flex_negllh_var: calculate the negative log-likelihood with PBT, GSI...

In delomast/fishCompTools: Tools to Assist With Fish Composition Estimates, Particularly Using Parental Based Tagging (PBT)

Description

more here...

Usage

flex_negllh_var(
  params,
  nPBT,
  nGSI,
  ohnc,
  t,
  utGSI,
  ohnc_gsi,
  utVar,
  ohnc_var,
  nCat
)

Arguments

params	vector of paramaters to optimize
nPBT	number of pbt groups to estimate
nGSI	number of GSI groups to estimate
ohnc	vector of number of observed (PBT assigned) hatchery fish in each PBT and GSI group (gsi groups should be 0)
t	vector of tag rates for all PBT and GSI groups (gsi groups should be 0)
utGSI	vector of number of un-PBT assigned fish in each GSI group
ohnc_gsi	matrix of counts of fish GSI assigned to various groups
utVar	matrix of numbers of un-PBT assigned fish in each GSI group (row) x category of the variable (column)
ohnc_var	matrix of counts of PBT-assigned fish in each category (rows are PBT groups)
nCat	the numbers of categories in the variable

Details

I expect that most users interested in MLE of composition will be best served by using MLEwrapper, which preps data, calls this function, and then returns the results in a nice format. This function calculates the likelihood for a given set of parameters, and may be useful to users who want MLE but want more control over how the data is used and/or the optimization procedure. This calculates a simplified version of the negative log-likelihood (constants removed) for computational efficiency.

delomast/fishCompTools documentation built on Jan. 11, 2021, 1:51 a.m.