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")
# 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. 1-37In 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-
getFishlet 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