data.tree

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implemented workaround for issue #160

3

Workaround for the issue in `as.Node.data.frame` when one node and one column of the data.frame share the same name. Note: the suggested workaround adds a new argument (`suffix`) to the...

simschul

toNewick() returns wrong branch length

1

Hi, I tried to follow the vignette to convert a dataframe to Newick format, but I the branch length in the output are wrong, although the overall shape of the...

Lan-h

as.Node.data.frame raises error when column name of data.frame equals the name of one node

1

Thank you so much for your very helpful R-package! I encountered one issue: I get an error message (`Error: $ operator is invalid for atomic vectors`) when converting the following...

simschul

docs: add equivalent of ape::drop.tip

3

It would be helpful to include an example in the docs of how to prune a `data.tree` object in the same manner as `ape::drop.tip`

nick-youngblut

Hi! I'm using the Node class for most tree manipulations. I propagate annotations up the tree from the leaves using the vignette's methods (including unique "sample" id's under which many...

kylekimler

Hello, this error will be thrown using function `data.tree::as.phylo.Node` if a parenthesis character was part of an *internal* node label: `Error in FUN(X[[i]], ...): attempt to set index 2/2 in...

danlooo

Slow conversion between data.tree and Newick format

4

Is there a way to speed up this conversion, specifically with `ToNewick`? ``` library(ape) data(bird.families) system.time(bf

cysouw

Custom serialization

1

Saving environments results in huge files. Instead of environments, we could simply save as list of list. Essentially, what we get when calling `ToListExplicit`

gluc

Changing name will keep reference

1

``` data(acme) acme$IT$name

gluc

Hi. I am trying to Find a node in a tree with non-unique names. Lets say, I have this - ``` data(acme) acme$Research$AddChild("IT") ``` When i use `FindNode(acme,"IT")` It is...

Jeeva-Ganesan