In SCAR/biotaxa: Visualising the growth and prediction of taxonomic diversity and identifying taxonomic incompleteness and imprecision

knitr::opts_chunk$set(echo = TRUE)

This is to demonstrate the use of biotaxa to explore whether there is a scale-free power law in taxonomic richnesses.

library(biotaxa)
Arthropoda <- subset(data_m, Phyla == "Arthropoda")
head(Arthropoda)

Find all of the classes of Mollusca

classes_msa <- unique(Arthropoda$Classes)

remove empty data

classes_msa <- as.character(classes_msa[classes_msa != ""])
classes_msa

Find the lower taxa (order) richness of each class in Mollusca

orders_distiller <- frequencyrank(classes_msa[1], "Order")[1]
orders_distiller <- orders_distiller[orders_distiller != ""]

lower_taxa_richness <- function(taxa, rank) {
  dim(frequencyrank(taxa, rank))[1]
}

tbl <- data.frame(mapply(lower_taxa_richness, orders_distiller, "Genus"))

Anton suggests to look at Amphipoda

SCAR/biotaxa documentation built on May 20, 2019, 3:05 p.m.