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Build a single linkage row

Source: R/0-linkage_table.R
linkage_row.Rd

Returns a one-row linkage table with defaults for the optional columns, for tests and for assembling a table row by row.

Usage

linkage_row(
  process,
  param,
  X_col,
  species = NA_integer_,
  sex = NA_integer_,
  age_bin = NA_integer_,
  fleet = NA_integer_,
  design_col = NA_character_,
  link = "identity",
  init = 0,
  init_supplied = FALSE,
  lower = -Inf,
  upper = Inf,
  prior_family = "none",
  prior_p1 = NA_real_,
  prior_p2 = NA_real_,
  re_group = NA_character_,
  re_struct = NA_character_,
  est_phase = 1L,
  re_index = NA_integer_,
  sigma_index = NA_integer_,
  re_time = NA_real_,
  re_sigma_init = NA_real_,
  re_sigma_prior_family = NA_character_,
  re_sigma_prior_p1 = NA_real_,
  re_sigma_prior_p2 = NA_real_,
  re_rho_init = NA_real_,
  re_rho_prior_family = NA_character_,
  re_rho_prior_p1 = NA_real_,
  re_rho_prior_p2 = NA_real_,
  re_obs_value = NA_real_,
  re_obs_sd = NA_real_,
  re_obs_est = NA,
  re_integrate = NA,
  re_pos = NA_integer_
)

Arguments

process, param, X_col

required identifying fields.

species, sex, age_bin, fleet

stratum ids, NA = every level; fleet is a 1-based Fleet_code, used by catchability, selectivity and composition-weight linkages.

design_col

name of the design matrix column.

link function; one of LINKAGE_LINKS.

init

initial value (default 0).

init_supplied

TRUE if the user supplied init (default FALSE).

lower, upper

bounds (default -Inf, Inf).

prior_family

one of PRIOR_FAMILIES. "none" = no prior.

prior_p1, prior_p2

family-specific prior parameters; ignored when prior_family == "none".

re_group

random-effect grouping label; NA = fixed.

re_struct

random-effect covariance structure ("us"/"rw"/"ar1"); NA = fixed.

est_phase

estimation phase ordinal; 0 = fix at init.

re_index, sigma_index, re_time

random-effect fields filled by pool_linkages() (deviation slot, SD slot, time order); NA on fixed rows.

re_sigma_init, re_sigma_prior_family, re_sigma_prior_p1, re_sigma_prior_p2

the group's natural-scale SD start value (held fixed if given without a prior) and prior, from linkage_spec(init = , priors = ); NA on fixed rows.

re_rho_init, re_rho_prior_family, re_rho_prior_p1, re_rho_prior_p2

the ar1 group's correlation on (-1, 1), start value (held fixed if given without a prior) and prior, from linkage_spec(); NA otherwise.

re_obs_value, re_obs_sd

the Rogers QAR1 observed covariate value and measurement SD, from linkage_spec(observe = , obs_sd = ); NA when unobserved.

re_obs_est

TRUE to estimate the QAR1 measurement SD (linkage_spec(obs_sd_est = )); FALSE/NA holds it fixed.

re_integrate

FALSE for a penalized fixed effect rather than a Laplace-integrated random effect, from linkage_spec(integrate = ); TRUE/NA = integrated.

re_pos

0-based position of the deviation within beta_linkage_re or beta_linkage_re_pen, whichever holds it.

Value

A one-row Rceattle_linkage_table.