.LL)
##pp.MM <- length(coefs.MM)
##LLs <- exp(ZZ.LL %*% theta[1:pp.LL])
##MMs <- exp(ZZ.MM %*% theta[(pp.LL+1):(pp.LL+pp.MM)])
BDloglikelihood.PO.cov.helper(partialData,
coefs.LL, coefs.MM, beta.immig,
ZZ.LL, ZZ.MM,
n.fft)
}
## Reason for this function is that it's slightly more efficient if the
## loglikelihood is being computed repeatedly, as in getting the information
## numerically.
BDloglikelihood.PO.cov.helper <- function(partialData, coefs.LL, coefs.MM, beta.immig,
ZZ.LL, ZZ.MM=ZZ.LL,
n.fft=1024){ ##ctmcpo1 or ctmcpomany
LLs <- exp(ZZ.LL %*% coefs.LL);
MMs <- exp(ZZ.MM %*% coefs.MM);
NNs <- beta.immig*LLs
sum(mapply(BDloglikelihood.PO.CTMC_PO_1,
partialDat=getBDMCsPOlist(partialData), L=LLs,m=MMs,nu=NNs,
n.fft=n.fft,
SIMPLIFY=TRUE))
}
getBDinform.cov.numeric <- function(partialData,
coefs.LL, coefs.MM, beta.immig,
object.LL=NULL, data.LL=NULL,
object.MM=object.LL, data.MM=data.LL,
ZZ.LL=NULL, ZZ.MM=ZZ.LL,
delta=1e-4, r=4, n.fft=1024){
##get ZZ design matrices
if (!is.null(object.LL) && !is.null(data.LL)){
ZZ.LL <- model.matrix(object.LL,data.LL)
ZZ.MM <- model.matrix(object.MM,data.MM)
} ## else use the passed-in ZZ.LL and ZZ.MM vals.
## compute birth,death,immig rates from coefficients&covariates
pp.LL <- length(coefs.LL)
pp.MM <- length(coefs.MM)
myLogLike <- function(theta){ ##ctmcpo1 or ctmcpomany
BDloglikelihood.PO.cov.helper(partialData,
coefs.LL=theta[1:pp.LL],
coefs.MM=theta[(pp.LL+1):(pp.LL+pp.MM)],
beta.immig, ZZ.LL, ZZ.MM, n.fft)
}
##al the work is done by genD ...
Ihat <- -hessian(myLogLike, x=c(coefs.LL,coefs.MM), method.args=list(d=delta,r=r))
##return(Ihat)
DD <- t(genD(myLogLike, x=c(coefs.LL,coefs.MM),
method.args=list(d=delta,r=r))$D[1,1:(pp.LL+pp.MM),drop=FALSE])
list(Ihat=Ihat, DD2=DD %*% t(DD), DD=DD)
}
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