species_diversity: Get the species diversity indexes

Description Usage Arguments Value Author(s) References Examples

View source: R/species_diversity.R

Description

Calculate the diversity of species for the following indexes: Shannon, Simpson, Equitability, Pielou and Jentsch.

Usage

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species_diversity(df, species, plot = NA, NI_label = "", index = "all")

Arguments

df

A data frame.

species

Quoted name of the scientific names variable, or any variable used to differentiate the different species found in data. If supplied, will be used to classify the species in the diameter data.

plot

Optional parameter. Quoted name of the plot variable. used to differentiate the plots, and calculate the indexes by plot, or other subdivision variable.

NI_label

Label used for Species not identified. This parameter works along with species. The level supplied here will not be considered in the classification. Default "".

index

Character value for the desired index to be used. Can be either "H" for Shannon's diversity index, "S" for Total number of species in the community, "Hmax" for the maximum equitability, "J" for Pielou evenness, "QM" for the mixture coefficient of Jentsch, or "all", to get all indexes. Default: "all".

Value

a data frame with the indexes, or a numeric value of the desired index specified in the index argument.

Author(s)

Eric Bastos Gorgens e.gorgens@gmail.com

References

Souza, A. L. and Soares, C. P. B. (2013) Florestas Nativas: estrutura, dinamica e manejo. Vicosa: UFV.

Examples

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library(forestmangr)
data("exfm20")
head(exfm20)

# By default, the function returns all indexes:
species_diversity(exfm20, "scientific.name")

# It's possible to use a subdivision variable, like plot, to get
# the indexes for each subdivision:
species_diversity(exfm20, "scientific.name", "transect") 

# To only get one specific index, use the index argument:
species_diversity(exfm20, "scientific.name", index = "H")
species_diversity(exfm20, "scientific.name", index = "S")
species_diversity(exfm20, "scientific.name", index = "Hmax")
species_diversity(exfm20, "scientific.name", index = "J")

forestmangr documentation built on Aug. 16, 2021, 5:08 p.m.