Taxonlists overview

The function get_taxonlijsten_lists() queries D0156_00_Taxonlijsten and gives an overview of all the taxonlists and taxonlist versions available in the database. Only the latest version is shown (unless specified otherwise).

The following examples can be used as base to continue selecting the data you require.

Get the most recent version of the ‘Rode lijst van de Dagvlinders’:

rl_dagvlinders <- get_taxonlijsten_lists(con,
                              list = "%rode%dagvlinders%",
                              collect = TRUE
                           )

rl_dagvlinders
#> # A tibble: 1 × 9
#>   TaxonlijstType TaxonlijstCode Taxonlijst  PublicatieJaar Version ReferentieURL
#>   <chr>          <chr>          <chr>                <int> <chr>   <chr>        
#> 1 RL             <NA>           Rode lijst…           2021 latest  #https://pur…
#> # ℹ 3 more variables: Criteria <chr>, Validering <chr>, Vaststelling <chr>

Get all recent versions of red lists. This time we will not use collect = TRUE, which will return a lazy query:

rodelijst_recent <- get_taxonlijsten_lists(con,
                              list = "%rode lijst%"
                           )

Get all (most recent and older) taxonlist versions in the database:

listversions_all <- get_taxonlijsten_lists(con,
                              version = "all"
                           )

Red lists need to be validated (= compliant with IUCN criteria) and authorized by the minister. Get the status of red lists:

rodelijst_status <- get_taxonlijsten_lists(con,
                              list = "%rode lijst%",
                              collect = TRUE
                           )  %>%
select("Taxonlijst", "PublicatieJaar", "Criteria", "Validering",
       "Vaststelling")

rodelijst_status
#> # A tibble: 26 × 5
#>    Taxonlijst                    PublicatieJaar Criteria Validering Vaststelling
#>    <chr>                                  <int> <chr>    <chr>      <chr>       
#>  1 Rode lijst van de Amfibieën             2013 <NA>     <NA>       <NA>        
#>  2 Rode lijst van de Bladmossen            2017 IUCN     Gevalidee… Vastgesteld 
#>  3 Rode lijst van de Broedvogels           2016 IUCN     Gevalidee… Vastgesteld 
#>  4 Rode lijst van de Dagvlinders           2021 IUCN     Gevalidee… Tervaststel…
#>  5 Rode lijst van de Dansvliegen           2001 Lokaal   Niet-geva… Niet-vastge…
#>  6 Rode lijst van de Doodhoutke…           2015 IUCN     Gevalidee… Vastgesteld 
#>  7 Rode lijst van de Hauwmossen            2017 IUCN     Gevalidee… Vastgesteld 
#>  8 Rode lijst van de Landslakken           2006 Lokaal   Niet-geva… Niet-vastge…
#>  9 Rode lijst van de Levermossen           2017 IUCN     Gevalidee… Vastgesteld 
#> 10 Rode lijst van de Libellen              2021 IUCN     Gevalidee… Tervaststel…
#> # ℹ 16 more rows

Taxonlist features

The function get_taxonlijsten_features() queries D0156_00_Taxonlijsten and gives an overview of all features associated with taxa on a taxonlist version. This is an auxiliary function to check the accepted values (KenmerkwaardeCodes) of the feature parameter in the core function get_taxonlijsten_items.

Features are very context (list) dependent: it may be a red list status, an annex of a legislative list, a habitat, … Not all lists have associated features, e.g. Soortbeschermingsplannen are (at this moment) featureless.

The following examples can be used as base to continue selecting the data you require.

