Get stochastic survival rates by period, year and stage.

Each stage can vary by intercept, year trend, annual random effect, period random effect and period within annual random effect. All values are provided on the log-odds scale. Variation from random effects is stochastic. Year is scaled to Year - 1 for trend, which ensures that the intercept is the rate in the first year.

bbs_survival(
  intercept,
  nyear = 10,
  trend = rep(0, length(intercept)),
  annual_sd = rep(0, length(intercept)),
  period_sd = rep(0, length(intercept)),
  annual_period_sd = rep(0, length(intercept)),
  nperiod_within_year = 12
)

Arguments

intercept

A vector of the intercept of the log-odds survival by stage.

nyear

A whole number of the number of years.

trend

A vector of the effect of an increase of one year on the log-odds survival by stage.

annual_sd

A vector of the standard deviation of the annual variation of the log-odds survival by stage.

period_sd

A vector of the standard deviation of the period variation of the log-odds survival by stage.

annual_period_sd

A vector of the standard deviation of the period within annual variation on the log-odds survival by stage.

nperiod_within_year

A whole number of the number of periods in a year.

Value

An array of survival rates with dimensions period, year, stage.

Examples

survival <- bbs_survival(intercept = logit(c(0.94, 0.98, 0.98)), trend = c(0, 0, 0.2))