Function to import and export splits and networks

read.nexus.splits, write.nexus.splits, read.nexus.networx, write.nexus.networx can be used to import and export splits and networks with nexus format and allow to exchange these object with other software like SplitsTree. write.splits returns a human readable output.

Usage

read.nexus.splits(file)

write.nexus.splits(obj, file = "", weights = NULL, taxa = TRUE,
  append = FALSE)

write.nexus.networx(obj, file = "", taxa = TRUE, splits = TRUE,
  append = FALSE)

read.nexus.networx(file, splits = TRUE)

write.splits(x, file = "", zero.print = ".", one.print = "|",
  print.labels = TRUE, ...)

Arguments

file: a file name.
obj: An object of class splits.
weights: Edge weights.
taxa: logical. If TRUE a taxa block is added
append: logical. If TRUE the nexus blocks will be added to a file.
splits: logical. If TRUE the nexus blocks will be added to a file.
x: An object of class splits.
zero.print: character which should be printed for zeros.
one.print: character which should be printed for ones.
print.labels: logical. If TRUE labels are printed.
...: Further arguments passed to or from other methods.
labels: names of taxa.

Value

write.nexus.splits and write.nexus.networx write out the splits and networx object to read with other software like SplitsTree. read.nexus.splits and read.nexus.networx return an splits and networx object.

Note

read.nexus.splits reads in the splits block of a nexus file. It assumes that different co-variables are tab delimited and the bipartition are separated with white-space. Comments in square brackets are ignored.

Author

Klaus Schliep klaus.schliep@gmail.com

Examples


(sp <- as.splits(rtree(5)))
#>       t3 t4 t2 t5 t1
#>  [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 t3 t4 t2 t5 t1 ;
#> END;
#> 
#> BEGIN SPLITS;
#> 	DIMENSIONS ntax=5 nsplits=8;
#> 	FORMAT labels=left weights=yes confidences=no intervals=no;
#> 	MATRIX
#> 		1	0.576804658863693 	1,
#> 		2	0.0763594461604953 	1 3 4 5,
#> 		3	0.956285735592246 	1 2 4 5,
#> 		4	0.505531079834327 	1 2 3 5,
#> 		5	0.924366363789886 	1 2 3 4,
#> 		6	0.778544640168548 	1 2 3 4,
#> 		7	0.400843428215012 	1 2,
#> 		8	0.872974850703031 	1 2 5,
#> 	;
#> END;
spl <- allCircularSplits(5)
plot(as.networx(spl))

write.splits(spl, print.labels = FALSE)
#> 
#> 
#>  |.... 
#> 
#>  .|... 
#> 
#>  ..|.. 
#> 
#>  ...|. 
#> 
#>  ....| 
#> 
#>  ||... 
#> 
#>  .||.. 
#> 
#>  ..||. 
#> 
#>  ...|| 
#> 
#>  |...|