README.md

In alexology/biomonitoR: biomonitoring indices and metrics

biomonitoR

A package for managing taxonomic and functional information and for calculating indices for biomonitoring of running waters, with a focus on the macroinvertebrate community.

Installation

# install the devtools package and then
# The devtools package requires and updated version of Rtools.
library(devtools)

install_github("alexology/biomonitoR", ref = "main", build_vignettes = TRUE)

To install the newest version:

# install the devtools package and then
library(devtools)

install_github("alexology/biomonitoR", ref = "develop", build_vignettes = TRUE)

To install old and deprecated version:

# install the devtools package and then
library(devtools)

install_github("alexology/biomonitoR", ref = "old_version")

Basic usage

library(biomonitoR)

# load example dataset. biomonitoR package needs a dataset with taxa names in the first column called "Taxa" and samples on the columns. Take a look to macro_ex for an example:

data(macro_ex)

# Prepare data for the analysis.

data_bio <- as_biomonitor(macro_ex)
data_agr <- aggregate_taxa(data_bio)

# calculate genus and family richness
richness(data_agr, tax_lev = "Genus")
richness(data_agr, tax_lev = "Family")

# calculate shannon index
shannon(data_agr, tax_lev = "Family")

# calculate italian bmwp and aspt
bmwp(data_agr, method = "ita", agg = TRUE)
aspt(data_agr, method = "ita", agg = TRUE)

# calculate iberian bmwp and aspt
bmwp(data_agr, method = "spa")
aspt(data_agr, method = "spa")

Vignettes

To have some more information on how to use biomonitoR take a look to the vignettes:

# import data in biomonitoR
vignette("introduction", package = "biomonitoR")

# trait-based analysis
vignette("functional", package = "biomonitoR")

Acknowledgments

This package is based upon work from COST Action CA15113 (SMIRES, Science and Management of Intermittent Rivers and Ephemeral Streams,www.smires.eu), supported by COST (European Cooperation in Science and Technology).

References

Reference database is from freshwaterecology.info.

Schmidt-Kloiber, A. & Hering D. (2015): www.freshwaterecology.info - an online tool that unifies, standardises and codifies more than 20,000 European freshwater organisms and their ecological preferences. Ecological Indicators 53: 271-282. doi: 10.1016/j.ecolind.2015.02.007

alexology/biomonitoR documentation built on April 7, 2024, 10:15 a.m.