sanitizeRecaInput: Input sanitation for Reca

In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

Input sanitation for Reca

Description

Performs input sanitation for Reca

Usage

sanitizeRecaInput(
  AgeLength = NULL,
  WeightLength = NULL,
  Landings = NULL,
  GlobalParameters = NULL,
  stage = c("dataprep", "parameterize", "predict")
)

Arguments

AgeLength	list that is to be provided as the AgeLength argument to eca.estimate or eca.predict
WeightLength	list that is to be provided as the AgeLength argument to eca.estimate or eca.predict
Landings	list that is to be provided as the AgeLength argument to eca.estimate or eca.predict
GlobalParameters	list that is to be provided as the AgeLength argument to eca.estimate or eca.predict
stage	character specifying which stage the sanitation should be performed for. See details.

Details

The main interfaces to the Reca-package is eca.estimate and eca.predict. This have strict formatting requirements, well documented in the help pages for these functions, but they do not perform much input sanitation. This function checks that data is formatted in accordance with the requirements.

The input formats are shared between the eca.estimate and eca.predict and the formatting requirements are largely overlapping. Sanitation has therefore been conseptually divided into three stages, and which checks are to be performed is controlled by the argument 'stage'. The three stages are:

dataprep

check that data is correctly and consistently formatted, and check that all global parameters that have implications for data formatting are provided.

parameterize

check that arguments are valid input to eca.estimate

predict

check that arguments are valid input to eca.predict

Errors or warnings are raised on any issue, and this function does not have a meaningful return value.

All or some inputs to the Reca-functions may be provided for sanitation, and available checks will be run accordingly. As Reca impose some restriction on consistency in formatting between the different arguments, some checks require certain combination of arguments to be provided. For instance, checks on consistent encoding of variables in 'AgeLength' and 'Landings' are only performed if both 'AgeLength' and 'Landings' are provided.

StoXProject/RstoxFDA documentation built on Nov. 12, 2024, 3:42 a.m.