Use function with default values (get all features of the most recent list versions):

all_recent <- get_taxonlijsten_features(con)

Get features of all versions of the ‘Rode lijst van de Dagvlinders’:

rl_butterfly <- get_taxonlijsten_features(con, version = "all",
                                          list = "%rode%dagvlinders%",
                                          collect = TRUE)

Get features of Habitattypical fauna:

habitat_fauna <- get_taxonlijsten_features(con, list = "%Habitattyp%fauna%")

Note that the function also returns taxonlists without features:

no_feature <- get_taxonlijsten_features(con, list = "%SBP%", collect = TRUE)

no_feature
#> # A tibble: 27 × 7
#>    Taxonlijst             PublicatieJaar Version KenmerkCode KenmerkBeschrijving
#>    <chr>                           <int> <chr>   <chr>       <chr>              
#>  1 SBP Akkervogels                  2021 latest  <NA>        <NA>               
#>  2 SBP Beekprik, rivierd…           2017 latest  <NA>        <NA>               
#>  3 SBP Bever                        2015 latest  <NA>        <NA>               
#>  4 SBP Boomkikker                   2018 latest  <NA>        <NA>               
#>  5 SBP Bruine kiekendief            2018 latest  <NA>        <NA>               
#>  6 SBP Gladde slang                 2016 latest  <NA>        <NA>               
#>  7 SBP Grauwe kiekendief            2015 latest  <NA>        <NA>               
#>  8 SBP Grauwe klauwier              2017 latest  <NA>        <NA>               
#>  9 SBP Grote modderkruip…           2020 latest  <NA>        <NA>               
#> 10 SBP Hamster                      2015 latest  <NA>        <NA>               
#> # ℹ 17 more rows
#> # ℹ 2 more variables: KenmerkwaardeCode <chr>, KenmerkwaardeBeschrijving <chr>

Taxonlist items

The function get_taxonlijsten_items() queries D0156_00_Taxonlijsten and returns the taxa (list items) that are on a taxonlist. The interpreted taxa are given by default, but it is possible to add taxa as they were originally published.

Several examples are given, this can be used as base to continue selecting the data you require.

Get all taxa from list ‘Jachtdecreet’:

jachtdecreet <- get_taxonlijsten_items(con, list =  "Jachtdecreet",
                                       collect = TRUE)

Get all taxa on category 2 of ‘Soortenbesluit’:

soortenbesluit_cat2 <- get_taxonlijsten_items(con, list =  "soortenbesluit",
                                              feature = "cat2")

Get all taxonlist that include ‘Gentiaanblauwtje’ (you can search for scientific as well as Dutch names):

gentiaanblauwtje <- get_taxonlijsten_items(con, taxon = "Gentiaanblauwtje",
                                           collect = TRUE)

gentiaanblauwtje
#> # A tibble: 10 × 10
#>    Lijst    Publicatiejaar LaatsteVersie Taxongroep Naamwet_interpretatie Auteur
#>    <chr>             <int>         <int> <chr>      <chr>                 <chr> 
#>  1 Ecoprof…           2014             1 Dagvlinde… Phengaris alcon       <NA>  
#>  2 Habitat…           2013             1 Dagvlinde… Phengaris alcon       <NA>  
#>  3 Provinc…           2021             1 Dagvlinde… Phengaris alcon       <NA>  
#>  4 Provinc…           2021             1 Dagvlinde… Phengaris alcon       <NA>  
#>  5 Rode li…           2021             1 Dagvlinde… Phengaris alcon       <NA>  
#>  6 Soorten…           2009             1 Dagvlinde… Phengaris alcon       <NA>  
#>  7 Soorten…           2014             1 Dagvlinde… Phengaris alcon       <NA>  
#>  8 Subsidi…           2017             1 Dagvlinde… Phengaris alcon       <NA>  
#>  9 Subsidi…           2017             1 Dagvlinde… Phengaris alcon       <NA>  
#> 10 Subsidi…           2017             1 Dagvlinde… Phengaris alcon       <NA>  
#> # ℹ 4 more variables: NaamNed_interpretatie <chr>, Kenmerk <chr>,
#> #   KenmerkwaardeCode <chr>, Kenmerkwaarde <chr>

Get all taxa with status CR (critically endangered) from the Red list of Vascular plants (use function get_taxonlijsten_features() to see what feature codes are available):

critical <- get_taxonlijsten_items(con, feature = "CR",
                                   list = "Rode lijst%vaatpl%")

