get_community_matrix: Get community matrix from the TripleD database

Description Usage Arguments Details Value Examples

View source: R/create_community_matrix.R

Description

This functions lets you extract a community matrix (i.e. stations in rows, taxa in columns) from the TripleD databas.

Usage

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get_community_matrix(
  database,
  taxonomic_level,
  abundance_measure,
  include_incomplete = TRUE
)

Arguments

database

A dataframe, database output from the TripleD package.

taxonomic_level

The taxonomic level for which you want to create a community matrix. Options:

  • all

  • species (default)

  • genus

  • family

  • order

  • class

  • phylum

abundance_measure

The value in the cells. Options:

presence_absence

only 1 (present) or 0 (absence)

Density_nr_per_m2

individual count per square meter

Biomass_g_per_m2"

ash-free dry weight in grams per square meter

Density_nr_per_m3

individual count per cubic meter

Biomass_g_per_m3

ash-free dry weight in grams per cubic meter

include_incomplete

Include values based on incomplete data i.e. underestimations? (Default TRUE)

Details

Missing data filled with 0.

Value

Returns a dataframe with StationID as first row.

Examples

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get_community_matrix(database, "species", "Biomass_g_per_m2")
get_community_matrix(database, "phylum", "Density_nr_per_m2", include_incomplete = FALSE)

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