Predloga:Klad/dok

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[uredi kodo]

Ta predloga se uporablja za prikazovanje drevesastih diagramov, kjer so oznake nodusov in baze delujoče povezave. Taka drevesa so posebej uporabna za predstavljanje evolucijskih dreves.

Glej {{Cladex}} za dve dodatni funkciji:

  • Double lines leading to a node can be produced as easily as dotted lines.
  • Brackets or bars of a chosen colour can be placed to the right of a set of leaf nodes in the cladogram, thus allowing paraphyletic groups to be identified.

Osnovne funkcije

Uporaba[uredi kodo]


{{Klad
|label1=Baza
|1=Nodus
}}

izpiše

Baza

Nodus




{{Klad
|1={{Klad
   |label1=[[Poddrevo1]]
   |1=Veja1
   |label2=Poddrevo2
   |2=[[Veja2]]
   }}
}}

izpiše


Poddrevo1 

Veja1


Poddrevo2 

Veja2





{{Klad| style=font-size:75%;line-height:75%;
|1={{Klad
   |label1=Poddrevo1
   |1=Veja1
   |label2=Poddrevo2
   |2=Veja2
   }}
}}

izpiše


Poddrevo1

Veja1


Poddrevo2

Veja2




Note that the order of the parameters does not matter. Exactly the same output is produced by


{{Klad| style=font-size:75%;line-height:75%;
|1={{Klad
   |2=Veja2
   |1=Veja1
   |label1=Poddrevo1
   |label2=Poddrevo2
   }}
}}

Poddrevo1

Veja1


Poddrevo2

Veja2





{{Klad
|1={{Klad
   |1={{Klad| thickness=3
      |1=Veja1
      |2=Veja2
      }}
   |2=Leaf3
   }}
}}

izpiše




Veja1



Veja2




Leaf3




To replace a solid line leading to the Nth child with a dashed line, use |stateN=dashed.


{{Klad
|1={{Klad
   |1={{Klad
      |1=Veja1|state1=dashed
      |2=Veja2
      }}
   |2=Leaf3
   }}
}}

izpiše




Veja1



Veja2




Leaf3




Tips[uredi kodo]

An easy way of creating larger cladograms is to use the Newick format and proceed to edit it using a suitable text editor to produce the markup.

  1. Start with Newick format ((a,b),(c,d))
  2. Replace "(" with "{{Klad|"
  3. Replace ")" with "}}"
  4. Edit to replace commas with pipes and numbers
  5. Edit clade labels if needed

Alternatively, one can easily generate required clade code by downloading the free Windows utility, 'Claded', via link at http://code.google.com/p/claded, 'Claded' allowing editing of Cladograms using a tree control.


{{Klad
 |1={{Klad
    |1=a
    |2=b
    }}
 |2={{Klad
    |1=c
    |2=d
    }}
}}

Example Perl script to automate the conversion:

use constant N=>"\n";
use constant T=>"\t";

my $tree='((a,b),(c,d));'; # get sequence
$tree=~s/[\n\r]//g; # loose those spaces
$tree=~ s/\:[\.\d]+//g; # loose those lengths
while ($tree=~ m/\(/) {
	foreach my $clade ($tree=~ m/\(([^\(\)]+)\)/g) {
		my @branches=split /\,/,$clade;
		s/(\t+)/$1\t/g for @branches;
		die 'ERROR: degenerate/empty node!'.N if $#branches<1;
		$tree=~ s/\(\Q$clade\E\)/${\join('','{{clade',N,map(T.'|'.($_+1).'='.$branches[$_].N,0..$#branches),T.'}}')}/; # substitute
	}
	pos($tree)=0;
}
$tree=~s/(\t*)\t\}\}/$1\}\}/g; # lazy fix

print $tree;

Using a box[uredi kodo]

You can nest the templates and use links around the text. You may use non-breaking spaces (&nbsp;) to obtain spaces or to have labels that have spaces.

The entire cladogram can be placed in a box so that text flows nicely around it. You can use {{Cladogram}} to produce the box.

