In clone.out, the node options and tree structure are separated into different dataframes. This can cause issues including:
Costly and inaccurate lookup (for example. tree[tree$tip == vi$id])
Inconsistency between index of each data.frame
Since these dataframes both seem to express the same concept - each row representing data for a single subclone - they can likely be combined. This will require further examination, but is worth a look.
Related to #120
In
clone.out, the node options and tree structure are separated into different dataframes. This can cause issues including:tree[tree$tip == vi$id])Since these dataframes both seem to express the same concept - each row representing data for a single subclone - they can likely be combined. This will require further examination, but is worth a look.