Population Model CE Application to Vital Rates Year-Specific

Utility function to apply cumulative effects to vital rates.

Usage

pop_model_ce_apply_year(
  rates = NULL,
  CE_df = NULL,
  anadromous = FALSE,
  mat_stage = NULL
)

Arguments

rates

Life history vital rates list object.

CE_df

Cumulative effects data frame.

anadromous

Anadromous TRUE/FALSE.

mat_stage

Named numeric vector of mature life stages.

Value

a modified dat vital rates object after applying CE effects.

Details

Per-year sys.cap values are matched to simulation years via the Year column of CE_df (slot 1 of each internal rate list is the initialization entry and carries Year 1's value; slot t + 1 carries simulation year t's value). Stressors supplied as a single row (no Year information) are treated as constant and applied to every year. Years missing from CE_df are treated as unstressed (sys.cap = 1) with a warning. Each vital rate may be targeted at most once per stressor: life_stage tokens are resolved to their underlying vital rate (so aliases such as "s1", "stage_1" and "surv_1" are recognized as the same target), and duplicate targeting - via aliases, a repeated token, or duplicate rows - is an error. To apply two separate effects to the same life stage, create two distinctly named stressors (effects multiply).