Length-based indicators by year and source — length

From the length samples of each year and source:

Usage

length_indicators(
  x,
  species,
  iter = 1,
  source = NULL,
  Lc = NULL,
  lh = NULL,
  season_weight = c("none", "equal")
)

x: a floss_data, a read_dataset() list, or a floss_treatments (then one set of indicators per run, column run).
species: species name.
iter: iteration(s).
source: sources; default all.
Lc: length of first capture (cm) per source (named) or one value; default the modal length.
lh: optional list with linf, k, M, lm (cm, per year); default from the species settings or lhpars.
season_weight: how seasonal length samples are pooled into a year (lfd_annual()): "none" sums the counts (imbalanced sampling then biases the indicators), "equal" gives every season the same weight.

a data frame, one row per species, iteration, year and source.

Lc: length of first full capture, here the mid-point of the modal length bin of the pooled samples of the source (or given).
Lmean: mean length of fish at or above Lc; L95: 95th percentile; Lmax5: mean length of the largest 5% of fish.
Pmat, Popt, Pmega (Froese 2004): proportion of fish above the length at maturity, within 10% of the optimum length \(L_{opt} = 3L_\infty/(3 + M/k)\), and above 1.1 \(L_{opt}\).
Z_lbar: total mortality from mean length (Beverton and Holt 1956), \(Z = k(L_\infty - \bar L)/(\bar L - L_c)\). It assumes equilibrium: constant recruitment and mortality, and flat-topped selectivity.
Z_true (when the answer key is present): true Fbar + M in that year, to show when and why Z_lbar departs from it.