Get original and interpreted Cicindela taxa from list ‘Soortenbesluit’

cicindela <- get_taxonlijsten_items(con, list = "Soortenbesluit",
                                    taxon = "%Cicindela%", original = TRUE,
                                    collect = TRUE) %>%
select("Naamwet_origineel", "NaamNed_origineel", "Naamwet_interpretatie",
         "NaamNed_interpretatie")

cicindela
#> # A tibble: 5 × 4
#>   Naamwet_origineel   NaamNed_origineel             Naamwet_interpretatie
#>   <chr>               <chr>                         <chr>                
#> 1 Cicindela germanica <NA>                          Cicindela germanica  
#> 2 Cicindela spp       zandloopkevers - alle soorten Cicindela campestris 
#> 3 Cicindela spp       zandloopkevers - alle soorten Cicindela hybrida    
#> 4 Cicindela spp       zandloopkevers - alle soorten Cicindela maritima   
#> 5 Cicindela sylvatica <NA>                          Cicindela sylvatica  
#> # ℹ 1 more variable: NaamNed_interpretatie <chr>

Compare red list status on multiple list versions:

redlist_evolution <- get_taxonlijsten_items(con, version = "all",
                                    list = "rode lijst van de dagvlinders",
                                    collect = TRUE) %>%
select("Lijst", "Publicatiejaar", "Naamwet_interpretatie",
         "NaamNed_interpretatie", "KenmerkwaardeCode") %>%
pivot_wider(names_from = "Publicatiejaar", values_from = "KenmerkwaardeCode")

redlist_evolution
#> # A tibble: 75 × 6
#>    Lijst        Naamwet_interpretatie NaamNed_interpretatie `1996` `2011` `2021`
#>    <chr>        <chr>                 <chr>                 <chr>  <chr>  <chr> 
#>  1 Rode lijst … Aglais urticae        Kleine vos            LC     NT     EN    
#>  2 Rode lijst … Anthocharis cardamin… Oranjetipje           LC     LC     LC    
#>  3 Rode lijst … Apatura iris          Grote weerschijnvlin… EN     EN     LC    
#>  4 Rode lijst … Aphantopus hyperantus Koevinkje             LC     LC     LC    
#>  5 Rode lijst … Aporia crataegi       Groot geaderd witje   RE     RE     RE    
#>  6 Rode lijst … Araschnia levana      Landkaartje           LC     LC     LC    
#>  7 Rode lijst … Argynnis paphia       Keizersmantel         CR     LC     LC    
#>  8 Rode lijst … Aricia agestis        Bruin blauwtje        VU     LC     LC    
#>  9 Rode lijst … Callophrys rubi       Groentje              VU     VU     EN    
#> 10 Rode lijst … Carterocephalus pala… Bont dikkopje         VU     NT     VU    
#> # ℹ 65 more rows

More complex queries

These functions give most of the relevant basic information that is available in D0156_00_Taxonlijsten. If you need more, check the data model below to write your own queries.

Taxonlijst

A Taxonlijst is a list of taxa that belong together for one reason or another. That reason can be legal (Habitats Directive, Birds Directive, Species Decree, Hunting Decree, etc.), thematic (ecoprofiles, etc.) or somewhere in between (Red lists, Species Protection Plans). This may seem pretty straightforward at first glance, but the concept of a Taxonlijst is susceptible to interpretation.

TaxonlijstVersie

Taxonlijst may be revised or updated over time. A typical example is the 10-yearly revision of the Red Lists. In that case we are talking about different versions of a Taxonlijst.

