Bayesian inference for the Type 2 moult model with repeat measures

uz2_linpred_recap(
  moult_index_column,
  date_column,
  id_column,
  start_formula = ~1,
  duration_formula = ~1,
  sigma_formula = ~1,
  lump_non_moult = FALSE,
  active_moult_recaps_only = FALSE,
  data,
  init = "auto",
  flat_prior = TRUE,
  beta_sd = 0,
  log_lik = FALSE,
  use_phi_approx = FALSE,
  same_sigma = FALSE,
  ...
)

Arguments

moult_index_column

the name the column in data containing moult indices, i.e. a numeric vector of (linearized) moult scores (0 = old plumage,1 = new plumage).

date_column

the name the column in data containing sampling dates, encoded as days since an arbitrary reference date, i.e. a numeric vector

id_column

factor identifier. Usually a season-individual combination to encode within-season recaptures

start_formula

model formula for start date

duration_formula

model formula for duration

sigma_formula

model formula for start date sigma

lump_non_moult

logical; should pre- and post-moult observations be treated as indistinguishable? if TRUE, the type 2L model will be fitted.

active_moult_recaps_only

logical flag whether to ignore repeated observations outside the active moult phase

data

Input data frame

init

Specification of initial values for all or some parameters. Can be the string "auto" for an automatic guess based on the data, or any of the permitted rstan options: the digit 0, the strings "0" or "random", or a function. See the detailed documentation for the init argument in ?rstan::stan.

flat_prior

use uniform prior on start date and duration (TRUE) or vaguely informative truncated normal prior (FALSE). Defaults to TRUE.

beta_sd

use zero-centred normal priors for regression coefficients other than intercepts? If <= 0 the stan default of improper flat priors is used.

log_lik

boolean retain pointwise log-likelihood in output? This enables model assessment and selection via the loo package. Defaults to FALSE, can lead to very large output arrays if sample size is large.

use_phi_approx

logical flag whether to use stan's Phi_approx function to calculate the "old" likelihoods

same_sigma

logical flag, currently unused

...

Arguments passed to rstan::sampling (e.g. iter, chains).

Value

An object of class stanfit returned by rstan::sampling