taxize
package.taxizehelper
?taxizehelper
is a personal package that helps me use rOpenSci's taxize
package more succinctly. taxize
helps you retrieve up-to-date taxonomic information, so you can easily do things like:
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
install.packages("devtools")
devtools::install_github("DesiQuintans/taxizehelper")
library(taxizehelper)
taxizehelper
currently has only one function:
search_gnr(species_list)
--- Get taxonomic info for a list of taxa in a tidy dataframe.search_gnr()
to get a dataframe of taxonomic ranks# A list of insect species recorded within 1 km of my university.
data("wsu_hwk_insects")
print(wsu_hwk_insects)
#> [1] "Apis mellifera" "Heteronympha merope"
#> [3] "Yoyetta celis" "Vespula germanica"
#> [5] "Atrapsalta corticina" "Aleeta curvicosta"
#> [7] "Psaltoda plaga" "Galanga labeculata"
#> [9] "Hadrocolletes fulvus" "Cyclochila australasiae"
#> [11] "Pieris rapae" "Danaus chrysippus"
#> [13] "Yoyetta repetens" "Musgraveia sulciventris"
#> [15] "Tectocoris diophthalmus" "Cystosoma saundersii"
#> [17] "Synemon plana" "Papilio anactus"
#> [19] "Gastrimargus musicus" "Popplepsalta notialis"
#> [21] "Laccotrephes tristis" "Graphium macleayanum"
#> [23] "Geitoneura minyas" "Leptotes plinius"
#> [25] "Diamesus osculans" "Ptomaphila lacrymosa"
#> [27] "Tenodera australasiae" "Hippodamia variegata"
output <- search_gnr(wsu_hwk_insects)
#> Warning: package 'bindrcpp' was built under R version 3.4.4
class(output)
#> [1] "tbl_df" "tbl" "data.frame"
glimpse(output, width = 85)
#> Observations: 28
#> Variables: 22
#> $ user_supplied_name <chr> "Apis mellifera", "Heteronympha merope", "Yoyetta cel...
#> $ binomial <chr> "Apis mellifera", "Heteronympha merope", "Yoyetta cel...
#> $ kingdom <chr> "Metazoa", "Metazoa", "Metazoa", "Metazoa", "Metazoa"...
#> $ phylum <chr> "Arthropoda", "Arthropoda", "Arthropoda", "Arthropoda...
#> $ class <chr> "Insecta", "Insecta", "Insecta", "Insecta", "Insecta"...
#> $ order <chr> "Hymenoptera", "Lepidoptera", "Hemiptera", "Hymenopte...
#> $ family <chr> "Apidae", "Nymphalidae", "Cicadidae", "Vespidae", "Ci...
#> $ genus <chr> "Apis", "Heteronympha", "Yoyetta", "Vespula", "Atraps...
#> $ superkingdom <chr> "Eukaryota", "Eukaryota", "Eukaryota", "Eukaryota", "...
#> $ superclass <chr> "Hexapoda", "Hexapoda", "Hexapoda", "Hexapoda", "Hexa...
#> $ subclass <chr> "Pterygota", "Pterygota", "Pterygota", "Pterygota", "...
#> $ infraclass <chr> "Neoptera", "Neoptera", "Neoptera", "Neoptera", "Neop...
#> $ cohort <chr> "Holometabola", "Holometabola", "Paraneoptera", "Holo...
#> $ suborder <chr> "Apocrita", "Glossata", "Auchenorrhyncha", "Apocrita"...
#> $ infraorder <chr> "Aculeata", "Neolepidoptera", "Cicadomorpha", "Aculea...
#> $ superfamily <chr> "Apoidea", "Papilionoidea", "Cicadoidea", "Vespoidea"...
#> $ subfamily <chr> "Apinae", "Satyrinae", "Cicadettinae", "Vespinae", "C...
#> $ tribe <chr> "Apini", "Satyrini", "Cicadettini", "", "Cicadettini"...
#> $ subtribe <chr> "", "Hypocystina", "", "", "", "", "", "", "", "", ""...
#> $ subgenus <chr> "", "", "", "", "", "", "", "", "", "", "", "Anosia",...
#> $ path <chr> "|Eukaryota|Opisthokonta|Metazoa|Eumetazoa|Bilateria|...
#> $ ranks <chr> "|superkingdom||kingdom||||||phylum|||superclass|clas...
The ICN ranks are ordered so that you can access them with kingdom:genus
.
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