Fills species parameter table for medfate with trait data from harmonized data sources
Usage
fill_medfate_traits(
SpParams,
harmonized_trait_path,
parameters = NULL,
priorization = TRUE,
erase_previous = FALSE,
replace_previous = FALSE,
progress = TRUE,
verbose = FALSE
)Arguments
- SpParams
A species parameter data frame to be filled for package medfate.
- harmonized_trait_path
A directory path were RDS files with harmonized trait databases are.
- parameters
A string vector of parameters to be populated. If
NULLthen all possible medfate parameters are parsed.- priorization
A boolean flag to perform priorization of some data sources over others.
- erase_previous
A boolean flag to indicate that all previous values should be set to NA before populating with new data
- replace_previous
A boolean flag to indicate that non-missing previous values should be replaced with new data
- progress
A boolean flag to prompt progress.
- verbose
A boolean flag to prompt detailed process information.
Details
The function processes multiple parameters of medfate SpParams table. It identifies the row to modify by
matching column 'AcceptedName' of SpParams with the column acceptedName of harmonized trait parameter sources.
If the target taxon is a species, values are taken from those rows in trait_table where species names match.
If the target taxon is a genus, then values are taken from those rows where genus is the same.
If priorization = TRUE and column priority_column is available in data sources,
the function will prioritize sources with higher priority first, filling parameters with them before inspecting data sources
of lower priority.