moultmcmc: Bayesian inference for Underhill-Zucchini moult models and...

In pboesu/moultmcmc: Bayesian Inference for Avian Moult Phenology Models

Bayesian inference for Underhill-Zucchini moult models and expansions

Description

Bayesian inference for Underhill-Zucchini moult models and expansions

Usage

moultmcmc(
  moult_column,
  date_column,
  id_column = NULL,
  start_formula = ~1,
  duration_formula = ~1,
  sigma_formula = ~1,
  type = 2,
  lump_non_moult = FALSE,
  data,
  init = "auto",
  flat_prior = TRUE,
  beta_sd = 0,
  log_lik = FALSE,
  use_phi_approx = FALSE,
  active_moult_recaps_only = TRUE,
  same_sigma = FALSE,
  ...
)

Arguments

moult_column	the name the column in data containing moult indices, i.e. a numeric vector of (linearized) moult scores in [0,1] (0 = old plumage, 1 = new plumage; for model types 1-5), numerical moult codes (1 = old plumage, 2 = moulting, 3 = new plumage; for model type 1), or a mixed column created by consolidate_moult_records for model type 12.
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	(optional) factor identifier. Usually a season-individual combination to encode within-season recaptures, defaults to NULL. When provided moultmcmc will attempt to fit the relevant recaptures model.
start_formula	model formula for start date
duration_formula	model formula for duration
sigma_formula	model formula for start date sigma
type	integer (one of 1,2,3,4,5,12) referring to type of moult data and consequently model to be fitted (see details)
lump_non_moult	logical; should pre- and post-moult observations be treated as indistinguishable? if TRUE and type %in% c(1,2,12), the relevant lumped model will be fitted (see details).
data	Input data frame must contain a numeric column "date" and a column "moult_cat" which is a numeric vector of categorical moult codes (1 = old plumage,2 = moulting,3 = new plumage).
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 when sample size is large.
use_phi_approx	logical flag whether to use stan's Phi_approx function to calculate the "old" likelihoods
active_moult_recaps_only	logical flag whether to ignore repeated observations outside the active moult phase
same_sigma	logical flag, currently unused
...	Arguments passed to rstan::sampling (e.g. iter, chains).

Details

type refers to the type of moult data available (see Underhill and Zucchini (1998) and Underhill, Zucchini and Summers (1990)).

type = 1 sample is representative of entire population (not yet moulting, in moult, and birds which have completed moult). For type 1 data, any value between 0 and 1 (> 0 and < 1) can be used as the moult index for birds in active moult. The value used does not matter, only the fact that they are in moult. type = 2 (default) sample is representative of entire population (not yet moulting, in moult, and birds which have completed moult). Moult scores are required.

type = 3 sample is representative only of birds in moult. Individuals with moult scores 0 or 1 are ignored.

type = 4 sample is representative only of birds in moult and those that have completed moult. Individuals with moult scores 0 are ignored.

type = 5 sample is representative only of birds that have not started moult or that are in moult. Individuals with moult scores 1 are ignored.

Value

An object of class stanfit returned by rstan::sampling

pboesu/moultmcmc documentation built on Feb. 19, 2023, 6:03 a.m.