Package 'cofid'

Title: Copepod Fish Interaction Database
Description: A curated list of copepod-fish ecological interaction records. It contains the taxonomy of the copepod and the fish and the publication from which the information was obtained. This database contains only marine and brackish water fish species. It excludes fish species that inhabit only freshwater.
Authors: Angel Robles [aut, cre]
Maintainer: Angel Robles <[email protected]>
License: GPL (>= 3)
Version: 1.0.1
Built: 2025-03-07 06:04:42 UTC
Source: https://github.com/alrobles/cofid

Help Index

Copepod fish interaction database

Description

A list of interactions between copepods and fish based on WoRMS database. And curated by Francisco Neptalí Morales-Serna. This dataset was cleaned and formated by Angel Luis Robles Fernandez following the GloBi (Global interactions) database standard. The cleaned dataset is stored in 10.5281/zenodo.11002619

Usage

cofid

Format

## 'cofid' A data frame with 10, 334 rows and 9 columns:

source_taxon_external_id

WoRMS id of the parasite, i.e. AphiaID

source_taxon_name

Scientific name of the species

source_taxon_path

Taxon path of the parasite

source_specimen_life_stage

Life stage of the parasite

interaction_type

Type of interactio between parasite and host

target_taxon_external_id

WoRMS id of the host, i.e. AphiaID

target_taxon_name

Scientific name of the host

target_taxon_path

Taxon path of the host

study_citation

Source paper of the interaction

Source

Copepod fish interaction database <10.5281/zenodo.11511665>

Find copepod occurrence data for given copepod species. Given a copepod family, genus or species returns a list of copepod occurrences.

Description

Find copepod occurrence data for given copepod species. Given a copepod family, genus or species returns a list of copepod occurrences.

Usage

getCopepods(species = NULL, genus = NULL, family = NULL, citation = TRUE)

Arguments

species

Copepod species to filter
genus

Copepod genus to filter
family

Copepod family to filter
citation

boolean. Should the output include the citation information? default is FALSE

Value

A data.frame with copepod fish interactions

Examples

getCopepods(genus = "Caligus")

Find copepod occurrence data for given host fish. Given a fish family, genus or species returns a list of copepod occurrences on that host

Description

Find copepod occurrence data for given host fish. Given a fish family, genus or species returns a list of copepod occurrences on that host

Usage

getFish(species = NULL, genus = NULL, family = NULL, citation = TRUE)

Arguments

species

Fish species to filter
genus

Fish genus to filter
family

Fish family to filter
citation

boolean. Should the output include the citation information? default is FALSE

Value

A data.frame with copepod fish interactions

Examples

getFish(genus = "Molva")