View source for WP:Automated taxobox system/advanced taxonomy

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Sometimes, taxonomy is not as simple as we might like, so taxonomy templates need to handle more unusual features and a taxobox needs to contain more information than just ranks and taxon names.  Some advanced cases are described here. Do ask at [[Wikipedia talk:Automated taxobox system]] if you need more information.

== Taxon variants ==
Sometimes it is desirable to have slightly different taxonomy templates for what is fundamentally the same taxon – "taxon variants". The convention in these cases is to use put "/''variant-identifier''" after the name of the taxon: for example, [[Template:Taxonomy/Corallinaceae]] and [[Template:Taxonomy/Corallinaceae/stem-group]]. The "taxon variant" identified by the "/''variant-identifier''" can pick up most of its data by using the <code>same_as</code> parameter. Thus [[Template:Taxonomy/Corallinaceae/stem-group]] has {{para|same_as|Corallinaceae}}.

Conventional values for "/''variant-identifier''" include:
* "/stem-group" and "/total-group"; both should be hyphenated. These would have {{para|rank|stem group}} and {{para|rank|total group}} respectively. Example – [[Template:Taxonomy/Chelicerata/stem-group]].
* "/skip" – used when it is necessary to skip to a higher level in the taxonomic hierarchy. Example [[Template:Taxonomy/Avialae/skip]]; here <code>parent</code> is set to skip Class Reptilia to avoid bird taxonomies showing both this class and Class Aves. See [[#Skip taxonomy templates]].
* "/?" – used when it is not certain that this is the correct taxon. The link text will automatically have " (?)" after the taxon name. Example – [[Template:Taxonomy/Graptolithina/?]]. See [[#Questionable assignments]].
* "/displayed" – used when it is appropriate to show an ancestor taxon only for a certain group of its descendant taxa, while picking up all other parameter values from the "plain" taxonomy template for the same taxon. The variant taxon has {{para|always_display|yes}} while using <code>same_as</code> for all the other parameters.
* "/''taxon''" – used of necessity for all taxonomy templates with titles like "Template:Taxonomy/Incertae sedis/''taxon''", since there isn't a single "''incertae sedis''" taxon. See [[#Incertae sedis taxonomy templates|#''Incertae sedis'' taxonomy templates]].

==Skip taxonomy templates==
{{anchor|"Dummy" taxonomy templates}}
A "skip taxonomy template" has the same title as a normal taxonomy template, but with "/skip" added to the end. Internally the skip taxonomy template at "Template:Taxonomy/''taxon-name''/skip" is coded like this:

<pre><nowiki>{{Don't edit this line {{{machine code|}}}
|same_as = taxon-name
|parent = parent-taxon-name
}}</nowiki></pre>

This says that ''taxon-name''/skip has the same values of rank, extinction status, etc. as ''taxon-name'', except that its parent is ''parent-taxon-name'', which will be higher up the taxonomic hierarchy. (When creating a skip taxonomy template, it can be prefilled if you use the correct page naming convention.)

To use a skip taxonomy template, the taxonomy template at the level below it must have {{para|parent|''parent-taxon-name''/skip}}.

See [[Template:Taxonomy/Ornithurae/skip]] as an example. Note the ".....&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;....." lines in the right-hand table that show where levels have been skipped, and the information at the bottom of the left-hand table.

To link an automatic taxobox to a skip taxonomy template, put {{para|taxon|''taxon-name''/skip}} in the taxobox template in the article.

== Questionable assignments ==
{| class="infobox biota" style="text-align: left; width: 200px; font-size: 100%" 
|-
! colspan=2 style="text-align: center; background-color: #999" |Example output
|-
| {{grey|Order:}}
| {{grey|Radiodonta}}
|-
| Family:
| {{grey|Anomalocarididae}}&nbsp;(?)
|-
| {{grey|Genus:}}
| {{grey|''Pambdeleurion''}}
|}
In the example, ''[[Pambdelurion]]'' might belong to the family Anomalocarididae: but this is questionable, so in the taxobox, the family should be shown with "(?)" following it. [[Template:Taxonomy/Pambdelurion]] has {{para|parent|Anomalocarididae/?}}. Then [[Template:Taxonomy/Anomalocarididae/?]] uses {{para|same_as|Anomalocaridae}} to pick up the relevant information.

If a template of the form "Template:Taxonomy/''taxon''/?" does not yet exist, a link will walk you through how to create it.

[[:Category:Taxonomy templates with query]] shows taxonomy templates with questionable assignments.

