cml {mixstock} | R Documentation |
Find the conditional maximum likelihood estimate (assuming marker frequencies in the sources are exactly equal to the sample frequencies) of the contributions of different sources to a mixed stock
cml(x, start.type="lsolve", fuzz=0, bounds=1e-4, ndepfac=1000,method="L-BFGS-B",lower=NULL,upper=NULL, ndeps=NULL, control=NULL,debug=FALSE,transf="part",grad=cml.grad,...)
x |
a list with elements mixsamp (a vector of the sampled
markers in the mixed stock) and sourcesamp (a matrix,
with markers in rows and sources in columns, of markers in the
source samples) |
grad |
function giving the gradient of the likelhood |
start.type |
starting values to use: equal (equal
contributions from each source); random (multinomial sample
with equal probabilities); rand2 (sample out of a transformed
normal distribution); a number between 1 and the number of sources;
that source starts with 0.95 contribution and the rest start with
0.05/(R-1); default lsolve , the linear solution to the problem |
fuzz |
min. value (1-min is the max.) for starting contributions |
bounds |
(bounds,1-bounds) are the lower and upper bounds for mle calculations |
ndepfac |
factor for computing numerical derivatives; numerical derivative stepsize is computed as bounds/ndepfac [OBSOLETE with gradient function?] |
method |
optimization method, to be passed to optim |
debug |
produce debugging output? |
lower |
lower bound |
upper |
upper bound |
ndeps |
scaling factor for optimization |
control |
other control arguments to optim |
transf |
(character) "full": use arctan transform to transform (-Inf,Inf) to (0,1) or vice versa; "part": don't; "none"; no transform |
... |
other arguments to mle or optim
(e.g. hessian=FALSE to suppress (slow) hessian calculation, etc.) |
By default, uses mle
which in turn uses optim
with method="L-BFGS-B"
to do bounded optimization
an object of class mixstock.est
, containing the results of
the fit
Ben Bolker
true.freq <- matrix(c(0.65,0.33,0.01,0.01, 0.33,0.65,0.01,0.01),ncol=2) true.contrib <- c(0.9,0.1) x <- simmixstock0(true.freq,true.contrib,50,100,1004) cml.est <- cml(x) cml.est