Example
Neornithes  
Paleognathae

 


 Neognathae 
 

Other birds


Galloanserae 

Anseriformes


    

Galliformes



Craciformes






Sample of {{Cladogram}}
{{cladogram|title=Example
|caption=Sample of {{tl|Cladogram}}
|clades={{Klad| style=font-size:75%;line-height:75%;
    |label1=[[Neornithes]]  
    |1={{Klad
        |label1=[[Paleognathae]]
        |1= 
        |label2= [[Neognathae]] 
        |2={{Klad
            |1=Other birds
            |label1= 
            |label2=[[Galloanserae]] 
            |2={{Klad
                |1=[[Anseriformes]]
                |label2=    
                |2={{Klad
                    |1=[[Galliformes]]
                    |2=[[Craciformes]]
                    }}
                }}
            }}
        }}
    }}
}}

Controlling the layout of sisters[uredi kodo]

When one sister is represented as a leaf node and the other as a labelled subclade, they do not appear to be at the same level. Consider this cladogram:



Banksia subser. Sphaerocarpae (5 taxa)


Banksia subser. Leptophyllae

Banksia telmatiaea



(4 other taxa)




Although Banksia subser. Sphaerocarpae and Banksia subser. Leptophyllae are sisters, their names are not aligned in the cladogram. If this is considered undesirable, one solution is to use a label in both cases, as shown hereafter, which now shows the sisters at the same level.


Banksia subser. Sphaerocarpae

(5 taxa)


Banksia subser. Leptophyllae

Banksia telmatiaea



(4 other taxa)




Another 'trick' is to introduce a dummy clade. The dotted line hereafter shows where an extra clade has been inserted:



Banksia subser. Sphaerocarpae



Banksia subser. Leptophyllae

Banksia telmatiaea



(4 other taxa)





To achieve this, instead of

{{Klad
|1=Sister1
|label2=Sister2
|2={{Klad
   ...
   }}
}}

use

{{Klad
|1=Sister1
|2={{Klad
   |label1=Sister2
   |2={{Klad
       ...
      }}
   }}
}}

Limitations[uredi kodo]

Label length[uredi kodo]

Labels produced by |labelN=, where N is 1, 2, ..., can lead to poor layout of the resulting cladogram. (This does not apply to the text of leaves, i.e. text produced by |N=.) To avoid problems:

  • Labels should be kept as short as possible, ideally a single word
  • Any necessary spaces in labels should be represented as &nbsp; not as actual spaces.
  • Line breaks (i.e. <br/>) should not be used.

Browser differences[uredi kodo]

Browser variation: left – Internet Explorer, Firefox; right – Safari, Chrome, Opera

Cladograms are drawn by generating hidden tables. The horizontal and vertical lines making up the tree are actually the edges of table cells. The tables are then drawn by the browser or user agent using its internal algorithms. As these differ from browser to browser, the trees produced will not look the same on all browsers.

In particular, od april 2012 there are two algorithms for laying out tables with empty cells, used by two groups of browsers. Browsers like Internet Explorer and Firefox use one algorithm, producing cladograms like the two on the left in the diagram. Browsers like Safari, Chrome and Opera use another algorithm, producing cladograms like the two on the right in the diagram.

No automated "fix" for these differences exists at present.

If there is a choice over the ordering of the terminal nodes (leaves) of the tree, cladograms look best in the second group of browsers if as much branching as possible is at the bottom of the cladogram. Typically this is produced by arranging the terminal nodes downwards on the page in order of their evolutionary divergence. Compare the bottom row of the diagram to the top row.

Large cladograms[uredi kodo]

There are limitations on the size and complexity of the cladograms which can be drawn:

  • A maximum of 17 children is allowed per node. It may seem that this could easily be increased by editing the template, but see the next point.
  • Cladograms can only be expanded up to a certain level of complexity because the MediaWiki software limits the resources available for template expansion. The cladogram at APG_III_system#Phylogeny has had to be broken into three parts, because the entire cladogram exhausts the allowed resources (in this case the allowed expansion depth). Any change to the template could result in large cladograms failing to display correctly. In general, don't exceed a depth of 19, i.e. don't nest one clade template inside another more than 19 times.

Inclusion in books[uredi kodo]

There are many known bugs in rendering tables in the software which produces Wikipedia books; see the book tool feedback page. Od julij 2011 these result in the lines in cladograms not displaying in books.