Complete strict parameters for medfate

Taxonomy-based imputation of strict parameters in medfate.

Usage

complete_medfate_strict(
  SpParams,
  params = NULL,
  progress = TRUE,
  verbose = FALSE
)

Arguments

SpParams

A species parameter data frame to be completed

params

A character vector with strict parameters to be completed. If missing, all strict parameters will be checked for completion.

progress

A boolean flag to prompt progress.

verbose

A boolean flag to prompt detailed process information.

Value

A species parameter data frame with imputed strict parameter values

Details

The function performs imputation of strict parameters on the basis of non-missing values in taxonomically-close taxa. Strict parameters are defined as such in SpParamsDefinition. First, if the taxon with missing values is a subspecies, the function looks for values at the species level. Missing values at the species level are filled with data at the genus, family, order or group levels, depending on the availability of information. Quantitative values are averaged, whereas for qualitative values the first non-missing value is used. Beware that imputation can result in errors if the initial amount of information is scarce. Therefore, users should revised the output of this function and correct potential errors manually, whenever detected.