README.md

README-MMIcalc

#> Last Update: 2017-03-08 17:17:47

Calculation of metrics for multi-metric index (MMI) for benthic macroinvertebrates or fish. Inputs are 3 files (master taxa list (with phylogeny, autecological information, and any operation taxonomic units (OTUs), stations (with location and any regional information), and a taxa samples file (with StationID, SampleID, TaxonID, Count, and Exclude code).

Installation

library(devtools) #install if needed

install_github("leppott/MMIcalc")

Purpose

Generate metric values for each provided sample. Then calculate metric scores and combine into index score. Scoring is based on a user defined table of IndexName, IndexRegion, MetricName, Direction in response to increasing perturbation, ScoringRegime (1/3/5 or 0:100), and High and Low values.

Status

Development stage. File input is assumed to already be aggregated. Benthos and Fish are working. Algae is a placeholder. Not all metrics are included. By default all metrics are calculated and if user doesn't specify metric names then all will be returned.

Usage



leppott/MMIcalc documentation built on May 21, 2019, 5:10 a.m.