Applying taxlist to species lists on diversity records

Miguel Alvarez

2018-01-05

1. Getting started

The package taxlist aims to implement an object class and functions (methods) for handling taxonomic data i R. The homonymous object class taxlist can be further linked to biodiversity records (e.g. for observations in vegetation plots).

The taxlist package is developed on the repository GitHub (https://github.com/kamapu/taxlist) and can be installed in your R-session using the package devtools:

library(devtools)
install_github("kamapu/taxlist", build_vignettes=TRUE)

Since this package is already available in the Comprehensive R Archive Network (CRAN), it is also possible to install it using the function install.packages:

install.packages("taxlist", dependencies=TRUE)

Of course, you have to load taxlist into your R-session.

library(taxlist)

For accessing to this vignette, use following command:

vignette("taxlist-intro")

2. Extracting a species list from a vegetation table

2.1 Example data

One of the main tasks of taxlist is to structure taxonomic information for a further linkage to biodiversity records. This structure have to be on the one side consistent with taxonomic issues (e.g. synonyms, hierarchies, etc.), on the other side have to be flexible for containing different depth of information availability (from plain species lists to hierarchical structures).

In this guide, we will work with a species list from phytosociological relevés collected at the borderline between the Democratic Republic of the Congo and Rwanda (Mullenders 1953 Vegetatio 4(2): 73–83).

The digitized data can be loaded by following command:

The data is formatted as data.frame in R, including the names of the species in the first column:

##                 TaxonName 3094 3093 3092 3095 3096 3097 3098
## 1   Eragrostis tenuifolia    + <NA> <NA> <NA> <NA> <NA> <NA>
## 2        Cyperus sublimis <NA>    + <NA> <NA> <NA> <NA> <NA>
## 3    Digitaria abyssinica    +    1    2    2    2    3    1
## 4 Hyparrhenia filipendula <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 5    Erigeron floribundus    +    1 <NA> <NA> <NA> <NA> <NA>
## 6            Aerva lanata    +    1 <NA> <NA> <NA> <NA> <NA>

2.2 From plain list to taxlist

As already mentioned, the first column in the cross table contains the names of the species occurring in the observed plots. Thus, we can use this character vector to construct a taxlist object. This can be achieved through the function df2taxlist.

## object size: 8.5 Kb 
## validation of 'taxlist' object: TRUE 
## 
## number of names: 35 
## number of concepts: 35 
## trait entries: 0 
## number of trait variables: 0 
## reference entries: 0

Note that the function summary provides a quick overview in the content of the resulting object. This function can be also applied to a specific taxon:

## ------------------------------ 
## concept ID: 5 
## view ID: none 
## level: none 
## parent: none 
## 
## # accepted name: 
## 5 Erigeron floribundus  
## ------------------------------

2.3 Resolving taxonomic names with taxize

One of the main concerns is to resolve nomenclatorial issues, especially when working with historical data or combining data from different sources. For this purpose, taxlist implements a method for the function tnrs (package taxize):

## object size: 8.5 Kb 
## validation of 'taxlist' object: TRUE 
## 
## number of names: 35 
## number of concepts: 35 
## trait entries: 0 
## number of trait variables: 0 
## reference entries: 0
## object size: 14.6 Kb 
## validation of 'taxlist' object: TRUE 
## 
## number of names: 45 
## number of concepts: 35 
## trait entries: 0 
## number of trait variables: 0 
## reference entries: 0

While after this procedure, the number of taxa remained as 35, the number of taxon names increased, indicating that some of the names in the original source are currently considered as synonyms. This is for example the case of Erigeron floribundus:

## ------------------------------ 
## concept ID: 5 
## view ID: none 
## level: none 
## parent: none 
## 
## # accepted name: 
## 36 Conyza sumatrensis var. leiotheca (S.F. Blake) Pruski & G. Sancho 
## 
## # synonyms (1): 
## 5 Erigeron floribundus  
## ------------------------------

At this point it is important to mention that while most resolvers are offering ways to replace names by accepted ones, in taxlist objects both, accepted names and synonyms are preserved. Only typographical errors and names of authors will be changed in the object. This is important in the compilation of diversity records (i.e. vegetation plot databases), where the stored data have to be faithful to the source. Thus data connected to a taxon name can be automatically assigned to the correspondent taxon concept without to modify the record’s entry. An overview to the accepted names and possible changes can be displayed as follows:

