getCWM: Obtain Community Weighted Means
In LimaRAF/TreeCo: An R Package to Manage TreeCo Database

getCWM

R Documentation

Obtain Community Weighted Means

Description

Calculate the Community Weighted Means (CWM), particularly for data in the TreeCo format.

Usage

getCWM(
  tree.data = NULL,
  trait.data = NULL,
  group = "ordem",
  spp.name = "Name_submitted",
  tax.rank = "taxon.rank",
  trait.list = c("wsg_gcm3", "MaxHeight_m", "SeedMass_g", "extinction", "endemism",
    "LeafArea", "LeafType", "dispersal.syndrome", "succesional.group",
    "ecological.group"),
  indets = c("unidentified"),
  rm.flora = TRUE,
  treeco.cwm = TRUE,
  reduce.cats = TRUE,
  habit = "habito",
  life.form = "life.form",
  ab.metric = "counts"
)

Arguments

`tree.data`	the data frame with tree abundance data.
`trait.data`	the data frame with tree species trait data.
`group`	vector with the the column that should be used to aggregate the data. Default to 'ordem'.
`spp.name`	the name of the columns containing the (morpho)species names. Default to the TreeCo column 'species.correct'.
`tax.rank`	the name of the columns containing the name taxonomic resolution. Default to the TreeCo column 'taxon.rank'.
`trait.list`	a vector with the names of the traits should be included in the calculations.
`indets`	a vector of characters containing the unidentified classes in ‘tax.rank'. Default to the TreeCo classes ’unidentified', 'family' and 'genus'.
`rm.flora`	should the records of (morpho)species not found within the main sampling but found in the floristics or natural regeneration of the same survey. Default to TRUE.
`treeco.cwm`	should the palms, ferns and/or shrubs be removed prior to the calculation of the CWM of wood density, potential height and seed mass? Default to TRUE.
`reduce.cats`	should the categories of dispersal and ecological groups be simplified previous to the analysis? Default to TRUE.
`habit`	the name of the columns containing the species habit information (i.e. 'tree', 'shrub', 'others')
`life.form`	the name of the columns containing the species life form information (i.e. 'woody_tree', 'woody_vines_and_subshrubs', 'palm', 'tree_fern', 'succulent_tree' or 'palmoids').
`ab.metric`	the abundance metric that should be used to weight the community-level trait means: 'counts' or 'biomass'. Default to 'counts'.

Details

The function .... TO BE FINISHED

If the argument 'treeco.cwm' is TRUE: - Information on species 'habit' and 'life.form' are necessary for filtering somes species out of the CWM from certain traits. - The CWM for each trait is calculated with a different set of species. For Wood Density, CWM excluded non woody species (e.g. palms and ferns). For Max. Height, CWM excludes shrubs (H and/or DBH typically <4m and 10 cm). Seed mass was calculated without tree ferns."

If the argument 'treeco.cwm' is TRUE: - The function reduces the dispersal syndrome to abiotic (anemochoric and autochoric) and zoochoric; hydrochory is disregarded