traitCover: Assess Trait Species Coverage

In LimaRAF/TreeCo: An R Package to Manage TreeCo Database

Assess Trait Species Coverage

Description

Calculate the number of individuals and taxa per survey that have any information available for selected species traits.

Usage

traitCover(
  tree.data = NULL,
  trait.data = NULL,
  group = "ordem",
  spp.name = "Name_submitted",
  trait.list = c("wsg_gcm3", "MaxHeight_m", "SeedMass_g", "extinction", "endemism",
    "LeafArea", "LeafType", "dispersal.syndrome", "ecological.group"),
  rm.flora = TRUE,
  trait.miss = 3
)

Arguments

tree.data	the data frame with tree abundance data in the TreeCo format
trait.data	the data frame with edited and averaged trait data in the TreeCo format
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'.
trait.list	a vector with the names of the traits should be included in the calculations.
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.
trait.miss	cutoff of number of missing traits

Details

For each selected group, the function calculates the percentage of individuals and species that have information for all the traits listed in 'trait.list'. This can be used as a measure of the trait coverage within each group.

The function also returns a metric of how complete the trait information is for each group (i.e. survey). This metric is obtained by assigned for each taxa the number of missing traits, which goes from zero (all traits are available) to the maximum number of traits listed in 'trait.list'. These number of missing traits are standardized by the maximum number of traits, so they vary between 0 and 1. Finally, these values are weighted by the number of individuals/taxa of each level of missing traits. That is, this metric is the weighted average of the number of missing traits per taxa. The closer to zero, more complete the taxa are in terms of the traits available.

Some TreeCo surveys contain extra species lists from outside the sampling plots/transects. These lists are often obtaining from floristic surveys in the same sites where the sampling was conducted. Other surveys stored in TreeCo present the records for species present in the adult and natural regeneration components of the forest. If a species is present in the floristic survey but not in the plots, the species enters the database with an abundance value equal to zero. Similarly, if a species is present in the natural regeneration but not in the adult component, the species enters the database with an abundance between zero and one. This records are excluded by default, using the argument 'rm.flora'.

Value

a data frame with number of individuals (N) and taxa (S) for the each group and the percentage of N and S with all selected traits (columns 'N.traits' and 'S.traits'), as well as a metric of the completeness of the traits within each group (columns 'miss.traits.N' and 'miss.traits.S').

Author(s)

Renato A. F. de Lima

See Also

indetSpecies

LimaRAF/TreeCo documentation built on Sept. 25, 2024, 12:41 p.m.