##   TaxonConceptID TaxonUsageID                         TaxonName
## 1              1            1             Eragrostis tenuifolia
## 2              2            2                  Cyperus sublimis
## 3              3            3              Digitaria abyssinica
## 4              4            4           Hyparrhenia filipendula
## 5              5           36 Conyza sumatrensis var. leiotheca
##                        AuthorName
## 1    (A. Rich.) Hochst. ex Steud.
## 2             (C.B. Clarke) Dandy
## 3     (Hochst. ex A. Rich.) Stapf
## 4                 (Hochst.) Stapf
## 5 (S.F. Blake) Pruski & G. Sancho

3. Built-in data set

3.1 Easplist

The installation of taxlist includes the data Easplist, which is formatted as a taxlist object. This data is a subset of the species list used by the database SWEA-Dataveg (GIVD ID AF-006):

## object size: 739.8 Kb 
## validation of 'taxlist' object: TRUE 
## 
## number of names: 5337 
## number of concepts: 3935 
## trait entries: 51 
## number of trait variables: 1 
## reference entries: 2 
## 
## concepts with parents: 3745 
## concepts with children: 1214 
## 
## hierarchical levels: form < variety < subspecies < species < genus < family 
## number of concepts in level form: 1
## number of concepts in level variety: 110
## number of concepts in level subspecies: 81
## number of concepts in level species: 2528
## number of concepts in level genus: 1025
## number of concepts in level family: 189

3.2 Access to slots

The common ways to access to the content of slots in S4 objects are either using the function slot(object, name) or the symbol @ (i.e. object@name). Additional functions, which are specific for taxlist objects are taxon_names, taxon_relations, taxon_traits and taxon_views (see the help documentation).

Additionally, it is possible to use the methods $ and [ , the first for access to information in the slot taxonTraits, while the second can be also used for other slots in the object.

## Ch  H Hy  T 
##  5  7  3 36

3.3 Subsets

Methods for the function subset are also implemented in this package. Such subsets usually apply pattern matching (for character vectors) or logical operations and are analogous to query building in relational databases. The subset method can be apply to any slot by setting the value of the argument slot.

Or the very same results:

Similarly, you can look for a specific name.

3.4 Hierarchical structure

Objects belonging to the class taxlist can optionally content parent-child relationships and taxonomic levels. Such information is also included in the data Easplist, as shown in the summary output.

## object size: 739.8 Kb 
## validation of 'taxlist' object: TRUE 
## 
## number of names: 5337 
## number of concepts: 3935 
## trait entries: 51 
## number of trait variables: 1 
## reference entries: 2 
## 
## concepts with parents: 3745 
## concepts with children: 1214 
## 
## hierarchical levels: form < variety < subspecies < species < genus < family 
## number of concepts in level form: 1
## number of concepts in level variety: 110
## number of concepts in level subspecies: 81
## number of concepts in level species: 2528
## number of concepts in level genus: 1025
## number of concepts in level family: 189

Note that such information can get lost once applied subset, since the respective parents or children from the original data set are not anymore in the subset. May you like to recover parents and children, you can use the functions get_paretns or get_children, respectively.

## ------------------------------ 
## concept ID: 206 
## view ID: 1 
## level: species 
## parent: none 
## 
## # accepted name: 
## 206 Cyperus papyrus L. 
## 
## # synonyms (2): 
## 52612 Cyperus papyrus subsp. antiquorum (Willd.) Chiov. 
## 52613 Cyperus papyrus subsp. nyassicus Chiov. 
## ------------------------------
## ------------------------------ 
## concept ID: 206 
## view ID: 1 
## level: species 
## parent: 53660 
## 
## # accepted name: 
## 206 Cyperus papyrus L. 
## 
## # synonyms (2): 
## 52612 Cyperus papyrus subsp. antiquorum (Willd.) Chiov. 
## 52613 Cyperus papyrus subsp. nyassicus Chiov. 
## ------------------------------ 
## concept ID: 53660 
## view ID: 2 
## level: genus 
## parent: 54607 
## 
## # accepted name: 
## 53660 Cyperus NA 
## ------------------------------ 
## concept ID: 54607 
## view ID: 2 
## level: family 
## parent: none 
## 
## # accepted name: 
## 54607 Cyperaceae NA 
## ------------------------------

4. Applying taxlist to syntaxonomic schemes

4.1 Example of a phytosociological classification

To illustrate the flexibility of the taxlist objects, the next example will handle a syntaxonomical scheme. As example it will be used a scheme proposed by the author for aquatic and semi-aquatic vegetation in Tanzania (Alvarez 2017 Phytocoenologia in review). The scheme includes 10 associations classified into 4 classes: