calcBMWP_CR: Calculate the Costa Rican BMWP biotic index for freshwater...

In robbriers/bioticCR: Calculation of Costa Rican BMWP Biotic Index

Description

Calculates the Costa Rican version of the BMWP freshwater invertebrate biotic index.

Usage

calcBMWP_CR(df, type = "num")

Arguments

df

A dataframe containing list of taxon names and their abundances in samples, along with sample identifiers. Default format is for taxon names to be in the first column and sample abundances in subsequent columns with identifers as column headers. See built-in almond dataset for an example. If data are in the transposed format i.e taxa as columns and samples as rows, the transposedata function can be used prior to calculation.

type

Indicates type of data being processed. Options are "num" for numeric data, "log" for integer log abundance categories (1-5) or "alpha" for alphabetic abundance categories (A-E). Default value is "num".

Value

A data frame consisting of columns of index values with samples in rows.

Examples

# calculate the Costa Rican version of the BMWP index for
# the built in 'almond' dataset
# 'type' does not have to specified as default is used
# ("num")

calcBMWP_CR(almond)

# example of processing data in alphabetic log abundance categories
# using the 'type' argument

# 'braidburn' dataset contains alphabetic log category data
# see ?braidburn for details

# calculate the Costa Rican BMWP index for this dataset

calcBMWP_CR(braidburn, "alpha")

# example of processing data in numeric log abundance categories
# using the 'type' argument

# 'greenburn' dataset contains numeric log category data
# see ?greenburn for details

# calculate the Costa Rican BMWP index for this dataset

calcBMWP_CR(greenburn, "log")

robbriers/bioticCR documentation built on May 29, 2019, 8:37 a.m.