This R packages contains an expert curated Copepod Fish database. This database was taxonomically curated by Francisco Neptalí Morales-Serna. The data cleaning, standarization and wrapping as an R packages was done by Ángel Luis Robles-Fernandez

Installation

Install from CRAN:

install.packages("cofid")

You can install the development version of cofid from GitHub with:

# install.packages("devtools")
# devtools::install_github("alrobles/cofid")
install.packages("cofid", repos = c('https://alrobles.r-universe.dev', 'https://cloud.r-project.org'))
# load the data to your environment
data(cofid, "cofid")

Dataset

The dataset contains $10, 344$ copepod - fish interaction records. The fields in the data set are:

source_taxon_external_id: the id number provided by World Register of Marine Species
source_taxon_name: The scientific name of the copepod species
source_taxon_path: Taxonomical hierarchy of the copepod. Only contains 7 levels
source_specimen_life_stage: The life stage of the record
interaction_type: The type of interaction between copepod and fish The records are mainly ectoparasitic (7654). There are 74 endoparasitic and 7 parasitic
target_taxon_external_id: The host fish id number provided by World Register of Marine Species
target_taxon_name: Host fish species scientific name
target_taxon_path: Taxonomical hierarchy of the host fish. Only contains 7 levels
study_citation: Original study where the record cand be found

Functionality

cofid R package has two helping funtions. * getCopepods let the user filter the dataset given a family, genus or species of copepod

library(cofid)
Caligus <- getCopepods(genus = "Caligus")
head(Caligus)
#>      source_taxon_name   target_taxon_name
#> 2073   Caligus affinis Pomatomus saltatrix
#> 2074   Caligus affinis     Umbrina cirrosa
#> 2075 Caligus alalongae    Thunnus alalunga
#> 2076 Caligus alalongae      Thunnus obesus
#> 2077 Caligus alalongae      Thunnus obesus
#> 2078 Caligus alalongae      Thunnus obesus
#>                                                                                                                                                                                                                                                       study_citation
#> 2073                                                                     Oldewage, W.H. & J.G. van As. (1989). Occurrence and distribution of Caligus (Copepoda: Siphonostomatoida) in African coastal waters. Revue de Zoologie Africaine 103(1):91-98, appendix 1.
#> 2074                                                                                                                    Kensley, B. & J.R. Grindley. (1973). South African parasitic Copepoda. Annals of the South African Museum 62(3):69-130, figs. 1-35. (x-1973)
#> 2075 Raibaut, A., C. Combes & F. Benoit. (1998). Analysis of the parasitic copepod species richness among Mediterranean fish. <em>In: Dahms, H.U., T. Glatzel, H.J. Hirche, S. Schiel & H.K. Schminke, (eds.). Proceedings of the 6th International Conference on Co
#> 2076                                                                     Oldewage, W.H. & J.G. van As. (1989). Occurrence and distribution of Caligus (Copepoda: Siphonostomatoida) in African coastal waters. Revue de Zoologie Africaine 103(1):91-98, appendix 1.
#> 2077                                                                                                                         Dippenaar, S.M. (2005). Reported siphonostomatoid copepods parasitic on marine fishes of southern Africa. Crustaceana 77(11):1281-1328.
#> 2078 Capart, A. (1959). Copépodes parasites. <em>Résultats Scientifiques de l'Expédition Océanographique Belge dans les Eaux Côtieres Afrricaines de l'Atlantique Sud (1948-1949). Institut Royale des Sciences Naturelles de Belgique.</em> 3(5):59-126, figs. 1-37

In addition, the user can also retrive the data withouth citation for convenience:

Caligidae <- getCopepods(family = "Caligidae", citation = FALSE)
head(Caligidae)
#>         source_taxon_name    target_taxon_name
#> 2050 Caligodes laciniatus   Strongylura leiura
#> 2051 Caligodes laciniatus       Tylosurus acus
#> 2052 Caligodes laciniatus     Tylosurus choram
#> 2053 Caligodes laciniatus Tylosurus crocodilus
#> 2054 Caligodes laciniatus  Platybelone argalus
#> 2055 Caligodes laciniatus       Ablennes hians

getFish let the user filter the dataset given a family, genus or species of fish:

library(cofid)
Molva_molva <- getFish(species = "Molva molva", citation = FALSE)
head(Molva_molva)
#>            source_taxon_name target_taxon_name
#> 562       Cresseyus confusus       Molva molva
#> 2214          Caligus curtus       Molva molva
#> 2387       Caligus elongatus       Molva molva
#> 4184 Lernaeocera branchialis       Molva molva
#> 4317       Lernaeocera lusci       Molva molva
#> 6962 Chondracanthus brotulae       Molva molva

Online access

You can try online the dataset.