prepare_bioconversion: Prepare the bioconversion file

In dswdejonge/TripleD: Construct a TripleD database.

Description

This wrapper function adds valid taxon names to the bioconversion file and also calculates mean conversion values for all higher taxonomic levels.

Usage

prepare_bioconversion(
  conversion_data = NULL,
  worms = NULL,
  input_folder = "inputfiles",
  data_folder = "data",
  out_folder = "data",
  as_CSV = FALSE
)

Arguments

conversion_data	Dataframe with bioconversion data matching the given requirements from the attributes_bioconversion file. If NULL (default) the bioconversion.csv will be searched for and loaded from the input_folder.
worms	Dataframe with query and valid names from worms. If NULL (default), the file "worms.rda" is searched for in the data_folder.
input_folder	The folder where to find the bioconversion.csv file. Default is 'inputfiles'.
out_folder	The external data is stored in this folder. Default is 'data'.
as_CSV	If you also want to store the collected external data as CSV, set to TRUE. Default is FALSE.

Value

This function does not return an object, but stores a dataframe in the specified out_folder under the name 'conversion_data.rda'.

dswdejonge/TripleD documentation built on June 18, 2020, 12:24 p.m.