specimens-class: An S4 class containing specimen collections.

In kamapu/specimens: Handling Specimen Collections

An S4 class containing specimen collections.

Description

A list of collections of specimens considering duplicated specimens and history of determination. This package was targeting collection databases from the perspective of a collector and designed for collections of herbarium specimens but also applicable to collections of other organisms, for instance zoological collections as well.

Slots

collections

A data frame or an object of class sf including variables associated to a collection, meaning a sample of a species in a locality. Mandatory columns are here coll_nr (unique identifier of the collection), leg (name of collector), and coll_date (date of collection set as class Date).

specimens

A data frame with information specifical to single specimens. It may be one specimen per collection or many (duplicates). This database list can contain the final destination of the specimens, in the case of plant specimens, the herbarium. Mandatory columns in this table are spec_id (unique identifier for specimens) and coll_nr (a foreign key pointing to the homonimous column in slot 'collections').

history

A data frame containing the history of determination. In the case of herbarium specimens, the update of the species determination. Mandatory columns are fid (unique identifier), spec_id (foreign key pointing to homonimous columns in slot 'specimens'), det (the name of determining person), det_date (date of update set as class Date), and taxon_name (the scientific name of specimen according to the determinator).

Author(s)

Miguel Alvarez [e-mail]

Examples

showClass("specimens")

## Create an empty object
spec <- new("specimens")

kamapu/specimens documentation built on March 1, 2024, 11:15 a.m.