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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 
#>