# 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)

# install the devtools package and then
library(devtools)

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

# install the devtools package and then
library(devtools)

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

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")

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

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