Convert a data frame into a vegtable object.

Conversion of a data frame containing a cross table of abundance or cover of species in single plots.

This function coerces a data frame containing a vegetation cross table into a vegtable object. The input data frame x may include information on the layers or not.

Usage

df2vegtable(x, species, layer, ...)

# S4 method for class 'data.frame,numeric,numeric'
df2vegtable(x, species, layer, ...)

# S4 method for class 'data.frame,numeric,missing'
df2vegtable(x, species, layer, ...)

Arguments

x: A data frame formatted for a taxlist object.
species: Numeric or integer indicating the position of the column with species names.
layer: Numeric or integer indicating the position of the column with layers.
...: Further arguments passed from or to other methods.

Value

A vegtable object.

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## Creating data set 'dune_veg'
library(vegan)
#> Loading required package: permute
#> Loading required package: lattice
#> This is vegan 2.6-6.1

## Load data from vegan
data(dune)
data(dune.env)

## Conversion to vegtable
dune_veg <- data.frame(
  species = colnames(dune), t(dune),
  stringsAsFactors = FALSE, check.names = FALSE
)
dune_veg <- df2vegtable(dune_veg, species = 1)

summary(dune_veg)
#> ## Metadata 
#>    object size: 24.9 Kb 
#>    validity: TRUE 
#> 
#> ## Content 
#>    number of plots: 20 
#>    plots with records: 20 
#>    variables in header: 1 
#>    number of relations: 0 
#> 
#> ## Taxonomic List 
#>    taxon names: 30 
#>    taxon concepts: 30 
#>    validity: TRUE 
#> 

## Adding environmental variables
dune.env$ReleveID <- as.integer(rownames(dune.env))
header(dune_veg) <- dune.env

summary(dune_veg)
#> ## Metadata 
#>    object size: 28.9 Kb 
#>    validity: TRUE 
#> 
#> ## Content 
#>    number of plots: 20 
#>    plots with records: 20 
#>    variables in header: 6 
#>    number of relations: 0 
#> 
#> ## Taxonomic List 
#>    taxon names: 30 
#>    taxon concepts: 30 
#>    validity: TRUE 
#>