In PaulESantos/diversity.tool: Tools for biodiversity data manipulation

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  message = FALSE
)
library(tidyverse)
library(diversity.tool)

diversity.tool

The goal of diversity.tool is to ...

Installation

You can install the development version from GitHub with:

# install.packages("pak")
pak::pkg_install("PaulESantos/diversity.tool")

Example

This is a basic example which shows you how to solve a common problem:

• Transform community matrix to tibble:

library(diversity.tool)
library(vegan)
data("dune")
dune_tbl <- dune |> comm_to_tbl()
dune_tbl

• Or build a community matrix from a tibble:

dune_comm <- dune_tbl |> 
  tbl_to_comm(site, species, abundance)
dune_comm[1:6, 1:6]

• IVI index

data("bci")

bci |> 
  ivi_index(sub_plot, species, area_basal)

• Rank-abundance calculation:

• All sample units as one community

dune |> 
  rankabund()

• Each sample units as a different community

dune |> 
  rankabund(group = "site")

+Rank-abundance plot

dune |> 
  rankabund_plot()

• Transform a dist matrix to tibble:

dune_dist <- vegdist(dune[1:10, 1:10])

dune_dist


dune_dist_tbl <- diversity.tool::as_distbl(dune_dist)

dune_dist_tbl

• Transform to long format:

dune_dist_tbl |> 
  long_distbl()

Citation

To cite the ppendemic package, please use:

citation("diversity.tool")

PaulESantos/diversity.tool documentation built on July 29, 2022, 8:20 a.m.