knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
In this article we will show how to find for species that must be added to the mega-tree, before running the FishPhyloMaker
function. When there are few species that must be added, the interactive insertion process is ease to follow. However, when we are dealing with big data bases with many species, it is desirable that before to initiate the insertion process with FishPhyloMaker
function we know which species must be inserted and at which position in phylogenetic tree. So, in order to facilitate this process the function whichFishAdd
take all species informed by the user and provide a classification of each level in which the species be inserted when running FishPhyloMaker
function. The code of classification follows similar classification from that presented in the insertion process:
First, lets read {FishPhyloMaker}
package and the data containing more than 650 fish species with occurrence in the Neotropical region.
library(FishPhyloMaker) data("fish_SAmerica")
Then, we will check for the names of the species in the data base through the function FishTaxaMaker
, and inform manually the Family and the Order of the species that were not find in Fishbase. This procedure is better explained in other articles
taxon_data <- FishTaxaMaker(data = fish_SAmerica) Loricariidae Siluriformes Anostomidae Characiformes Anostomidae Characiformes Anostomidae Characiformes Serrasalmidae Characiformes Auchenipteridae Siluriformes Auchenipteridae Siluriformes Auchenipteridae Siluriformes
taxon_data contain the taxonomic information for all species, and can be used in whichFishAdd
function to perform the classification of each species.
class_fish <- whichFishAdd(data = taxon_data)
class_fish is a data frame that contain in insertion column an indication of which level each species must be inserted (or if the species are already on tree). This data can be used previous than FishPhyloMaker
to find for phylogenetic position of the absent species.
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.