As from January 2017, the minimum content of an /? taxonomy template is of the form:
<pre>{{Don't edit this line {{{machine code|}}}
| same_as =
}}</pre>
where {{para|same_as}} is set to the taxon that is questionable. The "(?)" is added automatically by the automated taxobox system, based on the "/?" in the title of the taxonomy template.
{{clear}}

===Questionable assignment (two levels)===
{| class="infobox biota" style="text-align: left; width: 200px; font-size: 100%" 
|-
! colspan=2 style="text-align: center; background-color: #999" | Example output
|-
| ''Clade'':
| {{grey|Polysporangiophyta}}&nbsp;(?)
|-
| Class:
| {{grey|Horneophytopsida}}&nbsp;(?)
|-
| {{grey|Genus:}}
| {{grey|''Tortilicaulis''}}
|}
In the example, ''[[Tortilicaulis]]'' probably belongs to the class Horneophytopsida within the clade Polysporangiophyta, but cannot be assigned to either with certainty. To indicate this, [[Template:Taxonomy/Tortilicaulis]] has {{para|parent|Horneophytopsida/?/?}}. [[Template:Taxonomy/Horneophytopsida/?/?]] in turn has {{para|parent|Polysporangiophyta/?}}, making use of [[Template:Taxonomy/Polysporangiophyta/?]].

If a template of the form "Template:Taxonomy/''taxon''/?/?" does not yet exist, a link will walk you through how to create it.
 
The minimum content of a /?/? taxonomy template is of the form:
<pre>{{Don't edit this line {{{machine code|}}}
| same_as =
| parent = .../?
}}</pre>
where {{para|same_as}} is set to the taxon that is questionable; its parent in turn is set to the expected parent with "/?" added.

This process can be continued indefinitely. A taxonomy template with ''N'' repeats of "/?" at the end of its title should have its parent set to a taxon name followed by ''N''-1 repeats of "/?". {{As of|2017|January}}, there is no automated support for creating such templates beyond ''N'' = 2.
{{clear}}

==''Incertae sedis'' taxonomy templates==
{| class="infobox biota" style="text-align: left; width: 200px; font-size: 100%" 
|-
! colspan=2 style="text-align: center; background-color: #999" | Example output
|-
| {{grey|Phylum:}}
| {{grey|Arthropoda}}
|-
| Class:
| ''[[incertae sedis]]''
|-
| {{grey|Genus:}}
| {{grey|''Skania''}}
|}
In the example, ''[[Skania]]'' is definitely an arthropod genus, but its relationship to other arthropods – and in particular the class that it should be placed in – is unknown. To use the technical term, it is ''incertae sedis''.  Therefore, at [[Template:Taxonomy/Skania]], we set {{Para|parent|Incertae sedis/Arthropoda}}. There must then be [[Template:Taxonomy/Incertae sedis/Arthropoda]].

If a template with a name of the form "Template:Taxonomy/Incertae sedis/''taxon''" does not yet exist, a link will walk you through how to create it.

{{As of|2017|January}}, the minimum content of an ''incertae sedis'' taxonomy template is of the form:
<pre>{{Don't edit this line {{{machine code|}}}
| parent =
| rank =
}}</pre>
(The appropriate value for {{para|link}} will be set by default if the 'taxon' name starts with "Incertae sedis".)
{{clear}}

<!--
== Paraphyly ==
{| class="infobox biota" style="text-align: left; width: 200px; font-size: 100%" 
|-
! colspan=2 style="text-align: center; background-color: #999" | Example: Porifera
|-
| {{grey|Kingdom:}}
| {{grey|Animalia}}
|-
| Phylum:
| [[Sponge|"Porifera"]]
|-
| {{grey|Class:}}
| {{grey|Some sponge class}}
|}
A [[paraphyletic]] group is one that contains some, but not all, of its descendants. No special taxonomy template is necessary if the group is always considered paraphyletic, other than putting the link text inside quotation marks, e.g. {{para|link|Porifera{{!}}"Porifera"}}, using the convention that "..." denotes a paraphyletic group.

In other cases, a variant taxonomy template may be useful. For instance, although birds evolved from theropod dinosaurs, they may or may not be included in the term "dinosaur". The paraphyletic view could be encoded in "Template:Taxonomy/Dinosauria/paraphyly" as
<pre>{{Don't edit this line {{{machine code|}}}
|same_as = Dinosauria
|link = Dinosaur|"Dinosauria"
}}</pre>
Then in the taxonomic hierarchy, some taxon would have {{para|parent|Dinosauria|paraphyly}}.
-->
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