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A package for calculating indices for biomonitoring of running waters with a focus on macroinvertebrate community. Still in development.
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README.md

biomonitoR

A package for calculating indices for biomonitoring of running water with a focus on macroinvertebrate community. Still in development. See www.biomonitor.it for tips.

Installation

# install the devtools package and then
library(devtools)

install_github("alexology/biomonitoR")

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(macro_ex)
data.bio <- asBiomonitor(macro_ex)
data.agR <- aggregatoR(data.bio)

# calculate genus and family richness
richness(data.agR, "Genus")
famNumb(data.agR, "Family")

# calculate shannon index
shannon(data.agR, taxLev = "Family")

# calculate italian bmwp and aspt
bmwp(data.agR, method="ita_agg")
aspt(data.agR, method="ita_agg")

# calculate iberian bmwp and aspt
bmwp(data.agR, method="spa")
aspt(data.agR, method="spa")

To do list

  1. Check and fill missing data in reference taxa list;
  2. Update taxonomy of the reference datasets (e.g. those for the calculation of BMWP, LIFE, etc.) according to the freshwaterecology.info list;
  3. Implement other indices (e.g. metrics of I2M2, PSI, SPEAR, etc.);
  4. Implement combTaxa, a function to combine taxa of a particular taxonomic level in order to find the best combination of taxa that fit with a target environmental variable;
  5. Improve help;
  6. Test biomonitoR extensively.

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

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