prepTraits: Prepare TreeCo Species Trait Table
In LimaRAF/TreeCo: An R Package to Manage TreeCo Database

prepTraits

R Documentation

Prepare TreeCo Species Trait Table

Description

Clean trait records, get derived information and average the species trait information at family, genus, species and infraspecific levels.

Usage

prepTraits(
  trait.data = NULL,
  spp.name = "Name_submitted",
  tax.rank = "taxon.rank",
  trait.status = "status",
  trait.list = c(WSG = "wsg_gcm3", H = "MaxHeight_m", DBH = "MaxDbh_cm", MinLL =
    "MinLeafLength_cm", MinLW = "MinLeafWidth_cm", MaxLL = "MaxLeafLength_cm", MaxLW =
    "MaxLeafWidth_cm", LA = "LeafArea", SM = "SeedMass_g", EXT = "extinction", END =
    "endemism", LA = "LeafArea", LT = "LeafType", DS = "dispersal.syndrome", EG =
    "ecological.group"),
  rm.dead = TRUE,
  rm.indet = TRUE,
  rm.dup = TRUE
)

Arguments

`trait.data`	the data frame with the raw TreeCo trait table.
`spp.name`	character. The column name containing the species names. Defaults to "Name_submitted"
`tax.rank`	= "taxon.rank"
`trait.status`	character. The column name containing the entry status. Defaults to "status"
`trait.list`	a named vector with the column names of the traits should be included in the calculations.
`rm.dead`	logical. Should dead individuals be removed? Defaults to TRUE
`rm.indet`	logical. Should unidentified individuals be removed? Defaults to TRUE
`rm.dup`	logical. Should the duplicated or possibly duplicated entries (of wood density) be removed? Defaults to TRUE

Details

To be included

Value

a named list containing the edited and averaged trait data at the different taxonomic levels and the notes of the operations applied to obtain the new data frame.