download_diatbarcode: Download the diat.barcode database

In fkeck/diatbarcode: Access the diat.barcode database

Download the diat.barcode database

Description

This function downloads the database in a given location on your computer. The function allows to download different flavors of the original database.

Usage

download_diatbarcode(path = NULL, flavor = "original",
  version = "last")

Arguments

path	the path where the downloaded file is to be saved. If NULL, the temporary directory.
flavor	a flavor of the Diat.barcode database (see Details section).
version	a character string giving the version. Use "last" (default) to get the last version available.

Details

The Diat.barcode database can be downloaded in different flavors. Currently available flavors are:

• original The original database.

• rbcl312_dada2_tax A pre-formated reference for taxonomic affiliation with DADA2.

• rbcl312_dada2_spe A pre-formated reference for exact species matching with DADA2.

The diat.barcode database is a library of barcodes which is curated and which guarantees good taxonomical homogeneity and good quality of sequences. Data have different sources:

• The culture collection of Thonon, INRA, TCC.

• The barcoding project of diatoms in UK.

• Public data (NCBI).

Several European labs participate in this curation:

• INRA – UMR Carrtel, FR–74200 Thonon–les–Bains, France.

• Botanischer Garten und Botanisches Museum Berlin–Dahlem, Freie Universität Berlin, Germany.

• Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, Uppsala, Sweden.

• Bowburn Consultancy, Durham, UK.

• Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK.

• Marine and Continental Waters, Institute for Food and Agricultural Research and Technology (IRTA), Catalonia, Spain.

• Laboratory for Evolutionary Ecology, center for Marine Research, Ruder Boskovic Institute, Rovinj, Croatia.

Value

Silently returns a list with informations about the downloaded file.

Licence

Diatbarcode and R-Syst are distributed under the terms of the Open Licence 2.0. Consult: https://www.etalab.gouv.fr/wp-content/uploads/2018/11/open-licence.pdf

References

Rimet, Frederic; Gusev, Evgenuy; Kahlert, Maria; Kelly, Martyn; Kulikovskiy, Maxim; Maltsev, Yevhen; Mann, David; Pfannkuchen, Martin; Trobajo, Rosa; Vasselon, Valentin; Zimmermann, Jonas; Bouchez, Agnès, 2018, "Diat.barcode, an open-access barcode library for diatoms", https://doi.org/10.15454/TOMBYZ, Portail Data Inra, V1

Rimet F., Chaumeil P., Keck F., Kermarrec L., Vasselon V., Kahlert M., et al. (2016). R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database 2016, baw016. https://doi.org/10.1093/database/baw016

fkeck/diatbarcode documentation built on March 1, 2025, 4:49 a.m.