rFishTaxa
Introduction
Eschmeyer's Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable online database. This rFishTaxa package helps users to obtain valid taxonomic fish information for biodiversity estimates, conservation issues, etc.
:arrow_double_down: Installation
Current beta / GitHub release:
Installation using R package devtools:
if (!requireNamespace(c("devtools","tibble"), quietly = TRUE))
install.packages("devtools","tibble")
devtools::install_github("Otoliths/rFishTaxa",build_vignettes = TRUE)
:beginner: Example
Load the rFishTaxa package
options(warn = -1)
library(rFishTaxa)
library(magrittr)
library(dplyr)Genera/Species of Fishes by Family/Subfamily through 2022:
db <- species_family()
head(db)****************************************
Eschmeyer's Catalog of Fishes online database show that the number of available names for use at the species level as of 8 August 2022 is 61,376, the number of valid genera is 5,229, and the number of valid species is 36,292, of which 18,372 are found in freshwater.
****************************************
# A tibble: 1,036 x 10
class order family subfamily available_genera valid_genera genera_last_ten~ available_speci~ valid_species species_last_te~
<chr> <chr> <chr> <chr> <int> <int> <int> <int> <int> <int>
1 Myxi~ Myxi~ Myxini Myxini NA NA NA NA NA NA
2 Myxi~ Myxi~ Myxin~ Myxinifo~ NA NA NA NA NA NA
3 Myxi~ Myxi~ Myxin~ Myxinidae 19 6 1 104 88 13
4 Rubi~ Rubi~ Rubic~ Rubicund~ 1 1 1 4 4 0
5 Epta~ Epta~ Eptat~ Eptatret~ 10 1 0 65 55 10
6 Myxi~ Myxi~ Myxin~ Myxininae 8 4 0 35 29 3
7 Petr~ Petr~ Petro~ Petromyz~ NA NA NA NA NA NA
8 Petr~ Petr~ Petro~ Petromyz~ NA NA NA NA NA NA
9 Petr~ Petr~ Petro~ Petromyz~ 19 8 0 102 43 4
10 Geot~ Geot~ Geotr~ Geotriid~ 9 1 0 14 2 0
# ... with 1,026 more rowsSearching for genera in a family:
r1 <- search_cas(query = c("cyprinidae","balitoridae"),type = "genus_family")
head(r1)# A tibble: 6 x 6
query genus_author genus author family status
<chr> <chr> <chr> <chr> <chr> <chr>
1 asptosyax, B Aaptosyax Rainboth 1991 Aaptosyax Rainboth 1991 Cyprinidae Validation
2 yprininae, tribe Labeo Cuvier 1816 Labeo Cuvier 1816 Cyprinidae Synonym
3 tautonymy, fifteen Labeo Cuvier 1816 Labeo Cuvier 1816 Cyprinidae Synonym
4 ccrossocheilus, Kottelat Acrossocheilus Oshima 1919 Acrossocheilus Oshima 1919 Cyprinidae Validation
5 yprininae, tribe Puntioplites Smith 1929 Puntioplites Smith 1929 Cyprinidae Synonym
6 genneiogarra, Kottelat Ageneiogarra Garman 1912 Ageneiogarra Garman 1912 Cyprinidae Validation# Each matching row by family
db$family <- ifelse(!is.na(db$subfamily),paste0(db$family,"_",db$subfamily),db$family)
r1 <- r1 %>% left_join(db[,1:4],by = "family")
r1$family <- gsub("_.*","",r1$family)
head(r1)# A tibble: 6 × 9
query genus_author genus author family status class order subfa…¹
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 asptosyax, B Aaptosyax Rainboth 1991 Aaptosyax Rainboth 1… Cypri… Valid… Acti… Cypr… Cyprin…
2 yprininae, tribe Labeo Cuvier 1816 Labeo Cuvier 1816 Cypri… Synon… Acti… Cypr… Labeon…
3 tautonymy, fifteen Labeo Cuvier 1816 Labeo Cuvier 1816 Cypri… Synon… Acti… Cypr… Labeon…
4 ccrossocheilus, Kottelat Acrossocheilus Oshima 1919 Acrossocheilus Oshima 1919 Cypri… Valid… Acti… Cypr… Across…
5 yprininae, tribe Puntioplites Smith 1929 Puntioplites Smith 1929 Cypri… Synon… Acti… Cypr… Cyprin…
