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Validate species parameter data frame

Source: R/species_params.R
validSpeciesParams.Rd

Check validity of species parameters.

Usage

validSpeciesParams(species_params)

Arguments

species_params

The user-supplied species parameter data frame

Value

A valid species parameter data frame

This function throws an error if

  • the species column does not exist or contains duplicates

  • the maximum size is not specified for all species

If a weight-based parameter is missing but the corresponding length-based parameter is given, as well as the a and b parameters for length-weight conversion, then the weight-based parameters are added. If both length and weight are given, then weight is used and a warning is issued if the two are inconsistent.

If a w_inf column is given but no w_max then the value from w_inf is used. This is for backwards compatibility. But note that the von Bertalanffy parameter w_inf is not the maximum size of the largest individual, but the asymptotic size of an average individual.

Some inconsistencies in the size parameters are resolved as follows:

  • Any w_mat that is not smaller than w_max is set to w_max / 4.

  • Any w_mat25 that is not smaller than w_mat is set to NA.

  • Any w_min that is not smaller than w_mat is set to 0.001 or w_mat /10, whichever is smaller.

The row names of the returned data frame will be the species names. If species_params was provided as a tibble it is converted back to an ordinary data frame.

The function tests for some typical misspellings of parameter names, like wrong capitalisation or missing underscores and issues a warning if it detects such a name.

Note that the species parameters returned by this function are not guaranteed to produce a viable model. More checks of the parameters are performed by the individual rate-setting functions (see setParams() for the list of these functions).

See also

species_params()