MLEwrapper: Find maximum likelihood estimates for composition

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

Description

The likelihood is maximized using optim and some typically close, but quick to calculate, starting values. If estimating composition of a separate variable, all samples with missing data for this variable must be removed prior to running this function.

Usage

MLEwrapper(
  trapData,
  tags,
  GSIcol,
  PBTcol,
  strataCol,
  adFinCol,
  AI = TRUE,
  optimMethod = "Nelder-Mead",
  variableCols = NULL,
  ...
)

Arguments

trapData	a dataframe with a rwo for each individual and columns for GSI assignment, PBT assignment, etc.
tags	a dataframe with the first column containing names of PBT groups, and the second column containing tag rates
GSIcol	name of column containing GSI assignments. If you have no GSI information, create a column with the same value for all samples.
PBTcol	name of column containing PBT assignments
strataCol	name of column indicating the strata the observation belongs to
adFinCol	name of column containing adipose fin status - TRUE (or AI) being intact FALSE (or AD) being clipped, NA missing
AI	TRUE to analyze ad-intact fish, FALSE to analyze ad-clipped fish
optimMethod	the method to use first with optim. If this method fails, "Nelder-Mead" is attempted and a warning is issued.
variableCols	name of column containing the variable to estimate composition for (optional)
...	other arguments to pass to optim

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