startvec0: Produce (raw) starting vector of parameters for mixed stock...

In mixstock: functions for mixed stock analysis

Description

Provides raw (untransformed) starting vector of source contribution parameters for mixed stock analysis.

Usage

startvec0(sourcesamp, mixsamp=NULL, type="equal", sd=1, lmin=0.001)
startvec(sourcesamp, mixsamp=NULL, type="equal", 
         marktype="sample",a=1,cond=FALSE,transf="full",
fuzz=0,sd=1)
lsolve(n, s, tol = 1e-05, warn = FALSE)

Arguments

sourcesamp	Marker frequencies in sources, or a list with source and mixed samples, or a turtle.data object.
mixsamp	Marker frequencies in mixed stock
type	Various options for setting starting contributions. equal: equal contributions from all sources. random: random multinomial sample with equal multinomial probabilities. rand2: random sample from transformed normal variates with mean 0 and standard deviation sd. A number n between 1 and the number of sources inclusive gives a starting condition with 95% of the contribution from source n and the other 5% evenly split between the other sources. The default is to attempt a solution of the linear equation (sourcesamp*f=mixsamp) and use these values as the starting contributions.
sd	standard deviations for starting type rand2
lmin	When doing linear solutions, the boundary values are {lmin, 1-lmin.
marktype	method for starting marker frequencies: sample uses the observed sample probabilities; random used observed sample probabilities; weighted does a Bayes-weighted start (a la Masuda and Pella)
cond	Conditional likelihood? (i.e. cond=TRUE gives just the parameters for source contributions, not parameters for source marker frequencies)
a	prior strength parameter
transf	transform ("full","part", or "none")
fuzz	fuzz parameter for moving parameters away from the boundary
n	source samples (HxR matrix)
s	mixed stock samples (vector)
tol	tolerance for linear fit
warn	warn if numeric problems with solution

Value

A parameter vector of the contributions from each of the sources: just the raw source contributions in the case of startvec0, or source contributions and possibly marker frequencies (transformed or untransformed) in the case of startvec.

Note

lsolve attempts to get a starting value by solving the linear equation (solve(n,s,tol=tol))

Author(s)

Ben Bolker

Examples

 data(simex)
 startvec0(simex)
 startvec(simex,transf="part")
 startvec(simex)

mixstock documentation built on May 2, 2019, 6:48 p.m.