prepAbundances: Prepare TreeCo Species Abundance Table

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

Prepare TreeCo Species Abundance Table

Description

To be included

Usage

prepAbundances(
  tree.data = NULL,
  spp.name = "species.correct",
  site.name = "SiteCode",
  plot.id = "ordem",
  record.id = "RecordID",
  tax.rank = "taxon.rank",
  N.name = "N",
  AB.name = "AB",
  obs.name = "obs",
  linhas = NULL,
  rm.sites = NULL,
  rm.plots = NULL,
  rm.tax = c("liana", "bamboo", "herb", "exclude"),
  rm.dead = TRUE,
  rm.cf = TRUE,
  rm.infra = TRUE,
  replace.synonym = TRUE,
  rm.spp = NULL,
  rm.extra = TRUE,
  minN = 1
)

Arguments

tree.data	the data frame with tree abundance data.
spp.name	= "species.correct"
site.name	= "SiteCode"
plot.id	= "ordem"
record.id	= "RecordID"
tax.rank	= "taxon.rank"
N.name	= "N"
AB.name	= "AB"
obs.name	= "obs"
linhas	= NULL
rm.sites	= NULL
rm.plots	= NULL
rm.tax	= c("liana","bamboo","herb","exclude")
rm.dead	logical. Should dead individuals be removed? Defaults to TRUE
rm.cf	= FALSE
rm.infra	= FALSE
replace.synonym	= FALSE
rm.spp	character. A list of species names to be removed from the abundance data.
rm.extra	logical. Should the additional abundance data for size cutoffs different than the TreeCo preffered cutoff (e.g. DAP>3.2cm, DAS>3.2 inteade of DAP>5cm) etc. be removed? Defaults to TRUE.
minN	= 1

Details

User needs to choose the operations he wants to execute over the original species abundance dataset

Value

a named list containing new data frame and the notes of the operations selected and applied to obtain the new data frame.

Author(s)

Renato A. F. de Lima

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