Vegetation in East African Wetlands

Vegetation plots collected in several East African countries, including some species characteristics.

Description

Dataset of 325 vegetation plots combining original samples from the field and data collected from phytosociological publications. This data set also contains information on life forms for the recorded species.

The data was published by Behn et al. (2022) and uploaded to Zenodo as .

Usage

# Load the data
wetlands <- readRDS("wetlands.rds")

The data set is a list with four elements:

• wetlands$env is a data frame with plot attributes
• wetlands$spp is a data frame with attributes of recorded species
• wetlands$obs is the record of species in the plots structured as database list
• wetlands$cross is the vegetation matrix of plots by species

names(wetlands)

[1] "env"   "spp"   "obs"   "cross"

head(wetlands$env)
head(wetlands$spp)
head(wetlands$obs)

There is also an alternative data set formatted by the package vegtable:

library(vegtable)
wetlands <- readRDS("wetlands-vegtable.rds")

wetlands

## Metadata 
   name: East African Wetlands
   authors: K. Behn and M. Alvarez
   year: 2021
   object size: 419.3 Kb 
   validity: TRUE 

## Content 
   number of plots: 325 
   plots with records: 325 
   variables in header: 12 
   number of relations: 3 

## Taxonomic List 
   taxon names: 1354 
   taxon concepts: 601 
   validity: TRUE 

This format allows complex data processing with shorter code. The content of the data is included in four slots:

• wetlands@species including the taxonomic list formatted by the package taxlist. This object support taxonomy, use of synonyms, species attributes and bibliographic references.
• wetlands@header which is a data frame with plot (observation) attributes.
• wetlands@relations includes data frames with information on classes of categorical variables in header.
• wetlands@samples with the records of species in plots.

An overview of the associated taxonomic list can be retrieved by following command.

wetlands@species

object size: 244.6 Kb 
validation of 'taxlist' object: TRUE 

number of taxon usage names: 1354 
number of taxon concepts: 601 
trait entries: 320 
number of trait variables: 4 
taxon views: 6 

concepts with parents: 599 
concepts with children: 266 

hierarchical levels: form < variety < subspecies < species < genus < family < phylum 
number of concepts in level form: 0
number of concepts in level variety: 0
number of concepts in level subspecies: 0
number of concepts in level species: 335
number of concepts in level genus: 202
number of concepts in level family: 62
number of concepts in level phylum: 2

In this case, the taxonomic list includes parent-child relationships and synonyms. We can check for the case of Cyperus papyrus L..

summary(wetlands@species, "Cyperus papyrus")

------------------------------ 
concept ID: 206 
view ID: 1 
level: species 
parent: 54853 Cyperus L. 

# accepted name: 
202469 Cyperus papyrus L. 

# synonyms (2): 
205001 Cyperus papyrus ssp. antiquorum (Willd.) Chiov. 
205002 Cyperus papyrus ssp. nyassicus Chiov. 
------------------------------

indented_list(wetlands@species, "Cyperus papyrus")

Magnoliophyta NA
 Cyperaceae Juss.
  Cyperus L.
   Cyperus papyrus L.