FishTaxaMaker: Generate a list of species Auxiliary function to obtain...

In FishPhyloMaker: Phylogenies for a List of Finned-Ray Fishes

Description

Generate a list of species Auxiliary function to obtain taxonomic classification and check the names of species present in species pool

Usage

FishTaxaMaker(data, allow.manual.insert = TRUE)

Arguments

data	A character vector with species names or a community matrix with species names in columns
allow.manual.insert	Logical, if TRUE (default), the user must type the names of Family and Order of species not found in Fishbase

Value

List with three elements.

- A data frame containing the taxonomic classification of valid species accordingy to Fishbase

- A data frame with three columns containing the name of species (s), the Family (f) and Order (o) that can be used in
   FishPhyloMaker function
   
- A character vector containing all names of species that was not find in Fishbase

Examples

 ## Not run: 
 data(neotropical_comm)
 data_comm <- neotropical_comm[, -c(1, 2)]
 taxon_data <- FishTaxaMaker(data_comm, allow.manual.insert = TRUE)
 Characidae
 Characiformes
 Characidae
 Characiformes
 Characidae
 Characiformes
 Loricariidae
 Siluriformes
 Characidae
 Characiformes
 Cichlidae
 Cichliformes
 Crenuchidae
 Characiformes
 Gymnotidae
 Gymnotiformes
 Loricariidae
 Siluriformes
 Loricariidae
 Siluriformes
 Loricariidae
 Siluriformes
 Loricariidae
 Siluriformes
 Heptapteridae
 Siluriformes
 Characidae
 Characiformes
 Loricariidae
 Siluriformes
 Characidae
 Characiformes

## End(Not run)

FishPhyloMaker documentation built on Sept. 15, 2021, 9:09 a.m.