n2k_inla: Create an 'n2kInla' object

In inbo/n2kanalysis: Generic Functions to Analyse Data from the 'Natura 2000' Monitoring

Create an n2kInla object

Description

A new n2kInla model is created when data is a data.frame.

In case data is an n2kInla object, then only the model and status are updated. All other slots are unaffected.

Usage

n2k_inla(data, ..., model_fit)

## S4 method for signature 'data.frame,ANY'
n2k_inla(
  data,
  status = "new",
  result_datasource_id,
  scheme_id,
  family = "poisson",
  formula,
  species_group_id,
  location_group_id,
  model_type,
  first_imported_year,
  last_imported_year,
  duration,
  last_analysed_year,
  analysis_date,
  lin_comb = NULL,
  minimum = "",
  imputation_size,
  parent = character(0),
  seed,
  replicate_name = list(),
  control = list(),
  parent_status = "converged",
  parent_statusfingerprint,
  extra,
  ...,
  model_fit
)

## S4 method for signature 'n2kInla,inla'
n2k_inla(data, status, raw_imputed = NULL, ..., model_fit)

Arguments

data	a data.frame with the data to analyse
...	other arguments. See below
model_fit	The fitted model
status	A single character indicating the status of the model. Defaults to "waiting".
result_datasource_id	A string identifying the data source.
scheme_id	A single integer holding the id of the scheme.
family	the family to use in the INLA model.
formula	A single character identifying the comparison.
species_group_id	A string identifying the species group.
location_group_id	A string identifying the location group.
model_type	The type of the models. Must start with "inla comparison:".
first_imported_year	Oldest year considered in the data.
last_imported_year	Most recent year considered in the data.
duration	The width of the moving window. Defaults to the last_imported_year - first_imported_year + 1.
last_analysed_year	Most recent year in the window. Defaults to last_imported_year.
analysis_date	A POSIXct date indicating the date that the dataset was imported.
lin_comb	A model matrix to calculate linear combinations.
minimum	The name of the variable which holds the minimum counts. Only relevant in case of multiple imputation.
imputation_size	The required number of imputations defaults to 0.
parent	The file fingerprint of the optional parent analysis.
seed	A single integer used as a seed for all calculations. A random seed will be inserted when missing.
replicate_name	A list with the names of replicates. Defaults to an empty list. Used in case of f(X, ..., replicate = Z). Should be a named list like e.g. list(X = c("a", "b", "c")).
control	A named list passed to INLA::inla() when fitting the model.
parent_status	The status of the parent analysis.
parent_statusfingerprint	The status fingerprint of the parent analysis.
extra	a data.frame with extra observations not used in the model. They will be added in subsequent analyses.
raw_imputed	the optional rawImputed object

inbo/n2kanalysis documentation built on Feb. 17, 2024, 1:32 a.m.