Splits representation of graphs and trees.

as.splits produces a list of splits or bipartitions.

Usage

allSplits(k, labels = NULL)

allCircularSplits(k, labels = NULL)

as.splits(x, ...)

# S3 method for class 'splits'
as.matrix(x, zero.print = 0L, one.print = 1L, ...)

# S3 method for class 'splits'
as.Matrix(x, ...)

# S3 method for class 'splits'
print(x, maxp = getOption("max.print"), zero.print = ".",
  one.print = "|", ...)

# S3 method for class 'splits'
c(..., recursive = FALSE)

# S3 method for class 'splits'
unique(x, incomparables = FALSE, unrooted = TRUE, ...)

# S3 method for class 'phylo'
as.splits(x, ...)

# S3 method for class 'multiPhylo'
as.splits(x, ...)

# S3 method for class 'networx'
as.splits(x, ...)

# S3 method for class 'splits'
as.prop.part(x, ...)

# S3 method for class 'splits'
as.bitsplits(x)

# S3 method for class 'bitsplits'
as.splits(x, ...)

compatible(obj1, obj2 = NULL)

Arguments

k

number of taxa.

labels

names of taxa.

x

An object of class phylo or multiPhylo.

...

Further arguments passed to or from other methods.

zero.print

character which should be printed for zeros.

one.print

character which should be printed for ones.

maxp

integer, default from options(max.print), influences how many entries of large matrices are printed at all.

recursive

logical. If recursive = TRUE, the function recursively descends through lists (and pairlists) combining all their elements into a vector.

incomparables

only for compatibility so far.

unrooted

todo.

obj1, obj2

an object of class splits.

Value

as.splits returns an object of class splits, which is mainly a list of splits and some attributes. Often a splits object will contain attributes confidences for bootstrap or Bayesian support values and weight storing edge weights. compatible return a lower triangular matrix where an 1 indicates that two splits are incompatible.

Note

The internal representation is likely to change.

See also

prop.part, lento, as.networx, distanceHadamard, read.nexus.splits

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

(sp <- as.splits(rtree(5)))
#>       t4 t5 t1 t3 t2
#>  [1,]  |  .  .  .  .
#>  [2,]  .  |  .  .  .
#>  [3,]  .  .  |  .  .
#>  [4,]  .  .  .  |  .
#>  [5,]  .  .  .  .  |
#>  [6,]  |  |  |  |  |
#>  [7,]  |  |  .  .  .
#>  [8,]  .  .  |  |  |
#>  [9,]  .  .  .  |  |
write.nexus.splits(sp)
#> #NEXUS
#> 
#> [Splits block for Spectronet or SplitsTree]
#> [generated by phangorn 2.12.1.1 ]
#> 
#> BEGIN TAXA;
#> 	DIMENSIONS ntax=5;
#> 	TAXLABELS t4 t5 t1 t3 t2 ;
#> END;
#> 
#> BEGIN SPLITS;
#> 	DIMENSIONS ntax=5 nsplits=8;
#> 	FORMAT labels=left weights=yes confidences=no intervals=no;
#> 	MATRIX
#> 		1	0.478118034312502 	1,
#> 		2	0.924074469832703 	1 3 4 5,
#> 		3	0.976170694921166 	1 2 4 5,
#> 		4	0.356726912083104 	1 2 3 5,
#> 		5	0.431473690550774 	1 2 3 4,
#> 		6	0.129372348077595 	1 2,
#> 		7	0.59876096714288 	1 2,
#> 		8	0.731792511884123 	1 2 3,
#> 	;
#> END;
spl <- allCircularSplits(5)
plot(as.networx(spl))