6 genneiogarra, Kottelat Ageneiogarra Garman 1912 Ageneiogarra Garman 1912 Cypri… Valid… Acti… Cypr… Labeon…
# … with abbreviated variable name ¹subfamilySearching for species in a family:
r2 <- search_cas(query = "balitoridae",type = "species_family")
head(r2)# A tibble: 6 x 6
query species_author species author family status
<chr> <chr> <chr> <chr> <chr> <chr>
1 abbreviata, Homaloptera Jinshaia abbreviata (Günther 1892) Jinshaia abbreviata (Günther 189~ Balit~ Valid~
2 acuticauda, Sinohomaloptera Hemimyzon yaotanensis (Fang 1931) Hemimyzon yaotanensis (Fang 1931) Balit~ Synon~
3 amphisquamata, Homaloptera Homalopterula amphisquamata (Weber & de Beaufort 1916) Homalopterula amphisquamata (Weber & de ~ Balit~ Valid~
4 anisura, Platycara Balitora brucei Gray 1830 Balitora brucei Gray 1830 Balit~ Synon~
5 annamitica, Balitora Balitora annamitica Kottelat 1988 Balitora annamitica Kottelat 1988 Balit~ Valid~
6 annandalei, Bhavania Bhavania annandalei Hora 1920 Bhavania annandalei Hora 1920 Balit~ Valid~Searching for species in a genus:
r3 <- search_cas(query = "Brachyplatystoma",type = "species_genus")
head(r3)# A tibble: 6 x 6
query species_author species author family status
<chr> <chr> <chr> <chr> <chr> <chr>
1 affine, Platystoma Brachyplatystoma filamentosum (Lichtenstein 1819) Brachyplatystoma filamentosum (Lichtenstein ~ Pimel~ Synon~
2 capapretum, Brachyplatystoma Brachyplatystoma capapretum Lundberg & Akama 2005 Brachyplatystoma capapretum Lundberg & Aka~ Pimel~ Valid~
3 cunaguaro, Ginesia Brachyplatystoma juruense (Boulenger 1898) Brachyplatystoma juruense (Boulenger 189~ Pimel~ Synon~
4 dawall, Hypophthalmus Brachyplatystoma vaillantii (Valenciennes 1840) Brachyplatystoma vaillantii (Valenciennes ~ Pimel~ Synon~
5 filamentosus, Pimelodus Brachyplatystoma filamentosum (Lichtenstein 1819) Brachyplatystoma filamentosum (Lichtenstein ~ Pimel~ Valid~
6 gigas, Platystoma Brachyplatystoma filamentosum (Lichtenstein 1819) Brachyplatystoma filamentosum (Lichtenstein ~ Pimel~ Synon~Searching for species related to a species or subspecies:
r4 <- search_cas(query = c("Anguilla nebulosa", "Clupisoma sinense"),type = "species")
head(r4)
r4 %>% left_join(species_family()[,1:4],by = "family")# A tibble: 2 x 9
query species_author species author family status class order subfamily
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 nebulosa, Anguilla Anguilla nebulosa McClelland 1844 Anguilla nebulosa McClelland 1844 Anguillidae Validation Anguill~ Angu~ Anguilli~
2 sinensis, Platytropius Clupisoma sinense (Huang 1981) Clupisoma sinense (Huang 1981) Ailiidae Validation Ailiidae Aili~ Ailiidae :heart: Contribution
Latin-Chinese Dictionary of Fishes Names Introduction In the last 20-30 years, significant progress has been made in the work of fish. However the contents of a few published Latin-Chinese dictionaries of world's fish names are still incomplete and cannot satisfy the increasing demand by the Chinese language people for the purpose's such as research, teaching, conservation, fisheries, or aquatic trade use.
Future versions try to add Lantin-Chinese Dictionary of Fish Names by Classification System to this package.
Contributions to this package are welcome. The preferred method of contribution is through a GitHub pull request. Feel also free to contact us by creating an issue.
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