commdf-class: Class for commdf objects

In dinilu/EPDr: Interact with the European Pollen Database (EPD)

Description

This object stores information regarding the particles counts in each biological sample of an entity but in vector or table format rather than the original format in the EPD database. Note, however, that data here comes from the table SAMPLES from the database or an epd.entity-class object. Contrary to data in epd.entity-class objects, this are intended to be manipulated and modified if necessary.

Slots

taxanames

character. Names of the taxa included in the object.

taxa_

numeric. Identification numbers of the taxa.

taxaaccepted

numeric. Identification numbers for the accepted taxa. This is useful to unify taxonomy across entities from different authors, that may have used slightly different taxa names.

taxamhvar

numeric. Identification numbers for the higher taxa levels of each taxa. This is the only taxonomical hierarchy that is available in the EPD. The approach is useful, but also very limited, since there is no intuitive way to homogenize the data at certain taxonomical level (e.g., at the genus level).

taxagroupid

character. Identify code (four characters code) indicating the group of taxa (e.g., TRSH for trees and shrubs or HERB for herbs). Check list_taxagroups for the whole list and further details.

counts

data.frame. Particles counts in a matrix format (sample x taxa). This format is more intuitive and handy for biologist (ecologist or palynologist) than the original format.

dinilu/EPDr documentation built on Aug. 22, 2019, 1:03 p.m.