indetSpecies: Number of Unidentifications per Survey

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

Number of Unidentifications per Survey

Description

Calculate the number of individuals and species that are not identified at different taxonomic levels (e.g. family, genus).

Usage

indetSpecies(
  tree.data = NULL,
  group = "ordem",
  spp.name = "species.correct",
  tax.rank = "taxon.rank",
  indets = c("unidentified", "family", "genus"),
  not.indets = c("species", "variety", "subspecies"),
  rm.flora = TRUE
)

Arguments

tree.data	the data frame with tree abundance 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'.
tax.rank	the name of the columns containing the name taxonomic resolution. Default to the TreeCo column 'taxon.rank'.
indets	a vector of characters containing the unidentified classes in ‘tax.rank'. Default to the TreeCo classes ’unidentified', 'family' and 'genus'.
not.indets	a vector of characters containing the identified classes in ‘tax.rank'. Default to the TreeCo classes ’species', 'variety' and 'subspecies'.
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 be included? Default to TRUE.

Details

The function returns the percentage of individuals and species that remained unidentified until a certain taxonomic rank, which is provided by the user. *The order of the vector provided in 'indets' must be from the lowest to the highest resolution within the unidentification levels*.

The taxonomic ranks include in TreeCo are, in descreasing order of taxonomic resolution: 'variety'/'subspecies', 'species', 'genus', 'family', 'unidentified', 'dead' and 'correction'. The class 'unidentified' include living trees for which not even a family name was assigned. The class 'correction' is restricted to the Minas Gerais state inventory data. This class enter the computations of the total number of individuals in the sample but not in the totoal number of taxa.

The proportions are cumulative and they respect the order of taxonomic levels provided by the user. By default, this means that proportions at genus level include the identifications at the genus, family and unidentified classes, proportions at family level include the identifications at family and unidentified resolutions.

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, suing the argument 'rm.flora'.

Value

a data frame with number of individuals (N) and of taxa (S) for the each group and the percentage of N and S unidentified at different taxonomic resolutions.

Author(s)

Renato A. F. de Lima

See Also

traitCover

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