calculateFishIBI: Calculates Fish IBI

In jasonelaw/nrsa: Calculate metrics for NRSA protocol data.

Description

Calculates a fish IBI based on Hughes et al "A process for developing and evaluating indices of fish assemblage integrity"

Usage

calculateFishIBI(site, order, species, length, anomaly,
  join.traits.by = "common_name", return.subindices = F,
  return.raw.metrics = F, ODFW.version = F)

Arguments

site	vector of site-visit identifiers
order	a numeric vector; stream order correspoding to the location
species	a vector of taxa names; must correspond to name field returned by fishTraits
length	a vector of fish lengths in centimeters
anomaly	a logical vector, TRUE if an anomaly was observed on the fish
join.traits.by	which field from the data.frame returned by fishTraits should be used to match the species
return.subindices	logical, should the subindices be returned or just the IBI?
return.raw.metrics	should raw metrics be returned rather than IBI values?

Details

The fishTraits (unexported, use nrsa:::fishTraits to view code) function returns a data.frame with trait data for the IBI.

jasonelaw/nrsa documentation built on Nov. 8, 2019, 11:34 a.m.