Clean/Tidy to one row per taxa*Visit — filter

Deprecated in favour of the simpler workflow involving make_taxonomy then bin_taxa (along with other bins, say, geographic and temporal). Required attributes are then added to each taxa; context and/or taxa + context before reducing to distinct context and associated attributes.

filter_taxa(
  df,
  taxa_col = "original_name",
  context,
  extra_cols = NULL,
  required_rank = "species",
  do_cov = FALSE,
  do_life = FALSE,
  lucov = NULL,
  lulife = NULL,
  taxonomy
)

Arguments

df: Dataframe to clean, filter and tidy with respect to taxonomy.
taxa_col: Character. Name of column with taxa.
context: Character. Name of columns defining context.
extra_cols: Character. Name of any extra columns to keep.
required_rank: Character. Default is 'species'. What level of the taxonomic hierarchy is required for results. Records above this level are filtered.
do_cov: Logical. Should cover (needs to be supplied in df) be appended to output.
do_life: Logical. Should lifeform (needs to be supplied in df) be appended to output.
lucov: Dataframe lookup for cover.
lulife: Dataframe lookup for lifeform.
taxonomy: list with (at least) named elements lutaxa and taxonomy. Usually resulting from call to envClean::make_taxonomy().
do_ind: Logical. Should ind (needs to be supplied in df) be appended to output.

Value

Dataframe with columns taxa, context and, possibly, extracols , lifeform and cover