create_variable_mapping: Create the variable_mapping table

In EDIorg/ecocomDP: Tools to Create, Use, and Convert ecocomDP Data

Create the variable_mapping table

Description

Create the variable_mapping table

Usage

create_variable_mapping(
  observation,
  observation_ancillary = NULL,
  location_ancillary = NULL,
  taxon_ancillary = NULL
)

Arguments

observation	(tbl_df, tbl, data.frame) The observation table.
observation_ancillary	(tbl_df, tbl, data.frame) The optional observation_ancillary table.
location_ancillary	(tbl_df, tbl, data.frame) The optional location_ancillary table.
taxon_ancillary	(tbl_df, tbl, data.frame) The optional taxon_ancillary table.

Details

This function collects specified data tables, extracts unique variable_name values from each, converts into long (attribute-value) form with the table name and variable_name values to the resulting table's "table_name" and "variable_name" columns, respectively. The resulting table's "mapped_system", "mapped_id", and "mapped_label" are filled with NA and are to be manually filled.

Value

(tbl_df, tbl, data.frame) The variable_mapping table.

Examples

flat <- ants_L0_flat

# Create inputs to variable_mapping()

observation <- create_observation(
  L0_flat = flat, 
  observation_id = "observation_id", 
  event_id = "event_id", 
  package_id = "package_id",
  location_id = "location_id", 
  datetime = "datetime", 
  taxon_id = "taxon_id", 
  variable_name = "variable_name",
  value = "value",
  unit = "unit")

observation_ancillary <- create_observation_ancillary(
  L0_flat = flat,
  observation_id = "observation_id", 
  variable_name = c("trap.type", "trap.num", "moose.cage"))

location_ancillary <- create_location_ancillary(
  L0_flat = flat,
  location_id = "location_id",
  variable_name = "treatment")

taxon_ancillary <- create_taxon_ancillary(
  L0_flat = flat,
  taxon_id = "taxon_id",
  variable_name = c(
    "subfamily", "hl", "rel", "rll", "colony.size", 
    "feeding.preference", "nest.substrate", "primary.habitat", 
    "secondary.habitat", "seed.disperser", "slavemaker.sp", 
    "behavior", "biogeographic.affinity", "source"),
  unit = c("unit_hl", "unit_rel", "unit_rll"))

# Create variable_mapping table

variable_mapping <- create_variable_mapping(
  observation = observation,
  observation_ancillary = observation_ancillary,
  location_ancillary = location_ancillary, 
  taxon_ancillary = taxon_ancillary)

variable_mapping

EDIorg/ecocomDP documentation built on Aug. 22, 2024, 9:34 a.m.