make_species_list: Generate a species list containing unique levels from a...

In MikkoVihtakari/MarineDatabase: Export data to Norwegian Polar Institute's marine database

Description

Generate a data frame containing unique species names, summed abundances and search terms to be used by confirm_species_list.

Usage

make_species_list(
  dat,
  sp.col = "species",
  ab.col = NULL,
  st.col = NULL,
  exp.col = NULL
)

Arguments

dat	Data frame containing taxonomy information. Must be in long format.
sp.col	Character specifying the column name that contains species names in dat.
ab.col	Character specifying the column name that contains species abundances in dat.
st.col	Character specifying the column name that contains station names in dat.
exp.col	Character specifying the column name that contains expedition in dat.

Value

Returns speciesList object containing a list of unique species entries in dat ($data) and summary information ($sum_info). $data contains following columns:

• or_name The original species names (as unique levels in dat).

• expedition Expeditions during which the species occurred. Several expeditions are separated by ;.

• ab Summed abundance for a species entry.

• n Number of stations where the species name was encountered (n)

• perAb Summed abundance for a species entry as a percentage of total summed abundance ($sum_info$abSum).

• fo Frequency of occurrence for a species entry (total number of stations is given in $sum_info$N).

• search_term A tidied search term for confirm_species_list function.

• type Type of species (spores, symbionts and epiphytes are separated, otherwise NA).

• certainty Certainty of species identification (includes sp., spp., aff., cf. and unknown).

Author(s)

Mikko Vihtakari

See Also

confirm_species_list for confirming the species names against a database.

MikkoVihtakari/MarineDatabase documentation built on July 7, 2020, 2:16 a.m.