HNC_expand_unkGSI: Estimates the composition of ascensions and incorporates...

In delomast/escapeLGD: Escapement Estimation at Lower Granite Dam

Estimates the composition of ascensions and incorporates uncertainty in GSI assignments

Description

Estimates the composition of ascensions and incorporates uncertainty in GSI assignments

Usage

HNC_expand_unkGSI(
  trap,
  stratAssign_comp,
  boots = 2000,
  pbt_var,
  timestep_var,
  physTag_var,
  adclip_var,
  sampID,
  tagRates,
  H_vars,
  HNC_vars,
  W_vars,
  wc_binom,
  GSI_draws,
  n_point = 100,
  GSI_var,
  method = c("Account", "MLE")
)

Arguments

trap	a tibble with data about the trapped fish
stratAssign_comp	tibble with sWeek, stratum showing what stratum each sWeek corresponds to for composition estimation using the trap data
boots	The number of bootstap iterations to run
pbt_var	The column name of the PBT group variable (tag rates are defined for these groups)
timestep_var	The column name of the timestep variable (corresponds to sWeek in stratAssign_comp)
physTag_var	The column name of a logical variable defining whether or not a sample had a physical tag (e.g. CWT) identifying it as hatchery origin with 100% certainty
adclip_var	The column name of the variable defining ad-fin status (values are "AD" or "AI")
tagRates	A tibble with two columns, the first listing PBT groups and the second giving their tag rates
H_vars	A character vector defining one or two variables to estimate composition of the H group
HNC_vars	A character vector defining one or two variables to estimate composition of the HNC group. If method is "MLE" and two variables are defined, the first must be the pbt_var.
W_vars	A character vector defining one or two variables to estimate composition of the W group
wc_binom	The output of expand_wc_binom_night
GSI_draws	a tibble with the first column individuals names, the rest GSI values fro draws from the posterior (each column a draw). Used in order.
n_point	number of iterations in the bootstrap loop (only resampling GSI values) for calculating point estimates
GSI_var	the column name in trap that has the GSI values.
method	Either "Account" to use the accounting style estimator or "MLE" to use the maximum likelihood estimator

delomast/escapeLGD documentation built on June 9, 2025, 10:52 p.m.