In FRBCesab/forcis: An R Client to Access the FORCIS Database

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The R package forcis is an interface to the FORCIS database on global foraminifera distribution (Chaabane et al. 2023). This database includes data on living planktonic foraminifera diversity and distribution in the global oceans from 1910 until 2018 collected using plankton tows, continuous plankton recorder, sediment traps and plankton pump from the global ocean.

This vignette is an overview of the main features.

Installation

To install the forcis package, run:

## Install < remotes > package (if not already installed) ----
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

## Install dev version of < forcis > from GitHub ----
remotes::install_github("FRBCesab/forcis")

The forcis package depends on the sf package which requires some spatial system libraries (GDAL and PROJ). Please read this page if you have any trouble to install forcis.

Setup

First, let's attach the required packages.

library(forcis)

Download FORCIS database

The FORCIS database consists of a collection of five csv files hosted on Zenodo. These csv are regularly updated and we recommend to use the latest version

Let's download the latest version of the FORCIS database with download_forcis_db():

# Create a data/ folder ----
dir.create("data")

# Download latest version of the database ----
download_forcis_db(path = "data", version = NULL)

By default (version = NULL), this function downloads the latest version of the database. The database is saved in data/forcis-db/version-99/, where 99 is the version number.

N.B. The package forcis is designed to handle the versioning of the database on Zenodo. Read the Database versions for more information.

Import FORCIS data

In this vignette, we will use the plankton nets data of the FORCIS database. Let's import the latest release of the data.

file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
                         package = "forcis")
net_data <- read.table(file_name, dec = ".", sep = ";")

# Import plankton nets data ----
net_data <- read_plankton_nets_data(path = "data")

N.B. Here we use a subset of the plankton nets data, not the whole dataset.

Select a taxonomy

The FORCIS database provides three different taxonomies:

• LT: lumped taxonomy
• VT: validated taxonomy
• OT: original taxonomy

See the associated data paper for further information.

After importing the data and before going any further, the next step involves choosing the taxonomic level for the analyses.

Let's use the function select_taxonomy() to select the VT taxonomy (validated taxonomy):

# Select taxonomy ----
net_data_vt <- select_taxonomy(net_data, taxonomy = "VT")

To go further

Additional vignettes are available depending on user wishes:

• the Database versions vignette provides information on how to deal with the versioning of the database
• the Select, reshape, and filter data vignette shows examples to select, filter and reshape the FORCIS data
• the Data conversion vignette describes the conversion functions available in forcis to compute abundances, concentrations, and frequencies
• the Data visualization vignette describes the plotting functions available in forcis

References

Chaabane S, De Garidel-Thoron T, Giraud X, Schiebel R, Beaugrand G, Brummer G-J, Casajus N, Greco M, Grigoratou M, Howa H, Jonkers L, Kucera M, Kuroyanagi A, Meilland J, Monteiro F, Mortyn G, Almogi-Labin A, Asahi H, Avnaim-Katav S, Bassinot F, Davis CV, Field DB, Hernández-Almeida I, Herut B, Hosie G, Howard W, Jentzen A, Johns DG, Keigwin L, Kitchener J, Kohfeld KE, Lessa DVO, Manno C, Marchant M, Ofstad S, Ortiz JD, Post A, Rigual-Hernandez A, Rillo MC, Robinson K, Sagawa T, Sierro F, Takahashi KT, Torfstein A, Venancio I, Yamasaki M & Ziveri P (2023) The FORCIS database: A global census of planktonic Foraminifera from ocean waters. Scientific Data, 10, 354. DOI: 10.1038/s41597-023-02264-2.

FRBCesab/forcis documentation built on Oct. 25, 2024, 9:26 a.m.