Create the variable_mapping table

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.

Value

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

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
#> # A tibble: 19 x 6 #> variable_mapping_id table_name variable_name mapped_system mapped_id #> <chr> <chr> <chr> <chr> <chr> #> 1 1 observation abundance NA NA #> 2 2 observation_an~ trap.type NA NA #> 3 3 observation_an~ trap.num NA NA #> 4 4 observation_an~ moose.cage NA NA #> 5 5 location_ancil~ treatment NA NA #> 6 6 taxon_ancillary subfamily NA NA #> 7 7 taxon_ancillary hl NA NA #> 8 8 taxon_ancillary rel NA NA #> 9 9 taxon_ancillary rll NA NA #> 10 10 taxon_ancillary colony.size NA NA #> 11 11 taxon_ancillary feeding.preferen~ NA NA #> 12 12 taxon_ancillary nest.substrate NA NA #> 13 13 taxon_ancillary primary.habitat NA NA #> 14 14 taxon_ancillary secondary.habitat NA NA #> 15 15 taxon_ancillary seed.disperser NA NA #> 16 16 taxon_ancillary slavemaker.sp NA NA #> 17 17 taxon_ancillary behavior NA NA #> 18 18 taxon_ancillary biogeographic.af~ NA NA #> 19 19 taxon_ancillary source NA NA #> # ... with 1 more variable: mapped_label <chr>