fit_model: Fit an 'n2kModel' object

In INBO-Natura2000/n2kanalysis: Generic Functions to Analyse Data from the 'Natura 2000' Monitoring

Fit an n2kModel object

Description

Fit an n2kModel object

Usage

fit_model(x, ...)

## S4 method for signature 'character'
fit_model(
  x,
  base,
  project,
  status = c("new", "waiting"),
  verbose = TRUE,
  ...,
  bucket
)

## S4 method for signature 'n2kAggregate'
fit_model(x, ...)

## S4 method for signature 'n2kComposite'
fit_model(x, base, project, status = "new", ...)

## S4 method for signature 'n2kHurdleImputed'
fit_model(x, base, project, status = c("new", "waiting"), ...)

## S4 method for signature 'n2kInla'
fit_model(
  x,
  status = "new",
  ...,
  timeout = NULL,
  seed = get_seed(x),
  num_threads = NULL,
  parallel_configs = TRUE
)

## S4 method for signature 'n2kInlaComparison'
fit_model(x, base, project, status = "new", verbose = TRUE, ...)

## S4 method for signature 'n2kManifest'
fit_model(
  x,
  base,
  project,
  status = c("new", "waiting"),
  verbose = TRUE,
  ...,
  local = tempfile("fit_model"),
  first = FALSE
)

## S4 method for signature 'n2kModelImputed'
fit_model(x, ...)

## S4 method for signature 's3_object'
fit_model(x, status = c("new", "waiting"), ...)

Arguments

x	the n2kModel
...	other arguments. See details
base	The root of a project. Can be either a directory on a file system or an AWS S3 bucket object. Extracted from bucket or x when missing.
project	The subdirectory of the project. Is relative the base. Extracted from x when missing.
status	A vector with status levels naming the levels which should be calculated. Defaults to "new".
verbose	A logical indicating if the function should display the name of the file and the status. Defaults to TRUE.
bucket	The name of the AWS S3 bucket. Only used when base is missing.
timeout	the optional number of second until the model will time out
seed	See the same argument in INLA::inla.qsample() for further information. In order to produce reproducible results, you ALSO need to make sure the RNG in R is in the same state, see the example in INLA::inla.posterior.sample(). When seed is non-zero, num_threads is forced to "1:1" and parallel_configs is set to FALSE, since parallel sampling would not produce a reproducible sequence of pseudo-random numbers.
num_threads	The number of threads to use in the format "A:B" defining the number threads in the outer (A) and inner (B) layer for nested parallelism. ⁠A "0"⁠ will be replaced intelligently. seed != 0 requires serial computations.
parallel_configs	Logical. If TRUE and not on Windows, then try to run each configuration in parallel (not Windows) using A threads (see num_threads), where each of them is using B:0 threads.
local	A local folder into which objects from an AWS S3 bucket are downloaded.
first	A logical. first = TRUE implies to fit only the first object in the manifest with matching status. first = FALSE implies to fit all objects in the manifest with matching status. Defaults to FALSE.

Details

• status: A vector with status levels naming the levels which should be recalculated. Defaults to c("new", "waiting").

• verbose: A logical indicating if the function should display the name of the file and the status. Defaults to TRUE.

INBO-Natura2000/n2kanalysis documentation built on Feb. 15, 2024, 11:24 a.m.