Description Usage Arguments Methods tested Author(s) References See Also Examples
AllDists()
calculates the distances between two trees, using a suite
of distance measures.
1 |
tr1, tr2 |
Phylogenetic trees of class |
verbose |
Logical specifying whether to print messages allowing the user to keep track of progress. |
pid
: Phylogenetic Information Distance (Smith 2020), normalized
against the phylogenetic information content of the splits in the trees
being compared.
msid
: Matching Split Information Distance (Smith 2020), normalized
against the phylogenetic information content of the splits in the trees
being compared.
cid
: Clustering Information Distance (Smith 2020), normalized
against the entropy of the splits in the trees being compared.
qd
: Quartet divergence (Smith 2019), normalized against its maximum
possible value for n-leaf trees.
nye
: Nye et al. tree distance (Nye et al. 2006), normalized against
the total number of splits in the trees being compared.
jnc2
, jnc4
: Jaccard-Robinson-Foulds distances with k = 2, 4,
conflicting pairings prohibited ('no-conflict'), normalized against
the total number of splits in the trees being compared.
jco2
, jco4
: Jaccard-Robinson-Foulds distances with k = 2, 4,
conflicting pairings permitted ('conflict-ok'), normalized against
the total number of splits in the trees being compared.
ms
: Matching Split Distance (Bogdanowicz & Giaro 2012), unnormalized.
mast
: Size of Maximum Agreement Subtree (Valiente 2009), unnormalized.
masti
: Information content of Maximum Agreement Subtree, unnormalized.
nni_l
, nni_L
, nni_t
, nni_U
, nni_u
:
Lower, best lower, tight upper, best upper, and
upper bounds for nearest-neighbour interchange distance (Li et al. 1996),
unnormalized.
'Best' lower bounds jump sharply when mismatched regions of a tree become
large enough that a tight upper bound cannot be exactly calculated, so
are discontinuous and cannot readily be compared between trees.
spr
: Approximate subtree prune and regraft SPR distance,
unnormalized.
tbr_l
, tbr_u
: Lower and upper bound for tree bisection and reconnection
(TBR) distance, calculated using
TBRDist; unnormalized.
rf
: Robinson-Foulds distance (Robinson & Foulds 1981), unnormalized.
icrf
: Robinson-Foulds distance, splits weighted by phylogenetic
information content (Smith 2020), unnormalized.
path
: Path distance (Steel & Penny 1993), unnormalized.
Martin R. Smith (martin.smith@durham.ac.uk)
Bogdanowicz2012TreeDist
\insertRefLi1996TreeDist
\insertRefKendall2016TreeDistData
\insertRefNye2006TreeDist
\insertRefRobinson1981TreeDist
\insertRefSmith2019TreeDist
\insertRefSmithDistTreeDist
\insertRefSteel1993TreeDist
\insertRefValiente2009TreeDist
Other pairwise tree distances:
CompareAllTrees()
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