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 splits
as.matrix(x, zero.print = 0L, one.print = 1L, ...)

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

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

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

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

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

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

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

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

# S3 method for splits
as.bitsplits(x)

# S3 method for 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.

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 3.0.0.1 ]
#> 
#> 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))