Nothing
## ---- eval=FALSE---------------------------------------------------------
# install.packages("biotic")
## ---- eval=FALSE---------------------------------------------------------
# install.packages("devtools")
## ---- eval=FALSE---------------------------------------------------------
# devtools::install_github('robbriers/biotic')
## ------------------------------------------------------------------------
# load library
library(biotic)
# show the format of the built-in almond dataset
head(almond)
## ------------------------------------------------------------------------
# calculate the BMWP index for the River Almond dataset
# 'index' and 'type' do not have to specified as defaults are used
# ("BMWP" and "num")
calcindex(almond)
# calculate the PSI index for the almond samples
# 'type' argument again not needed as the data are numeric abundances
calcindex(almond, "PSI")
## ------------------------------------------------------------------------
# example of processing data in alphabetic log abundance categories
# using the 'type' argument
# 'braidburn' dataset contains alphabetic log category data
# see ?braidburn for details
# calculate the Whalley revised BMWP index (including N-taxa and ASPT)
calcindex(braidburn, "Whalley", "alpha")
# example of processing data in numeric log abundance categories
# using the 'type' argument
# 'greenburn' dataset contains numeric log category data
# see ?greenburn for details
# calculate the LIFE index for this dataset
calcindex(greenburn, "LIFE", "log")
## ------------------------------------------------------------------------
# calculate the BMWP index for almond samples
calcBMWP(almond)
# calculate the AWIC index for almond samples
calcAWIC(almond)
# calculate the WHPT abundance-weighted index for Green Burn samples
# (numeric log abundance categories)
calcWHPT_AB(greenburn, "log")
# calculate LIFE index for Braid Burn samples (alphabetic log categories)
calcLIFE(braidburn, type="alpha")
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