A Taxonlijst has at least one TaxonlijstVersie, but it can have multiple versions. As a rule of thumb a new Taxonlijstversie can be related to a new publication. An example is the Union list of invasive alien species. This Taxonlijst is regularly amended. Each amendment is considered a new TaxonlijstVersie because it can be traced back to a citable, consolidated version:

Taxonlijstitem

All elements (taxa) on a Taxonlijstversie are called TaxonlijstItem These are the taxon(group) names as they were originally published. Often this will be species names, but it might as well be a description of a taxongroup that requires further interpretation. The Species Decree (Soortenbesluit) for example, includes many descriptive items such as:

• Cladonia spp. Subgen. Cladina (rendiermossen)
• Calosoma spp (poppenrovers - alle soorten)
• Formica rufa s.l. (rode bosmier s.l. (kale bosmier, behaarde bosmier en zwartrugbosmier))
• Odonata (libellen: alle soorten met uitzondering van die welke specifiek in deze bijlage worden vermeld)
• …

It also happens that names are published incorrectly (typos, errors in the authors, incorrect scientific or Dutch name, etc.). Even then, the names are copied literally as they were published, including errors. An example: In the Blueprints for species monitoring in Flanders (a list of Natura 2000 and other Flemish priority species) we find Veenmosorchis - Dactylorhiza sphagnicola. Two different species are confused here, namely Veenorchis - Dactylorhiza sphagnicola and Veenmosorchis - Hammarbya paludosa. We include the incorrect version in the TaxonlijstItem table, the correct interpretation only takes place afterwards.

A Dutch name may be published without a scientific name or vice versa, scientific names are published either with or without an author’s name, it all doesn’t matter: we just copy things as they appear in the original list. Hence, the TaxonlijstItem table always allows you to recall the list exactly as it was published. There is no direct link with the Taxon table, that link will be made in the table TaxonlijstItemInterpretatie.

TaxonlijstitemInterpretatie

This table links the name as it was originally published (TaxonlijstItem) with one or more taxa. We call this link the interpretation of the original name. Usually the interpretation will be unambiguous and one-to-one, but in other cases a translation must be done. For example, the reindeer mosses from the example above refer to 6 species occurring in Flanders:

The erroneous publication of Veenmosorchis - Dactylorhiza sphagnicola is interpreted as follows:

In practice, you will usually want to request the interpreted taxa.

The data model only allows one interpretation, so you cannot define versions of interpretations. That is a pragmatic choice. The intention is also to interpret taxa down to the species level whenever possible.

Taxon

This is the reference table with the taxa of this database. When managing this table, a number of important principles must be taken into account. The taxon model has been deliberately kept very simple. There are no taxonomic hierarchies, nor is it possible to define synonymy between taxa. It is strongly discouraged to maintain more than one record in the Taxon table for a particular taxon. Let’s take the High Brown Fritillary (Bosrandparelmoervlinder) as an example. This is the corresponding Taxon record:

The species is also known under the synonym Argynnis adippe and was previously called Adippevlinder in Dutch. So you might be tempted to add more records in the Taxon table:

But that is not how it works. For each taxon there should be only one record, i.e. the name that is considered by the administrator of the Taxon table as the currently accepted scientific and currently accepted Dutch name. Synonyms can of course occur as an original TaxonlijstItem. For example, we see that in the first version of the Red List of Butterflies the old Dutch name ‘Adippevlinder’ was used. The second version only contained Dutch names. They are all linked to the single entry Fabriciana adippe - Bosrandparelmoervlinder in the Taxon table:

By allowing only one record per taxon in the Taxon table, you are sure to get all relevant lists when requesting an overview for a taxon. The drawback is that you need to know the currently accepted name.

Kenmerk (= feature)

The TaxonlijstItem that appear on a TaxonlijstVersion may or may not have associated features. Typical examples of features are the Red List category or the Annex on which a TaxonlijstItem is listed. These are the features that are currently defined in the database:

Kenmerkwaarde

Each feature has a set of allowed feature values. The feature value codes are the input values for the feature argument in get_taxonlijsten_items():

TaxonlijstItemAttribuut

This is the relation table linking a TaxonlijstItem to its feature values. A TaxonlijstItem can have multiple feature values for the same feature. For example: the moor frog is linked to 3 habitat types on the taxon list of habitattypical fauna species: