aggregateAbundances: Aggregate TreeCo Species Abundance Table per Group
In LimaRAF/TreeCo: An R Package to Manage TreeCo Database

aggregateAbundances

R Documentation

Aggregate TreeCo Species Abundance Table per Group

Description

by ordem or SiteCode

Usage

aggregateAbundances(
  tree.data = NULL,
  site.data = NULL,
  spp.group = "species.correct",
  site.group = "ordem",
  cols.to.sum = c("N", "AB", "DA", "DoA", "DR", "DoR", "F", "IVC", "IVI"),
  cols.to.paste = c("ordem", "refID", "SiteCode", "SubSite", "Name_submitted", "family",
    "genus", "epiteth", "infra.epiteth", "authorship", "species.correct", "taxon.rank",
    "family.original", "genus.original", "species.original", "author.original", "notes",
    "accession", "coletor", "number", "DetBy", "DetDate", "obs"),
  effort = "effort_ha"
)

Arguments

`tree.data`	a data frame with tree abundance data.
`site.data`	a data frame with site and plot metadata (optional).
`spp.group`	a column with the species names to be used for aggregation.
`site.group`	a column with the site or plot codes/names to be used for aggregation.
`cols.to.sum`	a vector with the names of the columns in 'tree.data' to be summed over species and groups (generally the numerical variables)
`cols.to.paste`	a vector with the names of the columns in 'tree.data' to be be pasted over species and groups (generally the categorical variables)
`effort`	the name of the columns in 'site.data' containg the effort of each inventory in hectares