Manipulating Lists of Trees
These are extraction and replacement operators for lists of trees
stored in the class "multiPhylo"
.
## S3 method for class 'multiPhylo' x[i] ## S3 method for class 'multiPhylo' x[[i]] ## S3 method for class 'multiPhylo' x$name ## S3 replacement method for class 'multiPhylo' x[...] <- value ## S3 replacement method for class 'multiPhylo' x[[...]] <- value ## S3 replacement method for class 'multiPhylo' x$... <- value
x, value |
an object of class |
i |
index(ices) of the tree(s) to select from a list; this may be a vector of integers, logicals, or names. |
name |
a character string specifying the tree to be extracted. |
... |
index(ices) of the tree(s) to replace; this may be a vector of integers, logicals, or names. |
The subsetting operator [
keeps the class correctly
("multiPhylo"
).
The replacement operators check the labels of value
if x
has a single vector of tip labels for all trees (see examples).
An object of class "phylo"
([[
, $
) or of class
"multiPhylo"
([
and the replacement operators).
Emmanuel Paradis
x <- rmtree(10, 20) names(x) <- paste("tree", 1:10, sep = "") x[1:5] x[1] # subsetting x[[1]] # extraction x$tree1 # same than above x[[1]] <- rtree(20) y <- .compressTipLabel(x) ## up to here 'x' and 'y' have exactly the same information ## but 'y' has a unique vector of tip labels for all the trees x[[1]] <- rtree(10) # no error try(y[[1]] <- rtree(10)) # error try(x[1] <- rtree(20)) # error ## use instead one of the two: x[1] <- list(rtree(20)) x[1] <- c(rtree(20)) x[1:5] <- rmtree(5, 20) # replacement x[11:20] <- rmtree(10, 20) # elongation x # 20 trees
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