bb_fit_survival_ml: Fit Survival Model with Maximum Likelihood

In poissonconsulting/bboutools: Boreal Caribou Survival, Recruitment and Population Growth

Fit Survival Model with Maximum Likelihood

Description

Fits hierarchical survival model with Maximum Likelihood using Nimble Laplace approximation.

Usage

bb_fit_survival_ml(
  data,
  min_random_year = 5,
  year_trend = FALSE,
  include_uncertain_morts = FALSE,
  year_start = 4L,
  inits = NULL,
  quiet = FALSE
)

Arguments

data	The data.frame.
min_random_year	A whole number of the minimum number of years required to fit year as a random effect (as opposed to a fixed effect).
year_trend	A flag indicating whether to fit a year trend effect. Year trend cannot be fit if there is also a fixed year effect (as opposed to random effect).
include_uncertain_morts	A flag indicating whether to include uncertain mortalities in total mortalities.
year_start	A whole number between 1 and 12 indicating the start of the caribou (i.e., biological) year. By default, April is set as the start of the caribou year.
inits	A named vector of the parameter initial values. Any missing values are assigned a default value of 0. If NULL, all parameters are assigned a default value of 0.
quiet	A flag indicating whether to suppress messages and progress bars.

Details

If the number of years is > min_random_year, a fixed-effects model is fit. Otherwise, a mixed-effects model is fit with random intercept for each year. If year_trend is TRUE and the number of years is > min_random_year, the model will be fit with year as a continuous effect (i.e. trend) and no fixed effect of year. If year_trend is TRUE and the number of years is <= min_random_year, the model will be fit with year as a continuous effect and a random intercept for each year.

The model is always fit with random intercept for each month.

The start month of the Caribou year can be adjusted with year_start.

Value

A list of the Nimble model object and Maximum Likelihood output with estimates and standard errors on the transformed scale.

See Also

Other model: bb_fit_recruitment(), bb_fit_recruitment_ml(), bb_fit_survival()

Examples

if (interactive()) {
  fit <- bb_fit_survival_ml(bboudata::bbousurv_a)
}

poissonconsulting/bboutools documentation built on July 16, 2025, 11:14 p.m.