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Input sanitation for Reca

Source: R/RecaFormatChecks.R
sanitizeRecaInput.Rd

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.