Nothing
"optspacing" <- function(cost,G=NULL,sel.frac=NULL,cross)
{
if(cross=="bc")
optspacing.bc(cost,G,sel.frac)
else if(cross=="f2")
optspacing.f2(cost,G,sel.frac)
else
stop("Unknown cross ", cross, ".")
}
"optspacing.bc" <-
function(cost,G=NULL,sel.frac=NULL)
{
if(is.null(sel.frac))
{
tmp <- optim(par=c(50,0.5),fn=function(x,cost,G)
{-info2cost.bc(x[2],cost,x[1],G)},
method="L-BFGS-B",
lower=c(.Machine$double.eps,.Machine$double.eps),
upper=c(Inf,1),
G=G,cost=cost)$par
names(tmp) <- c("Marker spacing (cM)", "Selection fraction")
tmp
}
else
{
tmp <- optimize(f = function(d, sel.frac, cost, G)
{info2cost.bc(sel.frac, cost, d, G)},
lower = .Machine$double.eps,
upper = G, G = G, sel.frac = sel.frac,
cost = cost,maximum=TRUE)$maximum
tmp <- c(tmp,sel.frac)
names(tmp) <- c("Marker spacing (cM)", "Selection fraction")
tmp
}
}
"optspacing.f2" <-
function(cost,G=NULL,sel.frac=NULL)
{
if(is.null(sel.frac))
{
tmp <- optim(par=c(50,0.5),fn=function(x,cost,G)
{-info2cost.f2(x[2],cost,x[1],G)},
method="L-BFGS-B",
lower=c(.Machine$double.eps,.Machine$double.eps),
upper=c(Inf,1),
G=G,cost=cost)$par
names(tmp) <- c("Marker spacing (cM)", "Selection fraction")
tmp
# list(d=tmp[1],sel.frac=tmp[2])
}
else
{
tmp <- optimize(f = function(d, sel.frac, cost, G)
{info2cost.f2(sel.frac, cost, d, G)},
lower = .Machine$double.eps,
upper = G, G = G, sel.frac = sel.frac,
cost = cost,maximum=TRUE)$maximum
tmp <- c(tmp,sel.frac)
names(tmp) <- c("Marker spacing (cM)", "Selection fraction")
tmp
}
}
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