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

knitr::opts_chunk$set(echo = TRUE)

bioticCR

Introduction

The bioticCR package calculates the Costa Rican version of the BMWP freshwater invertebrate biotic index.

Installation

In order to install the development version, you need to first install the 'devtools' package.

install.packages("devtools")

Then use the 'install_github' function within this package to load the development version from GitHub.

devtools::install_github('robbriers/bioticCR')

Input format

The data are assumed to be stored in a dataframe with the first column containing a list of taxon names and subsequent columns containing sample headers and individual taxon abundances. Absences should be recorded as 'NA' rather than zero (so NA or blank cells in a csv file imported via read.csv), although the calculations will work with zero abundances as well, but this is not recommended. In addition to actual abundances, log categories (1-5) or alphabetic log categories (A-E) can also be processed, through specification of the data type (see below).

If you have data that are stored in a 'tidy' format sensu Wickham, then these can be converted to the correct format for this package using the reshape2 package, or the tidyr package prior to calculation.

An example of the default layout of data can be seen by accessing the built-in 'almond' dataset.

# load library
library(bioticCR)

# show the format of the built-in almond dataset
head(almond)

Functions

There is one main function 'calcBMWP_CR'. This calculates the value of the Costa Rican version of BMWP for the sample data. The first argument to the function is the object containing the data. A second (optional) argument relates to the format of the dataset.The options are "num" for numeric abundances, "log" for integer log categories (1-5) or "alpha" for alphabetic log abundance categories (A-E). If the data are in the default format (actual integer abundances) then it can be omitted. The use of these is best illustrated through examples using the built-in datasets ('almond', 'braidburn' and 'greenburn').

# calculate the Costa Rican BMWP index for the River Almond dataset
# 'type' does not have to specified as the default is used
# ("num")

calcBMWP_CR(almond)

To process data in either integer or alphabetic log categories, the 'type' argument should specify either "log" or "alpha". An example is shown below.

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

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

calcBMWP_CR(braidburn, "alpha")

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